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| 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
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| 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.
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| 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-/-
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| Contributor(s) |
Zviran A, Novershtern N, Rais Y, Mor N, Hanna J |
| Citation(s) |
30122475, 30554962 |
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| Submission date |
Aug 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Noa Novershtern |
| E-mail(s) |
noa.novershtern@weizmann.ac.il
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| Organization name |
Weizmann Institute of Science
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| Department |
Molecular Genetics
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| Street address |
Weizmann Institute
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| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (43)
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| GSM2735171 |
PolyA_Mbd3f/-_Day3 |
| GSM2735172 |
PolyA_Mbd3f/-_Day4 |
| GSM2735173 |
PolyA_Mbd3f/-_Day5 |
| GSM2735174 |
PolyA_Mbd3f/-_Day6 |
| GSM2735175 |
PolyA_Mbd3f/-_Day7 |
| GSM2735176 |
PolyA_Mbd3f/-_Day8 |
| GSM2735177 |
PolyA_Mbd3f/-_IPS |
| GSM2735178 |
PolyA_Mbd3f/-_ES |
| GSM2735179 |
PolyA_WT-1_MEF |
| GSM2735180 |
PolyA_WT-1_Day2 |
| GSM2735181 |
PolyA_WT-1_Day4 |
| GSM2735182 |
PolyA_WT-1_Day6 |
| GSM2735183 |
PolyA_WT-1_Day8 |
| GSM2735184 |
PolyA_WT-1_IPS |
| GSM2735185 |
PolyA_WT-1_ES |
| GSM2735186 |
PolyA_Gatad2a-/-_MEF |
| GSM2735187 |
PolyA_Gatad2a-/-_Day1 |
| GSM2735188 |
PolyA_Gatad2a-/-_Day2 |
| GSM2735189 |
PolyA_Gatad2a-/-_Day3 |
| GSM2735190 |
PolyA_Gatad2a-/-_Day4 |
| GSM2735191 |
PolyA_Gatad2a-/-_Day5 |
| GSM2735192 |
PolyA_Gatad2a-/-_Day6 |
| GSM2735193 |
PolyA_Gatad2a-/-_Day7 |
| GSM2735194 |
PolyA_Gatad2a-/-_Day8 |
| GSM2735195 |
PolyA_Gatad2a-/-_IPS |
| GSM2735196 |
PolyA_WT-2_MEF |
| GSM2735197 |
PolyA_WT-2_Day2 |
| GSM2735198 |
PolyA_WT-2_Day4 |
| GSM2735199 |
PolyA_WT-2_Day6 |
| GSM2735200 |
PolyA_WT-2_Day8 |
| GSM2735201 |
PolyA_WT-2_IPS |
| GSM3290271 |
OSK over expression + cMyc over expression, reprogramming, day 4 |
| GSM3290272 |
cMyc over expression reprogramming, day 4 |
| GSM3290273 |
OSK over expression reprogramming, day 4 |
| GSM3290274 |
reprogramming with siMyc (for cMyc, nMyc, lMyc), day 3 |
| GSM3290275 |
reprogramming with Myc inhibitor, day 3 |
| GSM3290276 |
reprogramming with siMyc (for cMyc, nMyc, lMyc), day 7 |
| GSM3290277 |
reprogramming with si-Scramble (control), day 7 |
| GSM3290278 |
reprogramming with si-Scramble (control), MEF replicate 1 |
| GSM3290279 |
reprogramming with si-Scramble (control), MEF replicate 2 |
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| 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 |
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| Relations |
| BioProject |
PRJNA397534 |
| SRA |
SRP115010 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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