|
| Status |
Public on Jun 22, 2022 |
| Title |
mTAIL-seq_shRnf219-1 |
| Sample type |
SRA |
| |
|
| Source name |
V6.5
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 (female) x 129/S (male)
cell line: V6.5
cell type: mES
shRNA: Rnf219 shRNA
|
| Treatment protocol |
Non-targeting shRNA or Rnf219 shRNA in the presence of 8 ug/ml of polybrene. 24 hours later, ES cells were selected with 2 ug/ml of puromycin for additional 48 hours and then were grown one passage off feeders for 30 min before harvesting
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extract total RNA by TRIzol
mTAIL-seq library was constructed as previously described_x000D_(Lim, J., Lee, M., Son, A., et al. (2016). mTAIL-seq reveals dynamic poly(A)_x000D_tail regulation in oocyte-to-embryo development. Genes Dev. 30,_x000D_1671–1682.) with an additional gel purification after 5' _x000D_adapter ligation.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
processed data file: SHC_vs_shRnf219.xls
|
| Data processing |
We used STAR to align read1 to the reference genome (mm10) to get the detail alignment. Then, paired reads were mapped using STAR to allow soft-clipping to the alignments. We filter the read2 by removing read without the tag (GTCAG) on positions 15–25 nt from the 5’-end. Those consecutive poly(A) on filtered read2 not entirely aligned to the genome were considered as putative poly(A) tags. Using reference genome annotation (GENCODE vM23), we assigned these putative poly(A) tags by considering read1 alignment overlapped with annotated genes. Then we could calculate the poly(A) length for each poly(A) tag and assign these poly(A) length to each gene
Assembly: UCSC mm10 (GRCm38)
Supplementary files format and content: Excel shows the median poly(A) tail length of each gene.
Library strategy: mTAIL-Seq
|
| |
|
| Submission date |
Jun 21, 2022 |
| Last update date |
Nov 29, 2022 |
| Contact name |
Xiaoxu Liu |
| E-mail(s) |
liuxiaoxu1010@126.com
|
| Organization name |
Southeast University
|
| Department |
Institute of Life Sciences
|
| Lab |
the Key Laboratory of Developmental Genes and Human Disease
|
| Street address |
2 Sipailou
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210018 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE146511 |
Functional characterization of RNF219 |
|
| Relations |
| BioSample |
SAMN29226926 |
| SRA |
SRX15815370 |
