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Status |
Public on Jun 26, 2014 |
Title |
Suv39h dn 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: Suv39h double null
|
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)
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from 106 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, 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_dn_A1_R1.fastq.gz ; tot_dn_A1_R2.fastq.gz Raw files for Rep 2: tot_dn_A2_R1.fastq.gz ; tot_dn_A2_R2.fastq.gz Raw files for Rep 3: tot_dn_B_R1.fastq.gz ; tot_dn_B_R2.fastq.gz
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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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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 |
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Relations |
BioSample |
SAMN02737336 |
SRA |
SRX527848 |