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Sample GSM1267666 Query DataSets for GSM1267666
Status Public on Dec 09, 2013
Title WT_fib_RNASeq
Sample type SRA
 
Source name Tailtip fibroblasts
Organism Mus musculus
Characteristics strain: C57BL/6J
genotype: WT
cell type: adult tailtip fibroblasts
Growth protocol Tailtip fibroblasts were cultured in 89% DMEM, 10% FCS and 1% penicillin-streptomycin. E13.5 embryos were isolated using standard techniques.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from fibroblasts and embryos using TriZol Reagent.
Paired-end strand-specific RNA-Seq libraries were prepared from fibroblast and embryo RNA using the dUTP method and libraries were sequenced using the Illumina HiSeq instrument.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1000
 
Description Processed data files are tabular files generated from fastq raw files and input into EdgeR
Data processing Illumina Casava1.7 software used for basecalling.
Raw reads were groomed using Fastqgroomer and filtered for read quality.
Reads were mapped using TopHat v1.4.0 using the settings: -p 4 -r 24 -a 8 -m 0 -I 70 -l 500000 -g 20 --library-type fr-firststrand --no-novel-indels --no-coverage-search --no-closure-search --mate-std-dev 27 --initial-read-mismatches 0 --segment-mismatches 0 -segment
Galaxy pipeline was used to filter for unique hits generating interval files which were used to create read pile-ups by the Galaxy inner join package.
Read pile-up files were input into EdgeR to calculate differential expression between libraries and also pile-ups were converted to bed files for this submission.
Genome_build: Mouse mm9
Supplementary_files_format_and_content: abundance
 
Submission date Nov 18, 2013
Last update date May 15, 2019
Contact name Donncha S Dunican
Organization name IGMM / MRC HGU
Street address Western General Hospital
City Edinburgh
ZIP/Postal code EH4 2XU
Country United Kingdom
 
Platform ID GPL15103
Series (2)
GSE52477 Lsh regulates LTR retrotransposon repression independent of Dnmt3b function (RNA-Seq)
GSE52479 Lsh regulates LTR retrotransposon repression independent of Dnmt3b function
Relations
BioSample SAMN02404844
SRA SRX378825

Supplementary file Size Download File type/resource
GSM1267666_WT_fib_LINE.txt.gz 726.9 Kb (ftp)(http) TXT
GSM1267666_WT_fib_LTR.txt.gz 27.3 Kb (ftp)(http) TXT
GSM1267666_WT_fib_downstream_LINE.txt.gz 1.4 Mb (ftp)(http) TXT
GSM1267666_WT_fib_downstream_LTR.txt.gz 20.4 Kb (ftp)(http) TXT
GSM1267666_WT_fib_upstream_LINE.txt.gz 1.4 Mb (ftp)(http) TXT
GSM1267666_WT_fib_upstream_LTR.txt.gz 20.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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