Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bombycidae strain:BmN4

ABSTRACT: Siwi and BmAgo3 IPed piRNA profile in BmN4 cells

PROVIDER: PRJDB17074 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR514992.fastq.gz	Fastqsanger.gz
	DRR514993.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Genome assembly of silkworm BmN4 cells

Project description:BmN4 cells are cultured cells derived from Bombyx mori ovaries and widely used to study transposon silencing by PIWI-interacting RNAs (piRNAs). A high-accurate genome sequence of BmN4 cells is required to analyze the piRNA pathway using RNA-seq. The genome sequence of BmN4 cells was assembled using Pacific Biosciences (PacBio) HiFi and Oxford Nanopore technology Ultralong (ONT-UL) reads. Microscopic observation and image analysis showed that BmN4 cells were octoploid on average, and the number of chromosomes per cell was highly variable. We concluded the haplotype-resolved assembly of such a complex genome would be difficult; therefore, we assembled a consensus genome sequence. RNA-seq analysis of Siwi knockdown cells also revealed that Siwi-piRISC may target Countdown (Cd), an LTR retrotransposon. By comparing the consensus genome sequence with the reads, we identified differences between haplotypes, particulary structural variants, suggesting that some transposons, including Countdown, increased their copy number in BmN4 cells.

2025-02-03 | GSE288600 | GEO

Bombyx mori strain:BmN4

Project description:piRNA profile of Zuc knockdown in BmN4 cells

| PRJDB17073 | ENA

Bombyx mori strain:BmN4

Project description:strand specific RNA sequence of BmAgo2 or Siwi depleted BmN4 cells

| PRJDB5927 | ENA

High throughput sequencing of Siwi and BmAGO3 associated piRNAs from Bombyx mori BmN4 cells

Project description:In germ cells, piRNAs are amplified through the Ping-Pong cycle that depends on reciprocal Slicer-mediated target RNA cleavage by two PIWI members. A germ-specific DEAD-box protein Vasa is required for the process. However, Vasa’s function is poorly understood. Here, we show that target RNAs cleaved by a Bombyx mori (silkworm) PIWI, Siwi, remain to be bound with the protein upon cleavage, but are released in the presence of Vasa in B. mori (BmVasa) and ATP. Under normal conditions, BmVasa co-purifies with Siwi, but not with second B. mori PIWI BmAgo3. However, when BmVasa loses the ATP-binding and RNA-unwinding activities, BmVasa avidly associates with Siwi and BmAgo3, which contains transposon transcripts predominantly in sense orientation, the sources of BmAgo3-piRNAs. Without BmVasa, BmAgo3 is devoid of piRNAs. Thus, BmVasa actively releases target RNAs from Siwi, upon its cleavage, to urge BmAgo3-piRNA complex formation in the Ping-Pong cycle, enabling continuous supply of piRNAs in germ cells.

2014-12-31 | GSE58221 | GEO

Siwi cooperates with Par-1 kinase to regulate mitochondrial Papi scaffolding Siwi-piRISC biogenesis

Project description: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. Here, we show that Siwi targets Par-1 kinase to mitochondrial Papi to promote its phosphorylation at Ser547 in the auxiliary domain and that this modification enhances the ability of Papi to bind Siwi-bound piRNA precursors via the KH domains. Papi S547A mutant still bound to Siwi, like wild-type (WT) Papi, although it evaded phosphorylation by Par-1: Consequently, Papi lost the ability to bind RNAs, abrogating the generation of Siwi-piRISC. Papi mutant lacking the Tudor and auxiliary domains escaped coordinated regulation by Siwi and Par-1 and lost their bias to bind piRNA precursors. Pseudo-phosphorylation mutants of Papi restored Siwi-piRISC formation in Papi-lacking cells, but their ability to bind RNAs required Siwi, similar to WT Papi. Par-1-dependent, multilayered mechanism by which Siwi regulates the role of Papi in Siwi-piRISC biogenesis was revealed.

2022-01-25 | GSE179432 | GEO

High throughput sequencing of Siwi associated piRNAs from Bombyx mori BmN4 cells

Project description:High throughput sequencing of Siwi associated piRNAs from Bombyx mori BmN4 cells

| PRJNA678231 | ENA

RNA associating with PIWI proteins in Bombyx mori BmN4 cells

Project description:RNAs associating with PIWI proteins were Immunoisolated from BmN4 cells. Sequence libraries were generated with NEBNext Small RNA Library Prep Set for Illumina(NEB). Libraries were sequenced using Illumina MiSeq (single-end, 51 cycles).

2020-09-02 | GSE150444 | GEO

High throughput sequencing of Siwi associated piRNAs from Bombyx mori BmN4 cells

2021-02-01 | GSE161405 | GEO

RNAi silencing of the SoxE gene suppresses cell proliferation in silkworm BmN4 cells

Project description:Transcriptional profiling of silkworm BmN4-SID1 cells comparing the test of BmSoxE knockdown with the control of EGFP Knockdown.

2014-06-28 | GSE53240 | GEO

Knockdown of BmSoxE gene in silkworm BmN4-SID1 cells

Project description:Transcriptional profiling of silkworm BmN4-SID1 cells comparing the test of BmSoxE knockdown with the control of EGFP Knockdown. Two-condition experiment, BmSoxE knockdown vs EGFP Knockdown. Biological replicates: 3. One replicate per array.

2014-06-28 | E-GEOD-53240 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data