|
| Status |
Public on Aug 17, 2017 |
| Title |
pHCEnC ZEB1 siRNA 24hr 191 |
| Sample type |
SRA |
| |
|
| Source name |
primary corneal endothelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cornea
cell type: endothelial
immortalization: none
culture medium: F99
|
| Growth protocol |
Cultured cells were either grown in F99 or Human Endothelial SFM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriReagent extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNeasy Clean-Up Kit.
Enrichment for poly(A) RNAs was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module, followed by library preparation using the PrepX Complete ILM DNA Library Kit. Libraries were prepared as per the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file: Processed data ZEB1 KD pHCEnC.xls
Sample name: Sample 6
|
| Data processing |
The FASTQ files containing the RNA-sequencing data were uploaded to the Partek Flow servers for alignment to the hg38 genome using the TopHat2 aligner, which output the results in BAM files
The BAM files were uploaded to the Partek Genomics Suite software and the reads and read-depth were transformed to reads per kilobase per million (RPKM) values, a normalized quantity that accounts for gene size.
These data were annotated using the Ensemble 82 transcript database.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a txt file with Ensemble 82 gene symbol ID in the first column. Sample names are given on the first row with RPKM values for each gene running down the column.
|
| |
|
| Submission date |
Nov 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Anthony J. Aldave |
| E-mail(s) |
Aldave@jsei.ucla.edu
|
| Organization name |
Stein Eye Institute, UCLA
|
| Department |
Ophthalmology
|
| Lab |
Cornea Genetics Laboratory
|
| Street address |
200 Stein Plaza DSERC 3-143
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE90489 |
Transcriptomic Profiling of Posterior Polymorphous Corneal Dystrophy |
|
| Relations |
| BioSample |
SAMN06053548 |
| SRA |
SRX2373822 |
