|
| Status |
Public on Jul 29, 2011 |
| Title |
DG690_S2_EXP |
| Sample type |
SRA |
| |
|
| Source name |
cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: Delta-dcr1::kanMX6, otr1R(SphI)::ura4, ura4-DS/E, ade6-210, leu1-32, his7-366
strain: DG690
developmental stage: dividing
chip antibody: Abcam ab5095
average insert size + standard dev: 125,32
|
| Treatment protocol |
Samples from log phase dg21 and dg690 S. pombe strains were fixed (dividing cells) or first treated with 15mM hydroxyurea (HU) (Sigma) for 4.5 hr, washed once in HU free media and fixed (HU arrested cells)
|
| Growth protocol |
Samples were grown to OD=0.2 in YEA media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was purified, sonicated and incubated with following anti-RNA Polymerase II antibodies from Abcam: clone pospho-S2 (ab5095), and clone phospho-S5 (ab5131). For ChIP-seq, immunoprecipitated DNA was polished, ligated and amplified with the Illumina ChIP-seq sample preparation kit according to the manufacturerâs instructions. Average insert size 145bp.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
S2 phosphorylated RNA polII in dcr1 KO dividing cells
|
| Data processing |
Analysis was carried out by a custom pipeline using Bowtie to align reads to the S. pombe genome and MACS 1.4 for significance enrichment calls. The Bed files on the Series record were generated by MACS (http://liulab.dfci.harvard.edu/MACS/) and represent the areas of significant difference between two genotypes (WT vs dcr1-). MACS allows for direct comparison of ChIP-seq signal, as long as the strains used do not differ much in sequence. This experiment was done in two different conditions (log phase vs HU treatment).
|
| |
|
| Submission date |
Jul 28, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Mikel Zaratiegui |
| E-mail(s) |
zaratieg@cshl.edu
|
| Phone |
5163678836
|
| Fax |
5163678369
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Department |
Delbruck Bldg.
|
| Lab |
Martienssen
|
| Street address |
1 Bungtown Rd
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL13988 |
| Series (2) |
| GSE30837 |
RNAi promotes heterochromatic silencing through replication-coupled release of RNA pol II (superseries) |
| GSE31016 |
RNAi promotes heterochromatic silencing through replication-coupled release of RNA pol II (ChIP-seq) |
|
| Relations |
| SRA |
SRX085360 |
| BioSample |
SAMN00690268 |
