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Sample GSM1090979 Query DataSets for GSM1090979
Status Public on May 15, 2013
Title Input3
Sample type SRA
Source name RAW264.7_Input
Organism Mus musculus
Characteristics cell line: RAW264.7
ip antibody/beads information: none
molecule subtype: RNA purified from lysate before IP
Treatment protocol RAW264.7 cells were treated with LPS (100 ng/ml, Sigma, L2630, E. coli serotype O111:B4) for 2 h.
Growth protocol RAW264.7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (PAA Laboratories), 2 mM L-glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin (all PAN Biotech) at 37°C in 5% CO2.
Extracted molecule total RNA
Extraction protocol Cells were mechanically disrupted using a tissue lyser. RNA was isolated before (Input) or after IP (ctrl IP or Roquin IP) with TriFast reagent.
RNA libraries were prepared for sequencing using the TruSeq RNA Sample Preparation Kit.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Sample 9
Data processing Basecalling with CASAVA v1.8.2
Mapping to the mouse genome NCBI build 37 with BWA.
Reads were summarized for gene models with the Bioconductor package easyRNASeq v1.2.5. The exon coordinates of RefSeq annotated mRNAs were obtained from the refGene table of the UCSC genome browser.
Differential abundance was tested for with the Bioconductor package DESeq v1.8.3.
Genome_build: NCBI build 37
Supplementary_files_format_and_content: The 'RoquinIP_processed.txt' file contains, for each sample, the count table obtained with easyRNASeq, the fold changes and the p-values computed with DESeq.
Submission date Mar 01, 2013
Last update date May 15, 2019
Contact name Georg Stoecklin
Organization name German Cancer Research Center
Street address Im Neuenheimer Feld 280
City Heidelberg
ZIP/Postal code 69120
Country Germany
Platform ID GPL13112
Series (1)
GSE44775 Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs.
SRA SRX248300
BioSample SAMN01974600

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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