|
| Status |
Public on Sep 04, 2015 |
| Title |
HCEC-B4G12_81 |
| Sample type |
SRA |
| |
|
| Source name |
corneal endothelial cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: endothelial
imortalization: SV40 TAg
culture medium: Human Endothelial-SFM
|
| 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 |
Sample 13
|
| 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 TopHat 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 77 transcript database.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a txt file with Ensemble 77 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 |
Feb 17, 2015 |
| 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) |
| GSE65991 |
Transcriptomic analysis of cultured corneal endothelial cells as a validation for their use in cell-replacement therapy |
|
| Relations |
| BioSample |
SAMN03352050 |
| SRA |
SRX879503 |
