{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2978YQVA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2978YQVA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2978YQVA](/measurement-sets/IGVFDS2978YQVA/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS2978YQVA/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2978YQVA](/measurement-sets/IGVFDS2978YQVA/) has sequence file(s) [IGVFFI4719EJGG](/sequence-files/IGVFFI4719EJGG/), [IGVFFI2343VDQB](/sequence-files/IGVFFI2343VDQB/), [IGVFFI9721QXSH](/sequence-files/IGVFFI9721QXSH/), [IGVFFI9315IHLL](/sequence-files/IGVFFI9315IHLL/), [IGVFFI5662LHGR](/sequence-files/IGVFFI5662LHGR/), [IGVFFI5349UFOZ](/sequence-files/IGVFFI5349UFOZ/), [IGVFFI5374SSMO](/sequence-files/IGVFFI5374SSMO/), [IGVFFI6448TEJG](/sequence-files/IGVFFI6448TEJG/), [IGVFFI3321HMGZ](/sequence-files/IGVFFI3321HMGZ/), [IGVFFI0864LZHT](/sequence-files/IGVFFI0864LZHT/), [IGVFFI6332YPUU](/sequence-files/IGVFFI6332YPUU/), [IGVFFI2391ZMYI](/sequence-files/IGVFFI2391ZMYI/), [IGVFFI6492FHPV](/sequence-files/IGVFFI6492FHPV/), [IGVFFI9323QYVO](/sequence-files/IGVFFI9323QYVO/), [IGVFFI4573MSCD](/sequence-files/IGVFFI4573MSCD/), [IGVFFI7395ZMHL](/sequence-files/IGVFFI7395ZMHL/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS2978YQVA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2978YQVA](/measurement-sets/IGVFDS2978YQVA/) has sequence file(s): [IGVFFI4719EJGG](/sequence-files/IGVFFI4719EJGG/), [IGVFFI2343VDQB](/sequence-files/IGVFFI2343VDQB/), [IGVFFI9721QXSH](/sequence-files/IGVFFI9721QXSH/), [IGVFFI9315IHLL](/sequence-files/IGVFFI9315IHLL/), [IGVFFI5662LHGR](/sequence-files/IGVFFI5662LHGR/), [IGVFFI5349UFOZ](/sequence-files/IGVFFI5349UFOZ/), [IGVFFI5374SSMO](/sequence-files/IGVFFI5374SSMO/), [IGVFFI6448TEJG](/sequence-files/IGVFFI6448TEJG/), [IGVFFI3321HMGZ](/sequence-files/IGVFFI3321HMGZ/), [IGVFFI0864LZHT](/sequence-files/IGVFFI0864LZHT/), [IGVFFI6332YPUU](/sequence-files/IGVFFI6332YPUU/), [IGVFFI2391ZMYI](/sequence-files/IGVFFI2391ZMYI/), [IGVFFI6492FHPV](/sequence-files/IGVFFI6492FHPV/), [IGVFFI9323QYVO](/sequence-files/IGVFFI9323QYVO/), [IGVFFI4573MSCD](/sequence-files/IGVFFI4573MSCD/), [IGVFFI7395ZMHL](/sequence-files/IGVFFI7395ZMHL/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS2978YQVA/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5940EPFP](/in-vitro-systems/IGVFSM5940EPFP/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM5940EPFP/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM5940EPFP](/in-vitro-systems/IGVFSM5940EPFP/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM5940EPFP/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS2978YQVA](/measurement-sets/IGVFDS2978YQVA/) has no `control_for`. The `control_file_sets` should be patched on the file sets it serves as a control for and this property, `control_for`, will be reverse calculated. File sets that specify a control type are expected to be a control for other file sets.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_control_for_control_type",
"path": "/measurement-sets/IGVFDS2978YQVA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2978YQVA](/measurement-sets/IGVFDS2978YQVA/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS2978YQVA/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS2978YQVA](/measurement-sets/IGVFDS2978YQVA/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
"level": 40,
"level_name": "WARNING",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS2978YQVA/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"file_set_type": "guide library",
"status": "in progress",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-12-01T00:05:32.482942+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4719EJGG/",
"accession": "IGVFFI4719EJGG",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:36:51.869255+00:00",
"file_format": "fastq",
"file_size": 5850030,
"href": "/sequence-files/IGVFFI4719EJGG/@@download/IGVFFI4719EJGG.fastq.gz",
"md5sum": "72f8b6cc9b3f9a810c1b9fb499d186d2",
"s3_uri": "s3://igvf-files/2023/12/05/44e59c85-2ef7-49fc-94fe-a9a2a35e9836/IGVFFI4719EJGG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep4_S412_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2343VDQB/",
"accession": "IGVFFI2343VDQB",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:35:59.046134+00:00",
"file_format": "fastq",
"file_size": 1359444,
"href": "/sequence-files/IGVFFI2343VDQB/@@download/IGVFFI2343VDQB.fastq.gz",
"md5sum": "c5c0119c8ef82a32b39d27a23dac391f",
"s3_uri": "s3://igvf-files/2023/12/05/51dae852-1fa6-4a90-83a1-175283aa017d/IGVFFI2343VDQB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep3_S403_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9721QXSH/",
"accession": "IGVFFI9721QXSH",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:34:49.220907+00:00",
"file_format": "fastq",
"file_size": 1366194,
"href": "/sequence-files/IGVFFI9721QXSH/@@download/IGVFFI9721QXSH.fastq.gz",
"md5sum": "0696d1caa435d93c72d024383f93c94f",
"s3_uri": "s3://igvf-files/2023/12/05/06f7b91f-141b-4b59-86b4-6313c012e661/IGVFFI9721QXSH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep1_S385_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9315IHLL/",
"accession": "IGVFFI9315IHLL",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:35:15.393951+00:00",
"file_format": "fastq",
"file_size": 1360443,
"href": "/sequence-files/IGVFFI9315IHLL/@@download/IGVFFI9315IHLL.fastq.gz",
"md5sum": "f5099c8250b443eb57407ee9b00e32da",
"s3_uri": "s3://igvf-files/2023/12/05/7e75608e-3432-4bb4-99de-b1dd4086b1f8/IGVFFI9315IHLL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep2_S394_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5662LHGR/",
"accession": "IGVFFI5662LHGR",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:36:34.321141+00:00",
"file_format": "fastq",
"file_size": 1387768,
"href": "/sequence-files/IGVFFI5662LHGR/@@download/IGVFFI5662LHGR.fastq.gz",
"md5sum": "e61c6e07550153fc08a8127474078ab7",
"s3_uri": "s3://igvf-files/2023/12/05/c0685bb8-f5fb-4c70-8ff4-62756c269351/IGVFFI5662LHGR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep4_S412_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5349UFOZ/",
"accession": "IGVFFI5349UFOZ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:35:32.678237+00:00",
"file_format": "fastq",
"file_size": 4526436,
"href": "/sequence-files/IGVFFI5349UFOZ/@@download/IGVFFI5349UFOZ.fastq.gz",
"md5sum": "24d9c3c88f8a2ac9fb372b0f8a404931",
"s3_uri": "s3://igvf-files/2023/12/05/f18b0adc-828d-4299-9f76-24866d560178/IGVFFI5349UFOZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep2_S394_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5374SSMO/",
"accession": "IGVFFI5374SSMO",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:35:24.077657+00:00",
"file_format": "fastq",
"file_size": 1316933,
"href": "/sequence-files/IGVFFI5374SSMO/@@download/IGVFFI5374SSMO.fastq.gz",
"md5sum": "b0b8f27e85748171f3a597e04ecf4f49",
"s3_uri": "s3://igvf-files/2023/12/05/a7d4e543-c70d-4f0f-8c1c-1d0f94feaeeb/IGVFFI5374SSMO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep2_S394_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6448TEJG/",
"accession": "IGVFFI6448TEJG",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:35:41.411043+00:00",
"file_format": "fastq",
"file_size": 5686693,
"href": "/sequence-files/IGVFFI6448TEJG/@@download/IGVFFI6448TEJG.fastq.gz",
"md5sum": "0faf012d659feb03ff4edc9feb76ecaa",
"s3_uri": "s3://igvf-files/2023/12/05/fca0ee7f-b73a-411b-b944-cbd9385cce90/IGVFFI6448TEJG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep2_S394_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3321HMGZ/",
"accession": "IGVFFI3321HMGZ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:35:06.599454+00:00",
"file_format": "fastq",
"file_size": 5871930,
"href": "/sequence-files/IGVFFI3321HMGZ/@@download/IGVFFI3321HMGZ.fastq.gz",
"md5sum": "824dc8dbf8caae64a9e54a2489807611",
"s3_uri": "s3://igvf-files/2023/12/05/53909ffe-43c6-499f-af9c-342bd428bf5f/IGVFFI3321HMGZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep1_S385_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0864LZHT/",
"accession": "IGVFFI0864LZHT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:34:57.853388+00:00",
"file_format": "fastq",
"file_size": 4702307,
"href": "/sequence-files/IGVFFI0864LZHT/@@download/IGVFFI0864LZHT.fastq.gz",
"md5sum": "2e04718e74e0ed0789638b936b14b4ef",
"s3_uri": "s3://igvf-files/2023/12/05/3f52a418-0cae-4c4e-ac0b-df356f9e4cbd/IGVFFI0864LZHT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep1_S385_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6332YPUU/",
"accession": "IGVFFI6332YPUU",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:36:42.999731+00:00",
"file_format": "fastq",
"file_size": 4720461,
"href": "/sequence-files/IGVFFI6332YPUU/@@download/IGVFFI6332YPUU.fastq.gz",
"md5sum": "d0a5c378a787ede96ac4535cc5150737",
"s3_uri": "s3://igvf-files/2023/12/05/841009c3-a075-4ac3-9144-92240da8e9cd/IGVFFI6332YPUU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep4_S412_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2391ZMYI/",
"accession": "IGVFFI2391ZMYI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:36:25.578228+00:00",
"file_format": "fastq",
"file_size": 1410897,
"href": "/sequence-files/IGVFFI2391ZMYI/@@download/IGVFFI2391ZMYI.fastq.gz",
"md5sum": "3a32f24d2c03f96636b01ab6f0fc05b3",
"s3_uri": "s3://igvf-files/2023/12/05/b6810f1e-4ee7-4469-851f-8324dcd64b0e/IGVFFI2391ZMYI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep4_S412_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6492FHPV/",
"accession": "IGVFFI6492FHPV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:35:50.445218+00:00",
"file_format": "fastq",
"file_size": 1333975,
"href": "/sequence-files/IGVFFI6492FHPV/@@download/IGVFFI6492FHPV.fastq.gz",
"md5sum": "e53a98decb0d4ae9ba6dadfacc544f5e",
"s3_uri": "s3://igvf-files/2023/12/05/6a1f73e8-cd40-43e8-a60d-13669d8a3a5d/IGVFFI6492FHPV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep3_S403_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9323QYVO/",
"accession": "IGVFFI9323QYVO",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:36:08.012247+00:00",
"file_format": "fastq",
"file_size": 4609716,
"href": "/sequence-files/IGVFFI9323QYVO/@@download/IGVFFI9323QYVO.fastq.gz",
"md5sum": "43ad2d409db2aae93f0fcd3282695f1c",
"s3_uri": "s3://igvf-files/2023/12/05/6a70794f-acc8-4f06-b20a-73aa40570cc9/IGVFFI9323QYVO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep3_S403_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4573MSCD/",
"accession": "IGVFFI4573MSCD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:34:40.635195+00:00",
"file_format": "fastq",
"file_size": 1325783,
"href": "/sequence-files/IGVFFI4573MSCD/@@download/IGVFFI4573MSCD.fastq.gz",
"md5sum": "c70d0d332470d61378417981d2b7231f",
"s3_uri": "s3://igvf-files/2023/12/05/746adf58-209c-4836-9238-9da7f510b804/IGVFFI4573MSCD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep1_S385_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7395ZMHL/",
"accession": "IGVFFI7395ZMHL",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:36:16.803696+00:00",
"file_format": "fastq",
"file_size": 5751265,
"href": "/sequence-files/IGVFFI7395ZMHL/@@download/IGVFFI7395ZMHL.fastq.gz",
"md5sum": "0a72551ccb46353c9eb4286077920a68",
"s3_uri": "s3://igvf-files/2023/12/05/2dfdefcc-40e8-4f41-91a8-0b4f1d93ecf0/IGVFFI7395ZMHL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinAll-PCRrep3_S403_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS3423PSID/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. This measurement set previously used Variant FlowFISH as a preferred_assay_title, but this enum is now removed. So it has been defaulted to Variant-EFFECTS.",
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:06:04.513290+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5940EPFP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5940EPFP",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:34:40.635195+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "50ed0e8a-7769-498e-b3ad-ee006e7bc639"
}