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Sample GSM2576787 Query DataSets for GSM2576787
Status Public on Jun 20, 2017
Title chip1_wce_rct1rrm
Sample type SRA
 
Source name chip1_wce_rct1rrm
Organism Schizosaccharomyces pombe
Characteristics strain: AY420
chip antibody: whole cell extract
Treatment protocol Yeast cells were grown to a concentration of ~1 X 10^7 cells/ml, then fixed in 1% formaldehyde at 25°C for 20 min. Fixation was stopped by adding glysine to a final concentration of 0.125 M, and cells were washed twice in 1XPBS then stored in -80°C until all strains were harvested.
Growth protocol All yeast strains were cultured in YES (yeast exact with supplements) media at 30 °C.
Extracted molecule genomic DNA
Extraction protocol Cells were spheroplasted by zymolyase at 37°C and then sonicated using a bioruptor for 8 cycles (30s ON 60s OFF). For each IP, 500-750 ug of chromatin were used with 3 to 5 ul antibody. 1 ng of DNA purified from ChIP experiments was made into libraries by using NEB enzymes. In brief, DNA was end-repaired by T4 DNA polymerase, Klenow fragment and T4 DNA PNK. “A” bases were added to the 3’ end of end-repaired DNA fragment with Klenow 3’ to 5’ exo minus and dATP. Barcoded Truseq adaptors (Illumina) were ligated to DNA fragments using quick ligase at 25°C. Five PCR cycles were performed prior to size selection. After size selection, purified DNA was PCR amplified with 6 to 12 cycles (Kapa HiFi HotStart ready mix). Barcoded libraries were pooled and sequenced on Illumina HiSeq platform.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Obtained reads were quality filtered using Trimmomatic and aligned to the S. pombe genome assembly ASM294v2.21 using Bowtie v2.1.0 and local alignment, with multi-mappers randomly distributed. All read counts were normalized to reads per million (RPM) using total library size. ChIP enrichment was calculated as the log2 of the ratio of normalized IP reads to normalized input (whole cell extract) reads. Quantification at individual features was performed by intersecting reads with the feature of interest.
Genome_build: ASM294v2
Supplementary_files_format_and_content: Coverage of ChIP enrichment calculated as the log2 of the ratio of normalized IP reads to normalized input (whole cell extract) reads in bigWig format.
 
Submission date Apr 13, 2017
Last update date May 15, 2019
Contact name Robert A Martienssen
E-mail(s) martiens@cshl.edu
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)
GSE97746 The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly [ChIP-seq]
GSE97749 The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly
Relations
BioSample SAMN06732587
SRA SRX2734706

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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