NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2228532 Query DataSets for GSM2228532
Status Public on Nov 22, 2016
Title wt repeat three
Sample type SRA
 
Source name WT_hippocampus
Organism Mus musculus
Characteristics strain: C57/Bl
genotype/variation: wild type
tissue: hippocampus
Treatment protocol N/A
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol mRNAeasy qiagen RNA extraction kit
Truseq illumina library kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Reads were demultiplexed
Adapters were trimmed from sequences using cutadapt tool
Reads that mapped to rRNA were removed
The rest of the reads were aligned to the mm10 genome built using Tophat (v2.0.10)
Read counting to Refseq genes was done with HTseq-count (version 0.6.1p1)
Differential expression analysis was performed with DESeq2 (1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes the raw counts, normalized counts, fold change, p-value and FDR
 
Submission date Jul 08, 2016
Last update date May 15, 2019
Contact name Gilgi Friedlander
Organization name Weizmann Institute of Science
Street address Hertzel st
City Rehovot
ZIP/Postal code 76100
Country Israel
 
Platform ID GPL17021
Series (2)
GSE84175 RNA-seq of hippocampus from wild type and CTCF cko animals
GSE84176 CTCF ChIP-seq of WT and RNA-seq of WT and CTCF cko mouse
Relations
BioSample SAMN05366647
SRA SRX1906237

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