|
| Status |
Public on May 01, 2024 |
| Title |
LN229 shNUDT21 1 |
| Sample type |
SRA |
| |
|
| Source name |
Epithelial morphology
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LN229
culture duration: 60 days
shRNA: NUDT21
|
| Treatment protocol |
Cells were transfected with either control siRNA or siRNA targeting NUDT21 using Lipofectamine 2000.
|
| Growth protocol |
U251 and LN229 were grown in DMEM+10%FBS. Low passage numbers were attained and cells were not grown for more than 2 months until a new passage was thawed out.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
72hrs after RNAi, cells were harvested for either Western Blot using SDS loading buffer or for RNA isolation using TriZol.
We reverse transcribed 1 ug of total RNA with the partial P7 adapter (Illumina_4N_21T) and dNTPs with the addition of spiked-in azido-nucleotides (AzVTPs) at 5:1. We click-ligated the p5 adapter (IDT) to the 5′ end of the cDNA with CuAAC. We then amplified the cDNA for 21 cycles with Universal primer and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200-300 base pairs. We pooled the libraries and sequenced single-end, 75 base-pair reads on a Nextseq 550 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
treatment LN229 cells with NUDT21 siRNA; sample 1
|
| Data processing |
Raw reads were trimed using fastp
Trimed reads were aligned to the reference genome using bowtie2
Samtools were used to sort, convert and index alignment files
Assembly: GRCh38
|
| |
|
| Submission date |
Apr 27, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Venkata Soumith Jonnakuti |
| E-mail(s) |
Venkata.Jonnakuti@bcm.edu
|
| Phone |
6502769164
|
| Organization name |
Baylor College of Medicine
|
| Street address |
2255 Braeswood Park Drive
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE230769 |
NUDT21 alters glioma migration through differential alternative polyadenylation of LAMC1 |
|
| Relations |
| BioSample |
SAMN34410710 |
| SRA |
SRX20121076 |
