|
| Status |
Public on Jul 30, 2018 |
| Title |
H3K27ac ChIP-seq in MSC infected with EWSFLI1 |
| Sample type |
SRA |
| |
|
| Source name |
primary tissue
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MSC
chip antibody: H3K27ac
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin from formaldehyde-fixed cells (2-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads(Beckman Coulter) after crosslink reversal, RNAse A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MSC.EWSFLI1.H3K27ac
|
| Data processing |
Reads were aligned to GRCh37 using bwa (version 0.6.2) After removal of PCR duplicates using Picard(http://broadinstitute.github.io/picard), read counts were normalized for sequencing depth and scaled to 10 million reads to generate bigwig files.
Genome_build: hg19
|
| |
|
| Submission date |
Nov 15, 2017 |
| Last update date |
May 31, 2019 |
| Contact name |
Sowmya Iyer |
| E-mail(s) |
[email protected]
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Pathology
|
| Street address |
149 13th St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL24268 |
| Series (2) |
| GSE106914 |
Epigenome editing of microsatellite repeat enhancers reveals specific regulatory functions and tumor dependencies [ChIP-Seq] |
| GSE106925 |
Epigenome editing of microsatellite repeat enhancers reveals specific regulatory functions and tumor dependencies |
|
| Relations |
| BioSample |
SAMN08027865 |
