|
| Status |
Public on Jun 22, 2018 |
| Title |
DMS114_parental |
| Sample type |
SRA |
| |
|
| Source name |
small cell lung cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DMS114
treatment: exponentially growing cells
|
| Treatment protocol |
All parental cell lines were gowring exponentially upon harvest. Cells were lentivirally infected with sgRNA for knockout.
|
| Growth protocol |
NCI-H1048 cells were cultured in HITES, NCI-H128 cells were cultured in RPMI with 20% FBS and penicillin/streptomycin. All other cells were cultured in RPMI with 10% FBS and penicillin/streptomycin or HITES, .
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol following the manufacture's protocol
RNA-seq library was prepared using Illumina TruSeq sample prep kit v2 according to the manufacture's protocol. Briefly, polyA RNA was selected and fragmented enzymatically. First strand of cDNA was synthesized using Super Script II reverse transcriptase, and then second strand was synthesized. Double-stranded cDNA was end-repaired, 3'-adenylated, ligated with indexed adaptor, and then PCR-amplified.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file:
parental_RPKM.txt
|
| Data processing |
Sequencing reads were mapped into reference human genome hg19 using TopHat2
Differentially expressed genes were analyzed using a Cufflinks tool, Cuffdiff, by masking structural RNAs
normalized to total mapped reads
Genome_build: hg19
Supplementary_files_format_and_content: txt, normalized RPKM
|
| |
|
| Submission date |
May 30, 2018 |
| Last update date |
Jun 22, 2018 |
| Contact name |
Olaf Klingbeil |
| E-mail(s) |
[email protected]
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Street address |
1 Bungtown Road
|
| City |
Cold Spring Harbor |
| State/province |
New York |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE115122 |
POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer [RNA-seq] |
| GSE115124 |
POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer |
|
| Relations |
| BioSample |
SAMN09284674 |
| SRA |
SRX4143050 |
