X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=htsworkflow%2Ffrontend%2Fexperiments%2Ffixtures%2Ftest_flowcells.json;h=15d00c60de68e10d233c95af20b6aa63f082b4c2;hb=ab74b21a3c45abc940a2154e584a01089c910cbe;hp=b744e2bed8146898e1affd0c7fe898d2b7cd81bc;hpb=90506d1562dc6ae689ef27f6881dda576457443f;p=htsworkflow.git diff --git a/htsworkflow/frontend/experiments/fixtures/test_flowcells.json b/htsworkflow/frontend/experiments/fixtures/test_flowcells.json index b744e2b..15d00c6 100644 --- a/htsworkflow/frontend/experiments/fixtures/test_flowcells.json +++ b/htsworkflow/frontend/experiments/fixtures/test_flowcells.json @@ -1,7 +1,64 @@ [ - {"pk": 1, "model": "samples.affiliation", + {"pk": 5, "model": "auth.user", + "fields": { + "username": "test", + "first_name": "", + "last_name": "", + "is_active": true, + "is_superuser": false, + "is_staff": false, + "last_login": "2009-01-01T00:00:01-0800", + "groups": [], + "user_permissions": [], + "password": "sha1$foo$5e4eefec1144a04becfb7da79244f07c487fc345", + "email": "", + "date_joined": "2009-01-01T00:01:01-0800" + } + }, + {"pk": 5, "model": "samples.htsuser", + "fields" : {} + }, + {"pk": 6, "model": "auth.user", + "fields": { + "username": "admintest", + "first_name": "", + "last_name": "", + "is_active": true, + "is_superuser": false, + "is_staff": true, + "last_login": "2009-01-01T00:00:01-0800", + "groups": [], + "user_permissions": [], + "password": "sha1$foo$5e4eefec1144a04becfb7da79244f07c487fc345", + "email": "", + "date_joined": "2009-01-01T00:01:01-0800" + } + }, + {"pk": 6, "model": "samples.htsuser", + "fields" : {} + }, + {"pk": 7, "model": "auth.user", + "fields": { + "username": "supertest", + "first_name": "", + "last_name": "", + "is_active": true, + "is_superuser": true, + "is_staff": true, + "last_login": "2009-01-01T00:00:01-0800", + "groups": [], + "user_permissions": [], + "password": "sha1$foo$5e4eefec1144a04becfb7da79244f07c487fc345", + "email": "", + "date_joined": "2009-01-01T00:01:01-0800" + } + }, + {"pk": 7, "model": "samples.htsuser", + "fields" : {} + }, + {"pk": 1, "model": "samples.affiliation", "fields": { - "users": [], + "users": [5], "contact": "group 1", "name": "affiliation 1", "email": "pk1@example.com" @@ -9,7 +66,7 @@ }, {"pk": 2, "model": "samples.affiliation", "fields": { - "users": [], + "users": [6], "contact": "group 2", "name": "affiliation 2", "email": "pk2@example.com" @@ -39,339 +96,359 @@ "email": "pk5@example.com" } }, - {"pk": 5, "model": "auth.user", - "fields": { - "username": "test", - "first_name": "", - "last_name": "", - "is_active": true, - "is_superuser": false, - "is_staff": false, - "last_login": "2009-01-01 00:00:01", - "groups": [], - "user_permissions": [], - "password": "sha1$foo$5e4eefec1144a04becfb7da79244f07c487fc345", - "email": "", - "date_joined": "2009-01-01 00:01:01" - } - }, - {"pk": 6, "model": "auth.user", - "fields": { - "username": "admintest", - "first_name": "", - "last_name": "", - "is_active": true, - "is_superuser": false, - "is_staff": true, - "last_login": "2009-01-01 00:00:01", - "groups": [], - "user_permissions": [], - "password": "sha1$foo$5e4eefec1144a04becfb7da79244f07c487fc345", - "email": "", - "date_joined": "2009-01-01 00:01:01" - } - }, - {"pk": 1, "model": "experiments.clusterstation", "fields": {"name": "old"}}, - {"pk": 2, "model": "experiments.clusterstation", "fields": {"name": "loaner"}}, - {"pk": 3, "model": "experiments.clusterstation", "fields": {"name": "new"}}, - {"pk": 1, "model": "experiments.sequencer", "fields": {"name": "Rotifer (HWI-EAS229)"}}, - {"pk": 2, "model": "experiments.sequencer", "fields": {"name": "Tardigrade"}}, - {"pk": 3, "model": "experiments.sequencer", "fields": {"name": "Sequenced somewhere else."}}, - {"pk": 153, "model": "experiments.flowcell", + {"pk": 1, "model": "experiments.clusterstation", + "fields": {"name": "old", "isdefault": false}}, + {"pk": 2, "model": "experiments.clusterstation", + "fields": {"name": "loaner", "isdefault": true}}, + {"pk": 3, "model": "experiments.clusterstation", + "fields": {"name": "new", "isdefault": false}}, + {"pk": 1, "model": "experiments.sequencer", + "fields": { "name": "Rotifer (HWI-EAS229)", + "model": "Illumina Genome Analyzer I", + "active": false, + "isdefault": false }}, + {"pk": 2, "model": "experiments.sequencer", + "fields": {"name": "Tardigrade", + "instrument_name": "ILLUMINA-EC5D15", + "model": "Illumina Genome Analyzer IIx", + "active": true, + "isdefault": true} + }, + {"pk": 3, "model": "experiments.sequencer", + "fields": {"name": "Sequenced somewhere else.", + "model": "Unknown", + "active": true, + "isdefault": false}}, + {"pk": 153, "model": "experiments.flowcell", "fields": { - "paired_end": true, - "run_date": "2009-09-11 22:12:13", - "read_length": 75, + "paired_end": true, + "run_date": "2007-09-27T22:12:13-0800", + "read_length": 36, "notes": "", "advanced_run": false, "control_lane": 2, "cluster_station": 3, "sequencer": 2, - "flowcell_id": "303TUAAXX" + "flowcell_id": "FC12150" } - }, + }, {"pk": 1193, "model": "experiments.lane", "fields": { "comment": "No change in cluster numbers, despite slight increase in pM", - "library": 10984, + "library": "10981", "cluster_estimate": 129000, "flowcell": 153, "lane_number": 1, "pM": "8" } - }, - {"pk": 10984, "model": "samples.library", + }, + {"pk": 1192, "model": "experiments.lane", + "fields": { + "comment": "Other library", + "library": "11070", + "cluster_estimate": 132000, + "flowcell": 153, + "lane_number": 1, + "pM": "7" + } + }, + + {"pk": "10981", "model": "samples.library", "fields": { - "library_id": "10981", - "ten_nM_dilution": false, - "avg_lib_size": 400, - "library_name": "Paired End Multiplexed Sp-BAC", - "creation_date": "2009-07-21", - "cell_line": 1, - "library_species": 10, - "library_type": null, - "made_by": "Igor", + "ten_nM_dilution": false, + "gel_cut_size": 400, + "library_name": "Paired End Multiplexed Sp-BAC", + "creation_date": "2009-07-21", + "cell_line": 1, + "library_species": 10, + "library_type": null, + "made_by": "Igor", "affiliations": [ 1,2 - ], - "replicate": 1, - "condition": 1, - "hidden": false, - "stopping_point": "Done", - "tags": [], - "made_for": "Andy Cameron", - "amplified_from_sample": null, - "notes": "Combined 10957-10968", - "undiluted_concentration": "5.1", - "successful_pM": null, - "experiment_type": 10, + ], + "replicate": 1, + "condition": 1, + "hidden": false, + "stopping_point": "Done", + "tags": [], + "made_for": "Andy Cameron", + "amplified_from_sample": null, + "notes": "Combined 10957-10968", + "undiluted_concentration": "5.1", + "successful_pM": null, + "experiment_type": 10, "antibody": null } - }, + }, {"pk": 1194, "model": "experiments.lane", "fields": { "comment": "", - "library": 11019, + "library": "11016", "cluster_estimate": 152000, "flowcell": 153, "lane_number": 2, "pM": "7" } - }, + }, { - "pk": 11019, - "model": "samples.library", + "pk": "11006", + "model": "samples.library", "fields": { - "library_id": "11016", - "ten_nM_dilution": false, - "avg_lib_size": 325, - "library_name": "Paired End Pfl #3 MP 7/24/9 a", - "creation_date": "2009-08-06", - "cell_line": 1, - "library_species": 2, - "library_type": 2, - "made_by": "Lorian", + "ten_nM_dilution": false, + "gel_cut_size": 325, + "library_name": "Paired End Pfl #3 MP 7/24/9", + "creation_date": "2009-08-05", + "cell_line": 1, + "library_species": 8, + "library_type": 2, + "made_by": "Lorian", + "affiliations": [ + 3 + ], + "replicate": 1, + "condition": 1, + "hidden": true, + "stopping_point": "1A", + "tags": [], + "made_for": "", + "amplified_from_sample": null, + "notes": "7/31/2009 16:08:22\tColor: Blue", + "undiluted_concentration": null, + "successful_pM": null, + "experiment_type": 8, + "antibody": null + } + }, + { + "pk": "11016", + "model": "samples.library", + "fields": { + "ten_nM_dilution": false, + "gel_cut_size": 325, + "library_name": "Paired End Pfl #3 MP 7/24/9 a", + "creation_date": "2009-08-06", + "cell_line": 1, + "library_species": 2, + "library_type": 2, + "made_by": "Lorian", "affiliations": [ 2 - ], - "replicate": 1, - "condition": 1, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "", - "amplified_from_sample": 11006, - "notes": "7/31/2009 16:08:22\tColor: Blue", - "undiluted_concentration": "35.5", - "successful_pM": null, - "experiment_type": 8, + ], + "replicate": 1, + "condition": 1, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "", + "amplified_from_sample": 11006, + "notes": "7/31/2009 16:08:22\tColor: Blue", + "undiluted_concentration": "35.5", + "successful_pM": null, + "experiment_type": 8, "antibody": null } - }, + }, {"pk": 1195, "model": "experiments.lane", "fields": { "comment": "", - "library": 11042, + "library": "SL039", "cluster_estimate": 162000, "flowcell": 153, "lane_number": 3, "pM": "7" } - }, + }, { - "pk": 11042, - "model": "samples.library", + "pk": "SL039", + "model": "samples.library", "fields": { - "library_id": "SL039", - "ten_nM_dilution": false, - "avg_lib_size": 300, - "library_name": "Paired ends 99 GM12892", - "creation_date": "2009-08-25", - "cell_line": 1, - "library_species": 8, - "library_type": 2, - "made_by": "Brian Williams", + "ten_nM_dilution": false, + "gel_cut_size": 300, + "library_name": "Paired ends 99 GM12892", + "creation_date": "2009-08-25", + "cell_line": 1, + "library_species": 8, + "library_type": 2, + "made_by": "Brian Williams", "affiliations": [ 3,4 - ], - "replicate": 1, - "condition": 1, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "Brian Williams", - "amplified_from_sample": null, - "notes": "fragment size = 300 bp, Amicon filtered\r\nnanodrop: 56.3", - "undiluted_concentration": "28.7", - "successful_pM": null, - "experiment_type": 4, + ], + "replicate": 1, + "condition": 1, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "Brian Williams", + "amplified_from_sample": 11006, + "notes": "fragment size = 300 bp, Amicon filtered\r\nnanodrop: 56.3", + "undiluted_concentration": "28.7", + "successful_pM": null, + "experiment_type": 4, "antibody": null } - }, + }, {"pk": 1196, "model": "experiments.lane", "fields": { "comment": "This lane's library had the second lowest concentration of all the libraries built at the same time (2.05ng/ul)", - "library": 11063, + "library": "11060", "cluster_estimate": 24000, "flowcell": 153, "lane_number": 4, "pM": "7" } - }, + }, { - "pk": 11063, - "model": "samples.library", + "pk": "11060", + "model": "samples.library", "fields": { - "library_id": "11060", - "ten_nM_dilution": false, - "avg_lib_size": 300, - "library_name": "Paired ends 100 VC_CN_4_M_MBB1185_s1", - "creation_date": "2009-09-01", - "cell_line": 1, - "library_species": 8, - "library_type": 2, - "made_by": "Brian Williams", + "ten_nM_dilution": false, + "gel_cut_size": 300, + "library_name": "Paired ends 100 VC_CN_4_M_MBB1185_s1", + "creation_date": "2009-09-01", + "cell_line": 1, + "library_species": 8, + "library_type": 2, + "made_by": "Brian Williams", "affiliations": [ 5 - ], - "replicate": 1, - "condition": 1, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "Brian Williams", - "amplified_from_sample": null, - "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 24.2", - "undiluted_concentration": "2.05", - "successful_pM": null, - "experiment_type": 4, + ], + "replicate": 1, + "condition": 1, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "Brian Williams", + "amplified_from_sample": 11006, + "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 24.2", + "undiluted_concentration": "2.05", + "successful_pM": null, + "experiment_type": 4, "antibody": null } - }, + }, {"pk": 1197, "model": "experiments.lane", "fields": { - "comment": "", - "library": 11064, + "comment": "stuff", + "library": "11061", "cluster_estimate": 140000, "flowcell": 153, "lane_number": 5, - "pM": "7" + "pM": "7", + "status": 2 } - }, + }, { - "pk": 11064, - "model": "samples.library", + "pk": "11061", + "model": "samples.library", "fields": { - "library_id": "11061", - "ten_nM_dilution": false, - "avg_lib_size": 300, - "library_name": "Paired ends 101 VC_CN_4_M_MBB1185_s2", - "creation_date": "2009-09-01", - "cell_line": 1, - "library_species": 8, - "library_type": 2, - "made_by": "Brian Williams", + "ten_nM_dilution": false, + "gel_cut_size": 300, + "library_name": "Paired ends 101 VC_CN_4_M_MBB1185_s2", + "creation_date": "2009-09-01", + "cell_line": 1, + "library_species": 8, + "library_type": 2, + "made_by": "Brian Williams", "affiliations": [ 2,4 - ], - "replicate": 1, - "condition": 1, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "Brian Williams", - "amplified_from_sample": null, - "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 33.1", - "undiluted_concentration": "12.9", - "successful_pM": null, - "experiment_type": 4, + ], + "replicate": 1, + "condition": 1, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "Brian Williams", + "amplified_from_sample": null, + "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 33.1", + "undiluted_concentration": "12.9", + "successful_pM": null, + "experiment_type": 4, "antibody": null } - }, + }, {"pk": 1198, "model": "experiments.lane", "fields": { "comment": "This lane's library had the lowest concentration of all the libraries built at the same time (1.2ng/ul)", - "library": 11065, + "library": "11062", "cluster_estimate": 2000, "flowcell": 153, "lane_number": 6, - "pM": "7" + "pM": "7", + "status": 0 } - }, + }, { - "pk": 11065, - "model": "samples.library", + "pk": "11062", + "model": "samples.library", "fields": { - "library_id": "11062", - "ten_nM_dilution": false, - "avg_lib_size": 300, - "library_name": "Paired ends 102 VC_AU_8_M_MBB4721_s1", - "creation_date": "2009-09-01", - "cell_line": 1, - "library_species": 8, - "library_type": 2, - "made_by": "Brian Williams", + "ten_nM_dilution": false, + "gel_cut_size": 300, + "library_name": "Paired ends 102 VC_AU_8_M_MBB4721_s1", + "creation_date": "2009-09-01", + "cell_line": 1, + "library_species": 8, + "library_type": 2, + "made_by": "Brian Williams", "affiliations": [ 4,5 - ], - "replicate": 1, - "condition": 1, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "Brian Williams", - "amplified_from_sample": null, - "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 13.9", - "undiluted_concentration": "1.2", - "successful_pM": null, - "experiment_type": 4, + ], + "replicate": 1, + "condition": 1, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "Brian Williams", + "amplified_from_sample": null, + "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 13.9", + "undiluted_concentration": "1.2", + "successful_pM": null, + "experiment_type": 4, "antibody": null } - }, + }, {"pk": 1199, "model": "experiments.lane", "fields": { "comment": "", - "library": 11066, + "library": "11063", "cluster_estimate": 120000, "flowcell": 153, "lane_number": 7, "pM": "7" } - }, + }, { - "pk": 11066, - "model": "samples.library", + "pk": "11063", + "model": "samples.library", "fields": { - "library_id": "11063", - "ten_nM_dilution": false, - "avg_lib_size": 300, - "library_name": "Paired ends 103 VC_AU_8_M_MBB4721_s2", - "creation_date": "2009-09-01", - "cell_line": 1, - "library_species": 8, - "library_type": 2, - "made_by": "Brian Williams", + "ten_nM_dilution": false, + "gel_cut_size": 300, + "library_name": "Paired ends 103 VC_AU_8_M_MBB4721_s2", + "creation_date": "2009-09-01", + "cell_line": 1, + "library_species": 8, + "library_type": 2, + "made_by": "Brian Williams", "affiliations": [ 1,3 - ], - "replicate": 1, - "condition": 1, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "Brian Williams", - "amplified_from_sample": null, - "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 46.9", - "undiluted_concentration": "24.5", - "successful_pM": null, - "experiment_type": 4, + ], + "replicate": 1, + "condition": 1, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "Brian Williams", + "amplified_from_sample": null, + "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 46.9", + "undiluted_concentration": "24.5", + "successful_pM": null, + "experiment_type": 4, "antibody": null } - }, + }, {"pk": 1200, "model": "experiments.lane", "fields": { "comment": "This lane's library had the third lowest concentration of all the libraries built at the same time (5.21ng/ul), but gave perfectly normal cluster numbers", - "library": 11067, + "library": "11064", "cluster_estimate": 157000, "flowcell": 153, "lane_number": 8, @@ -379,39 +456,38 @@ } }, { - "pk": 11067, - "model": "samples.library", + "pk": "11064", + "model": "samples.library", "fields": { - "library_id": "11064", - "ten_nM_dilution": false, - "avg_lib_size": 300, - "library_name": "Paired ends 104 VC_CN_7_M_MBB4898_s1", - "creation_date": "2009-09-01", - "cell_line": 1, - "library_species": 8, - "library_type": 2, - "made_by": "Brian Williams", + "ten_nM_dilution": false, + "gel_cut_size": 300, + "library_name": "Paired ends 104 VC_CN_7_M_MBB4898_s1", + "creation_date": "2009-09-01", + "cell_line": 1, + "library_species": 8, + "library_type": 2, + "made_by": "Brian Williams", "affiliations": [ 3,5 - ], - "replicate": 1, - "condition": 1, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "Brian Williams", - "amplified_from_sample": null, - "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 20.4", - "undiluted_concentration": "5.21", - "successful_pM": null, - "experiment_type": 4, + ], + "replicate": 1, + "condition": 1, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "Brian Williams", + "amplified_from_sample": null, + "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 20.4", + "undiluted_concentration": "5.21", + "successful_pM": null, + "experiment_type": 4, "antibody": null } }, - {"pk": 152, "model": "experiments.flowcell", + {"pk": 152, "model": "experiments.flowcell", "fields": { "paired_end": false, - "run_date": "2009-09-10 18:30:15", + "run_date": "2009-09-10T18:30:15-0800", "read_length": 38, "notes": "328461 4897273 RGT-0248815\r\n328479 4897265 RGT-0249274\r\n330421 4822845 SR-0005496", "advanced_run": false, @@ -420,11 +496,11 @@ "sequencer": 1, "flowcell_id": "42JTNAAXX" } - }, + }, {"pk": 1185, "model": "experiments.lane", "fields": { "comment": "", - "library": 11038, + "library": "11035", "cluster_estimate": 174000, "flowcell": 152, "lane_number": 1, @@ -432,39 +508,38 @@ } }, { - "pk": 11038, - "model": "samples.library", + "pk": "11035", + "model": "samples.library", "fields": { - "library_id": "11035", - "ten_nM_dilution": false, - "avg_lib_size": 300, - "library_name": "Paired ends 95 Gilberto_d3_control_LTA", - "creation_date": "2009-08-25", - "cell_line": 1, - "library_species": 9, - "library_type": 2, - "made_by": "Brian Williams", + "ten_nM_dilution": false, + "gel_cut_size": 300, + "library_name": "Paired ends 95 Gilberto_d3_control_LTA", + "creation_date": "2009-08-25", + "cell_line": 1, + "library_species": 9, + "library_type": 2, + "made_by": "Brian Williams", "affiliations": [ 3 - ], - "replicate": 1, - "condition": 1, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "Brian Williams", - "amplified_from_sample": null, - "notes": "fragment size = 300 bp, Amicon filtered\r\nnanodrop: 67.1", - "undiluted_concentration": "28.5", - "successful_pM": null, - "experiment_type": 4, + ], + "replicate": 1, + "condition": 1, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "Brian Williams", + "amplified_from_sample": null, + "notes": "fragment size = 300 bp, Amicon filtered\r\nnanodrop: 67.1", + "undiluted_concentration": "28.5", + "successful_pM": null, + "experiment_type": 4, "antibody": null } - }, + }, {"pk": 1186, "model": "experiments.lane", "fields": { "comment": "", - "library": 11040, + "library": "11037", "cluster_estimate": 173000, "flowcell": 152, "lane_number": 2, @@ -472,39 +547,38 @@ } }, { - "pk": 11040, - "model": "samples.library", + "pk": "11037", + "model": "samples.library", "fields": { - "library_id": "11037", - "ten_nM_dilution": false, - "avg_lib_size": 300, - "library_name": "Paired ends 97 Kuntz_PDHT", - "creation_date": "2009-08-25", - "cell_line": 1, - "library_species": 3, - "library_type": 2, - "made_by": "Brian Williams", + "ten_nM_dilution": false, + "gel_cut_size": 300, + "library_name": "Paired ends 97 Kuntz_PDHT", + "creation_date": "2009-08-25", + "cell_line": 1, + "library_species": 3, + "library_type": 2, + "made_by": "Brian Williams", "affiliations": [ 4 - ], - "replicate": 1, - "condition": 1, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "Brian Williams", - "amplified_from_sample": null, - "notes": "fragment size = 300 bp, Amicon filtered\r\nnanodrop: 52.7", - "undiluted_concentration": "25.5", - "successful_pM": null, - "experiment_type": 4, + ], + "replicate": 1, + "condition": 1, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "Brian Williams", + "amplified_from_sample": null, + "notes": "fragment size = 300 bp, Amicon filtered\r\nnanodrop: 52.7", + "undiluted_concentration": "25.5", + "successful_pM": null, + "experiment_type": 4, "antibody": null } - }, + }, {"pk": 1187, "model": "experiments.lane", "fields": { "comment": "", - "library": 11048, + "library": "11045", "cluster_estimate": 198000, "flowcell": 152, "lane_number": 3, @@ -512,118 +586,115 @@ } }, { - "pk": 11048, - "model": "samples.library", + "pk": "11045", + "model": "samples.library", "fields": { - "library_id": "11045", - "ten_nM_dilution": false, - "avg_lib_size": 250, - "library_name": "FLDN1 8/3/9 anti-AcH3 chip B6 a", - "creation_date": "2009-08-26", - "cell_line": null, - "library_species": 9, - "library_type": 1, - "made_by": "Lorian", + "ten_nM_dilution": false, + "gel_cut_size": 250, + "library_name": "FLDN1 8/3/9 anti-AcH3 chip B6 a", + "creation_date": "2009-08-26", + "cell_line": null, + "library_species": 9, + "library_type": 1, + "made_by": "Lorian", "affiliations": [ 5 - ], - "replicate": 1, - "condition": null, - "hidden": false, - "stopping_point": "2A", - "tags": [], - "made_for": "", - "amplified_from_sample": 11044, - "notes": "8/21/2009 11:57:54\tColor: Yellow", - "undiluted_concentration": "20.5", - "successful_pM": null, - "experiment_type": 2, + ], + "replicate": 1, + "condition": null, + "hidden": false, + "stopping_point": "2A", + "tags": [], + "made_for": "", + "amplified_from_sample": null, + "notes": "8/21/2009 11:57:54\tColor: Yellow", + "undiluted_concentration": "20.5", + "successful_pM": null, + "experiment_type": 2, "antibody": null } - }, + }, {"pk": 1188, "model": "experiments.lane", "fields": { "comment": "", - "library": 11049, + "library": "11046", "cluster_estimate": 212000, "flowcell": 152, "lane_number": 4, "pM": "7"} }, { - "pk": 11049, - "model": "samples.library", + "pk": "11046", + "model": "samples.library", "fields": { - "library_id": "11046", - "ten_nM_dilution": false, - "avg_lib_size": 250, - "library_name": "FLDN1 7/8/9 anti-DiMeH3K4 chip B6 a", - "creation_date": "2009-08-26", - "cell_line": null, - "library_species": 9, - "library_type": 1, - "made_by": "Lorian", + "ten_nM_dilution": false, + "gel_cut_size": 250, + "library_name": "FLDN1 7/8/9 anti-DiMeH3K4 chip B6 a", + "creation_date": "2009-08-26", + "cell_line": null, + "library_species": 9, + "library_type": 1, + "made_by": "Lorian", "affiliations": [ - 6 - ], - "replicate": 1, - "condition": null, - "hidden": false, - "stopping_point": "2A", - "tags": [], - "made_for": "", - "amplified_from_sample": 11045, - "notes": "8/21/2009 11:57:54\tColor: Blue", - "undiluted_concentration": "23.9", - "successful_pM": null, - "experiment_type": 2, + 4 + ], + "replicate": 1, + "condition": null, + "hidden": false, + "stopping_point": "2A", + "tags": [], + "made_for": "", + "amplified_from_sample": null, + "notes": "8/21/2009 11:57:54\tColor: Blue", + "undiluted_concentration": "23.9", + "successful_pM": null, + "experiment_type": 2, "antibody": null } - }, + }, {"pk": 1189, "model": "experiments.lane", "fields": { "comment": "", - "library": 11057, + "library": "11054", "cluster_estimate": 49000, "flowcell": 152, "lane_number": 5, "pM": "7" } - }, + }, { - "pk": 11057, - "model": "samples.library", + "pk": "11054", + "model": "samples.library", "fields": { - "library_id": "11054", - "ten_nM_dilution": false, - "avg_lib_size": 225, - "library_name": "HNDHT HLH hnd-1 strain HT115 fed anti-hlh-1 2% fix plate a", - "creation_date": "2009-08-31", - "cell_line": null, - "library_species": 3, - "library_type": 1, - "made_by": "Lorian", + "ten_nM_dilution": false, + "gel_cut_size": 225, + "library_name": "HNDHT HLH hnd-1 strain HT115 fed anti-hlh-1 2% fix plate a", + "creation_date": "2009-08-31", + "cell_line": null, + "library_species": 3, + "library_type": 1, + "made_by": "Lorian", "affiliations": [ 1 - ], - "replicate": 1, - "condition": null, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "", - "amplified_from_sample": 11051, - "notes": "8/26/2009 14:46:56\tColor: Purple", - "undiluted_concentration": "1.47", - "successful_pM": null, - "experiment_type": 2, + ], + "replicate": 1, + "condition": null, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "", + "amplified_from_sample": null, + "notes": "8/26/2009 14:46:56\tColor: Purple", + "undiluted_concentration": "1.47", + "successful_pM": null, + "experiment_type": 2, "antibody": null } - }, + }, {"pk": 1190, "model": "experiments.lane", "fields": { "comment": "", - "library": 11059, + "library": "11056", "cluster_estimate": 48000, "flowcell": 152, "lane_number": 6, @@ -631,119 +702,116 @@ } }, { - "pk": 11059, - "model": "samples.library", + "pk": "11056", + "model": "samples.library", "fields": { - "library_id": "11056", - "ten_nM_dilution": false, - "avg_lib_size": 225, - "library_name": "HNDM3 HLH hnd-1 strain mex-3 fed anti-hlh-1 2% fix plate a", - "creation_date": "2009-08-31", - "cell_line": null, - "library_species": 3, - "library_type": 1, - "made_by": "Lorian", + "ten_nM_dilution": false, + "gel_cut_size": 225, + "library_name": "HNDM3 HLH hnd-1 strain mex-3 fed anti-hlh-1 2% fix plate a", + "creation_date": "2009-08-31", + "cell_line": null, + "library_species": 3, + "library_type": 1, + "made_by": "Lorian", "affiliations": [ 2 - ], - "replicate": 1, - "condition": null, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "", - "amplified_from_sample": 11053, - "notes": "8/26/2009 14:46:56\tColor: Black", - "undiluted_concentration": "1.42", - "successful_pM": null, - "experiment_type": 2, + ], + "replicate": 1, + "condition": null, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "", + "amplified_from_sample": null, + "notes": "8/26/2009 14:46:56\tColor: Black", + "undiluted_concentration": "1.42", + "successful_pM": null, + "experiment_type": 2, "antibody": null } - }, + }, {"pk": 1191, "model": "experiments.lane", "fields": { "comment": "", - "library": 11060, + "library": "11057", "cluster_estimate": 4000, "flowcell": 152, "lane_number": 7, "pM": "7" } - }, + }, { - "pk": 11060, - "model": "samples.library", + "pk": "11057", + "model": "samples.library", "fields": { - "library_id": "11057", - "ten_nM_dilution": false, - "avg_lib_size": 225, - "library_name": "HNDM3 4H8 hnd-1 strain mex-3 fed 4H8 2% fix plate a", - "creation_date": "2009-08-31", - "cell_line": null, - "library_species": 3, - "library_type": 1, - "made_by": "Lorian", + "ten_nM_dilution": false, + "gel_cut_size": 225, + "library_name": "HNDM3 4H8 hnd-1 strain mex-3 fed 4H8 2% fix plate a", + "creation_date": "2009-08-31", + "cell_line": null, + "library_species": 3, + "library_type": 1, + "made_by": "Lorian", "affiliations": [ 3 - ], - "replicate": 1, - "condition": null, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "", - "amplified_from_sample": 11054, - "notes": "8/26/2009 14:46:56\tColor: Orange.", - "undiluted_concentration": "1.3", - "successful_pM": null, - "experiment_type": 2, + ], + "replicate": 1, + "condition": null, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "", + "amplified_from_sample": null, + "notes": "8/26/2009 14:46:56\tColor: Orange.", + "undiluted_concentration": "1.3", + "successful_pM": null, + "experiment_type": 2, "antibody": null } - }, + }, {"pk": 1192, "model": "experiments.lane", "fields": { "comment": "", - "library": 11068, + "library": "11065", "cluster_estimate": 5000, "flowcell": 152, "lane_number": 8, "pM": "7" } - }, + }, { - "pk": 11068, - "model": "samples.library", + "pk": "11065", + "model": "samples.library", "fields": { - "library_id": "11065", - "ten_nM_dilution": false, - "avg_lib_size": 300, - "library_name": "Paired ends 105 Kuntz PDM3", - "creation_date": "2009-09-01", - "cell_line": 1, - "library_species": 3, - "library_type": 2, - "made_by": "Brian Williams", + "ten_nM_dilution": false, + "gel_cut_size": 300, + "library_name": "Paired ends 105 Kuntz PDM3", + "creation_date": "2009-09-01", + "cell_line": 1, + "library_species": 3, + "library_type": 2, + "made_by": "Brian Williams", "affiliations": [ 4 - ], - "replicate": 1, - "condition": 1, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "Brian Williams", - "amplified_from_sample": null, - "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 30.5", - "undiluted_concentration": "2.47", - "successful_pM": null, - "experiment_type": 4, + ], + "replicate": 1, + "condition": 1, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "Brian Williams", + "amplified_from_sample": null, + "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 30.5", + "undiluted_concentration": "2.47", + "successful_pM": null, + "experiment_type": 4, "antibody": null } - }, + }, {"pk": 151, "model": "experiments.flowcell", "fields": { "paired_end": false, - "run_date": "2009-09-08 15:39:28", + "run_date": "2009-09-08T15:39:28-0800", "read_length": 38, "notes": "Rebuild of broken flowcell\r\n\r\n328461 4820241 RGT-0215719\r\n328479 4897265 RGT-0249510\r\n330421 4822845 SR-0005402\r\n", "advanced_run": false, @@ -756,318 +824,394 @@ {"pk": 1177, "model": "experiments.lane", "fields": { "comment": "", - "library": 11037, + "library": "11034", "cluster_estimate": 177000, "flowcell": 151, "lane_number": 1, "pM": "7" } - }, + }, {"pk": 1178, "model": "experiments.lane", "fields": { "comment": "", - "library": 11039, + "library": "11036", "cluster_estimate": 169000, "flowcell": 151, "lane_number": 2, "pM": "7" } - }, + }, { - "pk": 11039, - "model": "samples.library", + "pk": "11036", + "model": "samples.library", "fields": { - "library_id": "11036", - "ten_nM_dilution": false, - "avg_lib_size": 300, - "library_name": "Paired ends 96 Kuntz_PDE1", - "creation_date": "2009-08-25", - "cell_line": 1, - "library_species": 3, - "library_type": 2, - "made_by": "Brian Williams", + "ten_nM_dilution": false, + "gel_cut_size": 300, + "library_name": "Paired ends 96 Kuntz_PDE1", + "creation_date": "2009-08-25", + "cell_line": 1, + "library_species": 3, + "library_type": 2, + "made_by": "Brian Williams", "affiliations": [ 5 - ], - "replicate": 1, - "condition": 1, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "Brian Williams", - "amplified_from_sample": null, - "notes": "fragment size = 300 bp", - "undiluted_concentration": "30.6", - "successful_pM": null, - "experiment_type": 4, + ], + "replicate": 1, + "condition": 1, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "Brian Williams", + "amplified_from_sample": null, + "notes": "fragment size = 300 bp", + "undiluted_concentration": "30.6", + "successful_pM": null, + "experiment_type": 4, "antibody": null } - }, + }, { - "pk": 11037, - "model": "samples.library", + "pk": "11034", + "model": "samples.library", "fields": { - "library_id": "11034", - "ten_nM_dilution": false, - "avg_lib_size": 300, - "library_name": "Paired ends 94 Gilberto_d3_denerv_LTA", - "creation_date": "2009-08-25", - "cell_line": 1, - "library_species": 9, - "library_type": 2, - "made_by": "Brian Williams", + "ten_nM_dilution": false, + "gel_cut_size": 300, + "library_name": "Paired ends 94 Gilberto_d3_denerv_LTA", + "creation_date": "2009-08-25", + "cell_line": 1, + "library_species": 9, + "library_type": 2, + "made_by": "Brian Williams", "affiliations": [ 1 - ], - "replicate": 1, - "condition": 1, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "Brian Williams", - "amplified_from_sample": null, - "notes": "fragment size = 300 bp", - "undiluted_concentration": "27", - "successful_pM": null, - "experiment_type": 4, + ], + "replicate": 1, + "condition": 1, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "Brian Williams", + "amplified_from_sample": null, + "notes": "fragment size = 300 bp", + "undiluted_concentration": "27", + "successful_pM": null, + "experiment_type": 4, "antibody": null } - }, + }, + { + "pk": "12044", + "model": "samples.library", + "fields": { + "ten_nM_dilution": false, + "gel_cut_size": 225, + "library_name": "Pooled Indexed Test", + "creation_date": "2009-08-26", + "cell_line": null, + "library_species": 9, + "library_type": 5, + "multiplex_id": "1,2,3", + "made_by": "Lorian", + "affiliations": [ + 2 + ], + "replicate": 1, + "condition": null, + "hidden": false, + "stopping_point": "2A", + "tags": [], + "made_for": "", + "amplified_from_sample": null, + "notes": "8/21/2009 11:57:54\tColor: Orange", + "undiluted_concentration": "22.4", + "successful_pM": null, + "experiment_type": 2, + "antibody": null + } + }, { - "pk": 11047, - "model": "samples.library", + "pk": "13044", + "model": "samples.library", "fields": { - "library_id": "11044", - "ten_nM_dilution": false, - "avg_lib_size": 225, - "library_name": "p300 60h C2 FA KF 12/22/8 a", - "creation_date": "2009-08-26", - "cell_line": null, - "library_species": 9, - "library_type": 1, - "made_by": "Lorian", + "ten_nM_dilution": false, + "gel_cut_size": 225, + "library_name": "Dual Indexed Test", + "creation_date": "2009-08-26", + "cell_line": null, + "library_species": 9, + "library_type": 9, + "multiplex_id": "N701-N501", + "made_by": "Lorian", "affiliations": [ 2 - 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"library": 11047, + "library": "12044", "cluster_estimate": 196000, "flowcell": 151, "lane_number": 3, "pM": "7" } - }, + }, + {"pk": 1279, + "model": "experiments.lane", + "fields": { + "comment": "", + "library": "11045", + "cluster_estimate": 196000, + "flowcell": 151, + "lane_number": 3, + "pM": "7" + } + }, + {"pk": 1379, + "model": "experiments.lane", + "fields": { + "comment": "", + "library": "13044", + "cluster_estimate": 196000, + "flowcell": 151, + "lane_number": 4, + "pM": "7" + } + }, + { - "pk": 11047, - "model": "samples.library", + "pk": "11044", + "model": "samples.library", "fields": { - "library_id": "11044", - "ten_nM_dilution": false, - "avg_lib_size": 225, - "library_name": "p300 60h C2 FA KF 12/22/8 a", - "creation_date": "2009-08-26", - "cell_line": null, - "library_species": 9, - "library_type": 1, - "made_by": "Lorian", + "ten_nM_dilution": false, + "gel_cut_size": 225, + "library_name": "p300 60h C2 FA KF 12/22/8 a", + "creation_date": "2009-08-26", + "cell_line": null, + "library_species": 9, + "library_type": 1, + "made_by": "Lorian", "affiliations": [ 3 - 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"library": 11058, + "library": "11055", "cluster_estimate": 104000, "flowcell": 151, "lane_number": 5, "pM": "7" } - }, + }, { - "pk": 11058, - "model": "samples.library", + "pk": "11055", + "model": "samples.library", "fields": { - "library_id": "11055", - "ten_nM_dilution": false, - "avg_lib_size": 225, - "library_name": "HNDHT 4H8 hnd-1 strain HT115 fed 4H8 2% fix plate a", - "creation_date": "2009-08-31", - "cell_line": null, - "library_species": 3, - "library_type": 1, - "made_by": "Lorian", + "ten_nM_dilution": false, + "gel_cut_size": 225, + "library_name": "HNDHT 4H8 hnd-1 strain HT115 fed 4H8 2% fix plate a", + "creation_date": "2009-08-31", + "cell_line": null, + "library_species": 3, + "library_type": 1, + "made_by": "Lorian", "affiliations": [ 5 - ], - "replicate": 1, - "condition": null, - "hidden": false, - "stopping_point": "1Aa", - "tags": [], - "made_for": "", - "amplified_from_sample": 11052, - "notes": "8/26/2009 14:46:56\tColor: White.", - "undiluted_concentration": "2.17", - "successful_pM": null, - "experiment_type": 2, + ], + "replicate": 1, + "condition": null, + "hidden": false, + "stopping_point": "1Aa", + "tags": [], + "made_for": "", + "amplified_from_sample": null, + "notes": "8/26/2009 14:46:56\tColor: White.", + "undiluted_concentration": "2.17", + "successful_pM": null, + "experiment_type": 2, "antibody": null } - }, + }, {"pk": 1182, "model": "experiments.lane", "fields": { "comment": "", - "library": 11070, + "library": "11067", "cluster_estimate": 168000, "flowcell": 151, "lane_number": 6, "pM": "7" } - }, + }, { - "pk": 11070, - "model": "samples.library", + "pk": "11067", + "model": "samples.library", "fields": { - "library_id": "11067", - "ten_nM_dilution": false, - "avg_lib_size": 325, - "library_name": "Paired End SP-BAC Barcoding test 250-300 bp", - "creation_date": "2009-09-03", - "cell_line": 1, - "library_species": 10, - "library_type": 2, - "made_by": "Igor", + "ten_nM_dilution": false, + "gel_cut_size": 325, + "library_name": "Paired End SP-BAC Barcoding test 250-300 bp", + "creation_date": "2009-09-03", + "cell_line": 1, + "library_species": 10, + "library_type": 2, + "made_by": "Igor", "affiliations": [ 1 - ], - "replicate": 1, - "condition": 1, - "hidden": false, - "stopping_point": "Done", - "tags": [], - "made_for": "Andy Cameron", - "amplified_from_sample": null, - "notes": "12 SP BACs", - "undiluted_concentration": "1.45", - "successful_pM": null, - "experiment_type": 8, + ], + "replicate": 1, + "condition": 1, + "hidden": false, + "stopping_point": "Done", + "tags": [], + "made_for": "Andy Cameron", + "amplified_from_sample": null, + "notes": "12 SP BACs", + "undiluted_concentration": "1.45", + "successful_pM": null, + "experiment_type": 8, "antibody": null } - }, + }, {"pk": 1183, "model": "experiments.lane", "fields": { "comment": "", - "library": 11072, + "library": "11069", "cluster_estimate": 184000, "flowcell": 151, "lane_number": 7, "pM": "7" } - }, + }, { - "pk": 11072, - "model": "samples.library", + "pk": "11069", + "model": "samples.library", "fields": { - "library_id": "11069", - "ten_nM_dilution": false, - "avg_lib_size": 300, - "library_name": "Paired End AG-3d-1 AG domain of floral meristem day 3, rep 1", - "creation_date": "2009-09-02", - "cell_line": null, - "library_species": 6, - "library_type": 2, - "made_by": "Yuling Jiao", + "ten_nM_dilution": false, + "gel_cut_size": 300, + "library_name": "Paired End AG-3d-1 AG domain of floral meristem day 3, rep 1", + "creation_date": "2009-09-02", + "cell_line": null, + "library_species": 6, + "library_type": 2, + "made_by": "Yuling Jiao", "affiliations": [ 2 - ], - "replicate": 1, - "condition": null, - "hidden": false, - "stopping_point": "Done", - "tags": [], - "made_for": "", - "amplified_from_sample": null, - "notes": "nanodrop: Xng/ul.", - "undiluted_concentration": "18.3", - "successful_pM": null, - "experiment_type": 4, + ], + "replicate": 1, + "condition": null, + "hidden": false, + "stopping_point": "Done", + "tags": [], + "made_for": "", + "amplified_from_sample": null, + "notes": "nanodrop: Xng/ul.", + "undiluted_concentration": "18.3", + "successful_pM": null, + "experiment_type": 4, "antibody": null } - }, + }, {"pk": 1184, "model": "experiments.lane", "fields": { "comment": "", - "library": 11073, + "library": "11070", "cluster_estimate": 182000, "flowcell": 151, "lane_number": 8, @@ -1075,34 +1219,55 @@ } }, { - "pk": 11073, - "model": "samples.library", + "pk": "11070", + "model": "samples.library", "fields": { - "library_id": "11070", - "ten_nM_dilution": false, - "avg_lib_size": 300, - "library_name": "Paired End AG-5d-1 AG domain of floral meristem day 5, rep 1", - "creation_date": "2009-09-02", - "cell_line": null, - "library_species": 6, - "library_type": 2, - "made_by": "Yuling Jiao", + "ten_nM_dilution": false, + "gel_cut_size": 300, + "library_name": "Paired End AG-5d-1 AG domain of floral meristem day 5, rep 1", + "creation_date": "2009-09-02", + "cell_line": null, + "library_species": 6, + "library_type": 2, + "made_by": "Yuling Jiao", "affiliations": [ 3 - ], - "replicate": 1, - "condition": null, - "hidden": false, - "stopping_point": "Done", - "tags": [], - "made_for": "", - "amplified_from_sample": null, - "notes": "nanodrop: 40ng/ul\r\nCalibrated qbit with standards.\r\nMeasured 2ul library with qbit using HS kit.\r\n", - "undiluted_concentration": "20.3", - "successful_pM": null, - "experiment_type": 4, + ], + "replicate": 1, + "condition": null, + "hidden": false, + "stopping_point": "Done", + "tags": [], + "made_for": "", + "amplified_from_sample": null, + "notes": "nanodrop: 40ng/ul\r\nCalibrated qbit with standards.\r\nMeasured 2ul library with qbit using HS kit.\r\n", + "undiluted_concentration": "20.3", + "successful_pM": null, + "experiment_type": 4, "antibody": null } - } - + }, + {"pk": 200, "model": "experiments.flowcell", + "fields": { + "paired_end": true, + "run_date": "2007-09-27T22:12:13-0800", + "read_length": 36, + "notes": "", + "advanced_run": false, + "control_lane": 2, + "cluster_station": 3, + "sequencer": 2, + "flowcell_id": "30012AAXX (failed)" + } + }, + {"pk": 201, "model": "experiments.lane", + "fields": { + "comment": "", + "library": "11070", + "cluster_estimate": 182000, + "flowcell": 200, + "lane_number": 8, + "pM": "7" + } + } ]