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Status |
Public on Jul 06, 2018 |
Title |
CA12_3MC_2 (chip-seq) |
Sample type |
SRA |
|
|
Source name |
lymphoblastoid cell line
|
Organism |
Homo sapiens |
Characteristics |
treatment: 3-MC cell line: GM17212 chip antibody: D5S6H-lot 1 (Cell Signaling Technology)
|
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.
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|
|
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
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|
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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 |
SAMN09603996 |
SRA |
SRX4342283 |