|
| Status |
Public on Jun 26, 2014 |
| Title |
Suv39h dn Nuclear RNA-seq |
| Sample type |
SRA |
| |
|
| 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)
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
After nuclei isolation, only nuclear-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®)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
two biological replicates
Raw files for Rep 1: Nuc_dn_B1_R1.fastq.gz ; Nuc_dn_B1_R2.fastq.gz
Raw files for Rep 2: Nuc_dn_B2_R1.fastq.gz ; Nuc_dn_B2_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
|
| |
|
| 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 |
SAMN02737335 |
| SRA |
SRX527846 |
