{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5864UGFT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_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 sequencing kit",
"detail": "Measurement set [IGVFDS5864UGFT](/measurement-sets/IGVFDS5864UGFT/) has sequence file(s) [IGVFFI2901MSWB](/sequence-files/IGVFFI2901MSWB/), [IGVFFI5738GCOE](/sequence-files/IGVFFI5738GCOE/), [IGVFFI5264KOJB](/sequence-files/IGVFFI5264KOJB/), [IGVFFI7478BMNB](/sequence-files/IGVFFI7478BMNB/), [IGVFFI6767GQPX](/sequence-files/IGVFFI6767GQPX/), [IGVFFI8285QUQB](/sequence-files/IGVFFI8285QUQB/), [IGVFFI4202ZWWK](/sequence-files/IGVFFI4202ZWWK/), [IGVFFI6396HFWS](/sequence-files/IGVFFI6396HFWS/), [IGVFFI3230WTRR](/sequence-files/IGVFFI3230WTRR/), [IGVFFI6235MNEI](/sequence-files/IGVFFI6235MNEI/), [IGVFFI7915NGDF](/sequence-files/IGVFFI7915NGDF/), [IGVFFI5305KTDF](/sequence-files/IGVFFI5305KTDF/), [IGVFFI2838LQVE](/sequence-files/IGVFFI2838LQVE/), [IGVFFI4285ZZFD](/sequence-files/IGVFFI4285ZZFD/), [IGVFFI0960MBFN](/sequence-files/IGVFFI0960MBFN/), [IGVFFI9811QIHQ](/sequence-files/IGVFFI9811QIHQ/) 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/IGVFDS5864UGFT/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5864UGFT](/measurement-sets/IGVFDS5864UGFT/) has sequence file(s): [IGVFFI2901MSWB](/sequence-files/IGVFFI2901MSWB/), [IGVFFI5738GCOE](/sequence-files/IGVFFI5738GCOE/), [IGVFFI5264KOJB](/sequence-files/IGVFFI5264KOJB/), [IGVFFI7478BMNB](/sequence-files/IGVFFI7478BMNB/), [IGVFFI6767GQPX](/sequence-files/IGVFFI6767GQPX/), [IGVFFI8285QUQB](/sequence-files/IGVFFI8285QUQB/), [IGVFFI4202ZWWK](/sequence-files/IGVFFI4202ZWWK/), [IGVFFI6396HFWS](/sequence-files/IGVFFI6396HFWS/), [IGVFFI3230WTRR](/sequence-files/IGVFFI3230WTRR/), [IGVFFI6235MNEI](/sequence-files/IGVFFI6235MNEI/), [IGVFFI7915NGDF](/sequence-files/IGVFFI7915NGDF/), [IGVFFI5305KTDF](/sequence-files/IGVFFI5305KTDF/), [IGVFFI2838LQVE](/sequence-files/IGVFFI2838LQVE/), [IGVFFI4285ZZFD](/sequence-files/IGVFFI4285ZZFD/), [IGVFFI0960MBFN](/sequence-files/IGVFFI0960MBFN/), [IGVFFI9811QIHQ](/sequence-files/IGVFFI9811QIHQ/) 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/IGVFDS5864UGFT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5864UGFT](/measurement-sets/IGVFDS5864UGFT/) 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/IGVFDS5864UGFT/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS5864UGFT](/measurement-sets/IGVFDS5864UGFT/) 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/IGVFDS5864UGFT/"
}
]
},
"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"
},
"control_for": [
{
"@id": "/measurement-sets/IGVFDS4745BLLN/",
"accession": "IGVFDS4745BLLN",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8290UELV/",
"accession": "IGVFDS8290UELV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6761PEJX/",
"accession": "IGVFDS6761PEJX",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6622DPIT/",
"accession": "IGVFDS6622DPIT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6551IWAB/",
"accession": "IGVFDS6551IWAB",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5733FUWG/",
"accession": "IGVFDS5733FUWG",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0336ABEV/",
"accession": "IGVFDS0336ABEV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1783OBDQ/",
"accession": "IGVFDS1783OBDQ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4761MJPK/",
"accession": "IGVFDS4761MJPK",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6267YRNH/",
"accession": "IGVFDS6267YRNH",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5699JBLV/",
"accession": "IGVFDS5699JBLV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3532HUSQ/",
"accession": "IGVFDS3532HUSQ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9665GYVE/",
"accession": "IGVFDS9665GYVE",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0629YEMD/",
"accession": "IGVFDS0629YEMD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4715UUNW/",
"accession": "IGVFDS4715UUNW",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1402WRSD/",
"accession": "IGVFDS1402WRSD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4750CFGI/",
"accession": "IGVFDS4750CFGI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3537WUVG/",
"accession": "IGVFDS3537WUVG",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9084GQXI/",
"accession": "IGVFDS9084GQXI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6566NSFE/",
"accession": "IGVFDS6566NSFE",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1674OUCP/",
"accession": "IGVFDS1674OUCP",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8517SHZG/",
"accession": "IGVFDS8517SHZG",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8736JDCM/",
"accession": "IGVFDS8736JDCM",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2978YQVA/",
"accession": "IGVFDS2978YQVA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0403DJHI/",
"accession": "IGVFDS0403DJHI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8801DBGC/",
"accession": "IGVFDS8801DBGC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7403HHLV/",
"accession": "IGVFDS7403HHLV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3226EEYN/",
"accession": "IGVFDS3226EEYN",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8854UNCC/",
"accession": "IGVFDS8854UNCC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6512WYQI/",
"accession": "IGVFDS6512WYQI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8631OYNB/",
"accession": "IGVFDS8631OYNB",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9894YFSM/",
"accession": "IGVFDS9894YFSM",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4761PXVO/",
"accession": "IGVFDS4761PXVO",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1646OXQU/",
"accession": "IGVFDS1646OXQU",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6147NJBC/",
"accession": "IGVFDS6147NJBC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7009ITAD/",
"accession": "IGVFDS7009ITAD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1327XCCU/",
"accession": "IGVFDS1327XCCU",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0744DITV/",
"accession": "IGVFDS0744DITV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8356GTHO/",
"accession": "IGVFDS8356GTHO",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7791SSYA/",
"accession": "IGVFDS7791SSYA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinC_AmpliconSequencing"
],
"status": "released"
}
],
"control_type": "untransfected",
"creation_timestamp": "2023-11-30T22:49:34.691226+00:00",
"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/IGVFFI2901MSWB/",
"accession": "IGVFFI2901MSWB",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:32:16.518847+00:00",
"file_format": "fastq",
"file_size": 1235454,
"href": "/sequence-files/IGVFFI2901MSWB/@@download/IGVFFI2901MSWB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3e3eda2d-54fe-4f72-9fb5-1aa34972a689/IGVFFI2901MSWB.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrepNA-BinNeg-PCRrep3_S411_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5738GCOE/",
"accession": "IGVFFI5738GCOE",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep3_R1"
],
"content_type": "reads",
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"creation_timestamp": "2023-12-05T21:32:25.293840+00:00",
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"href": "/sequence-files/IGVFFI5738GCOE/@@download/IGVFFI5738GCOE.fastq.gz",
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"sequencing_platform": {
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"status": "released",
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},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrepNA-BinNeg-PCRrep3_S411_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5264KOJB/",
"accession": "IGVFFI5264KOJB",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:32:07.835758+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI5264KOJB/@@download/IGVFFI5264KOJB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0e1729b5-70b5-4c37-bf63-1dc8c8963786/IGVFFI5264KOJB.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrepNA-BinNeg-PCRrep3_S411_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7478BMNB/",
"accession": "IGVFFI7478BMNB",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:32:34.069237+00:00",
"file_format": "fastq",
"file_size": 5000072,
"href": "/sequence-files/IGVFFI7478BMNB/@@download/IGVFFI7478BMNB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4e05b06d-688d-43aa-b102-12afcbb6d6cb/IGVFFI7478BMNB.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-FFrepNA-BinNeg-PCRrep3_S411_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6767GQPX/",
"accession": "IGVFFI6767GQPX",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:31:25.004664+00:00",
"file_format": "fastq",
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