|
| Status |
Public on Dec 18, 2011 |
| Title |
NP_PolII [ChIP-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
Neuronal Progenitor (NP) Cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129Sv-C57Bl/6
genotype/variation: wild type
cell type: Neuronal Progenitors (NP)
chip antibody: anti-RNA Pol II
|
| 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))
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments were performed as described before (F. Mohn et al., Mol Cell 30, 755 (Jun 20, 2008)), starting with 70 µg of chromatin and 5 µg of the following (proprietary) antibodies: anti-JNK1/3, anti-phospho-JNK, anti-NF-YA, anti-RNA Pol II, anti-H3K4me2, and anti-H3K27me3. The ChIP libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illumina’s instructions and sequenced on the Genome Analyzer 2 following the manufacturer’s protocols. ChIP-real time PCR was performed using SYBR Green chemistry (ABI) and 1/40 of ChIP or 1:100 diluted Input DNA per PCR reaction. Primers sequences are available upon request.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
NP_PolII
|
| 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 |
Dec 01, 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 |
| GSE33252 |
Chromatin based modeling of transcription rates identifies the contribution of different regulatory layers to steady-state mRNA levels |
|
| Relations |
| SRA |
SRX032484 |
| BioSample |
SAMN00139302 |
| Named Annotation |
GSM632050_NP_PolII.wig.gz |
