GEO DataSets

(Submitter supplied) We sequenced mRNA from four biological replicates of each tissue before (T1) and after the onset of maturation (T2, T3, T4). A total of 3.2 billion paired-end reads were mapped against the Atlantic salmon reference genome with 72% mapping efficiency to create an average depth of 50 million reads per library. The number of differentially expressed genes (DEGs) increased with elapsed time following the onset of the long light photoperiod for the two BPG axis tissues (pituitary and ovary). more...

Organism:

Salmo salar

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24981

64 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.This contains multi-omics datasets transcriptomic (RNA-Seq), methylomic (WGBS), and epigenomics (ATAC-seq) obtained during onset of sexual maturation in Atlantic salmon. We used gene regulatory networks (GRNs) to integrate results from these multi-omic analyses to identify key regulators of maturation.

Organism:

Salmo salar

Type:

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

Platforms:

GPL23792 GPL24981 GPL28848

88 Samples

Download data: TSV

(Submitter supplied) We sequenced 12 ATAC-Seq lbraries from four biological replicates before (T1) and after the onset of maturation (T2, T3, T4) from liver. To characterise changes in chromatin state following long light initiation, we defined differentially accessible regions (DARs) where mapping counts differed significantly between T1 and other time points. This revealed a strong early remodelling in the chromatin state landscape, as most DARs were observed at T2 (n=1501) before decreasing in stepwise fashion at T3 (n=477) and T4. more...

Organism:

Salmo salar

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28848

12 Samples

Download data: TXT

(Submitter supplied) We performed a time course experiment, whereby animals were manipulated with photoperiod before tissues were collected across the time window when animals commence sexual development. We performed whole genome bisulfite sequencing of three salmon tissues (pituitary, ovary and liver) at both the beginning and end of the experiment, to take a first look at the patterns of DNA methylation and examine how they change in response to the onset of an important life history trait. more...

Organism:

Salmo salar

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23792

12 Samples

Download data: TSV

(Submitter supplied) here we report the data from six pre-puberty and six post-puberty Brahman heifers, tissue samples collected in liquid nitrogen for RNA sequencing (mRNA libraries)

Organism:

Bos indicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20723

72 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL6244 GPL3718

27 Samples

Download data: BED, BW, CEL, WIG

(Submitter supplied) The mechanistic links between transcription factors and the epigenetic landscape, which coordinate the deregulation of gene networks during cell transformation are largely unknown. We used an isogenic model of stepwise tumorigenic transformation of human primary cells to monitor the progressive deregulation of gene networks upon immortalization and oncogene-induced transformation. By combining transcriptome and epigenome data for each step during transformation and by integrating transcription factor (TF) - target gene associations, we identified 142 TFs and 24 chromatin remodelers/modifiers (CRMs), which are preferentially associated with specific co-expression paths that originate from deregulated gene programming during tumorigenesis. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

18 Samples

Download data: BED, BW, WIG

(Submitter supplied) The mechanistic links between transcription factors and the epigenetic landscape, which coordinate the deregulation of gene networks during cell transformation are largely unknown. We used an isogenic model of stepwise tumorigenic transformation of human primary cells to monitor the progressive deregulation of gene networks upon immortalization and oncogene-induced transformation. By combining transcriptome and epigenome data for each step during transformation and by integrating transcription factor (TF) - target gene associations, we identified 142 TFs and 24 chromatin remodelers/modifiers (CRMs), which are preferentially associated with specific co-expression paths that originate from deregulated gene programming during tumorigenesis. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL3718

3 Samples

Download data: CEL, TXT

(Submitter supplied) The mechanistic links between transcription factors and the epigenetic landscape, which coordinate the deregulation of gene networks during cell transformation are largely unknown. We used an isogenic model of stepwise tumorigenic transformation of human primary cells to monitor the progressive deregulation of gene networks upon immortalization and oncogene-induced transformation. By combining transcriptome and epigenome data for each step during transformation and by integrating transcription factor (TF) - target gene associations, we identified 142 Tfs and 24 chromatin remodelers/modifiers (CRMs), which are preferentially associated with specific co-expression paths that originate from deregulated gene programming during tumorigenesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

6 Samples

Download data: CEL

(Submitter supplied) The goal of this study was to gain a better understanding of the genetic background of gonadal maturation of the European eel and to use gene expression profiles to identify predictive markers for broodstock selection that can be measured in blood samples. Three-year-old farmed silver female European eels were injected with 20 mg salmon pituitary extract (SPE) once per week and sampled after 4 weekly hormone injections. more...

Organism:

Anguilla anguilla

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20640

6 Samples

Download data: XLSX

(Submitter supplied) The goal of this study was to gain a better understanding of the genetic background of gonadal maturation of the European eel and to use gene expression profiles to identify predictive markers for broodstock selection that can be measured in blood samples. To find leads for maturation markers we performed a pilot deep-sequencing transcriptome analysis of ovarian tissue derived from a yellow eel, a prepubertal silver eel and a post-spawning matured eel. more...

Organism:

Anguilla anguilla

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20639

3 Samples

Download data: XLSX

(Submitter supplied) The study investigated gene expression patterns in liver tissue to understand the biological functions of genes that are potentially involved in controlling / regulating feed efficiency in Nordic dairy cattle.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19172

38 Samples

Download data: TXT

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

Organism:

Cavia porcellus; Heterocephalus glaber

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22346 GPL21195

476 Samples

Download data

(Submitter supplied) Comparison of gene expression level by Illumina sequencing of naked mole-rat liver from breeders and non-breeders.

Organism:

Heterocephalus glaber

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21195

23 Samples

Download data: XLS

(Submitter supplied) Comparison of gene expression level by Illumina sequencing of nine different naked mole-rat tissue from breeders and non-breeders.

Organism:

Heterocephalus glaber

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21195

215 Samples

Download data: XLS

(Submitter supplied) Comparison of gene expression level by Illumina sequencing of ten different guinea pig tissue from breeders and non-breeders.

Organism:

Cavia porcellus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22346

238 Samples

Download data: XLS

(Submitter supplied) Study revealed new information about molecular functions of the vgll3, akap11 and six6 genes associated with age-at-maturity in Atlantic salmon

Organism:

Salmo salar

Type:

Expression profiling by array

Platform:

GPL27758

96 Samples

Download data: XLSX

(Submitter supplied) This study aimed at providing insights into the hypothesized functional link between olfactory sensing of the spawning ground and final sexual maturation. We have therefore assessed the presence and expression levels of olfactory genes by RNA sequencing (RNAseq) of the olfactory rosettes in homing chum salmon Oncorhynchus keta Walbaum from the coastal sea to 75 km upstream the rivers at the pre-spawning ground. more...

Organism:

Oncorhynchus keta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20852

12 Samples

Download data: FA, XLSX

(Submitter supplied) When puberty starts before males reach harvest size, animal welfare and sustainability issues occur in Atlantic salmon (Salmo salar) aquaculture. Hallmarks of male puberty are an increased proliferation activity in the testis and elevated androgen production. Examining transcriptional changes in salmon testis during the transition from immature to maturing testes may help understanding the regulation of puberty, potentially leading to procedures to modulate its start. more...

Organism:

Salmo salar

Type:

Expression profiling by array

Platform:

GPL26200

37 Samples

Download data: TXT

(Submitter supplied) Background The generalist dipteran pupal parasitoid Nasonia vitripennis injects 79 venom peptides into the host before egg laying. This venom induces several important changes in the host, including developmental arrest, immunosuppression, and alterations to normal metabolism. It is hoped that diverse and potent bioactivities of N. vitripennis venom provide an opportunity for the design of novel acting drugs. more...

Organism:

Nasonia vitripennis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21271

6 Samples

Download data: CSV