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Sample GSM2492289 Query DataSets for GSM2492289
Status Public on Oct 31, 2017
Title 293FT WT-2
Sample type SRA
 
Source name 293FT HEK cells
Organism Homo sapiens
Characteristics cell line: 293FT
Treatment protocol 293FT cells were transfected with guide RNA expressing plasmids targeting the first ATG of the HDAC2 gene, followed by puromycin selection to obtain clonal lines of HDAC2-null cells.
Growth protocol Cells were grown using standard cell culture techniquesin DMEM supplemented with 10% FBS and 1% L-glutamine
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cells at 60-70% confluence utilizing the Nucleospin RNA kit (Macherey-Nagel, Ref #740955.5)
KAPA mRNA stranded kit (KK8401, Roche Catalog07962169001) for library preparation with poly-A enrichment
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing  illumina bclfastq 2.16.0 version for pipeline
TopHat v2.0.14, library-type fr-firststrand
Reads were counted and organized into a matrix using bioconductor package "summarizeOverlaps"
EdgeR (edgeR_3.14.0) was used to perform differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Text files with differentially expressed genes, log fold change, p-value, and FDR
 
Submission date Feb 15, 2017
Last update date May 15, 2019
Contact name Paul Knoepfler
E-mail(s) knoepfler@ucdavis.edu
Organization name UC Davis School of Medicine
Department Cell Biology and Human Anatomy
Lab Knoepfler
Street address 1 Shields Ave
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL21290
Series (1)
GSE94947 RNA-seq of HDAC2-disrupted 293FT cells by CRISPR-Cas9
Relations
BioSample SAMN06339411
SRA SRX2564612

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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