|
| Status |
Public on Apr 05, 2016 |
| Title |
Day6, rep2 (Paired-end) |
| Sample type |
SRA |
| |
|
| Source name |
Human lung cancer
|
| Organism |
Homo sapiens |
| Characteristics |
time point: Day6
tissue: Lung
treatment: DOX
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extrated from cells using TRIzol reagent (ThermoFisher 15596) according to the protocol.
cDNA libraries for sequencing were prepared using the Illumina True-seq Stranded mRNA kit and protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Day6
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl human transcript (release 72) then hg19 whole genome using tophat v1.4.1 with parameters -a 8 -m 0 -I 300000 -p 8 -g 20 --library-type fr-firststrand -initial-read-mismatches 3 --segment-mismatches 2
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cuffdiff v2.2.0 with uniquely and properly mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: an excel file includes FPKM values for each Sample …
|
| |
|
| Submission date |
Nov 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yi Xing |
| Organization name |
UCLA
|
| Department |
Department of Microbiology, Immunology, & Molecular Genetics
|
| Street address |
650 Charles E. Young Dr. South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7278 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE75487 |
Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition [EMT.time course] |
| GSE75492 |
Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition |
|
| Relations |
| BioSample |
SAMN04301558 |
| SRA |
SRX1455947 |
