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Series GSE102348 Query DataSets for GSE102348
Status Public on Jul 15, 2018
Title High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems [RNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Reprogramming of somatic cells to induced pluripotent stem cells provoke immense interest both for clinical applications in regenerative medicine, and in understanding the regulation of cell identity. Previous characterization of the molecular events that underlie this process were limited by the low yield and by the stochastic dynamics of this process. Here we present an in-depth mapping of the molecular events that underlie an efficient and successful reprogramming, covering transcriptional, epigenetic and translational changes in a single day resolution.
 
Overall design Mbd3f/-, Gatad2a-/- or wild-type (WT-1,WT-2) MEFs that carry DOX-inducible OKSM cassette were used, and iPSC reprogramming was initiated by addition of DOX in FBS/LIF medium in 5% pO2 conditions. On day 3.5 after DOX initiation, medium was changed to LIF/KSR-based with the addition of two small molecule inhibitors for MEK/ERK and GSK3 signaling (2i). Cells were harvested every 24 hours until day 8, and processed for library preparation followed by high-throughput sequencing. Mbd3f/-, Gatad2a-/- and WT established iPSC line (after 3 passages or more), and Mbd3f/- or WT V6.5 mouse ESCs were used as positive controls. PolyA RNA-seq measured in each time point. WT-2 cell line is isogenic to Gatad2a-/-
 
Contributor(s) Zviran A, Novershtern N, Rais Y, Mor N, Hanna J
Citation(s) 30122475, 30554962
Submission date Aug 08, 2017
Last update date May 15, 2019
Contact name Noa Novershtern
E-mail(s) noa.novershtern@weizmann.ac.il
Organization name Weizmann Institute of Science
Department Molecular Genetics
Street address Weizmann Institute
City Rehovot
ZIP/Postal code 7610001
Country Israel
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (43)
GSM2735168 PolyA_Mbd3f/-_MEF
GSM2735169 PolyA_Mbd3f/-_Day1
GSM2735170 PolyA_Mbd3f/-_Day2
This SubSeries is part of SuperSeries:
GSE102518 High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems
Relations
BioProject PRJNA397534
SRA SRP115010

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
GSE102348_Gatad2a-_fpkm.txt.gz 1.3 Mb (ftp)(http) TXT
GSE102348_Mbd3f_-_fpkm.txt.gz 1.2 Mb (ftp)(http) TXT
GSE102348_Myc_pert.fpkm.txt.gz 1.1 Mb (ftp)(http) TXT
GSE102348_WT-1_fpkm.txt.gz 878.8 Kb (ftp)(http) TXT
GSE102348_WT-2_fpkm.txt.gz 770.1 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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