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Series GSE61349 Query DataSets for GSE61349
Status Public on Apr 27, 2015
Title Epigenetic and genetic features that lead to discovery of enhancer function
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The ability to measure epigenetic features, such as histone modifications and occupancy by transcription factors and co-activators, on a genome-wide scale is advancing the accuracy of CRM predictions. While integration of signals from multiple features is expected to improve predictions, the contribution of each feature to prediction accuracy is not known. We began with predictions of 4,915 erythroid enhancers based on genomic occupancy by TAL1, a key hematopoietic transcription factor that is strongly associated with gene induction in erythroid cells. Seventy of these DNA segments occupied by TAL1 (TAL1 OSs) were tested by transient transfections of cultured hematopoietic cells, and 56% of these were active as enhancers. Sixty-six TAL1 OSs were evaluated in transgenic mouse embryos, and 65% of these were active enhancers in various tissues. Inclusion of additional epigenetic features improved the prediction accuracy, with combinations of TAL1, GATA1, EP300, H3K4me1, and H3K27ac giving high accuracy of enhancer prediction (70%-75% success depending on method of clustering) while maintaining good sensitivity and specificity. Motifs that distinguish active from inactive TAL1 OSs implicate IRFs, STATs, and FOX protein families as candidate positive co-factors with TAL1, while REST (NRSF) and HOX family proteins are implicated in inactivity. While signals for evolutionary constraint were weak over the entire TAL1-bound DNA segments regardless of activity in either assay, phylogenetic preservation of a TF-binding site motif was associated with enhancer activity.
Overall design The contribution of 8 epigenetic features including H3K27ac to identification of enhancers in 24h-induced G1E-ER4 cells.
Contributor(s) Dogan N, Wu W, Morrissy CS, Chen K, Stronestrom A, Long M, Keller CA, Cheng Y, Jain D, Visel A, Pennacchio LA, Weiss MJ, Blobel GA, Hardison RC
Citation(s) 25984238
Submission date Sep 11, 2014
Last update date May 15, 2019
Contact name Ross Hardison
Organization name Pennsylvania State University
Street address 303 Wartik Lab
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (4)
GSM1502751 H3K27ac_replicate1
GSM1502752 H3K27ac_replicate2
GSM1502753 H3K27ac_treated with E2, replicate1
Reanalysis of GSM923567
Reanalysis of GSM923572
Reanalysis of GSM923576
Reanalysis of GSM946519
Reanalysis of GSM946520
Reanalysis of GSM946534
Reanalysis of GSM946537
Reanalysis of GSM946545
Reanalysis of GSM995449
Reanalysis of GSM912921
Reanalysis of GSM912893
BioProject PRJNA262049
SRA SRP047493

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

Supplementary file Size Download File type/resource
GSE61349_DoganSupplementalTables-1.xlsx 1.1 Mb (ftp)(http) XLSX
GSE61349_RAW.tar 14.0 Gb (http)(custom) TAR (of BIGWIG, BROADPEAK)
GSE61349_er4Pool.bigWig 5.1 Gb (ftp)(http) BIGWIG
GSE61349_er4Pool.broadpeak.gz 718.0 Kb (ftp)(http) BROADPEAK
GSE61349_g1ePool.bigWig 3.9 Gb (ftp)(http) BIGWIG
GSE61349_g1ePool.broadpeak.gz 611.4 Kb (ftp)(http) BROADPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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