NBDC Research ID: hum0274.v1
SUMMARY
Aims: mRNA exporters, NXF1 and CRM1, are known to function in mRNA export. However, since each target mRNA has not been identified genome-widely, it is not clear whether they export exclusive mRNA subsets. To reveal this point, we prepared the nuclear and the cytoplasmic RNAs under either exporter inhibited condition and carried out RNA-seq.
Methods: Knockdown of a target gene was performed in cultured human cells (HeLa), and RNA was extracted after fractionation into the nucleus and cytoplasm.
Participants/Materials: HeLa cells with knockdown of the target gene
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000294 | NGS (RNA-seq) | Controlled-access (Type I) | 2022/04/22 |
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MOLECULAR DATA
| Participants/Materials: |
HeLa cells with knockdown (KD) of a target gene: 20 samples control KD cultured with/without LeptomycinB (LMB: CRM1 inhibitor), nucleus and cytoplasm (duplicate): total 8 samples NXF1 KD, nucleus and cytoplasm (duplicate): total 4 samples MTR4 KD cultured with/without LMB, nucleus and cytoplasm (duplicate): total 8 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from the nucleus or cytoplasm fractions obtained from HeLa cells with knockdown of a target gene |
| Cell Lines | HeLa (ATCC) |
| Library Construction (kit name) | TruSeq Stranded mRNA Library Prep Kit |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000401 |
| Total Data Volume | 307.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Kenichi Fujita
Affiliation: Division of Gene Expression Mechanism, Fujita Healthy University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Early-Career Scientists | Integrated analysis of selective mRNA export by mRNA export factors, UAP56 and URH49 | 19K15807 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| - | |||
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000401 | 2022/12/26-2025/03/31 |
