|
| Status |
Public on Dec 15, 2011 |
| Title |
ES RNA b |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Stem (ES) Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Embryonic Stem (ES) cells
strain: 129Sv-C57Bl/6
|
| 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 differentiated Neurons (TN). Mouse embryonic fibroblasts were isolated from wild-type embryos (C57Bl/6).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Trizol (Invitrogen) following the manufacturer's instructions. Ribosomal RNA was removed using the Ribo-Zero kit (Epicentre). Libraries for sequencing were prepared with the Illumina small RNA-Seq Prep Kit (Cat#FC-102-1009) according to Illumina's Directional mRNA-Seq Library Prep. (Pre-Release Protocol Rev.A). The DNA was PCR amplified with Illumina primers for 12 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 |
| |
|
| 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. The wiggle files are showing the read counts in log2 scale.
|
| |
|
| Submission date |
Aug 15, 2011 |
| 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 (4)
|
| GSE30280 |
DNA binding factors shape the mouse methylome at distal regulatory regions [RNA_seq] |
| GSE31385 |
DNA binding factors shape the mouse methylome at distal regulatory regions [strand-specific-RNA-seq] |
| GSE33252 |
Chromatin based modeling of transcription rates identifies the contribution of different regulatory layers to steady-state mRNA levels |
| GSE34473 |
Chromatin based modeling of transcription rates identifies the contribution of different regulatory layers to steady-state mRNA levels. |
|
| Relations |
| SRA |
SRX091802 |
| BioSample |
SAMN00709343 |
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