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Sample GSM3602448 Query DataSets for GSM3602448
Status Public on Apr 11, 2019
Title PPCD CDDL 91 (P7)
Sample type SRA
Source name ex vivo corneal endothelium
Organism Homo sapiens
Characteristics cell type: endothelial
age: 67
disease: posterior polymorphous corneal dystrophy
Treatment protocol N/A
Growth protocol Cultured cells were grown 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
Data processing The FASTQ files containing the RNA-sequencing data were aligned with CLC Biomedical Genomic Workbench to the hg38 genome.
Using CLC Biomedical Genomic Workbench, 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 88 transcript database.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a txt file with Ensemble 88 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 13, 2019
Last update date Apr 11, 2019
Contact name Anthony John Aldave
Phone 3108256232
Organization name University of California, Los Angeles
Department Ophthalmology
Lab Aldave Lab
Street address 200 Stein Plaza, DS 3-143
City Los Angeles
State/province California
ZIP/Postal code 90095
Country USA
Platform ID GPL21290
Series (1)
GSE126487 Alterations in GRHL2-OVOL2-ZEB1 Axis and Aberrant Activation of Wnt Signaling Lead to Altered Gene Transcription in Posterior Polymorphous Corneal Dystrophy
BioSample SAMN10924220
SRA SRX5371477

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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