|
| Status |
Public on Mar 11, 2015 |
| Title |
H2AK119Ub MiG-empty ChIP-seq rep2 |
| Sample type |
SRA |
| |
|
| Source name |
H2AK119Ub MiG-empty ChIP-seq
|
| Organism |
Mus musculus |
| Characteristics |
cell line: EML
tissue: bone marrow
cell type: basophil
atcc catalog number: CRL-11691
chip antibody: H2AK119Ub (Cell Signaling Technologies (Danvers, MA), Cat# 8240)
|
| Biomaterial provider |
ATCC
|
| Treatment protocol |
EML cells were transduced with either MSCV-IRES-GFP (MiG-empty) or with retroviral constructs encoding ASXL1(1-479) + BAP1 and expanded for 15 days post-transduction
|
| Growth protocol |
EML cells cultured under conditions recommended by ATCC. ATCC Cat # CRL-11691
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
IP's for ChIP-seq were carried out on mono-nucleosomes generated from EML cells.
ChiP-seq libraries were constructed using NEB's ChIP-seq library preparation kit for SOLiD sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Description |
processed data file: peaks_H2AK119Ub.bed
|
| Data processing |
ChIP-seq reads were aligned using Bowtie (version 0.12.8), allowing only uniquely mapping reads, fragment sizes of 90-250bp, and removing duplicates.
Enriched areas were called using SICER with parameters as suggested in the documentation and for H2AK119Ub with win size=800 and gap size=2400.
Genome_build: mm9
Supplementary_files_format_and_content: BED files with SICER calls, DESeq result file, eXpress result files
|
| |
|
| Submission date |
Feb 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Anjana Rao |
| E-mail(s) |
arao@liai.orgo
|
| Organization name |
La Jolla Institute for Allergy and Immunology
|
| Department |
Department of Signaling and Gene Expression
|
| Street address |
9420 Athena Circle
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL15907 |
| Series (1) |
| GSE65555 |
Cancer-associated ASXL1 mutations may act as gain-of-function mutations of the ASXL1-BAP1 complex |
|
| Relations |
| BioSample |
SAMN03326192 |
| SRA |
SRX864145 |
