|
| Status |
Public on Mar 11, 2019 |
| Title |
Attached-iSPIB rep1 |
| Sample type |
SRA |
| |
|
| Source name |
non-small cell lung cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lung
cell type: squamous cell carcinoma cells
cell line: H1703
attachment status: attached
genotype/variation: SPIB knockdown
|
| Treatment protocol |
The H1703 floating 12h
|
| Growth protocol |
All cells were cultured as protocol on ATCC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Thermo RevertAid First Strand cDNA Synthesis Kit (Cat#K1622) was used with 1 ug of total mRNA for the construction of sequencing libraries.
mRNA libraries were prepared for sequencing using standard Thermo protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
test sample
A_iSPIB1
|
| Data processing |
Illumina Casava1.9 software used for basecalling.
Low quality reads and adaptor contamination are removed by NGSQC software, then mapped to hg19 genome by HISAT software
FPKM and expression difference analysis are performed and calculated by Cuffquant and the Cuffnorm software
Genome_build: hg19
Supplementary_files_format_and_content: Sample expression file containing normalized FPKM for each gene, by Microsoft Excel format
|
| |
|
| Submission date |
Nov 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhenyi Ma |
| E-mail(s) |
zhyma@tmu.edu.cn
|
| Phone |
86-22-83336533
|
| Organization name |
Tianjin Medical University
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
22 Qixiangtai Road
|
| City |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE106592 |
SPIB promotes anoikis resistance via elevated autolysosomal process in lung cancer cells [RNA-seq] |
|
| Relations |
| BioSample |
SAMN07982498 |
| SRA |
SRX3368168 |
