SAMN32519280
External Id
University of California, San Francisco
INSDC center name
2022-12-31T00:00:00Z
INSDC first public
2022-12-31T12:14:29.667Z
INSDC last update
SRS16328712
INSDC secondary accession
live
INSDC status
Human
NCBI submission model
Human.1.0
NCBI submission package
SRS16328712
SRA accession
56
age
GRCh38
assembly
Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94194
biomaterial_provider
HEI-193 cells were transduced with the perturb-seq library at 1,000X coverage at an MOI of 0.1, corresponding to approximately 95% of cells with a single integration. 72 hours following transduction, sgRNA+ cells were FACS sorted (BFP+) and were recovered in DMEM 10% FBS. Sorted cultures were treated with either 0Gy, 1.8Gy x 5 daily fractions, or 12.5Gy x 1 fraction of radiotherapy using the X-Rad 320 irradiator (Precision X-Ray). 12 hours following the final fraction of radiotherapy, cells were trypsinized and harvested in single cell suspension on the 10x Chromium Controller (10x Genomics). Single-cell Perturb-seq libraries were processed using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1with Feature Barcoding (10x Genomics), allowing direct capture of modified sgRNAs83, and sequenced on a illumina NovaSeq-6000.
design_description
VS_perturb_sgRNA_1_S11_L001_R1_001.fastq.gz
filename
VS_perturb_sgRNA_1_S11_L002_R1_001.fastq.gz
filename2
VS_perturb_sgRNA_1_S11_L001_R2_001.fastq.gz
filename3
VS_perturb_sgRNA_1_S11_L002_R2_001.fastq.gz
filename4
VS_perturb_sgRNA_1_S11_L001_I1_001.fastq.gz
filename5
VS_perturb_sgRNA_1_S11_L002_I1_001.fastq.gz
filename6
fastq
filetype
Illumina NovaSeq 6000
instrument_model
schwannoma
isolate
VS_perturb_sgRNA_1_S11
library_ID
Homo sapiens
http://purl.obolibrary.org/obo/NCBITaxon_9606
organism
ILLUMINA
platform
male
sex
cells
tissue
Perturb_sgRNA_HEI193_0Gy_1
title