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Sample GSM3449992 Query DataSets for GSM3449992
Status Public on Jun 13, 2019
Title evK_3
Sample type SRA
Source name corneal keratocytes
Organism Homo sapiens
Characteristics sample type: ex vivo
age group: adult
cell type: corneal keratocytes
Treatment protocol N/A
Growth protocol N/A
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
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 delimited 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 Oct 29, 2018
Last update date Jun 13, 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 GPL16791
Series (1)
GSE121922 Transcriptomic and gene ontology profiling of the human corneal cell types
BioSample SAMN10341959
SRA SRX4950954

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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