|
| Status |
Public on Feb 07, 2019 |
| Title |
nsg-1f12-2-PT1 H3K27ac ChIP Seq |
| Sample type |
SRA |
| |
|
| Source name |
CRC cell line
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: peritoneal tumors
chip antibody: rabbit anti-H3K27ac (Abcam #4729).
|
| Growth protocol |
LoVo cells were grown in media supplemented as previously described; COLO205-derived subclones were grown in RPMI-1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin for approximately 2.5 months, then subcloned and expanded.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-Seq libraries were prepared with NEB reagents as previously described. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of ~250 bp were band isolated from an agarose gel.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
One of 2 peritoneal tumors formed by intrasplenic injection of 1f12-2 cells into female nude mouse.
|
| Data processing |
Adapter and quality trimming of ChIP-Seq reads was done using FASTX Toolkit 0.0.13. Reads below 25bp in length or reads with Phred quality scores below 20 were discarded
ChIP-seq reads were aligned to hg19 with Bowtie2 version 2.2.6, using default parameters.
Potential PCR duplicates were removed from aligned ChIP Seq reads files
ChIP-Seq peaks were called using MACS v2.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq WIG tracks were generated using Deeptools 3.1.2 and normalized using the RPGC option
|
| |
|
| Submission date |
Feb 06, 2019 |
| Last update date |
Feb 12, 2019 |
| Contact name |
Peter Scacheri |
| E-mail(s) |
pxs183@case.edu
|
| Phone |
216-368-3458
|
| Organization name |
Case Western Reserve University
|
| Street address |
10900 Euclid Ave; BRB 647
|
| City |
Cleveland Heights |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE126188 |
Mismatch-repair signature mutations activate gene enhancers across human colorectal cancer epigenomes |
|
| Relations |
| BioSample |
SAMN10881752 |
| SRA |
SRX5343532 |
