 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 04, 2018 |
| Title |
A673_Input_DNA |
| Sample type |
SRA |
| |
|
| Source name |
Ewing sarcoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A673
cell type: Ewing sarcoma
chip antibody: None
cell number: 20,000,000
|
| Growth protocol |
A673 Ewing sarcoma cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and kept at 37℃ with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell lysates were clarified from sonicated nuclei and MEIS1-DNA complexes were isolated with antibody.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v1.1.2 with parameters -m 2 -k 2 --best --strata
Using Picard to mark and remove duplicate reads
using macs2 to peaks calling with parameters -q 0.01 --extsize 200 --nomodel
Genome_build: hg19
|
| |
|
| Submission date |
Jan 23, 2018 |
| Last update date |
Dec 04, 2018 |
| Contact name |
Lehang Lin |
| E-mail(s) |
linlh7@mail2.sysu.edu.cn
|
| Organization name |
Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University
|
| Street address |
107, West Yanjiang Road
|
| City |
Guangzhou |
| ZIP/Postal code |
510120 |
| Country |
China |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE109477 |
Genome-wide chromatin analysis of Ewing sarcoma (ChIP-seq) |
|
| Relations |
| BioSample |
SAMN08384641 |
| SRA |
SRX3591010 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
