GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2492288 Query DataSets for GSM2492288
Status Public on Oct 31, 2017
Title 293FT WT-1
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
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
BioSample SAMN06339412
SRA SRX2564611

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap