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Status |
Public on Jun 26, 2014 |
Title |
WT poly-A RNA-seq |
Sample type |
SRA |
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|
Source name |
Embryonic Stem cells
|
Organism |
Mus musculus |
Characteristics |
cell type: Embryonic Stem cells genotype: wt
|
Growth protocol |
ES cells were grown on gelatin coated plates with ES medium ( DMEM supplemented with 15% FCS, 1x Pen/strept, L-Glutamine 2mM, ß-mercaptoethanol 0.1 MM, Non Essential amino acids 1x, Sodium piruvate 1mM and LIF). MEFs were grown in DMEM supplemented with 10% FCS, 1x Pen/strept, L-Glutamine 2mM, ß-mercaptoethanol 0.1 MM, Non Essential amino acids 1x, Sodium piruvate 1mM. In vitro differentiation to NPCs was carried out as described before (Bibel et al., 2007)
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from 10^6 cells using TRIzol reagent (Invitrogen) and contaminating DNA was digested with Turbo DNase (Ambion). RNA libraries were prepared for sequencing following standard Illumina protocols (TruSeq RNA Sample Prep Kit v2 -Set A)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
three biological replicates Raw files for Rep 1: tot_wt_A1_R1.fastq.gz ; tot_wt_A1_R2.fastq.gz Raw files for Rep 2: tot_wt_A2_R1.fastq.gz ; tot_wt_A2_R2.fastq.gz Raw files for Rep 3: tot_wt_B_R1.fastq.gz ; tot_wt_B_R2.fastq.gz
|
Data processing |
Illumina Casava 1.7.0 and bcl2fastq 1.8.3 software used for basecalling. Bowtie version 2.0.0-beta6 with parameters -D 15 -R 2 -N 0 -L 32 -i S,1,0.75 -M 10000 was used to map reads agains the mm9 genome build. The default bowtie2 mapping of multi-reads to one of the possible genomic locations was used. Reads mapping with mismatches were removed. bigWig RPKM files were generated using bamCoverage from the deepTools package (http://deeptools.github.io). Scores represent the normalized number of reads overlaping bins of 10bp. The normalization scales the original depth of sequencing to RPKM for each 10 bp bin. Genome_build: mm9
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|
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Submission date |
Apr 25, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Thomas Manke |
Organization name |
Max-Planck-Institute for Immunobiology and Epigenetics
|
Department |
Bioinformatics and Deep-Sequencing Unit
|
Street address |
Stuebeweg 51
|
City |
Freiburg im Breisgau |
ZIP/Postal code |
79108 |
Country |
Germany |
|
|
Platform ID |
GPL13112 |
Series (1) |
GSE57092 |
Suv39h-dependent H3K9me3 represses intact retrotransposons in mouse embryonic stem cells |
|
Relations |
BioSample |
SAMN02737340 |
SRA |
SRX527847 |