|
| Status |
Public on Jan 31, 2020 |
| Title |
F99_P2_309 |
| Sample type |
SRA |
| |
|
| Source name |
corneal endothelium
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: corneal endothelium
media: F99
passage: P2
protocol: Tryp-LN-F99
|
| Treatment protocol |
N/A
|
| Growth protocol |
Cells were grown using two published protocols (Tryp-LN-F99 and ColA-ColIV-M4M5), and in a humidified incubation chamber at 37C with 5% CO2.
|
| Extracted molecule |
polyA 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.
RNA-seq libraries were prepared using the KAPA mRNA HyperPrep Kit using an automated liquid handler (Janus G3 – PerkinElmer) according to manufacturer’s instruction at the UCLA Institute for Quantitative and Computational Biology
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Raw reads in FASTQ files were aligned to the human hg38 genome build and transcript (Ensembl 92) quantities calculated using the kallisto (v0.44.0) per instructions.
Differential gene expression analysis was performed using the Sleuth (v0.30.0) R package. Differential expression was tested using a negative binomial test, and corrected for multiple testing using the Benjamini-Hochberg correction.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a tab delimeted txt file with Ensembl 92 gene symbol ID in the first column. Sample names are given on the first row with TPM values for each gene running down the column.
|
| |
|
| Submission date |
Jun 05, 2019 |
| Last update date |
Jan 31, 2020 |
| 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 |
GPL21290 |
| Series (1) |
| GSE132204 |
Phenotypic and functional characterization of corneal endothelial cells during in vitro expansion |
|
| Relations |
| BioSample |
SAMN11960262 |
| SRA |
SRX5973973 |
