{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2692VBHQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2692VBHQ",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW287"
],
"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 [IGVFDS1937JPZI](/auxiliary-sets/IGVFDS1937JPZI/) has sequence file(s) [IGVFFI8385HABJ](/sequence-files/IGVFFI8385HABJ/), [IGVFFI3275ZEBW](/sequence-files/IGVFFI3275ZEBW/), [IGVFFI1518BMVF](/sequence-files/IGVFFI1518BMVF/), [IGVFFI7286ZUUS](/sequence-files/IGVFFI7286ZUUS/) 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/IGVFDS1937JPZI/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1937JPZI](/auxiliary-sets/IGVFDS1937JPZI/) has sequence file(s): [IGVFFI8385HABJ](/sequence-files/IGVFFI8385HABJ/), [IGVFFI3275ZEBW](/sequence-files/IGVFFI3275ZEBW/), [IGVFFI1518BMVF](/sequence-files/IGVFFI1518BMVF/), [IGVFFI7286ZUUS](/sequence-files/IGVFFI7286ZUUS/) 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/IGVFDS1937JPZI/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2692VBHQ](/measurement-sets/IGVFDS2692VBHQ/) has sequence file(s) [IGVFFI9530TKDL](/sequence-files/IGVFFI9530TKDL/), [IGVFFI1291VGGB](/sequence-files/IGVFFI1291VGGB/), [IGVFFI8052QAVO](/sequence-files/IGVFFI8052QAVO/), [IGVFFI0588MNHI](/sequence-files/IGVFFI0588MNHI/), [IGVFFI2941KCXR](/sequence-files/IGVFFI2941KCXR/), [IGVFFI8090CHJY](/sequence-files/IGVFFI8090CHJY/), [IGVFFI2261NWNR](/sequence-files/IGVFFI2261NWNR/), [IGVFFI3066OUFL](/sequence-files/IGVFFI3066OUFL/) 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/IGVFDS2692VBHQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2692VBHQ](/measurement-sets/IGVFDS2692VBHQ/) has sequence file(s): [IGVFFI9530TKDL](/sequence-files/IGVFFI9530TKDL/), [IGVFFI1291VGGB](/sequence-files/IGVFFI1291VGGB/), [IGVFFI8052QAVO](/sequence-files/IGVFFI8052QAVO/), [IGVFFI0588MNHI](/sequence-files/IGVFFI0588MNHI/), [IGVFFI2941KCXR](/sequence-files/IGVFFI2941KCXR/), [IGVFFI8090CHJY](/sequence-files/IGVFFI8090CHJY/), [IGVFFI2261NWNR](/sequence-files/IGVFFI2261NWNR/), [IGVFFI3066OUFL](/sequence-files/IGVFFI3066OUFL/) 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/IGVFDS2692VBHQ/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2373RGIJ](/auxiliary-sets/IGVFDS2373RGIJ/) has sequence file(s) [IGVFFI7050AVQG](/sequence-files/IGVFFI7050AVQG/), [IGVFFI6282MCFD](/sequence-files/IGVFFI6282MCFD/), [IGVFFI5493BBTV](/sequence-files/IGVFFI5493BBTV/), [IGVFFI1454KXNR](/sequence-files/IGVFFI1454KXNR/) 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/IGVFDS2373RGIJ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2373RGIJ](/auxiliary-sets/IGVFDS2373RGIJ/) has sequence file(s): [IGVFFI7050AVQG](/sequence-files/IGVFFI7050AVQG/), [IGVFFI6282MCFD](/sequence-files/IGVFFI6282MCFD/), [IGVFFI5493BBTV](/sequence-files/IGVFFI5493BBTV/), [IGVFFI1454KXNR](/sequence-files/IGVFFI1454KXNR/) 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/IGVFDS2373RGIJ/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1937JPZI/",
"accession": "IGVFDS1937JPZI",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW287"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2373RGIJ/",
"accession": "IGVFDS2373RGIJ",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_HTO_LW287"
],
"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": "2024-02-21T21:28:51.084902+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": [
{
"@id": "/sequence-files/IGVFFI9530TKDL/",
"accession": "IGVFFI9530TKDL",
"aliases": [
"gary-hon:LW287_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:51:35.105818+00:00",
"file_format": "fastq",
"file_size": 848056460,
"href": "/sequence-files/IGVFFI9530TKDL/@@download/IGVFFI9530TKDL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/37913b5e-1085-4fb4-869d-28ad3200efe9/IGVFFI9530TKDL.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//LW287_S2_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1291VGGB/",
"accession": "IGVFFI1291VGGB",
"aliases": [
"gary-hon:LW287_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:51:46.412370+00:00",
"file_format": "fastq",
"file_size": 950460686,
"href": "/sequence-files/IGVFFI1291VGGB/@@download/IGVFFI1291VGGB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/d60250b7-0164-4635-9ee3-5d26fb1930b3/IGVFFI1291VGGB.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//LW287_S2_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8052QAVO/",
"accession": "IGVFFI8052QAVO",
"aliases": [
"gary-hon:LW287_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:51:58.445942+00:00",
"file_format": "fastq",
"file_size": 3001212186,
"href": "/sequence-files/IGVFFI8052QAVO/@@download/IGVFFI8052QAVO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/013f6412-7bbb-471d-b336-1584f35160bb/IGVFFI8052QAVO.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//LW287_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0588MNHI/",
"accession": "IGVFFI0588MNHI",
"aliases": [
"gary-hon:LW287_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:52:27.691202+00:00",
"file_format": "fastq",
"file_size": 7746113826,
"href": "/sequence-files/IGVFFI0588MNHI/@@download/IGVFFI0588MNHI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/3e75fa3b-a9f6-4a89-97da-18ffc0efd90c/IGVFFI0588MNHI.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//LW287_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2941KCXR/",
"accession": "IGVFFI2941KCXR",
"aliases": [
"gary-hon:LW287_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:53:37.580543+00:00",
"file_format": "fastq",
"file_size": 796583703,
"href": "/sequence-files/IGVFFI2941KCXR/@@download/IGVFFI2941KCXR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/6d895ff6-2b06-41f6-9e08-579e3109a041/IGVFFI2941KCXR.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//LW287_S2_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8090CHJY/",
"accession": "IGVFFI8090CHJY",
"aliases": [
"gary-hon:LW287_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:53:48.396242+00:00",
"file_format": "fastq",
"file_size": 880176910,
"href": "/sequence-files/IGVFFI8090CHJY/@@download/IGVFFI8090CHJY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/cae15c23-4a16-4d01-bf33-77b73c894baf/IGVFFI8090CHJY.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//LW287_S2_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2261NWNR/",
"accession": "IGVFFI2261NWNR",
"aliases": [
"gary-hon:LW287_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:53:59.814668+00:00",
"file_format": "fastq",
"file_size": 2739532382,
"href": "/sequence-files/IGVFFI2261NWNR/@@download/IGVFFI2261NWNR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/a6b8d1de-c0af-43f9-a21d-c1f76804a344/IGVFFI2261NWNR.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//LW287_S2_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3066OUFL/",
"accession": "IGVFFI3066OUFL",
"aliases": [
"gary-hon:LW287_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:54:26.962640+00:00",
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"href": "/sequence-files/IGVFFI3066OUFL/@@download/IGVFFI3066OUFL.fastq.gz",
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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//LW287_S2_L002_R2_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/IGVFSM1153INDY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1153INDY",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW287"
],
"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_LW287), 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": "2024-03-04T19:51:35.105818+00:00",
"submitter_comment": "Transcriptiome for LW287",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "b7e426f1-2366-4598-8009-1993c34e1c20"
}