|
Status |
Public on Aug 13, 2020 |
Title |
scRNA 3 |
Sample type |
SRA |
|
|
Source name |
corneal endothelium
|
Organism |
Homo sapiens |
Characteristics |
cell type: primary cultured human corneal endothelial cells passage: 1 treatment: scrambled RNA
|
Treatment protocol |
Confluent pHCEnC were transfected with 10nM anti-SLC4A11 siRNA (siRNA-CrCrGrArArArGrUrArCrCrUrGrArArGrUrUrArArArGrArACT) or scrambled siRNA (OriGene Technologies) using Lipofectamine LTX (Life Technologies). At 72 hrs post-transfection, the cells were lysed for RNA isolation.
|
Growth protocol |
Primary cultures of human corneal endothelial cells (pHCEnC) were isolated from donor corneas as previously described (Frausto, et al. 2016). Cells were plated in laminin coated cell culture plastic and cultured in a 1:1 mixture of F12-Ham’s and M199 (F99) medium. Experiments were performed when the cells achieved an intact and confluent monolayer.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA from cultured pHCEnC was isolated in TRI Reagent and purified with the RNeasy Clean-Up Kit (Qiagen). Purified total RNA from pHCEnC was prepared for RNA-seq libraries using KAPA mRNA HyperPrep Kit.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
scRNA 246_S3_R1_001 246_S3_R2_001
|
Data processing |
Alignment - HISAT2, --no-unal --no-discordant --no-mixed Assemble and Quantify - STRINGTIE DGE analysis - LIMMA and VOOM Genome_build: GRCh38 Supplementary_files_format_and_content: txt - list of DGE
|
|
|
Submission date |
Dec 26, 2019 |
Last update date |
Aug 13, 2020 |
Contact name |
Wenlin Zhang |
E-mail(s) |
w.zhang@jsei.ucla.edu
|
Organization name |
UCLA, Jules Stein Eye Institute
|
Street address |
200 Stein Plaza, Dserc 3-143
|
City |
Los Angeles |
State/province |
CA |
ZIP/Postal code |
90095 |
Country |
USA |
|
|
Platform ID |
GPL20301 |
Series (1) |
GSE142636 |
Transcriptome of Human Primary Corneal Endothelial Cells with SLC4A11 deficiency |
|
Relations |
BioSample |
SAMN13683643 |
SRA |
SRX7443232 |