|
| Status |
Public on Jan 04, 2016 |
| Title |
S5p_Kless_EtOH.wig |
| Sample type |
SRA |
| |
|
| Source name |
IMEC cell line
|
| Organism |
Homo sapiens |
| Characteristics |
generation of cells: primary breast epithelial cells
antibody: Ser5p_RNAPII
dox treatment: EtOH
construct: pInducer21-MYC-Kless-HA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Where indicated, MYC was induced with doxycycline (pInducer samples) or treated with EtOH as solvent control. Cells were crosslinked with 1% formaldehyde at 37°C for 10min. Cells were lysed and after centrifugation nuclei were re-suspended in RIPA buffer. DNA was sonicated with a Branson sonifier to obtain DNA fragments at nucleosomal size. Chromatin bound to target proteins (HA-tag) was preciüitated by incubation with Protein A dynabeads beads overnight. After several washings chromatin was eluted with 1 % SDS and crosslinking was reverted overnight. DNA was purified by Phenol/Chloroform extraction and enrichments were checked by qPCR.
Libraries for ChIP-seq samples were contructed following manufactor's intructions using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (E6240). Briefly, ChIP DNA was end repaired, A-tailed and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of a agarose gel and extracted with a Qiagen PCR purification column. Size-selected DNA was amplified with 18 PCR cycles.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalling was performed with the real time analysis (RTA) package within the Genome Analyzer Sequencing Control Software (SCS2.10).
Demultiplexing and generation of Fastq files was done with the CASAVA software only considering high quality sequences (PF-cluster).
Reads were aligned to the human genome (hg19) with BOWTIE v0.12.8 using standard-options
Peaks were called and wig-files were produced with MACS-1.4.2
All further analysis were performed in R or Bedtools
Genome_build: hg19
Supplementary_files_format_and_content: MACS-output files in wig-format are provided.
|
| |
|
| Submission date |
Jun 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Eilers |
| Organization name |
University of Wuerzburg
|
| Department |
Chair for Biochemistry and Molecular Biology
|
| Lab |
Martin Eilers
|
| Street address |
Am Hubland
|
| City |
Wuerzburg |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE70001 |
Ubiquitin-dependent turnover of MYC promotes loading of the PAF complex on RNA Polymerase II to drive transcriptional elongation (ChIP-seq) |
| GSE70009 |
Ubiquitin-dependent turnover of MYC promotes loading of the PAF complex on RNA Polymerase II to drive transcriptional elongation |
|
| Relations |
| BioSample |
SAMN03782275 |
| SRA |
SRX1065315 |
