GEO DataSets

(Submitter supplied) The functions of human PUM1 and PUM2 are considered to be redundant given that both PUF1 and PUF2 recognize the same PBE motif UGUANAUA. However pools of mRNAs published so far for PUM1 and PUM2 do not overlap. Therefore we sought to investigate the issue of redundancy in human cells. The both PUM proteins are less conserved in the region that is outside the PUM domain. We sought that interactors could be different. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20301

21 Samples

Download data: TXT

(Submitter supplied) While Nanos-mediated maintenance of germ cells in Drosophila and mice has been related to regulation of apoptosis, the relevance of these findings to human physiology is uncertain. We show here that the NM_199461.4(NANOS1_v001):c.[100C>A;240_242del]; NM_199461.4(NANOS1_i001):p.[(Pro34Thr);(Ser83del)] double mutation, which has previously been associated with a lack of germ cells in the testes of infertile patients, causes NANOS1 to functionally switch from being anti-apoptotic to pro-apoptotic in the human male germ cell line TCam-2.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

9 Samples

Download data: CSV

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

30 Samples

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(Submitter supplied) Approximately 1500 RNA-binding proteins (RBPs) profoundly impact mammalian cellular function by controlling distinct sets of transcripts, often using sequence-specific binding to 3′ untranslated regions (UTRs) to regulate mRNA stability and translation. Aside from their individual effects, higher-order combinatorial interactions between RBPs on specific mRNAs have been proposed to underpin the regulatory network. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

9 Samples

Download data: BED

(Submitter supplied) Approximately 1500 RNA-binding proteins (RBPs) profoundly impact mammalian cellular function by controlling distinct sets of transcripts, often using sequence-specific binding to 3′ untranslated regions (UTRs) to regulate mRNA stability and translation. Aside from their individual effects, higher-order combinatorial interactions between RBPs on specific mRNAs have been proposed to underpin the regulatory network. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

21 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

Platform:

GPL13112

23 Samples

Download data: BED

(Submitter supplied) we employ crosslinking immunoprecipitation (iCLIP) to reveal Pum1 and Pum2 binding mRNAs

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: BED

(Submitter supplied) We employ mRNA-seq to investigate transcriptome of Pum1-Knockout, Pum2-Knockout and WT conditons

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

15 Samples

Download data: XLSX

(Submitter supplied) The human members of the PUF family of proteins, PUM1 and PUM2, are RNA-binding proteins that post-transcriptionally regulate gene expression through binding to a PUM recognition element (PRE) in the 3′ UTR of target mRNAs, promoting RNA decay. Recent RNA-seq experiments in PUM1/2 knockdown conditions have identified hundreds of known and new human PUM targets through measurement of changes in steady state RNA levels. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL11154

27 Samples

Download data: TXT

(Submitter supplied) We used RNA-seq to measure transcript levels in human cells with the PUM1 and PUM2 proteins knocked down; by analyzing the differences in transcript abundances between those conditions, we were able to identify 927 targets showing significant changes in the presence of the PUM knockdown.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) The presence of the PUF (Pumilio/FBF) domain defines a conserved family of RNA-binding proteins involved in repressing gene expression. It has been suggested that a conserved function of PUF proteins is to repress differentiation and sustain the mitotic proliferation of stem cells. In humans, Pumilio2 (PUM2) is expressed in embryonic stem cells and adult germ cells. To identify mRNAs associated with human PUM2 protein in adipose tissue stem cells (ADSC), we used a modified Ribonucleoprotein-ImmunoPrecipitation Microarray (RIP-Chip). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

4 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL7142 GPL7141

19 Samples

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(Submitter supplied) To identify mRNAs associated with human PUM2 protein, we used a modified Ribonucleoprotein-ImmunoPrecipitation Microarray (RIP-Chip) approach on HeLa S3 cancer cells that express PUM2. PUM ribonucleoprotein (RNP) complexes were captured from cell-free extracts with specific anti PUM2 antibody coupled to protein A sepharose beads, and then eluted with SDS-EDTA. To control for non-specifically enriched RNAs, the same procedure was performed with beads that were not coupled with immunoprecipitating antibodies (mock samples). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL7142

7 Samples

Download data

(Submitter supplied) To identify mRNAs associated with human PUM1 protein, we used a modified Ribonucleoprotein-ImmunoPrecipitation Microarray (RIP-Chip) approach on HeLa S3 cancer cells that express PUM1. PUM ribonucleoprotein (RNP) complexes were captured from cell-free extracts with anti PUM1 specific antibody Bethyl Laboratories, #300-201A coupled to protein G (PUM1) sepharose beads, and then eluted with SDS-EDTA. To control for non-specifically enriched RNAs, the same procedure was performed with beads that were not coupled with immunoprecipitating antibody (mock samples). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL7142 GPL7141

12 Samples

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(Submitter supplied) Recent studies show that RNA-binding proteins (RBPs) and microRNAs (miRNAs) function in coordination with each other to control post-transcriptional regulation (PTR). Despite this, the majority of research to date has focused on the regulatory effect of individual RBPs or miRNAs. Here, we mapped both RBP- and miRNA-binding sites on human 3'UTRs and utilized this collection to better understand PTR. We show that the transcripts that lack competition for HuR binding are destabilized more after HuR depletion. We also confirm this finding for PUM1(2) by measuring genome-wide expression changes following the knockdown of PUM1(2) in HEK293 cells. Next, to find potential cooperative interactions, we identified the pairs of factors whose sites co-localize more often than expected by random chance. Upon examining these results for PUM1(2), we found that transcripts where the sites of PUM1(2) and its interacting miRNA form a stem-loop are more stabilized upon PUM1(2) depletion. Finally, using dinucleotide frequency and counts of regulatory sites as features in a regression model, we achieved an AU-ROC of 0.86 in predicting mRNA half-life in BEAS-2B cells. Altogether, our results suggest that future studies of PTR must consider the combined effects of RBPs and miRNAs, as well as their interactions.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

8 Samples

Download data: IDAT, TXT

(Submitter supplied) Maintenance and maturation of primordial germ cells is controlled by complex genetic and epigenetic cascades, and disturbances in this network lead to either infertility or malignant aberration. Transcription factor Tcfap2c / TFAP2C has been described to be essential for primordial germ cell maintenance and to be upregulated in several human germ cell cancers. Using global gene expression profiling, we identified genes deregulated upon loss of Tcfap2c in primordial germ cell-like cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS5382

Platform:

GPL1261

8 Samples

Download data: CEL

Analysis of embryonic stem cells (ESCs) depleted for transcription factor Tcfap2c and PGC-like cells (PGCLCs) derived from the Tcfap2c-deficient ESCs. TFAP2C is a member of the activator protein-2 (AP-2) family. Results provide insight into the role of TFAP2C in germ cell fate.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 cell type, 2 genotype/variation sets

Platform:

GPL1261

Series:

GSE45941

8 Samples

Download data: CEL

(Submitter supplied) Human embryonic stem cells (hESCs) exhibit unique cell cycle structure, self-renewal and pluripotency. The Forkhead box transcription factor M1 (FOXM1) is critically required for the maintenance of pluripotency in mouse embryonic stem cells and mouse embryonal carcinoma cells, but its role in hESCs remains unclear. Here, we show that FOXM1 expression was enriched in undifferentiated hESCs and was regulated in a cell cycle-dependent manner with peak levels detected at the G2/M phase. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: BW, NARROWPEAK

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL4133 GPL9115

93 Samples

Download data: BED

(Submitter supplied) We report the genome wide DNA binding patterns of wild type FOXM1 in asynchronous HeLa cells using chromatin precipitation followed by high-throughput sequencing (ChIP-seq). We find that FOXM1 is bound to the promoter of a number of cell cycle genes including PLK, AURKB, and CCNB1.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

2 Samples

Download data: BED