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Sample GSM4233275 Query DataSets for GSM4233275
Status Public on Aug 13, 2020
Title SLC4A11 KD 1
Sample type SRA
 
Source name corneal endothelium
Organism Homo sapiens
Characteristics cell type: primary cultured human corneal endothelial cells
passage: 1
treatment: SLC4A11 siRNA knock-down
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 SLC4A11 KD
253_S4_R1_001
253_S4_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 SAMN13683642
SRA SRX7443233

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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