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Series GSE68582 Query DataSets for GSE68582
Status Public on May 05, 2016
Title Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State During Somatic Cell Reprogramming
Organism Mus musculus
Experiment type Other
Expression profiling by high throughput sequencing
Summary The pluripotent genome is folded in a hierarchy of sophisticated topologies that markedly reconfigure during cell fate transitions. A critical unknown is whether chromatin folding is reversible and functionally linked to the re-establishment of pluripotency in somatic cell reprogramming. Here we integrate classic epigenetic marks with high-resolution architecture maps in embryonic stem (ES) cells, ES-derived neural progenitor cells (NPCs) and NPC-derived induced pluripotent stem (iPS) cells. Collectively we demonstrate that chromatin architecture is only partially reconfigured during somatic cell reprogramming and that pluripotent elements can retain architectural memory from their somatic cell of origin.
Overall design Analysis of higher-order chromatin chromatin architecture and gene expression in mouse ES cells, primary NPCs and NPC-derived iPSCs.
Contributor(s) Plona ZM, Beagan JA, Gilgenast TG, Kim J, Phillips-Cremins JE
Citation(s) 27152443
Submission date May 05, 2015
Last update date May 15, 2019
Contact name Jennifer E Phillips-Cremins
Organization name University of Pennsylvania
Department Bioengineering
Street address 415 Curie Blvd
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19104
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (20)
GSM1974095 v65_Rep1_5C_library
GSM1974096 v65_Rep2_5C_library
GSM1974097 v65_2i_Rep1_5C_library
BioProject PRJNA283133
SRA SRP058020

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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
GSE68582_BED_ES-NPC-iPS-LOCI_mm9.bed.gz 24.2 Kb (ftp)(http) BED
GSE68582_BED_binned_mm9_20kbbin_4kbstep-10samples.bed.gz 13.1 Kb (ftp)(http) BED
GSE68582_BED_binned_mm9_20kbbin_4kbstep-6samples.bed.gz 13.1 Kb (ftp)(http) BED
GSE68582_Beagan_et_al_5C_processed_classification_data_file_2_23_2016_6samples.txt.gz 3.7 Mb (ftp)(http) TXT
GSE68582_Beagan_et_al_5C_processed_data_file_2_23_2016_10samples.txt.gz 36.8 Mb (ftp)(http) TXT
GSE68582_Beagan_et_al_5C_processed_data_file_2_23_2016_6samples.txt.gz 25.0 Mb (ftp)(http) TXT
GSE68582_Beagan_et_al_normalized_10sample_gene_expression_w_coordinates_1_29_2016.txt.gz 513.3 Kb (ftp)(http) TXT
GSE68582_RAW.tar 30.8 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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