 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 13, 2021 |
| Title |
A549_siPLANE_4 |
| Sample type |
SRA |
| |
|
| Source name |
Lung adinocarcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
treatment: transfected with PLANE siRNA(siRNA2)
|
| 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.In this study,we used two different PLANE siRNAs, A549_siPLANE_1 & A549_siPLANE_2 were transfacted with siRNA1, and A549_siPLANE_3 & A549_siPLANE_4 were transfacted with siRNA2, NC was used for siRNA control
|
| 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 Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data.
Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq Bioconductor package, a model based on the negative binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, P-value of genes were setted <0.05 to detect differential expressed ones.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, log2foldchange, pvalue, qvalue
|
| |
|
| Submission date |
Apr 12, 2021 |
| Last update date |
Apr 13, 2021 |
| Contact name |
liu Teng |
| E-mail(s) |
tengliu2007@126.com
|
| 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 |
GPL20795 |
| Series (1) |
| GSE162215 |
The pan-cancer lncRNA PLANE regulates an alternative splicing program and promotes cancer pathogenesis |
|
| Relations |
| BioSample |
SAMN18715638 |
| SRA |
SRX10579954 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
