 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 02, 2017 |
| Title |
KC_21 |
| 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 |
SRX1585291 |
| BioSample |
SAMN04504378 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
