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Sample GSM2470557 Query DataSets for GSM2470557
Status Public on Apr 12, 2017
Title RNA_caf1Δdcr1Δ
Sample type SRA
Source name caf1Δdcr1Δ
Organism Schizosaccharomyces pombe
Characteristics strain number: 521
target molecule: total 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.
Total RNA was isolated applying the hot phenol method. The extracted nucleic acids were treated with DNAse I for 2 h at 37°C. DNAse was removed by a second phenol-chloroform-isoamylalcohol extraction and ethanol precipitation. 1 µg total RNA was degraded with Terminator nuclease (Epicentre) in buffer A at 30°C for 2 h.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
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 SAMN06275895
SRA SRX2522272

Supplementary file Size Download File type/resource
GSM2470557_RNA_caf1Ddcr1D_minus.igv.tdf 29.8 Mb (ftp)(http) TDF
GSM2470557_RNA_caf1Ddcr1D_plus.igv.tdf 29.7 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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