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Series GSE109965 Query DataSets for GSE109965
Status Public on May 17, 2018
Title Analysis of genetically diverse macrophages reveals local and domain-wide mechanisms that control transcription factor binding and function
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Other
Summary Non-coding genetic variation is a major driver of phenotypic diversity and allows investigation of mechanisms that control gene expression. Here, we systematically investigated the effects of >50 million variations from five strains of mice on mRNA, nascent transcription, transcription start sites and transcription factor binding in resting and activated macrophages. We observed substantial differences associated with distinct molecular pathways. Evaluation of genetic variation provided evidence for roles of ~100 TFs in shaping lineage-determining factor binding. Unexpectedly, a substantial fraction of strain-specific factor binding could not be explained by local mutations. Integration of genomic features with chromatin interaction data provided evidence for hundreds of connected cis-regulatory domains associated with differences in transcription factor binding and gene expression. This system and the >250 data sets establish a substantial new resource for investigation of how genetic variation affects cellular phenotypes.
 
Overall design 5'GRO-Seq, GRO-Seq, ATAC-Seq, ChIP-seq, RNA-seq, Bisulfite-Seq, Hi-C and PLAC-Seq for diverse strains of mice: BALB/cJ, C57BL/6J, C57BL/6J x PWK/PhJ, C57BL/6J x SPRET/EiJ, NOD/ShiLtJ, PWK/PhJ, SPRET/EiJ

Several of the Input samples have been used for multiple ChIP samples. Please see 'description' field for a list of the ChIP samples associated with the input sample.
 
Contributor(s) Link VM, Glass CK
Citation(s) 29779944
Submission date Jan 31, 2018
Last update date Mar 11, 2021
Contact name Christopher Glass
E-mail(s) ckg@ucsd.edu
Phone 858-534-6011
Organization name University of California, San Diego
Department CMM
Lab Glass Lab
Street address 9500 Gilman Dr.
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (294)
GSM2974596 BALB_BMDM_5GRO_KLA_1h_rep1
GSM2974597 BALB_BMDM_5GRO_KLA_1h_rep2
GSM2974598 BALB_BMDM_5GRO_notx_rep1
Relations
BioProject PRJNA432435
SRA SRP131922

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE109965_5GRO_processed_data.tar.gz 8.8 Mb (ftp)(http) TAR
GSE109965_ATAC-seq_processed_data.tar.gz 3.8 Mb (ftp)(http) TAR
GSE109965_BALBCJ_genome.tar.gz 830.1 Mb (ftp)(http) TAR
GSE109965_C57_BMDM_HiC_raw_interactions_1MB.txt.gz 6.7 Mb (ftp)(http) TXT
GSE109965_C57_cytosine_report.txt.gz 230.7 Mb (ftp)(http) TXT
GSE109965_ChIP-seq_processed_data.tar.gz 38.9 Mb (ftp)(http) TAR
GSE109965_GRO-Seq_processed_data.tar.gz 7.4 Mb (ftp)(http) TAR
GSE109965_GRO_Seq_all_strains_KLA_1h_TPM.txt.gz 2.0 Mb (ftp)(http) TXT
GSE109965_NODSHILTJ_genome.tar.gz 830.4 Mb (ftp)(http) TAR
GSE109965_PLAC_seq_consensus_interactions.txt.gz 1.3 Mb (ftp)(http) TXT
GSE109965_PWKPHJ_genome.tar.gz 837.1 Mb (ftp)(http) TAR
GSE109965_RNA-seq_processed_data.tar.gz 6.9 Mb (ftp)(http) TAR
GSE109965_SPRETEIJ_genome.tar.gz 845.7 Mb (ftp)(http) TAR
GSE109965_SPRET_BMDM_HiC_raw_interactions_1MB.txt.gz 6.4 Mb (ftp)(http) TXT
GSE109965_SPRET_cytosine_report.txt.gz 234.9 Mb (ftp)(http) TXT
GSE109965_mutations.bed.tar.gz 1.0 Gb (ftp)(http) TAR
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Raw data are available in SRA
Processed data are available on Series record
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