Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression variability in human and chimpanzee populations share common determinants

ABSTRACT: Gene expression variability in human and chimpanzee populations share common determinants

PROVIDER: PRJNA635670 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11868900.fastq.gz	Fastqsanger.gz
	SRR11869000.fastq.gz	Fastqsanger.gz
	SRR11868901.fastq.gz	Fastqsanger.gz
	SRR11869001.fastq.gz	Fastqsanger.gz
	SRR11868902.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 155

Similar Datasets

Gene expression variability in human and chimpanzee populations share common determinants

Project description:Inter-individual variation in gene regulation has been shown to be heritable and it is quite often associated with differences in disease susceptibility between individuals. While many human studies focused on mapping associations between genetic and gene regulatory variation, much less attention has been paid to the evolutionary processes that shape the observed differences in gene regulation between individuals in humans or any other primate. To begin addressing this gap, we performed a comparative expression quantitative trait loci (eQTL) mapping study in humans and chimpanzees, using gene expression data from primary heart samples. While expression variability in both species is strongly determined by non-genetic sources, such as cell type heterogeneity, we found evidence that the degree of inter-individual variation in gene regulation is generally conserved in humans and chimpanzees. In particular, we found a significant overlap of genes associated with eQTLs in the two species. We conclude that humans and chimpanzees share sources common determinants of gene expression variability, including genetically regulated constraints from stabilizing and diversifying selection pressures.

2020-05-29 | GSE151397 | GEO

Gene expression variability in human and chimpanzee populations share common determinants.

Project description:Inter-individual variation in gene expression has been shown to be heritable and is often associated with differences in disease susceptibility between individuals. Many studies focused on mapping associations between genetic and gene regulatory variation, yet much less attention has been paid to the evolutionary processes that shape the observed differences in gene regulation between individuals in humans or any other primate. To begin addressing this gap, we performed a comparative analysis of gene expression variability and expression quantitative trait loci (eQTLs) in humans and chimpanzees, using gene expression data from primary heart samples. We found that expression variability in both species is often determined by non-genetic sources, such as cell-type heterogeneity. However, we also provide evidence that inter-individual variation in gene regulation can be genetically controlled, and that the degree of such variability is generally conserved in humans and chimpanzees. In particular, we found a significant overlap of orthologous genes associated with eQTLs in both species. We conclude that gene expression variability in humans and chimpanzees often evolves under similar evolutionary pressures.

| S-EPMC7644215 | biostudies-literature

FOHM data share

Project description:FOHM data share

| PRJEB28249 | ENA

ChIP-seq analysis of human and chimpanzee iPS cells

Project description:ChIP-seq for H3K4me3 and H3K27me3 were conducted for iPS cells of human-1 (409-B2/HPS0076), human-2 (Nips-B2/HPS0223), chimpanzee-1 (kiku/0138F-1), and chimpanzee-2 (mari/0274F-2). The reads were mapped to the respective genomes (hg38 for human and panTro5 for chimpanzee).

2022-10-26 | GSE201295 | GEO

Transcriptome analysis of human and chimpanzee iPS cells

Project description:mRNA-seq were conducted for iPS cells of human-1 (409-B2/HPS0076), human-2 (Nips-B2/HPS0223), chimpanzee-1 (kiku/0138F-1), and chimpanzee-2 (mari/0274F-2). To compare gene expression levels, the reads were first mapped to the chimpanzee genome (panTro5), and mapped reads were then mapped to the human genome (hg38). Gene expression was anlyzed based on the hg38 annotation.

2022-10-26 | GSE201296 | GEO

Framingham SHARe Social Network

Project description:Framingham SHARe Social Network

| PRJNA75945 | ENA

Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors [chimpanzee]

Project description:Human accelerated regions (HARs) are evolutionarily conserved sequences that acquired human-specific nucleotide changes and reside in genomic regions associated with unique human traits and disease. The majority of HARs (96%) are noncoding, a few of which have been shown to be functional enhancers. Here, we comprehensively tested human and chimpanzee sequences of HARs (N=714) for enhancer activity using a lentivirus-based massively parallel reporter assay (lentiMPRA) in human and chimpanzee iPSC derived neural progenitors at two differentiation time points. We found that 43% (306/714) function as enhancers and over two-thirds (204/306) showed consistent differences in activity between human and chimpanzee sequences across conditions. We also tested all possible permutations of substitutions in seven HARs and found significant positive and negative interactions. Our study provides a comprehensive resource of functional neurodevelopmental HAR enhancers and shows that multiple interacting sites drive evolutionary activity differences.

2018-02-17 | GSE110759 | GEO

TE-derived small RNA analysis of human and chimpanzee iPS cells

Project description:Small RNA-seq were conducted for iPS cells of human-1 (409-B2/HPS0076), human-2 (Nips-B2/HPS0223), chimpanzee-1 (kiku/0138F-1), and chimpanzee-2 (mari/0274F-2). The human samples were mapped to the human genome (hg38) and the chimpanzee samples were mapped to the chimpanzee genome (panTro5). The mapped reads for individual TE copies (in the repeatmasker tables downloaded from UCSC genome browser) were counted, and those for the same subfamily were summed up. The counts were normalized by RPM (reads per million genome-mapped reads).

2022-10-26 | GSE201297 | GEO

Epigenome analysis of brain between human and chimpanzee

Project description:Genome wide DNA methylation profiling of brain and liver from human and chimpanzee. The Illumina HumanMethylation27 DNA Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs for each sample. Samples included liver and NeuN-positive/NeuN-negative/unsorted brain in three individuals from each of two species (human and chimpanzee).

2015-06-19 | GSE38804 | GEO

SHARe Asthma Resource Project (SHARP)

Project description:SHARe Asthma Resource Project (SHARP)

| PRJNA75421 | ENA