|
Status |
Public on Jun 10, 2013 |
Title |
shGata6Hopx.2 |
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 |
SRX157748 |
BioSample |
SAMN01085885 |