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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 [ChIP-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy 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/- or Gatad2a-/- (P66) 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 WT V6.5 mouse ESCs were used as positive controls. ChIP-seq of the following proteins was measured in each time point: Oct4/Pou5f1, c-Myc, Klf4, Sox2, PolII, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9me2, H3K9me3.
This series includes re-analyzed samples from GSE49766.
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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 10, 2017 |
| Last update date |
Jul 25, 2021 |
| 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 (3) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (144)
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| GSM2739908 |
Oct4 ChIP-seq, in Mbd3f/- system, Day4 |
| GSM2739909 |
Oct4 ChIP-seq, in Mbd3f/- system, Day5 |
| GSM2739910 |
Oct4 ChIP-seq, in Mbd3f/- system, Day6 |
| GSM2739911 |
Oct4 ChIP-seq, in Mbd3f/- system, Day7 |
| GSM2739912 |
Oct4 ChIP-seq, in Mbd3f/- system, Day8 |
| GSM2739913 |
Oct4 ChIP-seq, in Mbd3f/- system, ES |
| GSM2739914 |
c-Myc ChIP-seq, in Mbd3f/- system, Day1 |
| GSM2739915 |
c-Myc ChIP-seq, in Mbd3f/- system, Day2 |
| GSM2739916 |
c-Myc ChIP-seq, in Mbd3f/- system, Day3 |
| GSM2739917 |
c-Myc ChIP-seq, in Mbd3f/- system, Day4 |
| GSM2739918 |
c-Myc ChIP-seq, in Mbd3f/- system, Day5 |
| GSM2739919 |
c-Myc ChIP-seq, in Mbd3f/- system, Day6 |
| GSM2739920 |
c-Myc ChIP-seq, in Mbd3f/- system, Day7 |
| GSM2739921 |
c-Myc ChIP-seq, in Mbd3f/- system, ES |
| GSM2739922 |
c-Myc ChIP-seq, in Mbd3f/- system, IPS |
| GSM2739923 |
c-Myc ChIP-seq, in Mbd3f/- system, MEF |
| GSM2739924 |
H3K27ac ChIP-seq, in Mbd3f/- system, Day1 |
| GSM2739925 |
H3K27ac ChIP-seq, in Mbd3f/- system, Day2 |
| GSM2739926 |
H3K27ac ChIP-seq, in Mbd3f/- system, Day3 |
| GSM2739927 |
H3K27ac ChIP-seq, in Mbd3f/- system, Day4 |
| GSM2739928 |
H3K27ac ChIP-seq, in Mbd3f/- system, Day5 |
| GSM2739929 |
H3K27ac ChIP-seq, in Mbd3f/- system, Day6 |
| GSM2739930 |
H3K27ac ChIP-seq, in Mbd3f/- system, Day7 |
| GSM2739931 |
H3K27ac ChIP-seq, in Mbd3f/- system, Day8 |
| GSM2739932 |
H3K27ac ChIP-seq, in Mbd3f/- system, ES |
| GSM2739933 |
H3K27ac ChIP-seq, in Mbd3f/- system, IPS |
| GSM2739934 |
H3K27me3 ChIP-seq, in Mbd3f/- system, Day1 |
| GSM2739935 |
H3K27me3 ChIP-seq, in Mbd3f/- system, Day2 |
| GSM2739936 |
H3K27me3 ChIP-seq, in Mbd3f/- system, Day3 |
| GSM2739937 |
H3K27me3 ChIP-seq, in Mbd3f/- system, Day4 |
| GSM2739938 |
H3K27me3 ChIP-seq, in Mbd3f/- system, Day5 |
| GSM2739939 |
H3K27me3 ChIP-seq, in Mbd3f/- system, Day6 |
| GSM2739940 |
H3K27me3 ChIP-seq, in Mbd3f/- system, Day7 |
| GSM2739941 |
H3K27me3 ChIP-seq, in Mbd3f/- system, Day8 |
| GSM2739942 |
H3K27me3 ChIP-seq, in Mbd3f/- system, ES |
| GSM2739943 |
H3K27me3 ChIP-seq, in Mbd3f/- system, IPS |
| GSM2739944 |
H3K27me3 ChIP-seq, in Mbd3f/- system, MEF 1 |
| GSM2739945 |
H3K27me3 ChIP-seq, in Mbd3f/- system, MEF 2 |
| GSM2739946 |
H3K36me3 ChIP-seq, in Mbd3f/- system, Day1 |
| GSM2739947 |
H3K36me3 ChIP-seq, in Mbd3f/- system, Day2 |
| GSM2739948 |
H3K36me3 ChIP-seq, in Mbd3f/- system, Day3 |
| GSM2739949 |
H3K36me3 ChIP-seq, in Mbd3f/- system, Day4 |
| GSM2739950 |
H3K36me3 ChIP-seq, in Mbd3f/- system, Day5 |
| GSM2739951 |
H3K36me3 ChIP-seq, in Mbd3f/- system, Day6 |
| GSM2739952 |
H3K36me3 ChIP-seq, in Mbd3f/- system, Day7 |
| GSM2739953 |
H3K36me3 ChIP-seq, in Mbd3f/- system, Day8 |
| GSM2739954 |
H3K36me3 ChIP-seq, in Mbd3f/- system, ES |
| GSM2739955 |
H3K36me3 ChIP-seq, in Mbd3f/- system, IPS |
| GSM2739956 |
H3K36me3 ChIP-seq, in Mbd3f/- system, MEF |
| GSM2739957 |
H3K4me1 ChIP-seq, in Mbd3f/- system, Day1 |
| GSM2739958 |
H3K4me1 ChIP-seq, in Mbd3f/- system, Day2 |
| GSM2739959 |
H3K4me1 ChIP-seq, in Mbd3f/- system, Day3 |
| GSM2739960 |
H3K4me1 ChIP-seq, in Mbd3f/- system, Day4 |
| GSM2739961 |
H3K4me1 ChIP-seq, in Mbd3f/- system, Day5 |
| GSM2739962 |
H3K4me1 ChIP-seq, in Mbd3f/- system, Day6 |
| GSM2739963 |
H3K4me1 ChIP-seq, in Mbd3f/- system, Day7 |
| GSM2739964 |
H3K4me1 ChIP-seq, in Mbd3f/- system, Day8 |
| GSM2739965 |
H3K4me1 ChIP-seq, in Mbd3f/- system, ES |
| GSM2739966 |
H3K4me1 ChIP-seq, in Mbd3f/- system, IPS |
| GSM2739967 |
H3K4me1 ChIP-seq, in Mbd3f/- system, MEF |
| GSM2739968 |
H3K4me3 ChIP-seq, in Mbd3f/- system, Day1 |
| GSM2739969 |
H3K4me3 ChIP-seq, in Mbd3f/- system, Day2 |
| GSM2739970 |
H3K4me3 ChIP-seq, in Mbd3f/- system, Day3 |
| GSM2739971 |
H3K4me3 ChIP-seq, in Mbd3f/- system, Day4 |
| GSM2739972 |
H3K4me3 ChIP-seq, in Mbd3f/- system, Day5 |
| GSM2739973 |
H3K4me3 ChIP-seq, in Mbd3f/- system, Day6 |
| GSM2739974 |
H3K4me3 ChIP-seq, in Mbd3f/- system, Day7 |
| GSM2739975 |
H3K4me3 ChIP-seq, in Mbd3f/- system, Day8 |
| GSM2739976 |
H3K4me3 ChIP-seq, in Mbd3f/- system, ES |
| GSM2739977 |
H3K4me3 ChIP-seq, in Mbd3f/- system, IPS |
| GSM2739978 |
H3K9me2 ChIP-seq, in Mbd3f/- system, Day1 |
| GSM2739979 |
H3K9me2 ChIP-seq, in Mbd3f/- system, Day2 |
| GSM2739980 |
H3K9me2 ChIP-seq, in Mbd3f/- system, Day3 |
| GSM2739981 |
H3K9me2 ChIP-seq, in Mbd3f/- system, Day4 |
| GSM2739982 |
H3K9me2 ChIP-seq, in Mbd3f/- system, Day5 |
| GSM2739983 |
H3K9me2 ChIP-seq, in Mbd3f/- system, Day6 |
| GSM2739984 |
H3K9me2 ChIP-seq, in Mbd3f/- system, Day7 |
| GSM2739985 |
H3K9me2 ChIP-seq, in Mbd3f/- system, Day8 |
| GSM2739986 |
H3K9me2 ChIP-seq, in Mbd3f/- system, IPS |
| GSM2739987 |
H3K9me2 ChIP-seq, in Mbd3f/- system, MEF |
| GSM2739988 |
H3K9me3 ChIP-seq, in Mbd3f/- system, Day1 |
| GSM2739989 |
H3K9me3 ChIP-seq, in Mbd3f/- system, Day2 |
| GSM2739990 |
H3K9me3 ChIP-seq, in Mbd3f/- system, Day3 |
| GSM2739991 |
H3K9me3 ChIP-seq, in Mbd3f/- system, Day4 |
| GSM2739992 |
H3K9me3 ChIP-seq, in Mbd3f/- system, Day5 |
| GSM2739993 |
H3K9me3 ChIP-seq, in Mbd3f/- system, Day6 |
| GSM2739994 |
H3K9me3 ChIP-seq, in Mbd3f/- system, Day7 |
| GSM2739995 |
H3K9me3 ChIP-seq, in Mbd3f/- system, Day8 |
| GSM2739996 |
H3K9me3 ChIP-seq, in Mbd3f/- system, ES |
| GSM2739997 |
H3K9me3 ChIP-seq, in Mbd3f/- system, IPS |
| GSM2739998 |
H3K9me3 ChIP-seq, in Mbd3f/- system, MEF |
| GSM2739999 |
Klf4 ChIP-seq, in Mbd3f/- system, Day1 |
| GSM2740000 |
Klf4 ChIP-seq, in Mbd3f/- system, Day2 |
| GSM2740001 |
Klf4 ChIP-seq, in Mbd3f/- system, Day3 |
| GSM2740002 |
Klf4 ChIP-seq, in Mbd3f/- system, Day4 |
| GSM2740003 |
Klf4 ChIP-seq, in Mbd3f/- system, Day5 |
| GSM2740004 |
Klf4 ChIP-seq, in Mbd3f/- system, Day6 |
| GSM2740005 |
Klf4 ChIP-seq, in Mbd3f/- system, Day7 |
| GSM2740006 |
Klf4 ChIP-seq, in Mbd3f/- system, Day8 |
| GSM2740007 |
Klf4 ChIP-seq, in Mbd3f/- system, ES |
| GSM2740008 |
Klf4 ChIP-seq, in Mbd3f/- system, IPS |
| GSM2740009 |
Klf4 ChIP-seq, in Mbd3f/- system, MEF |
| GSM2740010 |
PolII ChIP-seq, in Mbd3f/- system, Day1 |
| GSM2740011 |
PolII ChIP-seq, in Mbd3f/- system, Day2 |
| GSM2740012 |
PolII ChIP-seq, in Mbd3f/- system, Day3 |
| GSM2740013 |
PolII ChIP-seq, in Mbd3f/- system, Day4 |
| GSM2740014 |
PolII ChIP-seq, in Mbd3f/- system, Day5 |
| GSM2740015 |
PolII ChIP-seq, in Mbd3f/- system, Day6 |
| GSM2740016 |
PolII ChIP-seq, in Mbd3f/- system, Day7 |
| GSM2740017 |
PolII ChIP-seq, in Mbd3f/- system, Day8 |
| GSM2740018 |
PolII ChIP-seq, in Mbd3f/- system, ES |
| GSM2740019 |
PolII ChIP-seq, in Mbd3f/- system, IPS |
| GSM2740020 |
PolII ChIP-seq, in Mbd3f/- system, MEF |
| GSM2740021 |
Sox2 ChIP-seq, in Mbd3f/- system, Day1 |
| GSM2740022 |
Sox2 ChIP-seq, in Mbd3f/- system, Day2 |
| GSM2740023 |
Sox2 ChIP-seq, in Mbd3f/- system, Day3 |
| GSM2740024 |
Sox2 ChIP-seq, in Mbd3f/- system, Day4 |
| GSM2740025 |
Sox2 ChIP-seq, in Mbd3f/- system, Day5 |
| GSM2740026 |
Sox2 ChIP-seq, in Mbd3f/- system, Day6 |
| GSM2740027 |
Sox2 ChIP-seq, in Mbd3f/- system, Day7 |
| GSM2740028 |
Sox2 ChIP-seq, in Mbd3f/- system, Day8 |
| GSM2740029 |
Sox2 ChIP-seq, in Mbd3f/- system, ES |
| GSM2740030 |
Sox2 ChIP-seq, in Mbd3f/- system, IPS |
| GSM2740031 |
K27Ac Chip-seq in Gatad2a-/- system, Day4 |
| GSM2740032 |
K27Ac Chip-seq in Gatad2a-/- system, MEF |
| GSM2740033 |
K27Ac Chip-seq in Gatad2a-/- system, Day2 |
| GSM2740034 |
K27Ac Chip-seq in Gatad2a-/- system, Day6 |
| GSM2740035 |
K27Ac Chip-seq in Gatad2a-/- system, Day8 |
| GSM2740036 |
Whole cell extract (Input) from Gatad2a-/- system, Day4 |
| GSM2912463 |
MBD3_f_-_IPS_Oct4_reanalyzed |
| GSM2912464 |
WT_4day_DOX_H3K27ac_reanalyzed |
| GSM2912465 |
WT_8day_DOX_H3K27ac_reanalyzed |
| GSM2912466 |
WT_IPS_H3K27ac_reanalyzed |
| GSM2912467 |
MBD3_f_-_MEF_H3K27ac_reanalyzed |
| GSM2912468 |
WT_MEF_H3K27ac_reanalyzed |
| GSM2912469 |
MBD3_f_-_MEF_H3K4me3_reanalyzed |
| GSM2912470 |
MBD3_f_-_MEF_WCE_reanalyzed |
| GSM2912471 |
MBD3_f_-_4day_DOX_WCE_reanalyzed |
| GSM2912472 |
MBD3_f_-_8day_DOX_WCE_reanalyzed |
| GSM2912473 |
MBD3_f_-_IPS_H3K4me3_reanalyzed |
| GSM2912474 |
WT_4day_DOX_WCE_reanalyzed |
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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 |
PRJNA397923 |
| SRA |
SRP115232 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE102517_RAW.tar |
199.2 Mb |
(http)(custom) |
TAR (of BED, TXT) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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