|
| Status |
Public on Mar 16, 2024 |
| Title |
tail_seq.dPAM2_2 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cell line
cell line: HeLa
cell type: immortalized cervical cancer cell
genotype: dPAM2 UNK
treatment: Dox for 24 hours
|
| Treatment protocol |
Inducible HeLa cells were treated or not for 24 hours with doxycycline (Dox)
|
| Growth protocol |
Inducible HeLa cells were maintained in Dulbecco’s Modified Eagle’s Medium, high glucose, pyruvate (Themo Fisher Scientific, 11995065) supplemented with 10% (v/v) fetal bovine serum (Thermo Fisher 10437) ; and 1% (w/v) penicillin/streptomycin Cells (Thermo Fisher Scientific, 1514022) were trypsinized and sub-cultured in incubator in 5% CO2 at 37 oC
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Direct-zol RNA miniprep kit (Zymo Research R2050) following manufacturer's instructions. Polyadenylated RNA was selected from total RNA using Poly(A) mRNA Magnetic Isolation kit (NEB E7490).
Poly(A)tail-seq libraries were constructed using Library Kit SQK-RNA002 and either Flowcell type FLO-MIN106D or FLO-PRO002 (Oxford Nanopore Technologies). One flowcell was used for each sample.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
PromethION |
| |
|
| Data processing |
When obtained the raw fast5 file from the sequencers, guppy (version 6.3.7-gpu) was used to call bases.
Minimap2 (version 2.26-r1175) was used to map the reads to hg38 gencode v35 transcripts.
tailfindr (version 1.4) and nanopolish (version 0.14.0) were used to estimate polyA tail length
Assembly: UCSC hg38
Supplementary files format and content: tab_delimimated tail lengths estimated from tailfindr and nanopolish, and gene mapping information for individual read.
Library strategy: Poly(A)tail-seq
|
| |
|
| Submission date |
Aug 10, 2023 |
| Last update date |
Mar 16, 2024 |
| Contact name |
Shiyang He |
| E-mail(s) |
[email protected]
|
| Organization name |
UCR
|
| Department |
Biochemistry
|
| Lab |
Murn lab
|
| Street address |
3401 Watkins Drive, Boyce Hall
|
| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
| |
|
| Platform ID |
GPL26167 |
| Series (2) |
| GSE240568 |
Regulation by the RNA-binding protein Unkempt at its effector interface [Tail seq] |
| GSE240571 |
Regulation by the RNA-binding protein Unkempt at its effector interface |
|
| Relations |
| BioSample |
SAMN36936147 |
| SRA |
SRX21329852 |
