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Sample GSM2470595 Query DataSets for GSM2470595
Status Public on Apr 12, 2017
Title H3RIP_caf1Δdcr1Δ 1
Sample type SRA
Source name caf1Δdcr1Δ
Organism Schizosaccharomyces pombe
Characteristics antibody for ip: Anti-H3: ab1791, abcam
strain number: 521
target molecule: H3 bound RNA
Growth protocol cells were grown in liquid, rich YES medium
Extracted molecule total RNA
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 DNA depletion.
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
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 ( 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:
Submission date Jan 27, 2017
Last update date May 15, 2019
Contact name Mario Halic
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
BioSample SAMN06275909
SRA SRX2522310

Supplementary file Size Download File type/resource
GSM2470595_H3RIP_caf1Ddcr1D1_minus.igv.tdf 33.2 Mb (ftp)(http) TDF
GSM2470595_H3RIP_caf1Ddcr1D1_plus.igv.tdf 33.2 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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