|
| Status |
Public on Jul 06, 2018 |
| Title |
CA12_3MC_2_input (chip-seq) |
| Sample type |
SRA |
| |
|
| Source name |
lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: 3-MC
cell line: GM17212
chip antibody: none
|
| Biomaterial provider |
Coriell lymphoblastoid cell line GM17212
https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM17212&PgId=166
|
| Treatment protocol |
Cells treated with 1uM 3-MC or 0.1% DMSO in fresh media for 24 hours
|
| Growth protocol |
Gown in RPMI 1640 + 15% FBS +1% P/S; passaged by spinning down at 120g for 5 minutes and resuspended in growth media; cultured in 37C with 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were pelleted at 300g for 5 minutes at 4C, resuspended in ice cold phosphate buffered saline and pelleted again. RNA was extracted using the miRNeasy RNA extraction kit. ChIP DNAs were extracted as described previously (PMID: 29268714).
ChIP-seq libraries were prepared according to manufacturer’s instructions in the ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI). The libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 4000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
OverlappedPeaksUniq.bed.gz
|
| Data processing |
Sequences were mapped to hg19 genome with BWA
Duplicates were removed
MACS2 was used to call narrow peaks
Bedtools was used to identify common peaks
Genome_build: hg19
Supplementary_files_format_and_content: tab separated bed of peaks in common between all four samples
|
| |
|
| Submission date |
Jul 05, 2018 |
| Last update date |
Jul 06, 2018 |
| Contact name |
Drew Neavin |
| E-mail(s) |
d.neavin@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Department |
Cellular Science
|
| Street address |
384 Victoria St
|
| City |
Darlinghurst |
| State/province |
New South Wales |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE116632 |
AHR ChIP-seq in lymphoblastoid cell line |
| GSE116638 |
Role of AHR in lymphoblastoid cell lines |
|
| Relations |
| BioSample |
SAMN09603995 |
| SRA |
SRX4342284 |
