|
| Status |
Public on May 22, 2019 |
| Title |
CES_PP_CTCF |
| Sample type |
SRA |
| |
|
| Source name |
CD19+ B-cells from peripheral blood of CLL patient
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD19+ B-cells from peripheral blood
disease: CLL
donor: PP
chip antibody: 61311 Active Motif rabbit Lot#31917004
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 4000 |
| |
|
| Data processing |
Base calls performed with Illumina RTA 2.7.7.
Reads were aligned using bowtie (options --best --strata -v 1 -m 1).
Peaks were called with MACS with standard settings.
genome_build: hs37d5
supplementary_files_format_and_content: bigWig files were generated using bamCoverage (deepTools). Coverage tracks were normalized to 1x.
Supplementary_files_format_and_content: bw
|
| |
|
| Submission date |
Oct 17, 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 |
GPL20301 |
| Series (1) |
| GSE113336 |
Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks |
|
| Relations |
| BioSample |
SAMN10255975 |
