|
| Status |
Public on May 04, 2021 |
| Title |
1D-HCT116-siNUTD21-Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
116-DDI cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: derivative colorectal cancer cell line with MAT2A detained intron (intron 8) deleted
treatment: NUDT21/CFIm25 (siNUDT21) siRNA for 96 hr
biological replicate: Rep1
|
| Treatment protocol |
siRNAs were transfected using RNAiMax and 24 hrs later the cells were split to allow doubling over the ensuing 72hrs (96 hrs total)
|
| Growth protocol |
Cells were grown under standard cell line conditions (DMEM media supplemented with Penn-strep/L-Gln/10%FBS) at 37C/5%CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol was used to extract RNA, which was subsequently treated with RQ1 Dnase steps and phenol:chloroform:isoamyl alcohol (25:24:1) and chloroform extracted.
Libraries were prepared by ClickSeq Technologies based on the protocol of Routh et al 2017 (PMC5499544).
PAC-seq. The general strategy is that first-strand synthesis is primed with a dT-p7-adaptor primer. The cDNA synthesis step is doped with an azide-containing chain-terminating nucleotide that is subsequently linked to a p5 sequencing adaptor with click chemistry.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
PAC-seq
|
| Data processing |
Library strategy: PAC-seq
Adaptor and poly(A) tail trimming and measurement by fastp and cutadapt
Mapping to hg19 using HISAT2.
Genome coverage calculated by bedtools
DPAC was used to identify poly(A) sites and clusters and to generate counts of clusters (Routh 2019; PMC6553543)
DESeq2 was used for differential analysis of poly(A) clusters.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files for each sample that used as input in gene count tables for DPAC and to calculate relative gene expression; Also included are two txt files of the gene counts and poly(A) cluster counts
|
| |
|
| Submission date |
Sep 25, 2020 |
| Last update date |
May 04, 2021 |
| Contact name |
Nicholas K Conrad |
| E-mail(s) |
nicholas.conrad@utsouthwestern.edu
|
| Phone |
2146480795
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Microbiology
|
| Street address |
6000 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75063 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE158591 |
NUDT21 regulates intron detention of the SAM synthetase MAT2A RNA |
|
| Relations |
| BioSample |
SAMN16265677 |
| SRA |
SRX9192851 |
