GEO DataSets

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

Organism:

Bombyx mori

Type:

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

Platform:

GPL29210

27 Samples

Download data: BIGWIG, BW, MCOOL

(Submitter supplied) Genome organization in diverse eukaryotes follows conserved principles including the formation of chromosome territories (CT), chromatin compartments, and TADs. Here, we describe the 3D architecture of holocentric chromosomes in the silkworm Bombyx mori. At the genome-wide scale, B. mori chromosomes are highly territorial lacking any visible trans contact pattern. At the chromosomal scale, B. mori chromosomes segregate into three chromatin compartments: an active A and an inactive B as described in other eukaryotes, and a third type, X, with a unique contact pattern. more...

Organism:

Bombyx mori

Type:

Other

Platform:

GPL29210

3 Samples

Download data: MCOOL

(Submitter supplied) Genome organization in diverse eukaryotes follows conserved principles including the formation of chromosome territories (CT), chromatin compartments, and TADs. Here, we describe the 3D architecture of holocentric chromosomes in the silkworm Bombyx mori. At the genome-wide scale, B. mori chromosomes are highly territorial lacking any visible trans contact pattern. At the chromosomal scale, B. mori chromosomes segregate into three chromatin compartments: an active A and an inactive B as described in other eukaryotes, and a third type, X, with a unique contact pattern. more...

Organism:

Bombyx mori

Type:

Other

Platform:

GPL29210

1 Sample

Download data: MCOOL

(Submitter supplied) Genome organization in diverse eukaryotes follows conserved principles including the formation of chromosome territories (CT), chromatin compartments, and TADs. Here, we describe the 3D architecture of holocentric chromosomes in the silkworm Bombyx mori. At the genome-wide scale, B. mori chromosomes are highly territorial lacking any visible trans contact pattern. At the chromosomal scale, B. mori chromosomes segregate into three chromatin compartments: an active A and an inactive B as described in other eukaryotes, and a third type, X, with a unique contact pattern. more...

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29210

3 Samples

Download data: BW, XLSX

(Submitter supplied) Genome organization in diverse eukaryotes follows conserved principles including the formation of chromosome territories (CT), chromatin compartments, and TADs. Here, we describe the 3D architecture of holocentric chromosomes in the silkworm Bombyx mori. At the genome-wide scale, B. mori chromosomes are highly territorial lacking any visible trans contact pattern. At the chromosomal scale, B. mori chromosomes segregate into three chromatin compartments: an active A and an inactive B as described in other eukaryotes, and a third type, X, with a unique contact pattern. more...

Organism:

Bombyx mori

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29210

20 Samples

Download data: BIGWIG

(Submitter supplied) Hyperproteinemia is a metabolic disorder characterized by abnormally elevated plasma protein concentrations (PPC) in humans and animals. Here, a genetic silkworm model with high PPC was employed to investigate the effect of elevated PPC on female reproduction. Transcriptomic analysis revealed that high PPC induces downregulation of the ovarian development-related genes and disrupts ovarian sugar metabolism. more...

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29210

12 Samples

Download data: TXT

(Submitter supplied) The silk gland development has a greater impact on silk yields in silkworms. Silk glands from three pure silkworm strains (A798, A306, and XH) with different silk gland weight phenotypes were compared using transcriptome, proteomics, and WGCNA. Five genes (BGIBMGA002524, BGIBMGA002629, BGIBMGA005659, BGIBMGA005711, and BGIBMGA010889) may be strongly associated with the growth of silk glands to be confirmed. more...

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23127

9 Samples

Download data: TXT

(Submitter supplied) We determined the RNA secondary structure of different retrotransposon by icSHAPE. The retrotransposon has differnet states including protein bound, DNA and protein bound.

Organism:

Bombyx mori

Type:

Other

Platform:

GPL29210

9 Samples

Download data: TXT

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

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29210 GPL18754

8 Samples

Download data

(Submitter supplied) Bombyx Vasa (BmVasa) assembles non-membranous organelle, nuage or Vasa bodies, in germ cells, known as the center for Siwi-dependent transposon silencing and concomitant Ago3-piRISC biogenesis. However, details of the body assembly remain unclear. Here, we show that the N-terminal intrinsically disordered region (N-IDR) and RNA helicase domain of BmVasa are responsible for self-association and RNA binding, respectively, but N-IDR is also required for full RNA-binding activity. more...

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29210

4 Samples

Download data: TXT

(Submitter supplied) Bombyx Vasa (BmVasa) assembles non-membranous organelle, nuage or Vasa bodies, in germ cells, known as the center for Siwi-dependent transposon silencing and concomitant Ago3-piRISC biogenesis. However, details of the body assembly remain unclear. Here, we show that the N-terminal intrinsically disordered region (N-IDR) and RNA helicase domain of BmVasa are responsible for self-association and RNA binding, respectively, but N-IDR is also required for full RNA-binding activity. more...

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18754

4 Samples

Download data: TXT

(Submitter supplied) We investigate tissue transcriptomic evolution across bilaterian animals by analyzing RNA-seq data from eight different tissues across twenty species.

Organism:

Bombyx mori; Drosophila melanogaster; Callorhinchus milii; Monodelphis domestica; Episyrphus balteatus; Branchiostoma lanceolatum; Danio rerio; Blattella germanica; Strongylocentrotus purpuratus; Octopus bimaculoides; Strigamia maritima; Tribolium castaneum; Aedes aegypti; Xenopus tropicalis; Cloeon dipterum

Type:

Expression profiling by high throughput sequencing

15 related Platforms

89 Samples

Download data: TSV

(Submitter supplied) This study aims to bridge the gap in our knowledge of Philippine-reared silkworm by analyzing the gene expression profiles in the silkworm silk glands through next generation sequencing. RNA was isolated from the silk glands of 5th instar larvae and mRNA-enriched libraries were sequenced with NextSeq 500 (Illumina). To compare gene expression profiles of strains from CAR (Benguet) and TCMO (Misamis Oriental), DESeq2 analysis was performed. more...

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30635

9 Samples

Download data: CSV, TXT

(Submitter supplied) The silk gland (SG) of the domesticated silkworm Bombyx mori, an economically important insect that has been used for silk production for over 5000 years, is a remarkable organ that produces vast amounts of silk with exceptional properties . Little is known about which SG cells execute silk protein synthesis and its precise spatiotemporal control. Here, we used single-cell RNA-seq to build a comprehensive cell atlas of the B. more...

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29210

3 Samples

Download data: MTX, TSV

(Submitter supplied) PIWI-interacting RNAs (piRNAs) bind to PIWI proteins to assemble the piRISC, which represses germline transposons. Maelstrom (Mael) is necessary for piRISC biogenesis in germ cells, but its function remains unclear. Here, we show that Mael interconnects Spindle-E (Spn-E), a key piRISC biogenesis factor, with unloaded Siwi, one of two silkworm PIWI members. Mael also assembles a subset of nuage, a non-membranous organelle involved in piRISC biogenesis. more...

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL18754 GPL29210

12 Samples

Download data: FASTA, TXT

(Submitter supplied) We report the ATAC-seq data that reveal chromatin accessibility during Bombyx mori development

Organism:

Bombyx mori

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29210

12 Samples

Download data: BW

(Submitter supplied) Bombyx Papi contains two K-homology (KH) domains and one Tudor domain, and acts as a scaffold for Siwi-piRISC biogenesis on the mitochondrial surface. To initiate this process, Papi binds first to Siwi via the Tudor domain and subsequently to piRNA precursors loaded onto Siwi via the KH domains. This second action depends on phosphorylation of Papi. However, its underlying mechanism remains unknown. more...

Organism:

Bombyx mori

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18754

6 Samples

Download data: TXT

(Submitter supplied) Purpose:The purpose of study these processes, is helpful to understand the mechanisms of genetic sterility of lepidopteran insects and achieve sterile insect technique (SIT) for pest control. Methods:Intact testes were dissected on day 5 of fifth-instar larvae and immediately frozen in liquid nitrogen for RNA-Seq. The testes from three silkworms were taken as one biological sample, and three samples per strain were prepared as biological replicates. more...

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30062

6 Samples

Download data: TXT

(Submitter supplied) Yun7Ge (Yun7Ge is represented by Ge in the high-throughput sequencing results) is a giant egg mutant found in the silkworm variety Yun7 (Yun7 is represented by Se in the high-throughput sequencing results). The amount of laid eggs and the hatching rate of Yun7Ge are reduced, which is not conducive to the reproduction. The target gene controlling giant egg trait is located on the Z chromosome (chromosome 1) was determined through genetic analysis. more...

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30062

4 Samples

Download data: TXT

(Submitter supplied) OThe N6-methyladenosine (m6A) RNA modification is widely used to alter the fate of mRNAs. Here we demonstrate that the C. elegans writer METT-10 (orthologue of mouse METTL16) deposits an m6A mark on the 3′ splice site (AG) of the SAM synthetase pre-mRNA which inhibits its proper splicing and protein production. The mechanism is triggered by a rich diet, and acts as an m6A-mediated switch to stop SAM production and regulate its homeostasis. more...

Organism:

Caenorhabditis elegans; Bombyx mori; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22765 GPL19757 GPL28266

42 Samples

Download data: BW, CSV, XLSX