|
| Status |
Public on Apr 11, 2019 |
| Title |
PPCD CDDL 91 (P7) |
| Sample type |
SRA |
| |
|
| Source name |
ex vivo corneal endothelium
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: endothelial
age: 67
disease: posterior polymorphous corneal dystrophy
|
| Treatment protocol |
N/A
|
| Growth protocol |
Cultured cells were grown 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 3000 |
| |
|
| Data processing |
The FASTQ files containing the RNA-sequencing data were aligned with CLC Biomedical Genomic Workbench to the hg38 genome.
Using CLC Biomedical Genomic Workbench, 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 88 transcript database.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a txt file with Ensemble 88 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 13, 2019 |
| Last update date |
Apr 11, 2019 |
| Contact name |
Anthony John Aldave |
| E-mail(s) |
aldave@jsei.ucla.edu
|
| Phone |
3108256232
|
| Organization name |
University of California, Los Angeles
|
| Department |
Ophthalmology
|
| Lab |
Aldave Lab
|
| Street address |
200 Stein Plaza, DS 3-143
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE126487 |
Alterations in GRHL2-OVOL2-ZEB1 Axis and Aberrant Activation of Wnt Signaling Lead to Altered Gene Transcription in Posterior Polymorphous Corneal Dystrophy |
|
| Relations |
| BioSample |
SAMN10924220 |
| SRA |
SRX5371477 |
