{
"@context": "/terms/",
"@id": "/tabular-files/IGVFFI4410YZQZ/",
"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI4410YZQZ",
"aliases": [
"gary-hon:WTC11_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_local"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"ERROR": [
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI4410YZQZ](/tabular-files/IGVFFI4410YZQZ/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 521928c40e2bdf2234d01082cf035998 does not match newly calculated md5sum 5529ced80d67d34b604a49a2e7a0404a.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI4410YZQZ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI4410YZQZ](/tabular-files/IGVFFI4410YZQZ/) has no `file_format_specifications`. Tabular files are expected to link to a file format specifications document describing the headers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_tabular_file_no_file_format_specifications",
"path": "/tabular-files/IGVFFI4410YZQZ/"
}
]
},
"award": {
"@id": "/awards/HG011996/",
"component": "functional characterization"
},
"barcode_map_for": [],
"content_md5sum": "bb47f7aa7953e65e1f9d937c395052c4",
"content_type": "unfiltered local differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T20:48:34.756501+00:00",
"file_format": "csv",
"file_set": {
"@id": "/analysis-sets/IGVFDS4252LFRU/",
"accession": "IGVFDS4252LFRU",
"file_set_type": "principal analysis",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2176YXFG/",
"accession": "IGVFSM2176YXFG",
"classifications": [
"differentiated cell specimen"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW438), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM8072YOLO/",
"accession": "IGVFSM8072YOLO",
"classifications": [
"differentiated cell specimen"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW437), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM8889XSOR/",
"accession": "IGVFSM8889XSOR",
"classifications": [
"differentiated cell specimen"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW436), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM4418NJET/",
"accession": "IGVFSM4418NJET",
"classifications": [
"differentiated cell specimen"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW435), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
"status": "preview",
"summary": "interference Perturb-seq: filtered feature barcode matrix, raw feature barcode matrix, sparse gene count matrix, unfiltered global differential expression, unfiltered local differential expression"
},
"file_size": 6592,
"gene_list_for": [],
"href": "/tabular-files/IGVFFI4410YZQZ/@@download/IGVFFI4410YZQZ.csv.gz",
"input_file_for": [],
"integrated_in": [],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"loci_list_for": [],
"md5sum": "521928c40e2bdf2234d01082cf035998",
"s3_uri": "s3://igvf-files/2024/12/18/94cb8573-25f3-4a4d-bcc7-7b55f3002a56/IGVFFI4410YZQZ.csv.gz",
"schema_version": "13",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/WTC11_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_local.csv.gz",
"summary": "unfiltered local differential expression",
"upload_status": "invalidated",
"uuid": "94cb8573-25f3-4a4d-bcc7-7b55f3002a56",
"validation_error_detail": "{\"md5sum\": \"original md5sum 521928c40e2bdf2234d01082cf035998 does not match newly calculated md5sum 5529ced80d67d34b604a49a2e7a0404a.\"}"
}