|
Status |
Public on Jun 13, 2016 |
Title |
WT_UT_rep1 |
Sample type |
SRA |
|
|
Source name |
Macrophages
|
Organism |
Mus musculus |
Characteristics |
cell type: Bone marrow-derived macrophages strain: C57BL/6 chip antibody: RNA Pol II
|
Treatment protocol |
WT and DKO BMDMs were left untreated or exposed to 10 ng/ml cell culture grade LPS (Escherichia coli 0111:B4, Sigma) for 1 hour.
|
Growth protocol |
Bone marrows cells from WT and DKO mice were cultured for 5 days in DMEM supplemented with 10% FBS and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor to generate BMDMs
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Lysates were clarified from sonicated nuclei and Pol II-DNA complexes were isolated with antibody DNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Basecalls performed using CASAVA version 1.8.2 ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 1.0.1 Reads have passed Illumina filters, and been trimmed using Sickle using quality threshold >20 Peaks were called using ChIPseeqer with the following setting: p < 10~-15, FDR <0.02) Annotation and downstream analysis was done using ChIPseeqer Genome_build: mm10 Supplementary_files_format_and_content: wig
|
|
|
Submission date |
Sep 29, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Yingli Shang |
E-mail(s) |
yinglishang@gmail.com
|
Organization name |
Hospital for Special Surgery
|
Street address |
535E 70th Street
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10021 |
Country |
USA |
|
|
Platform ID |
GPL13112 |
Series (1) |
GSE73568 |
ChIP-seq to profile LPS-induced RNA polymerase II transcription in bone marrow-derived macrophages from WT and Hes1 KO mice |
|
Relations |
BioSample |
SAMN04122644 |
SRA |
SRX1295675 |