|
| Status |
Public on Jul 09, 2023 |
| Title |
22rv ko ip1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
technology: m6A-Seq
genotype: FTO KO
cell line: 22Rv1
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
At 48-h post-transfection, total RNA was isolated from transfected cells with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen).
RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
High-quality reads were then mapped to hg19 reference genome by HISAT2 with uniquely mapped reads retained for the following analyses.
Normalization were performed by Deeptools.
Differential expression analysis was performed by DESeq2.
Peak calling was performed with exomePeak.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig normalized signal
|
| |
|
| Submission date |
Nov 23, 2021 |
| Last update date |
Jul 09, 2023 |
| Contact name |
Xiaolong Cui |
| E-mail(s) |
xiaolong.cui@northwestern.edu
|
| Organization name |
Northwestern University
|
| Department |
Department of Preventive Medicine
|
| Street address |
680 N Lake Shore Drive
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE189465 |
N6-methyladenosine modification is essential for prostate cancer cells |
|
| Relations |
| BioSample |
SAMN23415487 |
| SRA |
SRX13212198 |
