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Sample GSM2470587 Query DataSets for GSM2470587
Status Public on Apr 12, 2017
Title Caf1RIP_chr_wild_type 2
Sample type SRA
Source name wild type, 3x FLAG-Caf1
Organism Schizosaccharomyces pombe
Characteristics antibody for ip: anti-FLAG M2-Magnetic Beads (Sigma-Aldrich)
strain number: 773
target molecule: Caf1 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.
Crosslinked cells with 1% Formaldehyde for 15 minutes used. Caf1-associated RNA IP with chromatin fractionation: before sonication, the sample was centrifuged for 20 min at 21 000 x g at 4°C. The supernatant was taken as “soluble fraction”, the pellet was washed twice with lysis buffer, then resuspended in lysis buffer, which formed the “chromatin fraction”. Subsequent immunoprecipitation, 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 SAMN06275868
SRA SRX2522302

Supplementary file Size Download File type/resource
GSM2470587_Caf1RIP_wild_type2_chr_minus.igv.tdf 22.7 Mb (ftp)(http) TDF
GSM2470587_Caf1RIP_wild_type2_chr_plus.igv.tdf 22.6 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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