|
| Status |
Public on Nov 30, 2012 |
| Title |
WT1 RNA Polymerase II ChIP |
| Sample type |
SRA |
| |
|
| Source name |
Yeast cells, wild-type, Rpb1 ChIP
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: W303 wild-type
chip antibody: 4H8
|
| Treatment protocol |
1% formaldehyde cross-linked for 20 minutes at 25 °C, quenched for 5 minutes at 25 °C with 200 mM glycine.
|
| Growth protocol |
YPD 30 °C to mid-log phase.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP performed using standard techniques (Kristjuhan, A. & Svejstrup, J. Q. (2004). Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo. Embo J 23, 4243-4252) except cell breakage and antibody binding were performed in 500 mM NaCl-containing buffer. Chromatin extract was divided in two, to one sample 4H8 antibody was added and to the second non-specific mouse IgG. Purified DNA was subjected to the Illumina ChIP-Seq DNA Sample Prep Kit for library production.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
4H8 antibody was produced by Cancer Research UK LRI in-house antibody service. Can be purchased from Abcam Cat. No. ab5408.
|
| Data processing |
Base-calling was performed using Illumina CASAVA pipeline and standard parameters.
ChIP-seq reads were aligned to the S288c reference R64 genome assembly using Novoalign V2.07.18 with default parameters.
wig files were generated using samtools depth.
Genome_build: Saccharomyces cerevisiae S288C reference genome R64 downloaded from SGD (http://www.yeastgenome.org/).
Supplementary_files_format_and_content: wig files
|
| |
|
| Submission date |
May 31, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Wu Wei |
| E-mail(s) |
wuwei@embl.de
|
| Organization name |
EMBL Heidelberg
|
| Department |
Genome Biology Unit
|
| Lab |
Steinmetz Lab
|
| Street address |
EMBL Heidelberg,Meyerhofstraße 1
|
| City |
Heidelberg |
| ZIP/Postal code |
69117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13272 |
| Series (2) |
| GSE38382 |
RNA polymerase II collision interrupts convergent transcription (ChIP-seq) |
| GSE38384 |
RNA polymerase II collision interrupts convergent transcription |
|
| Relations |
| SRA |
SRX150895 |
| BioSample |
SAMN01001327 |
