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Sample GSM2932721 Query DataSets for GSM2932721
Status Public on Jun 07, 2018
Title dis2cs_Input_rep2
Sample type SRA
 
Source name spt5-13myc::kanMX6 dis2-11 leu1-32 ura4-D18 his3-D1 ade6-M210 h+
Organism Schizosaccharomyces pombe
Characteristics temperature c: 30
antibody: None
assay: ChIP-seq
Growth protocol ChIP-seq: S. pombe cultures were grown in YES media till OD600 ~ 0.4.
Extracted molecule genomic DNA
Extraction protocol ChIP-seq: After HCHO-crosslinking (15 min at 25°C) protein extract was prepared using Mini-beadbeater (Biospec; 30 sec "ON" and 30 sec "OFF"). Lysates were precleared with Protein A agarose beads and used for IP with respective antibodies.
ChIP-seq: Multiplexed ChIP-seq libraries were prepared using the Illumina TruSeq DNA Sample Preparation kit v2 with 75 ng of input or IP DNA and barcode adaptors.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing ChIP-seq: Paired-end sequencing (50-nt reads) was performed on an Illumina HiSeq 2000 (Genome Quebec Innovation Centre, McGill University).
ChIP-seq: Quality control and adapter trimming of the FASTQ (raw sequencing files) files were done in Galaxy using FastQC Read Quality reports (Galaxy Version 0.69) and trimmomatic flexible read trimming tool for Illumina NGS data (Galaxy Version 0.36.3) respectively.
ChIP-seq: After adaptor trimming and quality control, processed FASTQ files were aligned to the S. pombe genome using Bowtie2 (Galaxy Version 2.2.6.2).
ChIP-seq: Aligned sequences of each biological replicate were fed into MACS2 (Galaxy Version 2.1.1.20160309.0) to call peaks from alignment results. Generated “bedgraph treatment” files were converted into bigwig using “Wig/BedGraph-to-bigWig converter” (Galaxy Version 1.1.0), concatenated (Galaxy Version 1.0.1) to combine replicates of each sample, subtracted IgG reads from each and processed using computeMatrix (Galaxy Version 2.3.6.0) in DeepTools to prepare data for plotting a heatmap and/ or a profile of given regions.
Genome_build: ChIP-seq: S. pombe: ASM294v2.
Supplementary_files_format_and_content: ChIP-seq: processed files are in bigWig format. There are 26-bigWig files in total. 4 for pSpt5, 4 for Myc, 3 for IgG and 2 for Iuput for each strain (wt or dis2cs) including two biological replicates.
 
Submission date Jan 12, 2018
Last update date Jun 07, 2018
Contact name PABITRA K PARUA
E-mail(s) pabitra.parua@einsteinmed.eduy
Phone 7184304284
Organization name Albert Einstein College of Medicine
Department Molecular Pharmacology
Lab Forch-236
Street address 1300 Morris Park Avenue, Forchheimer 236, Molecular Pharmacology
City Bronx
State/province NY
ZIP/Postal code 10461
Country USA
 
Platform ID GPL20584
Series (1)
GSE102590 A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II
Relations
BioSample SAMN08358599
SRA SRX3557076

Supplementary file Size Download File type/resource
GSM2932721_pp_chipseq_MACS2_dis2cs_Input_r2.bigwig 50.7 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA
Processed data provided as supplementary file

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