GEO DataSets

(Submitter supplied) We report the whole genome transcriptomic responses of ape species (human, common chimpanzee) and AAMs (rhesus macaque and olive baboon) to bacterial and viral stimulation. We find stark differences in the responsiveness of these groups, with apes mounting a markedly stronger early transcriptional response to both viral and bacterial stimulation, altering the transcription of ∼40% more genes than AAMs. more...

Organism:

Papio anubis; Macaca mulatta; Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

151 Samples

Download data: TXT

(Submitter supplied) Variation in gene regulation is thought to have played an important role in the evolution of primates, and many studies have documented differences in mRNA expression levels across primate species. However, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are more directly tied to phenotypic differences. To address this question, we used high-resolution, quantitative mass spectrometry to collect thousands of protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines (LCLs). more...

Organism:

Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14954 GPL16809 GPL11154

16 Samples

Download data: TXT

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

Organism:

Caenorhabditis elegans; Pristionchus pacificus

Type:

Expression profiling by array

Platforms:

GPL10094 GPL14372

30 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Xenorhabdus nematophila for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. more...

Organism:

Pristionchus pacificus

Type:

Expression profiling by array

Platform:

GPL14372

4 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Serratia marcescens for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. more...

Organism:

Pristionchus pacificus

Type:

Expression profiling by array

Platform:

GPL14372

4 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Staphylococcus aureus for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. more...

Organism:

Pristionchus pacificus

Type:

Expression profiling by array

Platform:

GPL14372

3 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Xenorhabdus nematophila for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. more...

Organism:

Pristionchus pacificus

Type:

Expression profiling by array

Platform:

GPL14372

4 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of C. elegans young adult worms exposed to pathogen Xenorhabdus nematophila for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode Pristionchus pacificus to the same pathogen. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL10094

4 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of C. elegans young adult worms exposed to pathogen Serratia marcescens for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode Pristionchus pacificus to the same pathogen. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL10094

4 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of C. elegans young adult worms exposed to pathogen Staphylococcus aureus for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode Pristionchus pacificus to the same pathogen. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL10094

4 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of C. elegans young adult worms exposed to pathogen Bacillus thuringiensis DB27 for 4 hours versus age-matched worms exposed to onctrol lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode Pristionchus pacificus to the same pathogen. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL10094

3 Samples

Download data: GPR

(Submitter supplied) Host-influenza virus interplay at the transcript level has been extensively characterized in epithelial cells. Yet, there are no studies that simultaneously characterize human host and influenza A virus (IAV) genomes. We infected human bronchial epithelial BEAS-2B cells with two seasonal IAV/H3N2 strains, Brisbane/10/07 and Perth/16/09 (reference strains for past vaccine seasons) and the well-characterized laboratory strain Udorn/307/72. more...

Organism:

Influenza A virus (A/Perth/16/2009(H3N2)); Influenza A virus (A/Udorn/307/1972(H3N2)); Influenza A virus (A/Brisbane/10/2007(H3N2)); Homo sapiens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

36 Samples

Download data: FA, XLSX

(Submitter supplied) we used RNA-Seq to quantify the RNA editing level at more than 8,000 previously annotated exonic A-to-I RNA editing sites in two brain regions - prefrontal cortex and cerebellum - of humans, chimpanzees and rhesus macaques. We observed substantial conservation of RNA editing levels between the brain regions, as well as among the three primate species. Evolutionary changes in RNA editing were nonetheless evident among the species. more...

Organism:

Pan troglodytes; Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9160 GPL9378

8 Samples

Download data: TXT

(Submitter supplied) Comparative studies of gene regulation suggest an important role for natural selection in shaping gene expression patterns within and between species. Most of these studies, however, estimated gene expression levels using microarray probes designed to hybridize to only a small proportion of each gene. Here we used recently-developed RNA sequencing protocols, which side-step this limitation, to assess intra- and inter-species variation in gene regulatory processes in considerably more detail than was previously possible. more...

Organism:

Macaca mulatta; Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9160 GPL9115 GPL9378

36 Samples

Download data: TXT

(Submitter supplied) While genome sequencing has identified numerous non-coding alterations between primate species, which of these are regulatory and potentially relevant to the evolution of the human brain is unclear. Here, we annotate cis-regulatory elements (CREs) in the human, rhesus macaque and chimpanzee genome using ChIP-sequencing in different anatomical parts of the adult brain. We find high similarity in the genomic positioning of CREs between rhesus macaque and humans, suggesting that the majority of these elements were already present in a common ancestor 25 million years ago. more...

Organism:

Mus musculus; Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

Genome binding/occupancy profiling by high throughput sequencing

8 related Platforms

98 Samples

Download data: BEDGRAPH, BW, NARROWPEAK, TXT

(Submitter supplied) Differences in gene regulation between human and closely related species influence phenotypes that are distinctly human. While gene regulation is a multi-step process, the majority of research concerning divergence in gene regulation among primates has focused on transcription.  To gain a comprehensive view of gene regulation, we surveyed genome-wide ribosome occupancy, which reflects levels of protein translation, in lymphoblastoid cell lines derived from human, chimpanzee and rhesus macaque. more...

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19148 GPL16791 GPL19129

14 Samples

Download data: TXT

(Submitter supplied) Changes in gene transcription regulation are necessary for species to respond to changes in their environment. In particular, host-pathogen dynamics have been observed to entail rapid evolution of genes involved in the host innate immune system. Cytokines such as type I interferon alpha and beta trigger an antiviral cellular state controlled by members of the transcription factor families STAT and IRF. more...

Organism:

Macaca mulatta; Homo sapiens

Type:

Other

Platforms:

GPL18573 GPL21120

12 Samples

Download data: BED, BW

(Submitter supplied) The chimpanzee is the only model other than man for investigating the pathogenesis of viral hepatitis types A through E. Studies of the host response, including microarray analyses, have relied on the close relationship between these two primate species: chimpanzee samples are commonly tested with human-based reagents. In this study, the host response to two dissimilar viruses, hepatitis E virus (HEV) and hepatitis C virus (HCV), was compared in multiple experimentally-infected chimpanzees. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

44 Samples

Download data: CEL, TXT

(Submitter supplied) Transcriptional regulatory changes have been shown to contribute to phenotypic differences between species, but many questions remain about how gene expression evolves. Here we report the first comparative study of nascent transcription in primates. We used PRO-seq to map actively transcribing RNA polymerases in resting and activated CD4+ T-cells in multiple human, chimpanzee, and rhesus macaque individuals, with rodents as outgroups. more...

Organism:

Mus musculus; Macaca mulatta; Homo sapiens; Pan troglodytes; Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

8 related Platforms

24 Samples

Download data: BW

(Submitter supplied) Marburg virus is a genetically simple RNA virus that causes a severe hemorrhagic fever upon infection in humans and non-human primates. The mechanism of how this pathogenesis comes about is not well understood, but it is well accepted that pathogenesis is significantly driven by a hyperactive immune response. To better understand the overall response to Marburg virus challenge, we undertook a transcriptomic analysis of immune cells circulating in the blood following aerosol exposure of cynomolgus macaques to a lethal dose of Marburg virus. more...

Organism:

Macaca fascicularis; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10332

30 Samples

Download data: TXT