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Sample GSM2835842 Query DataSets for GSM2835842
Status Public on Mar 06, 2018
Title MEF_RNASeq_KO1_20435
Sample type SRA
 
Source name primary mouse embryonic fibroblasts
Organism Mus musculus
Characteristics tissue: primary mouse embryonic fibroblasts
genotype: Supt5hFl/- Rosa26ERT2-cre/+
Treatment protocol Primary MEFs were treated with 2 uM 4-HT for 72h and then harvested for all downstream applications.
Growth protocol Primary MEFs were prepared from d13.5 Supt5hFl/+Rosa26ERT2-cre/+ and Rosa26ERT2-cre/+ embryos and cultured in complete DMEM medium to passage 3.
Extracted molecule polyA RNA
Extraction protocol Cells were harvested as per the instructions in the TruSeq kit from Illumina.
Library preparation for mRNAseq was performed using the TruSeq kit from Illumina following their instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Adapters were trimmed from the 3' ends of the reads with cutadapt v1.10.
The trimmed reads larger than 18nt were aligned against the Fitz et al 25 rDNA of the respective organism using bowtie2 v 2.1.0 (--sensitive-local --score-min G,30,8 -N 0 --ignore-quals) to remove the rRNA reads.
rRNA cleaned reads were aligned to the genome with the TopHat splice junction mapper for RNA-seq reads v1.4.1.
Reads were quantified with featureCounts v1.5.0-p1.
Differentially expressed genes were obtained using DESeq2 v1.10.1 according to its standard comparison between two experimental conditions vignette. Differentially expressed genes were filtered for a p-adjusted value of < 0.05 and a fold-change greater 1.5 in either direction.
genome build: NCBI mm9
processed data files format and content: Tab-delimited table with raw counts and DESeq2 log2-foldchanges and adjusted p-values
 
Submission date Oct 30, 2017
Last update date May 15, 2019
Contact name Tobias Neumann
Organization name IMP
Street address Campus-Vienna-Biocenter 1
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platform ID GPL13112
Series (1)
GSE106313 Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window in elongation
Relations
BioSample SAMN07946538
SRA SRX3342586

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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