|
| Status |
Public on Dec 26, 2018 |
| Title |
dis2Δ, Spt5-T1E total-Pol II_IP_1 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Yeast cell extract
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Seb1-3XHA-TAP::kanMX; Spt5-T1A-3xFlag::natMX
method: ChIP-Seq
antibody: RNAPII (8WG16) antibody, Millipore, Cat#05-952
|
| Growth protocol |
S. pombe were grown in YES medium to exponential phase at 30°C
S. pombe were grown in YES medium to exponential phase at 30°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication and DNA was extracted by ChIP DNA Clean & Concentrator (Zymo Research).
Libraries were generated using the NEBNext fast DNA library Prep set for Illumina (E7335).
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication and DNA was extracted by ChIP DNA Clean & Concentrator (Zymo Research).
Libraries were generated using the NEBNext fast DNA library Prep set for Ion Torrent (E6270) or Illumina (E7335).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Crosslinked DNA
|
| Data processing |
ChIP-seq: Single end reads with a Phred score of less than 20 were removed using the the program Trimmomatic (version 0.36) and the remaining reads were aligned to the S. pombe genome (ASM294v2.25 from Pombase.org) using the short read aligner Bowtie (version 2.2.6).
Genome_build: S. pombe genome version ASM294v2.28
Supplementary_files_format_and_content: ChIP-Seq: the data is provided as bigwig files
|
| |
|
| Submission date |
Jul 30, 2018 |
| Last update date |
Dec 26, 2018 |
| Contact name |
Tea Kecman |
| E-mail(s) |
tea.kecman@gmail.com
|
| Organization name |
University of Oxford
|
| Department |
Biochemistry
|
| Street address |
South Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3QU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20584 |
| Series (1) |
| GSE111326 |
Elongation/termination factor exchange mediated by PP1 phosphatase orchestrates trancription termination |
|
| Relations |
| BioSample |
SAMN09737387 |
| SRA |
SRX4482726 |
