|
| 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 (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 |
SAMN06275909 |
| SRA |
SRX2522310 |
