GEO DataSets

(Submitter supplied) Using the assay for transposase-accessible chromatin by sequencing (ATAC-seq), we produce the first genome- wide maps of chromatin accessibility across all three adult honey bee phenotypes. We identify ~ 3000 regulatory regions in queen, ~ 4500 in worker and ~ 4000 in drone, with the vast majority of these sites located within intronic regions. Integrating ATAC-seq, RNA-seq and ChIP-seq data, we show a positive correlation between chromatin accessibility at introns, flanking H3K27ac modified nucleosomes and abundance of the respective mRNA transcript. more...

Organism:

Apis mellifera

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27915

27 Samples

Download data: NARROWPEAK

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

Organism:

Apis mellifera

Type:

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

Platform:

GPL27915

39 Samples

Download data: NARROWPEAK, TSV

(Submitter supplied) Using the assay for transposase-accessible chromatin by sequencing (ATAC-seq), we produce the first genome- wide maps of chromatin accessibility across all three adult honey bee phenotypes. We identify ~ 3000 regulatory regions in queen, ~ 4500 in worker and ~ 4000 in drone, with the vast majority of these sites located within intronic regions. Integrating ATAC-seq, RNA-seq and ChIP-seq data, we show a positive correlation between chromatin accessibility at introns, flanking H3K27ac modified nucleosomes and abundance of the respective mRNA transcript. more...

Organism:

Apis mellifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27915

6 Samples

Download data: TSV, TXT

(Submitter supplied) Using the assay for transposase-accessible chromatin by sequencing (ATAC-seq), we produce the first genome- wide maps of chromatin accessibility across all three adult honey bee phenotypes. We identify ~ 3000 regulatory regions in queen, ~ 4500 in worker and ~ 4000 in drone, with the vast majority of these sites located within intronic regions. Integrating ATAC-seq, RNA-seq and ChIP-seq data, we show a positive correlation between chromatin accessibility at introns, flanking H3K27ac modified nucleosomes and abundance of the respective mRNA transcript. more...

Organism:

Apis mellifera

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27915

6 Samples

Download data: NARROWPEAK

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

Organism:

Apis mellifera

Type:

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

Platform:

GPL23819

22 Samples

Download data: TXT

(Submitter supplied) We use chromatin immunoprecipitation and high throughput sequencing to produce the first genome-wide maps of chromatin structure in the honeybee at a key larval stage where developmental canalization into queen or worker is irreversible. We find extensive genome-wide differences in H3K4me3, H3K27ac and H3K36me3, many of which correlate with caste-specific transcription. Furthermore, we identify H3K27ac as a key chromatin modification that most robustly defines caste and suggest that these regions may harbour caste-specific cis-acting elements such as enhancers.

Organism:

Apis mellifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23819

8 Samples

Download data: TXT

(Submitter supplied) We use chromatin immunoprecipitation and high throughput sequencing to produce the first genome-wide maps of chromatin structure in the honeybee at a key larval stage where developmental canalization into queen or worker is irreversible. We find extensive genome-wide differences in H3K4me3, H3K27ac and H3K36me3, many of which correlate with caste-specific transcription. Furthermore, we identify H3K27ac as a key chromatin modification that most robustly defines caste and suggest that these regions may harbour caste-specific cis-acting elements such as enhancers.

Organism:

Apis mellifera

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23819

14 Samples

Download data: TXT

(Submitter supplied) Social caste determination in the honey bee is assumed to be determined by the dietary status of the young larvae and translated into physiological and epigenetic changes through nutrient-sensing pathways. We have employed microRNA gene-microarray, and observed that both worker jelly and royal jelly showed dynamic changes in miRNA content during the 4th to 6th day of larval development . Adding specific miRNAs to royal jelly elicited significant changes in queen larval mRNA expression and in morphological characters of the emerging adult queen bee. more...

Organism:

Apis mellifera

Type:

Non-coding RNA profiling by array

Platform:

GPL17659

3 Samples

Download data: TIFF, XLS

(Submitter supplied) By comparing mRNA profiles of the two groups of bee larvae (treated by miR-184 and water), we found that there were 279 mRNAs which were differently expressed between treated and control larvae (ratio>2 and p<0.01), of which 200 mRNAs were down-regulated in treated larvae, and 79 mRNAs were down-regulated in controls.

Organism:

Apis mellifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11166

2 Samples

Download data: TXT

(Submitter supplied) Social caste determination in the honey bee is assumed to be determined by the dietary status of the young larvae and translated into physiological and epigenetic changes through nutrient-sensing pathways. We have employed Illumina/Solexa sequencing to examine the small RNA content in the bee larval food source, and show that worker jelly is enriched in miRNA complexity and abundance relative to royal jelly. more...

Organism:

Apis mellifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11166

2 Samples

Download data: TXT

(Submitter supplied) In honey bees (Apis mellifera) the behaviorally and reproductively distinct queen and worker female castes derive from the same genome as a result of differential intake of royal jelly and are implemented in concert with DNA methylation. To determine if these very different diet-controlled phenotypes correlate with unique brain methylomes, we conducted a study to determine the methyl cytosine (mC) distribution in the brains of queens and workers at single-base-pair resolution using shotgun bisulfite sequencing technology. more...

Organism:

Apis mellifera

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11166

2 Samples

Download data: TXT

(Submitter supplied) Honey bee drones, queens and workers have vastly different phenotypes. Here we profile the the expression level of mRNAs and microRNAs of honeybee, drones, queens and workers at the L5 larval stage (91 hours +/- 1).

Organism:

Apis mellifera

Type:

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

Platforms:

GPL16097 GPL19174

30 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL17639

6 Samples

Download data: BED, NARROWPEAK

(Submitter supplied) Background: There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors to specific DNA sequence motifs across the genome. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17639

3 Samples

Download data: BED, NARROWPEAK

(Submitter supplied) Background: There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors to specific DNA sequence motifs across the genome. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

3 Samples

Download data: TXT

(Submitter supplied) Mating is a complex process, which is frequently associated with behavioural and physiological changes. However, understanding of the genetic underpinnings of these changes is limited. Honey bees are both a model system in behavioural genomics, and the dominant managed pollinator of human crops; consequently understanding the mating process has both pure and applied value. We used next-generation transcriptomics to probe changes in gene expression in the brains of honey bee queens, as they transition from virgin to mated reproductive status. more...

Organism:

Apis mellifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19770

12 Samples

Download data: TXT

(Submitter supplied) Background: Aggression is influenced by individual variation in temperament as well as behavioral plasticity in response to adversity. DNA methylation is stably maintained over time, but also reversible in response to specific environmental conditions, and may thus be a neuromolecular regulator of both of these processes. A previous study reported DNA methylation differences between aggressive Africanized and gentle European honey bees. more...

Organism:

Apis mellifera ligustica

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24122

24 Samples

Download data: CSV

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

Organism:

Apis mellifera

Type:

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

Platform:

GPL16097

188 Samples

Download data: BIGWIG, TXT

(Submitter supplied) We studied behavioral, brain transcriptomic and epigenetic responses of honey bees to social challenge. Bees were exposed to two intruders at different intervals. The initial exposure caused two behavioral effects at the individual level: an increase in the intensity of aggression toward a second intruder at 30 and 60 minutes, and an increased probability of responding aggressively toward a second intruder that persisted for two hours. more...

Organism:

Apis mellifera

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16097

8 Samples

Download data: BIGWIG, TXT

(Submitter supplied) We studied behavioral, brain transcriptomic and epigenetic responses of honey bees to social challenge. Bees were exposed to two intruders at different intervals. The initial exposure caused two behavioral effects at the individual level: an increase in the intensity of aggression toward a second intruder at 30 and 60 minutes, and an increased probability of responding aggressively toward a second intruder that persisted for two hours. more...

Organism:

Apis mellifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16097

180 Samples

Download data: TXT