NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2061706 Query DataSets for GSM2061706
Status Public on Feb 02, 2017
Title KC_30
Sample type SRA
 
Source name Cornea
Organism Homo sapiens
Characteristics disease state: KTCN
study: replication
tissue: cornea
Extracted molecule total RNA
Extraction protocol The corneas were transferred to 400 µl of lysis solution (Norgen Biotek, Thorold, ON, Canada) in a 2-mL microtube with Lysing Matrix D (MP Biomedicals, Irvine, CA, USA) and homogenized using a FastPrep®-24 Instrument (MP Biomedicals). Further total RNA extraction and purification steps were performed according to the manufacturer’s instructions supplied with a Total RNA Purification Kit (Norgen Biotek). To maximize the removal of residual DNA that could affect downstream analyses, an on-column DNase I (Zymo Research, Irvine, CA, USA) treatment was performed.
Libraries were prepared with a TruSeq Stranded Total RNA LT with Ribo-Zero™ Human/Mouse/Rat Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol, with slight modifications.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Short reads were trimmed using Trimmomatic version 0.32
Reads matching rRNAs were removed using Bowtie version 1.0.1
Reads were mapped to the reference genome using STAR version 2.4.0j
Mapped reads were assembed into transcripts using StringTie version 1.0.4
Assembled reads were merged with reference annotations using Cuffmerge version 2.2.1
Expression of genes and transcripts was estimated using Kallisto version 0.42.2.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Merged annotations created by Cuffmerge (GFF3 format); tab-delimited text files containing expression values of genes and transcripts (TPM values and raw estimated read counts)
 
Submission date Feb 16, 2016
Last update date May 15, 2019
Contact name Michal Kabza
Organization name Poznan University of Medical Sciences
Street address ul. Fredry 10
City Poznań
ZIP/Postal code 61-701
Country Poland
 
Platform ID GPL18460
Series (1)
GSE77938 Transcriptome profiling of human keratoconus corneas through RNA sequencing identifies collagen synthesis disruption and downregulation of core elements of TGF-β, Hippo, and Wnt pathways
Relations
SRA SRX1585297
BioSample SAMN04504384

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap