|
| Status |
Public on Jan 28, 2016 |
| Title |
Rpb2-HTP_Dhp1-1_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Yeast RNA
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: Dhp1-1 + Rpb2-HTP
|
| Treatment protocol |
The washed cells were UV-crossliked for 3 minutes at 254nm, then pelleted and flash frozen in liquid nitrogen
|
| Growth protocol |
Cultures were grown in full media (YEA) at 30ºC to O.D. of 2.0.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For extraction and library preparation protocol please refer to the Materials and Methods section.
For extraction and library preparation protocol please refer to the Materials and Methods section.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Rpb2 CRAC in dhp1-1 mutant cells, rep1
|
| Data processing |
Library protocol: CRAC-seq
Demultiplexing and removal of 3prime adapter conatmination and poly-A sequences was done in one step.
Reads were mapped to S. pombe genome, version ASM294v1.17, with Tophat2 software. (Tophat-2.0.14)
PCR duplicates were filtered out and genome-wide coverage was calculated using R Bioconductor packages.
Datasets were normalised for mean coverage over mRNA.
Genome_build: ASM294v1.17
Supplementary_files_format_and_content: BigWig format containing normalised genome-wide coverage
|
| |
|
| Submission date |
Jan 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Tamas Fischer |
| E-mail(s) |
tamas.fischer@bzh.uni-heidelberg.de
|
| Phone |
+49 6221 544728
|
| Organization name |
Biochemie Zentrum Heidelebrg
|
| Department |
BZH
|
| Lab |
AG Fischer
|
| Street address |
Im Neuenheimer Feld 328
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13988 |
| Series (2) |
| GSE77290 |
A NOVEL EPIGENETIC SILENCING PATHWAY INVOLVING the HIGHLY CONSERVED 5'-3' EXORIBONUCLEASE Dhp1/Rat1/Xrn2 in SCHIZOSACCHAROMYCES POMBE [CRAC-seq] |
| GSE77291 |
A NOVEL EPIGENETIC SILENCING PATHWAY INVOLVING the HIGHLY CONSERVED 5'-3' EXORIBONUCLEASE Dhp1/Rat1/Xrn2 in SCHIZOSACCHAROMYCES POMBE |
|
| Relations |
| BioSample |
SAMN04443149 |
| SRA |
SRX1549312 |
