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Sample GSM2048202 Query DataSets for GSM2048202
Status Public on Jan 28, 2016
Title Rpb2-HTP_Dhp1-1_rep2
Sample type SRA
 
Source name Yeast RNA
Organism Schizosaccharomyces pombe
Characteristics strain: Dhp1-1 + Rpb2-HTP
Treatment protocol The washed cells were UV-crossliked for 3 minutes at 254nm, then pelleted and flash frozen in liquid nitrogen
Growth protocol Cultures were grown in full media (YEA) at 30ÂșC to O.D. of 2.0.
Extracted molecule total RNA
Extraction protocol For extraction and library preparation protocol please refer to the Materials and Methods section.
For extraction and library preparation protocol please refer to the Materials and Methods section.
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description Rpb2 CRAC in dhp1-1 mutant cells, rep2
Data processing Library protocol: CRAC-seq
Demultiplexing and removal of 3prime adapter conatmination and poly-A sequences was done in one step.
Reads were mapped to S. pombe genome, version ASM294v1.17, with Tophat2 software. (Tophat-2.0.14)
PCR duplicates were filtered out and genome-wide coverage was calculated using R Bioconductor packages.
Datasets were normalised for mean coverage over mRNA.
Genome_build: ASM294v1.17
Supplementary_files_format_and_content: BigWig format containing normalised genome-wide coverage
 
Submission date Jan 27, 2016
Last update date May 15, 2019
Contact name Tamas Fischer
E-mail(s) tamas.fischer@bzh.uni-heidelberg.de
Phone +49 6221 544728
Organization name Biochemie Zentrum Heidelebrg
Department BZH
Lab AG Fischer
Street address Im Neuenheimer Feld 328
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL13988
Series (2)
GSE77290 A NOVEL EPIGENETIC SILENCING PATHWAY INVOLVING the HIGHLY CONSERVED 5'-3' EXORIBONUCLEASE Dhp1/Rat1/Xrn2 in SCHIZOSACCHAROMYCES POMBE [CRAC-seq]
GSE77291 A NOVEL EPIGENETIC SILENCING PATHWAY INVOLVING the HIGHLY CONSERVED 5'-3' EXORIBONUCLEASE Dhp1/Rat1/Xrn2 in SCHIZOSACCHAROMYCES POMBE
Relations
BioSample SAMN04443150
SRA SRX1549313

Supplementary file Size Download File type/resource
GSM2048202_CRAC.032.Rpb2.dhp1d.fw.BigWig 10.7 Mb (ftp)(http) BIGWIG
GSM2048202_CRAC.032.Rpb2.dhp1d.rev.BigWig 10.8 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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