{
"@context": "/terms/",
"@id": "/sequence-files/IGVFFI4071NQGH/",
"@type": [
"SequenceFile",
"File",
"Item"
],
"accession": "IGVFFI4071NQGH",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinB-PCRRep1_I2"
],
"assay_titles": [
"Variant-EFFECTS"
],
"audit": {},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"content_md5sum": "773e51763dbd9095b47501e7f20d32db",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:25:38.599566+00:00",
"externally_hosted": false,
"file_format": "fastq",
"file_set": {
"@id": "/measurement-sets/IGVFDS2419JBTK/",
"accession": "IGVFDS2419JBTK",
"file_set_type": "experimental data",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9146UAUA/",
"accession": "IGVFSM9146UAUA",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002796/",
"status": "released",
"term_name": "Jurkat"
}
],
"status": "preview",
"summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 26-50% expression of IL2RA) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours, modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/4b5f0d13-ec20-4b91-85f5-a009cd91451f/",
"purpose": "stimulation",
"status": "in progress",
"summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours",
"treatment_term_name": "phorbol 13-acetate 12-myristate"
},
{
"@id": "/treatments/cf87f410-54ee-48ef-b654-8443c4fee032/",
"purpose": "stimulation",
"status": "in progress",
"summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
}
]
}
],
"status": "preview",
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus"
},
"file_size": 1520414,
"gene_list_for": [],
"href": "/sequence-files/IGVFFI4071NQGH/@@download/IGVFFI4071NQGH.fastq.gz",
"illumina_read_type": "I2",
"index": "ACCAACTG:TTGT",
"input_file_for": [
"/tabular-files/IGVFFI9903UNGI/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"loci_list_for": [],
"maximum_read_length": 4,
"md5sum": "3b1403a9ae72d5a393dfeabd45ff38a2",
"mean_read_length": 4,
"minimum_read_length": 4,
"read_count": 190006,
"s3_uri": "s3://igvf-files/2024/11/22/fc21ebcd-3e4a-4277-be55-4a071978116e/IGVFFI4071NQGH.fastq.gz",
"schema_version": "14",
"seqspecs": [],
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"sequencing_run": 1,
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-PCRRep1-BinB_S2_I2_001.fastq.gz",
"summary": "I2 reads from sequencing run 1",
"upload_status": "validated",
"uuid": "fc21ebcd-3e4a-4277-be55-4a071978116e"
}