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Links from GEO DataSets

Items: 20

1.

Hominid-specific transposable elements and KRAB-ZFPs facilitate human embryonic genome activation and transcription in naïve hESCs

(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
Platform:
GPL16791
79 Samples
Download data: BED, TAB
Series
Accession:
GSE117395
ID:
200117395
2.

Hominid-specific transposable elements and KRAB-ZFPs facilitate human embryonic genome activation and transcription in naïve hESCs [ATAC-seq]

(Submitter supplied) Transposable elements (TEs) are key to the evolutionary turnover of regulatory sequences. How they can play such an essential role in spite of their genotoxic potential is unknown. Here, we demonstrate that KRABcontaining zinc finger proteins control the timely and pleiotropic engagement of TE-derived cis-regulators of transcription. We first observed that evolutionary recent TEs of the SVA, HERVK and HERVH subgroups are major contributors to chromatin opening during human embryonic genome activation and act as KLF-stimulated enhancers in naïve embryonic stem cells. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16791
10 Samples
Download data: BED
Series
Accession:
GSE130418
ID:
200130418
3.

Hominid-specific transposable elements and KRAB-ZFPs facilitate human embryonic genome activation and transcription in naïve hESCs [ChIP-seq]

(Submitter supplied) Transposable elements (TEs) are key to the evolutionary turnover of regulatory sequences. How they can play such an essential role in spite of their genotoxic potential is unknown. Here, we demonstrate that KRABcontaining zinc finger proteins control the timely and pleiotropic engagement of TE-derived cis-regulators of transcription. We first observed that evolutionary recent TEs of the SVA, HERVK and HERVH subgroups are major contributors to chromatin opening during human embryonic genome activation and act as KLF-stimulated enhancers in naïve embryonic stem cells. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16791
35 Samples
Download data: BED
Series
Accession:
GSE130417
ID:
200130417
4.

Hominid-specific transposable elements and KRAB-ZFPs facilitate human embryonic genome activation and transcription in naïve hESCs [RNA-seq]

(Submitter supplied) Transposable elements (TEs) are key to the evolutionary turnover of regulatory sequences. How they can play such an essential role in spite of their genotoxic potential is unknown. Here, we demonstrate that KRABcontaining zinc finger proteins control the timely and pleiotropic engagement of TE-derived cis-regulators of transcription. We first observed that evolutionary recent TEs of the SVA, HERVK and HERVH subgroups are major contributors to chromatin opening during human embryonic genome activation and act as KLF-stimulated enhancers in naïve embryonic stem cells. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
34 Samples
Download data: TAB
Series
Accession:
GSE130416
ID:
200130416
5.

ChIP-exo of human KRAB-ZNFs transduced in HEK 293T cells and KAP1 in hES H1 cells

(Submitter supplied) Encoded in the hundreds by the human genome, KRAB-containing zinc finger proteins (KRAB-ZFPs) constitute a rapidly evolving family of transcription factors with largely undefined functions. Here, by a combination of phylogenetic and genomic approaches, we retrace the evolutionary history of KRAB-ZFP genes and define the genomic targets of their human products. Through in silico analysis of 207 vertebrate genomes and chromatin immunoprecipitation / deep sequencing characterization of 257 human KRAB-ZFPs, we identify the root of the family in an early Devonian ancestor of tetrapods, describe its diversity amongst these species, and reveal that the majority of its human members primarily recognize transposable elements. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16791
237 Samples
Download data: BED
Series
Accession:
GSE78099
ID:
200078099
6.

Primate-specific Transcription Factors & Cis-Regulatory Elements Regulate Human Developmental Evolution.

(Submitter supplied) The human genome is composed of 4.5 million transposable elements (TE). The requirement for a TE to propagate through the genome during evolution is to be expressed to be retro-transpose into germ cells or pre-implantation embryo. Thus, many evolutionarily young TEs still contain DNA binding sites for pluripotency factors and are transiently expressed in the pre-implantation embryo. We observed that these and many other primate-restricted transposable elements have alternative binding sites for cell-type-specific transcription factors that allow them to be transcribed during human gastrulation. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16791
14 Samples
Download data: BED, TXT
Series
Accession:
GSE181120
ID:
200181120
7.

Chip-exo and Chip-seq of human KRAB-ZNFs transduced in HEK 293T cells

(Submitter supplied) Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL16791 GPL20301
139 Samples
Download data: BED
Series
Accession:
GSE200964
ID:
200200964
8.

Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
13 Samples
Download data: BW
Series
Accession:
GSE122856
ID:
200122856
9.

Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells [ChIP-seq]

(Submitter supplied) Transposable elements (TEs) appear to have contributed to the evolution of tissue-specific gene regulatory networks in contexts such as early development, pregnancy and innate immunity, amongst others. In mouse embryonic stem cells (ESCs), TE families such as RLTR13D6 bind key pluripotency-associated transcription factors and are enriched for histone marks that are characteristic of distal enhancers. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
4 Samples
Download data: BW
Series
Accession:
GSE122855
ID:
200122855
10.

Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells [RNA-seq]

(Submitter supplied) Transposable elements (TEs) appear to have contributed to the evolution of tissue-specific gene regulatory networks in contexts such as early development, pregnancy and innate immunity, amongst others. In mouse embryonic stem cells (ESCs), TE families such as RLTR13D6 bind key pluripotency-associated transcription factors and are enriched for histone marks that are characteristic of distal enhancers. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
9 Samples
Download data: TXT
Series
Accession:
GSE122854
ID:
200122854
11.

ChIP-exo and ChIP-seq of human KRAB-ZNFs transduced in HEK 293T cells

(Submitter supplied) Kruppel-associated box (KRAB)-containing zinc-finger proteins (KZFPs) represent the largest family of transcription factors encoded by higher vertebrates. Together with their heterochromatin-inducing cofactor KAP1, many act as repressors of endogenous retroelements (EREs) during early embryonic genome reprogramming, yet their widespread expression in adult tissues and enrichment at other genetic loci indicate additional roles. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL16791 GPL18573
30 Samples
Download data: BED
Series
Accession:
GSE120539
ID:
200120539
12.

Individual retrotransposon integrants are differentially controlled by KZFP/KAP1-dependent histone methylation, DNA methylation and TET-mediated hydroxymethylation in naïve embryonic stem cells

(Submitter supplied) The KZFP/KAP1 (KRAB zinc finger proteins/KRAB-associated protein 1) system plays a central role in the silencing of transposable elements (TEs) and the maintenance of parent-of-origin DNA methylation at imprinting control regions (ICRs) during the wave of genome-wide reprogramming that precedes implantation. In naïve murine embryonic stem cells (mESCs), the genome is maintained highly hypomethylated by a combination of active demethylation (operated by TET proteins) and lack of de novo methylation; in these cells, KAP1 is tethered by sequence-specific KZFPs to ICRs and TEs where it recruits histone and DNA methyltransferases to impose heterochromatin formation and DNA methylation. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL19057 GPL17021
28 Samples
Download data: BED, PILEUP, TXT
Series
Accession:
GSE95720
ID:
200095720
13.

Genetic deletion of ZNF91 in human embryonic stem cells leads to ectopic activation of SVAs and collective upregulation of KRAB zinc finger gene clusters

(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
14.

Control or KZFP KD hESC-derived organoids RNA-seqs

(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
15.

RNA-seq of untreated- or STING inhibitor treated control and ZNFKD iN.

(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
16.

Primate-restricted KRAB zinc finger proteins control gene expression in human brain

(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
Series
Accession:
GSE144192
ID:
200144192
17.

RNA-seq of ZNF417/ZNF587 KD or control H1 cells

(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
18.

RNAseq of hIPS cells at day 0 and hiPS-differentiated induced neuron at day 4 post neuronal induction

(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
19.

RNA-seq of HERVK-CRIPRi IPS and iN cells

(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
20.

KAP1 ChIP-seq in hESC

(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
Series
Accession:
GSE144150
ID:
200144150
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