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An evolutionary arms race between KRAB zinc finger genes 91/93 and SVA/L1 retrotransposons

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Sofie Salama

PROVIDER: E-GEOD-60211 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Human stem cell and mouse transchromosomic (hsa11) embryonic stem cell (with and without ectopic ZNF91 expression) ChIP-seq

Project description:We compared the binding patterns in embryonic stem cells of KAP1 and KRAB Zinc Finger (KZNF) proteins as well as H3K4me3 DNA under several conditions. Native human stem cells. Mouse stem cells containing a transchromosomic copy of human chromosome 11, with and without the introduction of plasmids containing KRAB Zinc Finger sequences. We show that certain KZNFs are responsible for the repression of certain retrotransposons in embryonic stem cells, preventing their spread across the genome. ChIP-seq of HESCs and mouse TC11 ESCs with ZNF91 plasmids and with empty vector plasmids. ChIP of KAP1, ZNF486, H3K4me3. At least 2 replicates of each condition.

2014-09-29 | E-GEOD-60210 | biostudies-arrayexpress

Human embryonic stem cell, rhesus embryonic stem cell and mouse transchromosomic (hsa11) embryonic stem cell (with and without ectopic ZNF91 expression) RNA-seq

Project description:We compared the expression in embryonic stem cells of KRAB ZNF proteins and retrotransposon elements in the human genome under several conditions. Native human stem cells. Mouse stem cells containing a transchromosomic copy of human chromosome 11, with and without the introduction of plasmids containing KRAB Zinc Finger sequences. We show that certain KZNFs are responsible for the repression of certain retrotransposons in embryonic stem cells, preventing their spread across the genome. RNA-seq of hESCs, rhESCs and mouse TC11 ESCs with ZNF91 plasmids (2 replicates), with empty vector plasmids (2 replicates), or no plasmids.

2014-09-29 | E-GEOD-60178 | biostudies-arrayexpress

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Project description:Sox2 is a pleiotropic transcription factor that regulates self-renewal and differentiation capacity in different types of stem cells, raising the possibility that it regulates similar transcriptional programs controlling common stemness. Embryonic stem (ES) cells and trophoblast stem (TS) cells are two developmentally related types of stem cells, which originate from distinct lineages of peri-implantation embryos. We have found that Sox2 is a critical regulator of self-renewal in both of two stem cells. Genome-wide analysis of Sox2 target genes using Affymetrix Exon Arrays and chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) unraveled that it regulates distinct transcriptional networks in ES and TS cells. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-10-17 | E-GEOD-28455 | biostudies-arrayexpress

Induction of trophoblast stem cells from embryonic stem cells by forced repression of Oct3/4.

Project description:To characterize the transdifferentiation of embryonic stem (ES) cells into trophoblast stem (TS) cells triggered by forced repression of Oct3/4, we performed whole-genome expression analysis after tetracycline (Tet)-induced knockout of Oct3/4. A Tet-inducible Oct3/4 knockout ES cell line ZHBTc4 was treated with Tet for 4 days in the presence of FGF4 and mouse embryonic fibroblasts (MEFs). A total of 15 samples from Day 0 to Day 4 were analyzed in three biological replicates.

2013-10-17 | E-GEOD-28452 | biostudies-arrayexpress

Dynamics of Sox2 occupancy during the differentiation of embryonic stem cells into trophoblast stem cells.

Project description:To understand the mechanism underlying the versatility in transcriptional regulation by Sox2, we compared genome-wide binding sites of Sox2 in embryonic stem (ES) cells and trophoblast stem (TS) cells by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). A tetracycline-inducible Oct3/4 knockout ES cell line ZHBTc4 was treated with Tet for 4 days in the presence of FGF4 and mouse embryonic fibroblasts (MEFs).

2013-10-17 | E-GEOD-28453 | biostudies-arrayexpress

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2013-10-17 | E-GEOD-28451 | biostudies-arrayexpress

Expression analysis in H9-hESCs to induce naive pluripotency

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2016-08-31 | E-MTAB-4567 | biostudies-arrayexpress

An evolutionary arms race between KRAB zinc finger genes 91/93 and SVA/L1 retrotransposons

Project description:This SuperSeries is composed of the SubSeries listed below.

2014-09-29 | GSE60211 | GEO

Transcriptome of ESCs, EpiSCs and reverted ES by MM401 (Mll1 inhibitor)

Project description:This study describes the transcriptome profiling of: 1) mouse ES cells and EpiSCs in LIF/serum-free (KSR) medium; 2) E14Tg2a (E14) ES cells in LIF/Serum with or without MM401 treatment; 3) rES reverted form EpiSC by MM401/LIF KSR treatment at P6, P30. RNA-Seq profiling on mouse pluripotent cells. Biological duplicates of each sample are labled as rep1/2.

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