|
| Status |
Public on May 22, 2019 |
| Title |
CES_ZV_H3K27me3 Sample 388 |
| Sample type |
SRA |
| |
|
| Source name |
CD19+ B-cells from peripheral blood of CLL patient
|
| Organism |
Homo sapiens |
| Characteristics |
disease: CLL
donor: ZV
chip antibody: Mouse monoclonal H3K27me3 (Abcam, ab6002)
treatment: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Patient derived cells were cross-linked with 1 % methanol-free formaldehyde for 10 min. After quenching with glycine, cells were washed three times with PBS and the cell pellet was frozen in liquid nitrogen. For analysis, the cell pellet was thawn and treated with 4U MNase per 1x106 cells for 15 min. MNase was stopped with 10x covaris buffer and the chromatin was sheared for an additional 15 min with the S2 covaris device and the soluble chromatin was then recovered and subjected to a background-minimizing pre-clearing step with an unspecific IgG antibody. For each ChIP-assay an equivalent of 3x106 cells were used with the antibodies. After the IP, chromatin was digested with RNaseA and proteinase K.
The purified DNA was cloned into illumina sequencing libraries with the NEBNext Ultra library preparation kit (NEB).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
bigWig
|
| Data processing |
Base calls performed with Illumina RTA 1.18.64.
Reads were aligned using bowtie (options --best --strata -v 1 -m 1).
SICER was used to determine enriched regions, peaks, with histone H3 serving again as a control.
hs37d5
bigWig files were generated using bamCoverage (deepTools). Coverage tracks were normalized to 1x.
|
| |
|
| Submission date |
Apr 18, 2018 |
| Last update date |
May 22, 2019 |
| Contact name |
Karsten Rippe |
| Phone |
+49-6221-54-51376
|
| Organization name |
DKFZ
|
| Department |
Division of Chromatin Networks
|
| Street address |
Im Neuenheimer Feld 267-BQ24
|
| City |
Heidelberg |
| State/province |
Germany |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE113336 |
Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks |
|
| Relations |
| BioSample |
SAMN08950669 |
