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Sample GSM2402804 Query DataSets for GSM2402804
Status Public on Aug 17, 2017
Title PPCD CDDL 290 (P6)
Sample type SRA
Source name ex vivo corneal endothelium
Organism Homo sapiens
Characteristics diagnosis: Posterior Polymorphous Corneal Dystrophy (PPCD)
tissue: cornea
cell type: endothelial
immortalization: none
culture medium: none
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 3000
Description processed data file: Processed data PPCD evHCEnC.xls
Sample name: Sample 11
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 TopHat2 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 82 transcript database.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a txt file with Ensemble 82 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 Nov 24, 2016
Last update date May 15, 2019
Contact name Anthony J. Aldave
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)
GSE90489 Transcriptomic Profiling of Posterior Polymorphous Corneal Dystrophy
BioSample SAMN06053543
SRA SRX2373827

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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