NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE242851 Query DataSets for GSE242851
Status Public on Jun 06, 2024
Title Cell fate decision by a morphogen-transcription factor-chromatin modifier axis
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Bulk RNA-sequences show the differences upon primitive endoderm cell related gene expression between JGES induced somatic cell reprogramming with or without BMP4 treatment, and between WT-SALL4 or delN12-SALL4 induced transdifferentiation from E13.5 mouse embryonic fibroblasts, primitive endoderm cell related gene are from our single cell RNA sequence data
So as to estimate the chromatin remodeling differences between SALL4-WT and SALL4-delN12 during single factor induced PrE formation, we performed Tn5 dependent ATAC-sequence to compare the open and close chromatin of the two group.
In order to identify the bingding differences of SALL4 and H3K27ac level diversity between SALL4-WT and SALL4-delN12 on PrE related genes, wo performed CUTandTAG experiments.
Single cell analysis provides clarity unattainable with bulk approaches. Here we apply single cell RNA-seq to a newly established mouse somatic cell reprogramming system with or without BMP4 treatment at Day 7, this reprogramming system are induced by four transcriptional factors Jdp2-Glis1-Esrrb-Sall4 or JGES and cultured in iCD3. We first show that cells could be clustered into four group, primitive endoderm cell like cells, pluripotent cells, endothelial cells, and intermediate state cells which are hard to be clarified, after BMP4 treatment, a placenta-like state arise, the percentage of endothelial cells and primitive endoderm cell like cells increase and pluripotent cells decrease sharply. Our results not only show the ability of JGES and BMP4 in different cell lineage induction but also provide a model to explore mechanisms of first and second cell lineage decision during early embryogenesis.
 
Overall design We analyzed the transcriptome expression of mixture cells generated during mouse somatic cell reprogramming and transdifferentiation
We analyzed the transcriptome expression of mixture cells generated during mouse somatic cell reprogramming with or without BMP4 treatment
ATAC-seq data shows the chromatin accessibility differences between SALL4-WT and SALL4-delN12 single factor indeuced PrE formation, four time points were checked, Day1, Day5, Day9 and Day11
CUT&Tag analysis was performed in PrE formation at day 6 to map SALL4 and H3K27ac binding sites.
 
Contributor(s) Ming J, Zhao C, Pei D
Citation(s) 39075094
Submission date Sep 11, 2023
Last update date Aug 26, 2024
Contact name jin ming
E-mail(s) mingjin@westlake.edu.cn
Phone 18801279010
Organization name Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
Lab duanqing pei
Street address 西湖大学
City zhejiang, china
ZIP/Postal code 310024
Country China
 
Platforms (2)
GPL21273 HiSeq X Ten (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (38)
GSM7771968 Day0 of JGES reprogramming without BMP4 treatment
GSM7771969 Day1 of JGES reprogramming without BMP4 treatment
GSM7771970 Day3 of JGES reprogramming without BMP4 treatment
Relations
BioProject PRJNA1015164

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
GSE242851_GeneSymbol_fpkm.txt.gz 1.3 Mb (ftp)(http) TXT
GSE242851_JGESOB_fpkm.txt.gz 791.6 Kb (ftp)(http) TXT
GSE242851_JGES_BMP4_Raw_Counts.txt.gz 99.3 Mb (ftp)(http) TXT
GSE242851_RAW.tar 1.7 Gb (http)(custom) TAR (of BED, BW)
SRA Run SelectorHelp
Raw data are available in SRA
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap