|
| Status |
Public on Jun 13, 2019 |
| Title |
evCEpC_3 |
| Sample type |
SRA |
| |
|
| Source name |
corneal epithelium
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: ex vivo
age group: adult
cell type: corneal epithelium
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| 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 |
| |
|
| 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 delimited 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 |
Oct 29, 2018 |
| Last update date |
Jun 13, 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) |
| GSE121922 |
Transcriptomic and gene ontology profiling of the human corneal cell types |
|
| Relations |
| BioSample |
SAMN10341962 |
| SRA |
SRX4950951 |
