|
| Status |
Public on Apr 16, 2021 |
| Title |
A549-ONT-NC-2 |
| Sample type |
SRA |
| |
|
| Source name |
Lung adinocarcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
treatment: transfected with negative control siRNA
control
|
| Treatment protocol |
A549 cells were seeded in 6-well plate (1.5X10^5/well). Transfections were performed after 24h by using Lipofectamine™ 3000 Transfection Reagent (Thermo Fisher, L3000-015) according to the manufacturer’s instructions.
|
| Growth protocol |
cells were maintained in DMEM (Biological Industries, #01-052-1ACS; Beit Haemek, Israel) supplemented with 10% fetal bovine serum (FBS, Biological Industries, #04-001-1A; Beit Haemek, Israel) and 1% penicillin-streptomycin (Biological Industries, #03-031-1BCS，Beit Haemek, Israel). Cells were cultured in a humidified incubator at 37 °C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol™ Reagent(Catalog number: 15596026,ThermoFisher Scientific) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Oxford Nanopore Technologies protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Data processing |
Raw reads were first filtered with minimum average read quality score=7 and minimum read length=500bp. Ribosomal RNA were discarded after mapping to rRNA database. Next, full-length, non-chemiric (FLNC) transcripts were determined by searching for primer at both ends of reads. Clusters of FLNC transcripts were obtained after mapping to reference genome with mimimap2, and consensus isoforms were obtained after polishing within each cluster by pinfish.
Consensus sequences were mapped to reference genome using minimap2. Mapped reads were further collapsed by cDNA_Cupcake package with min-coverage=85% and min-identity=90%. 5’ difference was not considered when collapsing redundant transcripts.
The criteria for fusion candidates is that a single transcript must: (1) must map to 2 or more loci,(2) minimum coverage for each loci is 5% and minimum coverage in bp is >= 1 bp,(3) total coverage is >= 95%,(4) distance between the loci is at least 10kb
Differential expression analysis of two samples was performed using the EBSeq R package. The resulting FDR (false discovery rate) were adjusted using the PPDE(posterior probability of being DE).The FDR < 0.05 and foldchange ≥ 1.5 was set as the threshold for significantly differential expression.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text file includes CPM values for each Sample,FDR,log2FC
|
| |
|
| Submission date |
Apr 15, 2021 |
| Last update date |
Apr 16, 2021 |
| Contact name |
liu Teng |
| E-mail(s) |
[email protected]
|
| Organization name |
Henan Provincial People’s Hospital and People’s Hospital of Zhengzhou University
|
| Department |
Translational Research Institute
|
| Street address |
No 7,Weiwu Road,Jinshui District
|
| City |
Zhengzhou |
| ZIP/Postal code |
450053 |
| Country |
China |
| |
|
| Platform ID |
GPL26167 |
| Series (1) |
| GSE172124 |
The pan-cancer lncRNA PLANE regulates an alternative splicing program and promotes cancer pathogenesis [ONT] |
|
| Relations |
| BioSample |
SAMN18746850 |
| SRA |
SRX10605792 |
