|
| Status |
Public on Jun 01, 2024 |
| Title |
miCLIP-seq-Input-KO1 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
cell line: C57BL/6
cell type: effector CD8 (CD44+CD62L-EYFP+CD8+)
genotype: Mettl3deltaGzmb
age: 6~8 weeks
rip antibody: none (input)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated from effector CD8+ T cells of Mettl3ΔGzmb and control mice , and subjected to m6A-miCLIP-SMARTer-seq protocol.
The procedures of m6A-miCLIP-SMARTer-seq were according to the previously reported methods (Yao et al., 2021).
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
m6A-miCLIP-SMARTer-Seq data were analyzed as previously described (Michael J Moore et al., 2014)
Adapters were trimmed off for all raw reads and R1 beads were combined with R2 reads that transformed to reverse complementary sequences.
PolyA tails and duplicated reads were removed by Cutadapt and fastq2collapse.pl respectively; besides, the barcodes of reads were trimmed.
Reads were mapped to the reference genome (mm10) using BWA.
The mutation information was tracked and PCR duplicates were removed separately by parseA-lignment.pl and tag2collapse.pl based on BWA’s results. Further, the mutation site and transition number (m) were calculated through CIMS.pl. Mutation sites were kept with parameters, k/m ≥ 0.01 and k/m ≤ 0.5. The remaining sites within the RRACH motif sequence were regarded as m6A
Assembly: mm10
Supplementary files format and content: bw format
|
| |
|
| Submission date |
Oct 14, 2022 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Shuyang Yu |
| E-mail(s) |
ysy@cau.edu.cn
|
| Organization name |
China Agricultural University
|
| Department |
College of Biological Sciences
|
| Street address |
2 Yuanmingyuan West Road
|
| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE215760 |
Mettl3-dependent m6A modification is essential for effector differentiation and memory formation of CD8+ T cells [miCLIP] |
| GSE215762 |
Mettl3-dependent m6A modification is essential for effector differentiation and memory formation of CD8+ T cells |
|
| Relations |
| BioSample |
SAMN31281033 |
| SRA |
SRX17889303 |
