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Sample GSM1612322 Query DataSets for GSM1612322
Status Public on Sep 04, 2015
Title HCEC-12_75
Sample type SRA
 
Source name corneal endothelial cell line
Organism Homo sapiens
Characteristics cell type: endothelial
imortalization: SV40 TAg
culture medium: F99
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 10
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 SAMN03352048
SRA SRX879500

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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