{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3495FUIW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3495FUIW",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW289"
],
"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 [IGVFDS6015JDKU](/auxiliary-sets/IGVFDS6015JDKU/) has sequence file(s) [IGVFFI6468GABU](/sequence-files/IGVFFI6468GABU/), [IGVFFI6456QWCW](/sequence-files/IGVFFI6456QWCW/), [IGVFFI0029ZRXZ](/sequence-files/IGVFFI0029ZRXZ/), [IGVFFI4585KPNO](/sequence-files/IGVFFI4585KPNO/) 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/IGVFDS6015JDKU/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6015JDKU](/auxiliary-sets/IGVFDS6015JDKU/) has sequence file(s): [IGVFFI6468GABU](/sequence-files/IGVFFI6468GABU/), [IGVFFI6456QWCW](/sequence-files/IGVFFI6456QWCW/), [IGVFFI0029ZRXZ](/sequence-files/IGVFFI0029ZRXZ/), [IGVFFI4585KPNO](/sequence-files/IGVFFI4585KPNO/) 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/IGVFDS6015JDKU/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1931QVXR](/auxiliary-sets/IGVFDS1931QVXR/) has sequence file(s) [IGVFFI2505GTMO](/sequence-files/IGVFFI2505GTMO/), [IGVFFI6068UCJF](/sequence-files/IGVFFI6068UCJF/), [IGVFFI1333KJVP](/sequence-files/IGVFFI1333KJVP/), [IGVFFI4370ZHGH](/sequence-files/IGVFFI4370ZHGH/) 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/IGVFDS1931QVXR/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1931QVXR](/auxiliary-sets/IGVFDS1931QVXR/) has sequence file(s): [IGVFFI2505GTMO](/sequence-files/IGVFFI2505GTMO/), [IGVFFI6068UCJF](/sequence-files/IGVFFI6068UCJF/), [IGVFFI1333KJVP](/sequence-files/IGVFFI1333KJVP/), [IGVFFI4370ZHGH](/sequence-files/IGVFFI4370ZHGH/) 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/IGVFDS1931QVXR/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3495FUIW](/measurement-sets/IGVFDS3495FUIW/) has sequence file(s) [IGVFFI4619JBKN](/sequence-files/IGVFFI4619JBKN/), [IGVFFI0029HYME](/sequence-files/IGVFFI0029HYME/), [IGVFFI3311SGCE](/sequence-files/IGVFFI3311SGCE/), [IGVFFI1599REKO](/sequence-files/IGVFFI1599REKO/), [IGVFFI1831BWFA](/sequence-files/IGVFFI1831BWFA/), [IGVFFI5866PQRS](/sequence-files/IGVFFI5866PQRS/), [IGVFFI6540FOZV](/sequence-files/IGVFFI6540FOZV/), [IGVFFI7073MZDL](/sequence-files/IGVFFI7073MZDL/) 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/IGVFDS3495FUIW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3495FUIW](/measurement-sets/IGVFDS3495FUIW/) has sequence file(s): [IGVFFI4619JBKN](/sequence-files/IGVFFI4619JBKN/), [IGVFFI0029HYME](/sequence-files/IGVFFI0029HYME/), [IGVFFI3311SGCE](/sequence-files/IGVFFI3311SGCE/), [IGVFFI1599REKO](/sequence-files/IGVFFI1599REKO/), [IGVFFI1831BWFA](/sequence-files/IGVFFI1831BWFA/), [IGVFFI5866PQRS](/sequence-files/IGVFFI5866PQRS/), [IGVFFI6540FOZV](/sequence-files/IGVFFI6540FOZV/), [IGVFFI7073MZDL](/sequence-files/IGVFFI7073MZDL/) 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/IGVFDS3495FUIW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1931QVXR/",
"accession": "IGVFDS1931QVXR",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW289"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6015JDKU/",
"accession": "IGVFDS6015JDKU",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_HTO_LW289"
],
"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": "2024-02-21T21:28:52.738874+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": "IGVFFI4619JBKN",
"aliases": [
"gary-hon:LW289_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:59:19.076267+00:00",
"file_format": "fastq",
"file_size": 953824605,
"href": "/sequence-files/IGVFFI4619JBKN/@@download/IGVFFI4619JBKN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/380e209c-dc23-4d6c-b690-463750da8ed4/IGVFFI4619JBKN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW289_S4_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0029HYME/",
"accession": "IGVFFI0029HYME",
"aliases": [
"gary-hon:LW289_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:01:55.997108+00:00",
"file_format": "fastq",
"file_size": 6854997126,
"href": "/sequence-files/IGVFFI0029HYME/@@download/IGVFFI0029HYME.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/4d570255-24d9-46f6-a229-9c99d594e9d2/IGVFFI0029HYME.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW289_S4_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3311SGCE/",
"accession": "IGVFFI3311SGCE",
"aliases": [
"gary-hon:LW289_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:59:07.530121+00:00",
"file_format": "fastq",
"file_size": 875197702,
"href": "/sequence-files/IGVFFI3311SGCE/@@download/IGVFFI3311SGCE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/6e7da687-00cd-4ac4-a11c-e78f327baff2/IGVFFI3311SGCE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW289_S4_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1599REKO/",
"accession": "IGVFFI1599REKO",
"aliases": [
"gary-hon:LW289_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:01:06.328794+00:00",
"file_format": "fastq",
"file_size": 825989722,
"href": "/sequence-files/IGVFFI1599REKO/@@download/IGVFFI1599REKO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/6faa0c69-332f-41b3-81de-3cecf5213414/IGVFFI1599REKO.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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW289_S4_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1831BWFA/",
"accession": "IGVFFI1831BWFA",
"aliases": [
"gary-hon:LW289_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:01:17.614159+00:00",
"file_format": "fastq",
"file_size": 903652404,
"href": "/sequence-files/IGVFFI1831BWFA/@@download/IGVFFI1831BWFA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/b1661c82-20f0-442a-a868-349ff973c533/IGVFFI1831BWFA.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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW289_S4_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5866PQRS/",
"accession": "IGVFFI5866PQRS",
"aliases": [
"gary-hon:LW289_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:59:31.047554+00:00",
"file_format": "fastq",
"file_size": 2863060614,
"href": "/sequence-files/IGVFFI5866PQRS/@@download/IGVFFI5866PQRS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/25435713-572e-4a50-b854-04361aef7e40/IGVFFI5866PQRS.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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW289_S4_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6540FOZV/",
"accession": "IGVFFI6540FOZV",
"aliases": [
"gary-hon:LW289_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:59:59.285328+00:00",
"file_format": "fastq",
"file_size": 7396576666,
"href": "/sequence-files/IGVFFI6540FOZV/@@download/IGVFFI6540FOZV.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW289_S4_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7073MZDL/",
"accession": "IGVFFI7073MZDL",
"aliases": [
"gary-hon:LW289_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:01:29.390920+00:00",
"file_format": "fastq",
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"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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW289_S4_L002_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7340YDHF/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"preferred_assay_title": "Perturb-seq",
"protocols": [
"https://www.protocols.io/view/experimental-procedures-for-tf-perturb-seq-ut-sout-denf3dbn"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1597KVRS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1597KVRS",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW289"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2302LCEO/",
"accession": "IGVFDS2302LCEO",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) cell line (cellular sub pool: subpool_LW289), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-03-04T19:59:07.530121+00:00",
"submitter_comment": "Transcriptiome for LW289",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "85804c71-b383-4b0a-8064-604b831d29af"
}