|
| Status |
Public on Aug 03, 2016 |
| Title |
A549_shIno80_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
human A549_shIno80
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lung cancer cell line
cell line: A549
|
| Treatment protocol |
Human lung cancer cell line A549 cells were infected with shNT or shIno80, and total RNA was extracted 4 days after infection. The RNA was submitted to RNA-Seq subsequently.
|
| Growth protocol |
A549 cells were obtained from ATCC, and cultured in DMEM supplemented with 10% fetal bovine serum (FBS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells using the GeneJet RNA purification kit (Thermo Scientific)
For RNA-seq, One microgram total RNA was used for sequencing library generation using the Truseq RNA Library Prep Kit V2 (Illumina) according to the manufacturer’s instructions. Truseq RNA Library Prep Kit V2 (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Gene expression 4 days after transfection
|
| Data processing |
Aligned with TopHat2 version 2.0.4 with the following parameters: -g 10
FPKM measurements obtained using CuffLinks version 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: text file with FPKM: 1st column = RefSeq ID, 2nd column = fragments per kilobase of exon per million mapped reads (FPKM value)
|
| |
|
| Submission date |
Aug 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Li Wang |
| Organization name |
NIH
|
| Street address |
111 T.W. Alexander Dr
|
| City |
Durham |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE85118 |
INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer [RNA-seq] |
| GSE85119 |
INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer |
|
| Relations |
| BioSample |
SAMN05505547 |
| SRA |
SRX1996512 |
