GEO DataSets

(Submitter supplied) The neurobiological origins of social behaviors are incompletely understood. Here we utilized synthetic biology approaches to reprogram the function of ZFP189, a transcription factor whose expression and function in rodent prefrontal cortex was previously demonstrated to be protective against stress-induced social deficits. We created novel synthetic ZFP189 transcription factors including ZFP189VPR, which activates the transcription of target genes and therefore exerts opposite functional control from the endogenous, transcriptionally repressive ZFP189WT. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

33 Samples

Download data: CSV, TXT

(Submitter supplied) Stress resilience involves numerous brain-wide transcriptional changes. Determining the organization and orchestration of these transcriptional events may reveal novel antidepressant targets, but this remains unexplored. Here, we characterize the resilient transcriptome with co-expression analysis and identify a single transcriptionally-active uniquely-resilient gene network. Zfp189, a previously unstudied zinc finger protein, is the top network key driver and its overexpression in prefrontal cortical (PFC) neurons preferentially activates this network, alters neuronal activity and promotes behavioral resilience. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

45 Samples

Download data: TXT

(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

(Submitter supplied) ZXDC1 augments the expression of various markers of monocyte/macrophage differentiation when over-expressed in the U937 cell line treated with the phorbol ester PMA. Likewise, knockdown of ZXDC1 restricts the induced expression of these markers. We sought to identify specfic gene targets of ZXDC1 during the process of monocyte/macrophage differentiation in U937 by performing gene expression profiling in cells exhibiting reduced expression of ZXDC1 compared to controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5070

Platform:

GPL570

12 Samples

Download data: CEL

Analysis of U937 myeloid cells treated with phorbol 12-myristate 13-acetate (PMA) and depleted for the zinc finger transcription factor ZXDC. PMA treatment induces myeloid cell differentiation. Results provide insight into the role of ZXDC in myeloid cell differentiation.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 agent, 2 protocol sets

Platform:

GPL570

Series:

GSE45417

12 Samples

Download data: CEL

(Submitter supplied) Transposable elements hold regulatory functions to impact cell fate determination by controlling gene expression, which when altered can promote oncogenesis. Despite accounting for half of the human genome, little is known about the transcriptional mechanisms that confer regulatory properties to transposable elements in pluripotent, mature versus oncogenic cell states. Through positional analysis over repetitive DNA sequence of H3K27ac ChIP-seq from 32 different normal cell and tissue states, we report pluripotent stem and mature cell states-specific “regulatory transposable elements”. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16791 GPL24676 GPL11154

130 Samples

Download data: BED, BEDGRAPH, TSV

(Submitter supplied) We investigated how cognitive stimulation impacts gene expression in the prefrontal cortex (PFC), a brain region known to regulate higher cognitive functions including the control of attention, in young and aged rats.

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18694

12 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30173 GPL24676

18 Samples

Download data: BW

(Submitter supplied) We used ChIP-seq to assess how abolition of KRAB binding by KAP1 (through structure-guided mutations in the KAP1-KRAB binding interface) changed the distribution of KAP1 on chromatin genome-wide.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

7 Samples

Download data: BW

(Submitter supplied) We used CUT&RUN to assess how abolition of KRAB binding by KAP1 (through structure-guided mutations in the KAP1-KRAB binding interface) changed the distribution of H3K9me3 epigenetic mark genome-wide.

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL30173 GPL24676

11 Samples

Download data: BW

(Submitter supplied) RNA-sequencing was used to screen all differentially expressed (DE) lncRNAs and mRNAs between the RSD and control groups. In mice experiencing RSD, 373 and 454 lncRNAs, along with 1142 and 654 mRNAs were significantly upregulated and downregulated, respectively.Available informatics evidence highlighted the likely role of synapse dysfunction and abnormal synaptic neurotransmission in these behaviors. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: XLSX

(Submitter supplied) We identified an enrichment in IFN-gamma dependent genes in the prefrontal cortex of group housed mice compared to single housed mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TSV

(Submitter supplied) Major depressive disorder (MDD) is a prevalent and life-threatening illness in modern society. The susceptibility to MDD is profoundly influenced by environmental factors, such as stressful lifestyle or traumatic events, which could impose maladaptive transcriptional program through epigenetic regulation. However, the underlying molecular mechanisms remain elusive. Here we report that stress-susceptible rodents exhibit lower levels of histone crotonylation in the medial prefrontal cortex (mPFC), concurrent with regional upregulation of chromodomain Y-like (CDYL), a crotonyl-CoA hydratase and histone methyllysine reader. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: TXT

(Submitter supplied) We performed RNAseq experiments to examine genome-wide transcriptional changes in PFC of shRNA-Kmt5b KD mice compared to GFP injected control mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT