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Sample GSM3853938 Query DataSets for GSM3853938
Status Public on Jan 31, 2020
Title F99_P2_309
Sample type SRA
 
Source name corneal endothelium
Organism Homo sapiens
Characteristics tissue: corneal endothelium
media: F99
passage: P2
protocol: Tryp-LN-F99
Treatment protocol N/A
Growth protocol Cells were grown using two published protocols (Tryp-LN-F99 and ColA-ColIV-M4M5), and in a humidified incubation chamber at 37C with 5% CO2.
Extracted molecule polyA 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.
RNA-seq libraries were prepared using the KAPA mRNA HyperPrep Kit using an automated liquid handler (Janus G3 – PerkinElmer) according to manufacturer’s instruction at the UCLA Institute for Quantitative and Computational Biology
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
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 delimeted 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 Jun 05, 2019
Last update date Jan 31, 2020
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 GPL21290
Series (1)
GSE132204 Phenotypic and functional characterization of corneal endothelial cells during in vitro expansion
Relations
BioSample SAMN11960262
SRA SRX5973973

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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