GEO DataSets

(Submitter supplied) Transposable element (TE) invasions have shaped vertebrate genomes over the course of evolution. They have contributed an extra layer of species-specific gene regulation by providing novel transcription factor binding sites. In humans, SVA elements are one of three still active TE families, and approximately 2800 SVA insertions exist in the human genome, half of which are human-specific. TEs are often silenced by KRAB zinc finger (KZNF) proteins recruiting co-repressor proteins that establish a repressive chromatin state. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21697 GPL20301 GPL11154

26 Samples

Download data: CSV, NARROWPEAK, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Macaca mulatta; Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL14954 GPL11154 GPL13112

25 Samples

Download data

(Submitter supplied) 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.

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154

15 Samples

Download data: XLSX

(Submitter supplied) 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.

Organism:

Mus musculus; Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14954 GPL11154 GPL13112

10 Samples

Download data: XLSX

(Submitter supplied) Domestication of transposable elements (TEs) into functional cis-regulatory elements is a widespread phenomenon. However, why some TEs are co-opted as functional enhancers while others are not is underappreciated. SINE-Vntr-Alus (SVAs) are the youngest group of transposons in the human genome, where ~3,700 copies are annotated, nearly half of which are human-exclusive. Many studies indicated that the SVAs are among the most frequently co-opted TEs in human gene regulation, but the mechanisms underlying such process have not yet been thoroughly investigated. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL24676

23 Samples

Download data: BED, BW, NARROWPEAK, TSV

(Submitter supplied) Control or KD hESC were differentiated into organoids as decribed in Methods. RNA was extracted from individual organoids at day 20 after commencing the STEMdiff™ Cerebral Organoid Kit protocol. Day 0 was designated as the day of transfer of hESC to a 96-well plate for differentiation into embryoid bodies .

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24268

6 Samples

Download data: TXT

(Submitter supplied) hiPSC were treated or not with STING inhibitor, transduced with KD or control lentivectors and differentiated in induced neurons.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24268

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

71 Samples

Download data: BED, TXT

(Submitter supplied) RNAseq of human embryonic stem cells depleted for ZNF417 and ZNF587 or control cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

7 Samples

Download data: TXT

(Submitter supplied) RNA-seq of hiPS or induced neurons depleted for ZNF417 and ZNF587 or control cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TXT

(Submitter supplied) dCas9KRAB and gRNA targeting HERVK TEs were used to repress the TEs in stem cells (hiPS) and in differentiated induced neurons (iN). As control, dCas9KRAB alone without gRNA was used.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TXT

(Submitter supplied) endogenous KAP1 ChIPseq remapping (previously published in GSE57989)

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: BED

(Submitter supplied) KZFP ChIP-seqs in H1 cells overexpressing the proteins

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: BED

(Submitter supplied) Active and repressive histones ChIPseqs in controls and ZNF417/587 depleted hESC.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

20 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL17021 GPL21493

280 Samples

Download data: BED, BIGWIG, TXT

(Submitter supplied) We report a retrotransposon-specific loss of CpG methylation in chromosome 4 KRAB-ZFP cluster (Chr4-cl) KO ES cells that are cultivated in conditions that induce DNA hypomethylation. The retrotransposon groups with the strongest DNA methylation loss are the main targets of the KRAB-ZFPs within the deleted gene cluster indicating that these KRAB-ZFPs prevent complete DNA demethylation at retrotransposons during global DNA demethylation.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL21493 GPL17021

4 Samples

Download data: TXT

(Submitter supplied) Mammalian genomes encode several hundred Krüppel-associated box zinc finger proteins (KRAB-ZFPs) that bind DNA in a sequence-specific manner through tandem arrays of C2H2-type zinc fingers and repress transcription via KRAB-dependent recruitment of the silencing cofactor KAP1. The KRAB-ZFP family rapidly amplified and diversified in mammals by segmental gene duplications, mutations, and zinc finger rearrangements likely in response to continued transposable element invasions, but the biological functions and in vivo requirement of these proteins has gone largely unexplored. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL21493

61 Samples

Download data: BIGWIG

(Submitter supplied) Mammalian genomes encode several hundred Krüppel-associated box zinc finger proteins (KRAB-ZFPs) that bind DNA in a sequence-specific manner through tandem arrays of C2H2-type zinc fingers and repress transcription via KRAB-dependent recruitment of the silencing cofactor KAP1. The KRAB-ZFP family rapidly amplified and diversified in mammals by segmental gene duplications, mutations, and zinc finger rearrangements likely in response to continued transposable element invasions, but the biological functions and in vivo requirement of these proteins has gone largely unexplored. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21493 GPL17021

74 Samples

Download data: BIGWIG, TXT

(Submitter supplied) We have shown that many mouse KRAB-ZFPs target retrotransposons which are generally marked by H3K9me3 and KAP1 in ES cells. To test whether these KRAB-ZFPs are require to establish and maintain repressive chromatin marks at these elements, we performed ChIP-seq with antibodies against KAP1 (2 KRAB-ZFP cluster KOs) and H3K9me3 (5 KRAB-ZFP cluster KOs). We show that KRAB-ZFP targeted retrotransposons show reduced KAP1 binding and H3K9me3 in these KO ES cells. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL21493

54 Samples

Download data: BIGWIG

(Submitter supplied) Genetic deletion of a large KRAB-ZFP gene cluster on chromosome 4 (Chr4-cl) leads to transcriptional reactivation of retrotransposons (mainly ETn elements) in ES cells. We therefore wanted to test whether ETn elements retrotranspose in Chr4-cl KO mice at higher frequency. For this we purified genomic DNA from WT and KO mice, enriched gDNA libraries using ETn capture probes and sequenced those libraries as paire-end reads. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

87 Samples

Download data: BED