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Sample GSM1898040 Query DataSets for GSM1898040
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

Supplementary file Size Download File type/resource
GSM1898040_WT_UT_rep1.wig.gz 393.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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