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Sample GSM2470605 Query DataSets for GSM2470605
Status Public on Apr 12, 2017
Title H3K9me2_ChIP_taz1Δ
Sample type SRA
 
Source name taz1Δ
Organism Schizosaccharomyces pombe
Characteristics antibody for ip: H3K9me2: ab1220 abcam
strain number: 633
target molecule: H3K9me2 bound DNA
Growth protocol cells were grown in liquid, rich YES medium
Extracted molecule genomic DNA
Extraction protocol RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB); DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.
Immunoprecipitation of crosslinked (1% formaldehyde, 15 min) cells, decrosslinking, protein degradation and RNA degradation.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Data processing base calling with RTA1.18.64
Sequenced reads were trimmed for the adaptor sequence, then mapped to the S.pombe genome with Novoalign (http://www.novocraft.com) randomly assigned.
Reads mapping with two or fewer mismatches were retained.
Enrichments were calculated with our house Perl scripts
Normalisation to reads per million for siRNA and ChIP experiments, normalisation to reads mapping to protein coding genes for RNAseq /RIPseq
Genome_build: Schizosaccharomyces_pombe.ASM294v1.18
Supplementary_files_format_and_content: can be viewed with IGV browser: http://www.broad.mit.edu/igv
 
Submission date Jan 27, 2017
Last update date May 15, 2019
Contact name Mario Halic
E-mail(s) halic@genzentrum.lmu.de
Organization name Ludwig-Maximilians-Universität
Department Biochemistry - Gene Center
Lab Halic
Street address Feodor-Lynen-Str.25
City Munich
ZIP/Postal code 81377
Country Germany
 
Platform ID GPL22681
Series (1)
GSE94129 Accumulation of RNA on chromatin disrupts heterochromatic silencing
Relations
BioSample SAMN06275848
SRA SRX2522320

Supplementary file Size Download File type/resource
GSM2470605_H3K9me2ChIP_taz1D.igv.tdf 1.1 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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