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Sample GSM2228530 Query DataSets for GSM2228530
Status Public on Nov 22, 2016
Title wt repeat one
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
BioSample SAMN05366645
SRA SRX1906235

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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