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Sample GSM3581128 Query DataSets for GSM3581128
Status Public on Apr 30, 2019
Title naïve LPM Bhlhe40 ChIP
Sample type SRA
 
Source name Peritoneal lavage
Organism Mus musculus
Characteristics strain: C57BL/6
treatment: untreated
tx conditions: NA
cell type: LPM
chip antibody: Novus Biologicals anti-Dec1 (Bhlhe40) NB100-1800, lot C1
gender: male
Treatment protocol See above
Growth protocol NA
Extracted molecule genomic DNA
Extraction protocol Bhlhe40 immunoprecipitation of bound, crosslinked DNA from LPMs
Genome Technology Access core (WUSTL)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
Description NA
Data processing FASTQ quality control, FastQC (0.11.3)
Read mapping, Bowtie (1.1.1) (mm10 reference genome)
Peak calling, MACS v1.4 (relative to input controls)
Peaks from unmapped regions and/or with fold-enrichment <5 were excluded
Normalized track generation, Deeptools (2.5.3)
Genome_build: Peak annotation, R package ChIPseeker (1.14.1)
Supplementary_files_format_and_content: bed, peaks, bw
 
Submission date Jan 28, 2019
Last update date May 01, 2019
Contact name Brian T Edelson
E-mail(s) bedelson@path.wustl.edu
Organization name Washington University in St. Louis
Department Pathology and Immunology
Lab Rm. 8304
Street address 425 S. Euclid Ave.
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platform ID GPL21493
Series (2)
GSE125729 Chromatin immunoprecipitation sequencing (ChIP-Seq) for Bhlhe40 from naïve and IL-4c-stimulated large peritoneal macrophages (LPMs)
GSE125730 Bhlhe40 mediates tissue-specific control of macrophage proliferation in homeostasis and type 2 immunity
Relations
BioSample SAMN10829922
SRA SRX5299298

Supplementary file Size Download File type/resource
GSM3581128_lpm_naive_light_peaks.bed.gz 26.5 Kb (ftp)(http) BED
GSM3581128_naive_LPM_Bhlhe40_bound_peaks.xlsx 307.4 Kb (ftp)(http) XLSX
GSM3581128_naive_bhlhe40_depth_norm.bw 113.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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