|
| Status |
Public on Jan 27, 2025 |
| Title |
NIH3T3-U1-1 |
| Sample type |
SRA |
| |
|
| Source name |
none
|
| Organism |
Mus musculus |
| Characteristics |
tissue: none
cell line: NIH3T3
cell type: mouse fibroblast cell line
genotype: U1 AMO treatment
treatment: AMO treatment
|
| Treatment protocol |
AMO transfection was carried out by electroporation method. Electrophoration was performed using a Bio-Rad Gene pulser at 960 μF and 280 V. After electroporation, cells were cultured for 12 hours in 6 well plates.. The sequence of the 25-mer U6 AMO is 5’-TGCTAATCTTCTCTGTATCGTTCCA-3’. The sequence of the 25-mer U1 AMO is 5’-GGTATCTCCCCTGCCAGGTAAGTAT-3’. The sequence of control AMO is 5’-CCTCTTACCTCAGTTACAATTTATA-3’. AMOs were ordered from Gene Tools.
|
| Growth protocol |
HeLa and HEK293 cells were obtained from ATCC and cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (Thermo Scientific). SW480, NIH3T3, and Neuro-2a cells were obtained from iCell Bioscience Inc. (Shanghai, China) and cultured in commercially available medium (Cat. No. iCell-h204-001b; iCell-m041-001b; iCell-m040-001b).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were extracted with Trizol
3'-seq library was prepared using lexogen kit (Cat. 016.24)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
lexogen 3’-seq kit (Cat. 016.24) was used to prepare the sequencing library.
|
| Data processing |
data processing steps were carried out using our published pipeline QuantifyPoly(A) (https://pubmed.ncbi.nlm.nih.gov/34255024/)
Assembly: hg38
Supplementary files format and content: bw files
|
| |
|
| Submission date |
Dec 15, 2023 |
| Last update date |
Jan 27, 2025 |
| Contact name |
chengguo yao |
| E-mail(s) |
yaochguo@mail.sysu.edu.cn
|
| Organization name |
sysu
|
| Department |
school of medicine
|
| Street address |
No. 74 zhongshan 2rd road
|
| City |
guangzhou |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE250342 |
U6 snRNP inhibits the premature cleavage and polyadenylation of pre-mRNAs (3'-Seq) |
| GSE250345 |
U6 snRNP inhibits the premature cleavage and polyadenylation of pre-mRNAs |
|
| Relations |
| BioSample |
SAMN38858995 |
| SRA |
SRX22906245 |
