|
| Status |
Public on Jun 10, 2013 |
| Title |
shGata6Hopx.1 |
| Sample type |
SRA |
| |
|
| Source name |
shGata6Hopx
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC9
cell type: human lung Adenocarcinoma
transfected with: lentivirus harboring shRNA of both GATA6 and HOPX
|
| Treatment protocol |
Doxycycline (1ug/ml) for 5 days
|
| Growth protocol |
RPMI1640 + 10%FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Illumina TrueSeq RNA Prep, Total RNA from triplicate samples were extracted using RNeasy Mini kit (Qiagen). The quality of RNA samples was first analyzed on Agilent Bioanalyzer. Single-end, barcoded sequence libraries were constructed with TruSeq RNA Sample Prep Kit (Illumina) and sequenced on a HiSeq 2000 instrument according to the manufacturer’s instructions with single-end 50 base pair reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
KD
|
| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were mapped to human transcriptome using tophat 1.4.1 with parameters -p4 --solexa-quals --min-anchor 12 --library-type fr-unstranded -G All_Isoforms_For_ExpressionTable.gtf
Reads per gene was calculated using HtSeq-count in union mode
Reads per gene was nomalized to the library size and differential expressed genes was detected using EdgeR R package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized count of reads for each gene and each sample.
|
| |
|
| Submission date |
Jul 05, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Don Nguyen |
| E-mail(s) |
don.nguyen@yale.edu
|
| Phone |
2037374514
|
| Organization name |
Yale Shcool of Medicine
|
| Street address |
310 Cedar St
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE39121 |
Lung adenocarcinoma metastasis is suppressed by the alveolar lineage transcription factors GATA6 and HOPX. |
|
| Relations |
| SRA |
SRX157747 |
| BioSample |
SAMN01085884 |
