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Evan_Littleton_BCO_000546 #162

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{
"bco_id": "http://biocomputeobject.org/BCO_000546",
"checksum": "0e2c2cc2998bd4fc194606827588b3377202ce08f9ea9d017bf92e4620708eb0",
"bco_spec_version": "1.3.0",
"provenance_domain": {
"name": "Multi-omics profiling reveals key signaling pathways in ovarian cancer controlled by STAT3",
"version": "1.0.0",
"license": "Attribution 4.0 International (CC BY 4.0)",
"created": "2019-10-15T19:03:27.501822",
"modified": "2019-10-15T23:42:00.496764",
"review": [
{
"status": "in-review",
"reviewer_comment": "Reviewed by BioCompute technical assistant, approval pending modification by author",
"reviewer": {
"orcid": "https://orcid.org/0000-0002-8824-4637",
"affiliation": "George Washington University",
"contribution": [
"curatedBy"
],
"name": "Janisha Patel",
"email": "janishapatel@gwu.edu"
},
"date": "2019-10-15"
}
],
"contributors": [
{
"name": "Evan Littleton",
"orcid": "",
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"affiliation": "George Washington University",
"contribution": [
"createdBy"
],
"email": "evanlittleton@gwu.edu"
},
{
"name": "Tiangong Lu",
"orcid": "",
"affiliation": "University of Michigan",
"contribution": [
"authoredBy"
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],
"email": ""
},
{
"name": "Nouri Neamati",
"orcid": "https://orcid.org/0000-0003-3291-7131",
"affiliation": "University of Michigan",
"contribution": [
"authoredBy"
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],
"email": "neamati@umich.edu"
},
{
"name": "Mats Ljungman",
"orcid": "https://orcid.org/0000-0003-1553-6695",
"affiliation": "University of Michigan",
"contribution": [
"authoredBy"
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],
"email": ""
},
{
"name": "Armand Bankhead, III",
"orcid": "",
"affiliation": "University of Michigan",
"contribution": [
"authoredBy"
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],
"email": ""
}
]
},
"usability_domain": [
"Transcriptomic and proteomic data used to understand cell-wide effects of STAT3 knockdown on ovarian cancer cells. Adapted from Tiangong Lu, Armand Bankhead III, Mats Ljungman, and Nouri Neamati. \"Multi-omics profiling reveals key signaling pathways in ovarian cancer controlled by STAT3.\" Theranostics. 2019; 9(19): 5478–5496. http://www.thno.org/v09p5478.htm"
],
"extension_domain": {},
"description_domain": {
"keywords": [
"STAT3",
"STAT3 knockout",
"Multi-omic genome-wide analysis",
"CRISPR-Cas9",
"Ovarian cancer"
],
"pipeline_steps": [
{
"name": "STAR",
"version": "2.5.2",
"step_number": 1,
"input_list": [
{
"access_time": "2019-10-15 T15:20:45",
"uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134375",
"filename": "SRA files"
}
],
"output_list": [
{
"access_time": "",
"uri": "",
"filename": "Publication did not give output/input files for any steps other than inputs for step 1 and outputs from step 4"
}
],
"prerequisite": [],
"description": "Alignment of reads to reference genome"
},
{
"name": "Cufflinks",
"version": "2.2.1",
"step_number": 2,
"input_list": [],
"output_list": [],
"prerequisite": [],
"description": "Quantification of aligned reads"
},
{
"name": "featureCounts",
"version": "1.6.1",
"step_number": 3,
"input_list": [],
"output_list": [],
"prerequisite": [],
"description": "Attainment of gene read counts from quantification"
},
{
"name": "DESeq2",
"version": "1.18.1",
"step_number": 4,
"input_list": [],
"output_list": [
{
"access_time": "2019-10-15 T15:25:30",
"uri": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735387/bin/thnov09p5478s1.pdf",
"filename": "Supplemental Data"
}
],
"prerequisite": [],
"description": "Differential expression analysis of RNA-seq data"
}
]
},
"execution_domain": {
"external_data_endpoints": [
{
"name": "Publication gave no information regarding scripts, parameters, or where the pipeline was executed",
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"url": ""
}
],
"environment_variables": {},
"script_driver": "",
"software_prerequisites": [],
"script": [
{
"uri": {
"access_time": "",
"uri": "",
"filename": ""
}
}
]
},
"parametric_domain": [
{
"step": "",
"param": "",
"value": ""
}
],
"io_domain": {
"input_subdomain": [
{
"uri": {
"access_time": "2019-10-15 T15:40:10",
"uri": " https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134375",
"filename": "SRA files"
}
}
],
"output_subdomain": [
{
"mediatype": "text",
"uri": {
"access_time": "2019-10-15 T15:40:10",
"uri": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735387/bin/thnov09p5478s1.pdf",
"filename": "Supplemental Data"
}
}
]
},
"error_domain": {}
}