{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2628PYOH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2628PYOH",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW278"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0109SCQO](/auxiliary-sets/IGVFDS0109SCQO/) has sequence file(s) [IGVFFI0359OPZH](/sequence-files/IGVFFI0359OPZH/), [IGVFFI1587BLSX](/sequence-files/IGVFFI1587BLSX/), [IGVFFI8395IXDC](/sequence-files/IGVFFI8395IXDC/), [IGVFFI6340VLIA](/sequence-files/IGVFFI6340VLIA/), [IGVFFI5123HTNM](/sequence-files/IGVFFI5123HTNM/), [IGVFFI5460OSRQ](/sequence-files/IGVFFI5460OSRQ/), [IGVFFI6913WKOH](/sequence-files/IGVFFI6913WKOH/), [IGVFFI3244CIGW](/sequence-files/IGVFFI3244CIGW/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0109SCQO/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0109SCQO](/auxiliary-sets/IGVFDS0109SCQO/) has sequence file(s): [IGVFFI0359OPZH](/sequence-files/IGVFFI0359OPZH/), [IGVFFI1587BLSX](/sequence-files/IGVFFI1587BLSX/), [IGVFFI8395IXDC](/sequence-files/IGVFFI8395IXDC/), [IGVFFI6340VLIA](/sequence-files/IGVFFI6340VLIA/), [IGVFFI5123HTNM](/sequence-files/IGVFFI5123HTNM/), [IGVFFI5460OSRQ](/sequence-files/IGVFFI5460OSRQ/), [IGVFFI6913WKOH](/sequence-files/IGVFFI6913WKOH/), [IGVFFI3244CIGW](/sequence-files/IGVFFI3244CIGW/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS0109SCQO/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8139DLEM](/auxiliary-sets/IGVFDS8139DLEM/) has sequence file(s) [IGVFFI7706SWGW](/sequence-files/IGVFFI7706SWGW/), [IGVFFI7788FDIR](/sequence-files/IGVFFI7788FDIR/), [IGVFFI6246XEYZ](/sequence-files/IGVFFI6246XEYZ/), [IGVFFI5269EMSE](/sequence-files/IGVFFI5269EMSE/), [IGVFFI7446JOPR](/sequence-files/IGVFFI7446JOPR/), [IGVFFI2624RMQV](/sequence-files/IGVFFI2624RMQV/), [IGVFFI7302FRGV](/sequence-files/IGVFFI7302FRGV/), [IGVFFI3447MKLI](/sequence-files/IGVFFI3447MKLI/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS8139DLEM/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8139DLEM](/auxiliary-sets/IGVFDS8139DLEM/) has sequence file(s): [IGVFFI7706SWGW](/sequence-files/IGVFFI7706SWGW/), [IGVFFI7788FDIR](/sequence-files/IGVFFI7788FDIR/), [IGVFFI6246XEYZ](/sequence-files/IGVFFI6246XEYZ/), [IGVFFI5269EMSE](/sequence-files/IGVFFI5269EMSE/), [IGVFFI7446JOPR](/sequence-files/IGVFFI7446JOPR/), [IGVFFI2624RMQV](/sequence-files/IGVFFI2624RMQV/), [IGVFFI7302FRGV](/sequence-files/IGVFFI7302FRGV/), [IGVFFI3447MKLI](/sequence-files/IGVFFI3447MKLI/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS8139DLEM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2628PYOH](/measurement-sets/IGVFDS2628PYOH/) has sequence file(s) [IGVFFI3549FRZL](/sequence-files/IGVFFI3549FRZL/), [IGVFFI3287GSDX](/sequence-files/IGVFFI3287GSDX/), [IGVFFI6854CNMR](/sequence-files/IGVFFI6854CNMR/), [IGVFFI0116GLJN](/sequence-files/IGVFFI0116GLJN/), [IGVFFI0240MDNW](/sequence-files/IGVFFI0240MDNW/), [IGVFFI2281LVOV](/sequence-files/IGVFFI2281LVOV/), [IGVFFI8935VLDH](/sequence-files/IGVFFI8935VLDH/), [IGVFFI5553EXGP](/sequence-files/IGVFFI5553EXGP/), [IGVFFI1044NEIU](/sequence-files/IGVFFI1044NEIU/), [IGVFFI1800XJLY](/sequence-files/IGVFFI1800XJLY/), [IGVFFI2581ZBYM](/sequence-files/IGVFFI2581ZBYM/), [IGVFFI7820TAWX](/sequence-files/IGVFFI7820TAWX/), [IGVFFI0907CMNL](/sequence-files/IGVFFI0907CMNL/), [IGVFFI1946LEGM](/sequence-files/IGVFFI1946LEGM/), [IGVFFI7535OPQC](/sequence-files/IGVFFI7535OPQC/), [IGVFFI5195OGCL](/sequence-files/IGVFFI5195OGCL/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS2628PYOH/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2628PYOH](/measurement-sets/IGVFDS2628PYOH/) has sequence file(s): [IGVFFI3549FRZL](/sequence-files/IGVFFI3549FRZL/), [IGVFFI3287GSDX](/sequence-files/IGVFFI3287GSDX/), [IGVFFI6854CNMR](/sequence-files/IGVFFI6854CNMR/), [IGVFFI0116GLJN](/sequence-files/IGVFFI0116GLJN/), [IGVFFI0240MDNW](/sequence-files/IGVFFI0240MDNW/), [IGVFFI2281LVOV](/sequence-files/IGVFFI2281LVOV/), [IGVFFI8935VLDH](/sequence-files/IGVFFI8935VLDH/), [IGVFFI5553EXGP](/sequence-files/IGVFFI5553EXGP/), [IGVFFI1044NEIU](/sequence-files/IGVFFI1044NEIU/), [IGVFFI1800XJLY](/sequence-files/IGVFFI1800XJLY/), [IGVFFI2581ZBYM](/sequence-files/IGVFFI2581ZBYM/), [IGVFFI7820TAWX](/sequence-files/IGVFFI7820TAWX/), [IGVFFI0907CMNL](/sequence-files/IGVFFI0907CMNL/), [IGVFFI1946LEGM](/sequence-files/IGVFFI1946LEGM/), [IGVFFI7535OPQC](/sequence-files/IGVFFI7535OPQC/), [IGVFFI5195OGCL](/sequence-files/IGVFFI5195OGCL/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS2628PYOH/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8139DLEM/",
"accession": "IGVFDS8139DLEM",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_sgRNA_LW278"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS0109SCQO/",
"accession": "IGVFDS0109SCQO",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_HTO_LW278"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
}
],
"award": {
"@id": "/awards/HG011996/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/95d84f03-8ce0-489c-a755-f33ced139c5d/",
"title": "Gary Hon"
},
"title": "Multiscale functional characterization of genomic variation in human developmental disorders"
},
"control_for": [],
"creation_timestamp": "2024-02-21T21:07:18.515909+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI3549FRZL",
"aliases": [
"gary-hon:LW278_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:10:57.093887+00:00",
"file_format": "fastq",
"file_size": 602801610,
"href": "/sequence-files/IGVFFI3549FRZL/@@download/IGVFFI3549FRZL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/84f48aa2-5801-47b1-99f4-75521f199947/IGVFFI3549FRZL.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW278_S16_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
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"accession": "IGVFFI3287GSDX",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:10:41.613966+00:00",
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"href": "/sequence-files/IGVFFI3287GSDX/@@download/IGVFFI3287GSDX.fastq.gz",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI6854CNMR",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:10:51.143365+00:00",
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"href": "/sequence-files/IGVFFI6854CNMR/@@download/IGVFFI6854CNMR.fastq.gz",
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"status": "released",
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},
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"upload_status": "validated"
},
{
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"accession": "IGVFFI0116GLJN",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:10:17.398886+00:00",
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"file_size": 100053352,
"href": "/sequence-files/IGVFFI0116GLJN/@@download/IGVFFI0116GLJN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/b4b2f9a0-eaa4-4a0c-a307-dc6c817847d7/IGVFFI0116GLJN.fastq.gz",
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"status": "released",
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},
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},
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"accession": "IGVFFI0240MDNW",
"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2024-03-01T17:10:26.753118+00:00",
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},
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"aliases": [
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],
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"creation_timestamp": "2024-03-01T17:10:32.721666+00:00",
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],
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"creation_timestamp": "2024-03-01T17:10:46.367254+00:00",
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},
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},
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"aliases": [
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],
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},
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},
{
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"aliases": [
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},
{
"@id": "/sequence-files/IGVFFI0907CMNL/",
"accession": "IGVFFI0907CMNL",
"aliases": [
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"creation_timestamp": "2024-03-01T18:46:13.963159+00:00",
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