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Sample GSM768587 Query DataSets for GSM768587
Status Public on Jul 29, 2011
Title DG21_S5_EXP
Sample type SRA
 
Source name cells
Organism Schizosaccharomyces pombe
Characteristics genotype: h-, otr1R(SphI)::ura4, ura4-DS/E, ade6-216, his7-366, leu1-32
strain: DG21
developmental stage: dividing
chip antibody: Abcam ab5131
average insert size + standard dev: 144,34
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 manufacturer’s instructions. Average insert size 145bp.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description S5 phosphorylated RNA polII in wt 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 SRX085359
BioSample SAMN00690267

Supplementary file Size Download File type/resource
GSM768587_b_alignment.txt.gz 660.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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