GEO DataSets

(Submitter supplied) To investigate the Binding density of BmGATA on silkworm genome

Organism:

Bombyx mori

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29210

2 Samples

Download data: BW

(Submitter supplied) RNA-seq of BmNPV cells infected by indicated mutant BmNPV to determine the impact on viral gene expression of the cis-interacting sites on BmNPV by knocking out them via RED system

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29210

15 Samples

Download data: TXT

(Submitter supplied) To investigate the transcriptional regulatory role of the transcription factor BmGATA, and the impact of BmNPV infection on its activation capacity

Organism:

Bombyx mori

Type:

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

Platform:

GPL29210

8 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) In this study, NanoString technology gene expression quantification platform was used to study the expression of toxin genes causing infections from Bacteria (Photorhabdus and Xenorhabdus), Nematode (H.indica, S.riobrave , S.carpocapsae) specific genes for detection and Immune related genes from the infected insects (Spodoptera frugiperda and Galleria mellonella). The study revealed the expression of different immune related genes from the infected insects (Spodoptera frugiperda and Galleria mellonella) and helped in understanding the trend of expression of gene in the samples from the healthy condition to the death stage. more...

Organism:

Bombyx mori; Heterorhabditis bacteriophora; Xenorhabdus; Photorhabdus; Spodoptera frugiperda; Galleria mellonella; Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL32011

10 Samples

Download data: RCC, TXT

(Submitter supplied) Ubiquitin-fold modifier 1 (UFM1) is attached to protein substrates through the sequential activity of an E1 (UBA5)-E2 (UBC1)-E3 (UBL1) cascade. UFBP1 is a conserved UFL1-interacting protein in mammals. However, there is no study on UFBP1 in silkworm yet. In this study, we identified a UFBP1 ortholog in B. mori genome. Spatio-Temporal expression profiles showed that BmUFBP1 expression was highly in midgut, fatbody, and at the moth stage. more...

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34106

6 Samples

Download data: XLS

(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; Tribolium castaneum; Aedes aegypti; Xenopus tropicalis; Cloeon dipterum; Blattella germanica; Strongylocentrotus purpuratus; Octopus bimaculoides; Strigamia maritima

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