|
| Status |
Public on Dec 18, 2011 |
| Title |
ES [RNA_Seq] |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Stem Cells (ESCs)
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129Sv-C57Bl/6
genotype/variation: wild type
cell type: Embryonic Stem Cells (ESCs)
|
| Growth protocol |
Wild-type embryonic stem cells (129Sv-C57Bl/6) were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007)) and differentiated to Neuronal Progenitors and further to Terminally diffentiated Neurons (TN)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using RNeasy Mini Kit (Invitrogen) following the manufacturer’s instructions. Libraries for sequencing were prepared with the Illumina mRNA-Seq 8-Sample Prep Kit (Cat# RS-100-0801) according to Illumina's instructions. After adapter ligation library fragments of ~250 bp were band isolated from an agarose gel. The cDNA was PCR amplified with Illumina primers for 15 cycles, purified and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
ES_RNA
|
| Data processing |
2007 M. musculus genome assembly (mm9) was used as a basis for all analyses. Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.
|
| |
|
| Submission date |
Nov 30, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Dirk Schuebeler |
| Organization name |
Friedrich Miescher Institute for Biomedical Research
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL9250 |
| Series (3) |
| GSE25532 |
A chromatin-modifying function of JNK during stem cell differentiation |
| GSE25533 |
A chromatin-modifying function of JNK during embryonic stem cell differentiation |
| GSE30280 |
DNA binding factors shape the mouse methylome at distal regulatory regions [RNA_seq] |
|
| Relations |
| Reanalyzed by |
GSE80797 |
| SRA |
SRX032448 |
| BioSample |
SAMN00139281 |
| Named Annotation |
GSM632013_ES_RNA.wig.gz |
