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Series GSE88789 Query DataSets for GSE88789
Status Public on Jan 24, 2017
Title Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific p300 bioChIP-seq
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary We report a method for high throughput mapping of transcriptional enhancers, genomic regulatory regions that activate lineage-specific transcription. Since tissue-specific enhancers are bound by the transcriptional co-activator p300, we developed murine knock-in alleles that permit Cre-dependent, lineage-specific p300 in vivo biotinylation and high affinity pulldown on immobilized streptavidin. Subsequent next generation sequencing of p300-bound genomic DNA identified lineage-specific enhancers. By driving this system with lineage-specific Cre transgenes, we mapped enhancers active in embryonic endothelial cells/blood or skeletal muscle. Analysis of these enhancer sequences identified new transcription factor heterodimer motifs that likely regulate transcription in these lineages. Furthermore, we identified candidate enhancers that regulate adult heart- or lung- specific endothelial cell specialization.
 
Overall design ES_p300_bioChIP x2, E12.5 forebrain_p300bioChIP x2 and H3K27Ac ChIP x2, E12.5 heart_p300bioChIP x2 and H3K27Ac ChIP x2, E11.5_embryo_p300_bioChIP x3, E11.5_Tie2Cre_EC_p300-bioChIP x3, E13.5_Myf5Cre_muscle prognitors_p300-bioChIP x3, adult_heart_p300-bioChIP x2, adult heart_lung_p300-bioChIP x3, adult_heart_EC_p300-bioChIP x3, adult_lung_EC_p300-bioChIP x3, E12.5 Cardiomyocyte_ATAC-seq x2, E10.5_Tie2Cre-TRAP x1
 
Contributor(s) Zhou P, Gu F, Zhang L, Akerberg BN, Ma Q, Li K, He A, Lin Z, Stevens SM, Zhou B, Pu WT
Citation(s) 28121289
Submission date Oct 14, 2016
Last update date May 15, 2019
Contact name Fei Gu
E-mail(s) alickgf@hotmail.com
Organization name Childrens hospital boston, Harvard Medical School
Department Cardiology
Lab William Pu
Street address 320 Longwood Ave.
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (40)
GSM2346434 ES_P300_input_rep1
GSM2346435 ES_P300_input_rep2
GSM2346436 ES_p300_rep1
Relations
BioProject PRJNA348551
SRA SRP091587

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
GSE88789_RAW.tar 5.4 Gb (http)(custom) TAR (of BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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