|
| Status |
Public on Jan 18, 2024 |
| Title |
Merged_A_HSC_Y1 |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: KSL
strain: C57BL/6
age: Young(3 months)
treatment: AlkB treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
200 ng small RNA fraction (<200 nt; mainly composed of mature tRNA) was purified from total RNA using MEGAclear Kit (Thermo).
Purified small RNA was deacylated by incubating in 0.1 M Tris-HCl, pH 9 at 37°C for 45 min. Half of the deacylated small RNA fraction was subjected to demethylation treatment by using AlkB in vivo reaction. RNA samples were dephosphorylated with PNK (NEB) and ligated to 3’ RNA linker using T4 RNA ligase2, truncated KQ (NEB). Reverse transcription was carried using different reverse transcriptase for different samples. 5’ adaptor was ligated to cDNA and then amplified by PCR. PCR products were purified by 8% TBE gel.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Trim_galore (version0.6.6 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for quality control and adaptor trimming. The minimum quality threshold was set to 20, and the reads length is 25~60nt. The remaining reads were further processed by removing the first 10 nt random barcode in the 5’ end.
Processed reads were mapped to mm10 tRNA(http://gtrnadb.ucsc.edu/genomes/eukaryota/Mmusc10/mm10-tRNAs.fa) and rRNA.
Count the tRF numbers and submitted to DEseq2 to different expression analysis.
Genome_build: mm10 smallRNA
|
| |
|
| Submission date |
Dec 16, 2020 |
| Last update date |
Jan 18, 2024 |
| Contact name |
Xiaoyu Li |
| E-mail(s) |
[email protected]
|
| Organization name |
Zhejiang University
|
| Department |
SCHOOL OF BASIC MEDICAL SCIENCES
|
| Lab |
Li Lab
|
| Street address |
866 Yuhangtang Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL28457 |
| Series (1) |
| GSE163301 |
Age-related noncanonical TRMT6–TRMT61A signaling impairs hematopoietic stem cells |
|
| Relations |
| BioSample |
SAMN17088979 |
| SRA |
SRX9689564 |
