{
"@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 publication",
"detail": "In vitro system [IGVFSM7075RRIN](/in-vitro-systems/IGVFSM7075RRIN/) 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/IGVFSM7075RRIN/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS5864UGFT](/measurement-sets/IGVFDS5864UGFT/) 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/IGVFDS5864UGFT/"
},
{
"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": {
"@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_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",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:32:25.293840+00:00",
"file_format": "fastq",
"file_size": 3895544,
"href": "/sequence-files/IGVFFI5738GCOE/@@download/IGVFFI5738GCOE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ac2405e4-4084-473b-942a-3ddc5bc009ed/IGVFFI5738GCOE.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_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",
"file_size": 1230365,
"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": {
"@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_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",
"file_size": 5827787,
"href": "/sequence-files/IGVFFI6767GQPX/@@download/IGVFFI6767GQPX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e9a89d41-c42f-48e0-87fd-d43470a85e51/IGVFFI6767GQPX.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-PCRrep1_S393_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8285QUQB/",
"accession": "IGVFFI8285QUQB",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:31:07.537849+00:00",
"file_format": "fastq",
"file_size": 1329921,
"href": "/sequence-files/IGVFFI8285QUQB/@@download/IGVFFI8285QUQB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/63dc380e-b4ee-4c2f-acea-133d4188248b/IGVFFI8285QUQB.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-PCRrep1_S393_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4202ZWWK/",
"accession": "IGVFFI4202ZWWK",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:31:51.004844+00:00",
"file_format": "fastq",
"file_size": 3918326,
"href": "/sequence-files/IGVFFI4202ZWWK/@@download/IGVFFI4202ZWWK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e38e73cf-d235-4e8c-8772-12c6f0b23dbf/IGVFFI4202ZWWK.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-PCRrep2_S402_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6396HFWS/",
"accession": "IGVFFI6396HFWS",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:30:58.691003+00:00",
"file_format": "fastq",
"file_size": 1374469,
"href": "/sequence-files/IGVFFI6396HFWS/@@download/IGVFFI6396HFWS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/550a10c2-8dc0-45ca-afaf-fc215a788751/IGVFFI6396HFWS.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-PCRrep1_S393_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3230WTRR/",
"accession": "IGVFFI3230WTRR",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:31:33.739857+00:00",
"file_format": "fastq",
"file_size": 1203204,
"href": "/sequence-files/IGVFFI3230WTRR/@@download/IGVFFI3230WTRR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3aa68e9d-6e86-4efa-b425-e98a84e64df2/IGVFFI3230WTRR.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-PCRrep2_S402_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6235MNEI/",
"accession": "IGVFFI6235MNEI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:33:00.462668+00:00",
"file_format": "fastq",
"file_size": 3914256,
"href": "/sequence-files/IGVFFI6235MNEI/@@download/IGVFFI6235MNEI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/04a0dab7-1c0c-4843-a470-31d65f3ca176/IGVFFI6235MNEI.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-PCRrep4_S420_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7915NGDF/",
"accession": "IGVFFI7915NGDF",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:32:42.786689+00:00",
"file_format": "fastq",
"file_size": 1247262,
"href": "/sequence-files/IGVFFI7915NGDF/@@download/IGVFFI7915NGDF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/310e8e34-c840-4736-bd35-0012fbefa5e9/IGVFFI7915NGDF.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-PCRrep4_S420_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5305KTDF/",
"accession": "IGVFFI5305KTDF",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:31:59.917961+00:00",
"file_format": "fastq",
"file_size": 5065301,
"href": "/sequence-files/IGVFFI5305KTDF/@@download/IGVFFI5305KTDF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ceb51bcf-d87c-4228-8718-d6e0a0e10af2/IGVFFI5305KTDF.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-PCRrep2_S402_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2838LQVE/",
"accession": "IGVFFI2838LQVE",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:33:09.225862+00:00",
"file_format": "fastq",
"file_size": 5012396,
"href": "/sequence-files/IGVFFI2838LQVE/@@download/IGVFFI2838LQVE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9ef3f61f-3081-4e8d-8f88-96b0870ac377/IGVFFI2838LQVE.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-PCRrep4_S420_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4285ZZFD/",
"accession": "IGVFFI4285ZZFD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:31:42.372612+00:00",
"file_format": "fastq",
"file_size": 1219077,
"href": "/sequence-files/IGVFFI4285ZZFD/@@download/IGVFFI4285ZZFD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4afc2443-f7cb-4205-b119-1ed3390380d8/IGVFFI4285ZZFD.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-PCRrep2_S402_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0960MBFN/",
"accession": "IGVFFI0960MBFN",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:32:51.676584+00:00",
"file_format": "fastq",
"file_size": 1216899,
"href": "/sequence-files/IGVFFI0960MBFN/@@download/IGVFFI0960MBFN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/20395ea1-f166-4145-b4a6-39652d906124/IGVFFI0960MBFN.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-PCRrep4_S420_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9811QIHQ/",
"accession": "IGVFFI9811QIHQ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:31:16.170307+00:00",
"file_format": "fastq",
"file_size": 4458547,
"href": "/sequence-files/IGVFFI9811QIHQ/@@download/IGVFFI9811QIHQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8c594c46-235f-4ceb-9754-acfb9542bbb5/IGVFFI9811QIHQ.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-PCRrep1_S393_R1_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": "2023-12-20T23:03:34.887828+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7075RRIN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7075RRIN",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl"
],
"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)",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T21:30:58.691003+00:00",
"summary": "untransfected prime editing Variant-EFFECTS",
"uuid": "5f789c5b-c158-405c-aa92-fcad5dab2aca"
}