|
| Status |
Public on Jun 10, 2016 |
| Title |
H460 NGFR knockdown biological replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
H460 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: non-small-cell lung cancer cell line
cell line: H460
|
| Treatment protocol |
Transfected with control or NGFR siRNA
|
| Growth protocol |
Cells were cultured in DMEM plus 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAGEN RNeasy mini Kit
Ribo-depletion: Ambion RiboMinus Eukaryote System v2
Library Preparation: Ion Total RNA-Seq Kit v2
Template Preparation: Ion PI Hi-Q Template OT2 200 Kit
Sequencing: Ion PI Hi-Q Sequencing 200 Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Align RNA-Seq reads with STAR
Align unmapped reads from Step 1 with bowtie2
Sort sam files
Merge bam files
Use SAMMatev2.6.1 to generate read counts and wiggle (coverage) files
Perform differential expression testing using EBSeq (100 iterations)
Genome_build: hg38
Supplementary_files_format_and_content: xlsx files including ensembl gene ID, gene name, read counts
|
| |
|
| Submission date |
Mar 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
HUA LU |
| E-mail(s) |
hlu2@tulane.edu
|
| Organization name |
TULANE UNIVERSITY
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
1430 Tulane Ave
|
| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70112 |
| Country |
USA |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE79051 |
RNA sequencing analysis of NGFR ablation in both p53-positive and negative non-small-cell lung cancer cell lines |
|
| Relations |
| BioSample |
SAMN04543852 |
| SRA |
SRX1622125 |
