Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide DNA binding patterns of KLF4 WT and mutant during reprogramming

ABSTRACT: On days 2 and 10 after transduction in an induction method, ChIP DNA samples were collected from reprogramming MEF transduced with SeVdp carrying a mutant or WT. ChIP-Seq was performed using an anti-human KLF4 antibody.

ORGANISM(S): Mus musculus

PROVIDER: GSE157762 | GEO | 2020/09/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide gene expression patterns in reprogramming MEF infected by SeVdp vectors carrying KLF4 WT or L507A mutant

Project description:To evaluate global gene expression pattern changes between KLF4 L507A and WT during reprogramming, RNA-Seq was performed on the samples collected from reprogramming MEF infected with SeVdp vectors carrying KLF4 WT or L507A mutant. Original MEF and resulting miPSCs (mouse iPSCs) were also used as samples. RNA-seq library was generated using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) and NEBNext rRNA Delepletion Kit (New England Biolabs) by Lab Droid “Maholo” (Robotic Biology Institute) automatically. Paired-end sequencing of the libraries was performed using Novaseq 6000 SP Sequencing system using SP 100 cycle kit (Illumina). Reads from RNA-seq experiments were mapped to the mouse genome (GRCm38 or mm10) and analyzed for differential gene expression and PCA (principal component analysis) using CLC Genomics Workbench (Qiagen) software.

2021-09-27 | GSE184449 | GEO

Genome-wide gene expression patterns in reprogramming MEF infected by SeVdp vectors carrying KLF4 WT or L507A mutant

Project description:Genome-wide gene expression patterns in reprogramming MEF infected by SeVdp vectors carrying KLF4 WT or L507A mutant

| PRJNA764699 | ENA

Gene expression data of fibroblasts transduced with LacZ or p63+KLF4.

2013-11-03 | GSE47746 | GEO

Gene expression analysis during reprogramming with sequential infecion of Oct4/Klf4/cMyc/Sox2

Project description:To further understand the mechanism of reprogramming, the mouse embryonic fibroblast cells were infected with Oct4, Klf4, c-Myc and Sox2 with special sequence. 1) Oct4 and Klf4 containing retrovirus was delivered on day 0. 2) Oct4, Klf4 and c-Myc were delivered on Day 1.5. 3) c-Myc and Sox-2 were deivered on Day 3. 4) Sox2 were delivered on Day 4.5. 5) Vitamin C containging medium were used from Day 6. The gene expression of Day 0 (MEF), Day 1.5, Day 3, Day 4.5 and Day 6 were analyzed with micro array to indentify the possible underlying mechanism. Especially the factors related to MET/EMT, cell cycle and epigenetic were focused. MEF cells were subjected for reprogramming with special protoocl: 1) Oct4 and Klf4 containing retrovirus were delivered on day 0. 2) Oct4, Klf4 and c-Myc were delivered on Day 1.5. 3) c-Myc and Sox-2 were deivered on Day 3. 4) Sox2 were delivered on Day 4.5. 5) Vitamin C containging medium were used from Day 6. RNA on Day 0 (MEF), Day 1.5, Day 3, Day 4.5 and Day 6 were collected for analysis.

2012-07-11 | E-GEOD-39260 | biostudies-arrayexpress

Gene expression data of fibroblasts transduced with LacZ or p63+KLF4.

Project description:To determine if fibroblasts could be reprogrammed to a keratinocyte phenotype p63+KLF4 or LacZ expressing retroviruses were transduced into primary human neonatal fibroblasts. Global gene expression profiling using U133 plus 2.0 arrays were used to deteremine the extent of reprogramming to a keratinocyte phenoypte upon transduction with p63+KLF4. Fibroblasts transduced with p63+KLF4 were also treated +/- high calcium to determine if treatment with calcium could induce differentiation of these cells. Microarray analysis was also performed on cells treated +/- calcium. For gene expression profiling, cultured human fibroblasts were infected with LacZ or p63+KLF4 expressing retroviruses. p63+KLF4 cells were also treated +/- calcium. Microarray analysis using Affymetrix HG-U133 2.0 plus arrays was performed on duplicate samples.

2013-11-03 | E-GEOD-47746 | biostudies-arrayexpress

KLF4 ChIP-seq at reprogramming 48 hours and Hic2, KLF4 ChIP-seq at reprogramming 48 hours with Hic2 overexpression

Project description:Mouse embryonic fibroblasts (MEFs) with doxycycline (Dox)-inducible reprogramming cassette MKOS-ires-mOrange and a Nanog-GFP reporter were transduced with lentiviral Dox-inducible Ty1-BFP (blue fluoresce protein with Ty1 tag in the N-terminus) or Hic2-Ty1 (Hic2 with Ty1 tag in the C-terminus) expression vector with MOI 5. One day later reprogramming was initiated by the administration of Dox. 48 hours later, the cells for Hic2 ChIP-seq with anti-Ty1 antibody were crosslinked with 2mM of Disuccinimidyl Glutarate (DSG) for 45 min at room temperature (RT) under constant agitation, before being cross-linked with 1% formaldehyde solution for 10 min at room temperature. For KLF4 ChIP-seq, cells were only cross-linked with 1% formaldehyde solution for 10 min at room temperature. ChIP-seq library was generated with the NEBNext Ultra-II DNA Library Prep kit. Each library was uniquely barcoded using NEBNext Multiplex Oligos for Illumina. Samples were sequenced with the NextSeq High 40PE.

2024-04-26 | E-MTAB-13170 | biostudies-arrayexpress

Histone profile for wild type MEF and secondary MEF with Dox-inducible vectors for Klf4, Sox2 and Oct4 (KSO)

Project description:Histone profile for wild type MEF and secondary MEF with Dox-inducible vectors for Klf4, Sox2 and Oct4 (KSO). ChIP-Seq data for H3K4me3, H3K27me3 and H3K9me3

2010-12-31 | E-GEOD-21271 | biostudies-arrayexpress

Gene expression analysis during reprogramming with sequential infecion of Oct4/Klf4/cMyc/Sox2

2012-07-12 | GSE39260 | GEO

Histone profile for wild type MEF and secondary MEF with Dox-inducible vectors for Klf4, Sox2 and Oct4 (KSO)

Project description:Histone profile for wild type MEF and secondary MEF with Dox-inducible vectors for Klf4, Sox2 and Oct4 (KSO).

2010-12-31 | GSE21271 | GEO

KLF4 knockdown in human keratinocytes

Project description:RNA sequencing (RNAseq) of N/TERT2G keratinocytes transduced with pooled siRNAs targeting KLF4, or non-targeting control siRNA (siCon)

2020-02-24 | GSE137410 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data