|
| Status |
Public on Aug 01, 2013 |
| Title |
HeLa_U6atac_AMO |
| Sample type |
SRA |
| |
|
| Source name |
HeLa_U6atac knockdown
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa PV
cell type: Human Carcinoma Cells
transfected with: antisense morpholino to U6atac
molecule subtype: nascent polyA mRNA
|
| Treatment protocol |
Cells transfected with antisense morpholino to control or U6atac using Neon system for 8 hours
|
| Growth protocol |
Cells grown in DMEM supplemented with 10% FBS and 1% antibiotics
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extractde using trizol, polyA mRNA extracted using Rneasy Kit, nascent RNA linked to Biotin and etracted on magnetic streptavidin beads
Libraries were prepared according to instructions accompanying the Nugen kits. Briefly, RNA was converted to cDNA using the Ovation RNA-seq System and starting with 100ng RNA. cDNA was amplified using SPIA protocol recommended by Nugen Kit. Libraries for RNA-seq were prepared from the amplified cDNA using Encore NGS Library System I.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 2
|
| Data processing |
RNA-seq reads were aligned to the reference genome (UCSC, hg19) using Tophat by default parameters
FPKMs were generated using BEDTools
The analysis of differential gene expression was performed using Cufflinks
Significant genes were detected based on FDR level at 0.05 using Benjamini-Hochberg correction for multiple-testing
alternative spliced genes were identified by MISO
Genome_build: hg19
Supplementary_files_format_and_content: xlsx files containing RPKMs
|
| |
|
| Submission date |
Jun 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ihab Younis |
| E-mail(s) |
younis@mail.med.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Department |
Biochemistry and Biophysics
|
| Lab |
Gideon Dreyfuss
|
| Street address |
415 Curie Blvd
|
| City |
philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE48263 |
Genome wide mapping of effects of U6atac knockdown on pre-mRNA splicing |
|
| Relations |
| BioSample |
SAMN02213058 |
| SRA |
SRX314812 |
