|
| Status |
Public on Jan 04, 2016 |
| Title |
S5p_K52o_EtOH |
| 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-K52o-HA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Where indicated, MYC K52o-HA was induced with doxycycline (pInducer samples) or treated with EtOH as solvent control. Where indicated MG-132 (10 µM) or EtOH as a control was added to the cells 4 hr prior to fixation. Cells were crosslinked with 1% formaldehyde 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 was precipitated by incubation with specific antibodies pre-adsorbed to 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 NextSeq 500 |
| |
|
| Data processing |
Basecalling and Demultiplexing was performed using BaseSpace from Illumina.
Reads were aligned to the human genome (hg19) with BOWTIE2 v2.1.0 using standard-options
Bedgraph files were generated using Bedtools
All further analysis were performed in R or Bedtools
Genome_build: hg19
Supplementary_files_format_and_content: Files in bedgraph format are provided.
|
| |
|
| Submission date |
Nov 20, 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 |
GPL18573 |
| 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 |
SAMN04285319 |
| SRA |
SRX1441868 |
