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Series GSE47459 Query DataSets for GSE47459
Status Public on Aug 15, 2013
Title Program specificity for Ptf1a in Pancreas versus Neural Tube Development correlates with distinct collaborating cofactors and chromatin accessibility
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Ptf1a is a lineage-specific basic-helix-loop-helix transcription factor critical in the development of both the pancreas and nervous system. How one transcription factor controls diverse programs of gene expression is a fundamental question in developmental biology. To uncover molecular strategies for the program-specific functions of Ptf1a, we identified bound genomic regions in vivo during development of both tissues. A majority of regions bound by Ptf1a are tissue-specific, lie near genes needed for proper formation and maturation of each tissue, and reflect regions of open chromatin.  Information for the specificity of Ptf1a binding and function is encoded in the DNA surrounding the Ptf1a-bound sites, since Ptf1a-bound regions are sufficient to direct tissue-restricted reporter expression when tested in transgenic mice. Fox and Sox factors were identified as lineage specific modifiers of Ptf1a binding, since binding motifs for these factors are enriched in Ptf1a-bound regions in pancreas and neural tube, respectively. Although Ptf1a and Foxa2 co-localize to sites in embryonic pancreas and can act synergistically in cell transfection assays, biochemical experiments detected no physical interaction between the two factors. These findings indicate that lineage-specific chromatin landscapes likely constrain the functions of Ptf1a, and identify Fox and Sox gene families as part of this process.
 
Overall design RNA-Seq: Examination of gene expression in Ptf1a expressing cells (NT E.12.5, Pancreas E15.5)
ChIP-Seq: Examination of chromatin occupancy in 2 tissue types (E12.5 NT and 17.5 Pancreas).
Faire-Seq: Examination of open chromatin in 2 tissue types (E12.5 NT and 17.5 Pancreas).
 
Contributor(s) Meredith DM, Borromeo MD, Deering TG, Casey B, Savage TK, Mayer PR, Hoang C, Tung K, Kumar M, Shen C, Swift GH, MacDonald RJ, Johnson JE
Citation(s) 23754747
Submission date May 29, 2013
Last update date Mar 19, 2019
Contact name Jane E Johnson
E-mail jane.johnson@utsouthwestern.edu
Organization name UT Southwestern Medical Center
Department Neuroscience
Street address 5323 Harry Hines Blvd
City Dallas
State/province TX
ZIP/Postal code 75390-9111
Country USA
 
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (18)
GSM1150320 RnaSeq_2.3Ptf1aGFP_NT
GSM1150322 RnaSeq_E15.5_Pancreas_WT
GSM1150323 ChIPseq_Ptf1a_NT_1
Relations
BioProject PRJNA205746
SRA SRP023264

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
GSE47459_RAW.tar 742.8 Mb (http)(custom) TAR (of BEDGRAPH)
GSE47459_RnaSeq_Ptf1a_FPKM_expression.txt.gz 225.5 Kb (ftp)(http) TXT
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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