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Sample GSM2470580 Query DataSets for GSM2470580
Status Public on Apr 12, 2017
Title Caf1RIP_sol_untagged 1
Sample type SRA
 
Source name wild type
Organism Schizosaccharomyces pombe
Characteristics antibody for ip: anti-FLAG M2-Magnetic Beads (Sigma-Aldrich)
strain number: 63
target molecule: background 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 (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 SAMN06275872
SRA SRX2522295

Supplementary file Size Download File type/resource
GSM2470580_Caf1RIP_background1_sol_minus.igv.tdf 33.6 Mb (ftp)(http) TDF
GSM2470580_Caf1RIP_background1_sol_plus.igv.tdf 33.6 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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