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| Status |
Public on Apr 07, 2020 |
| Title |
Normal5 |
| Sample type |
SRA |
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| Source name |
Optic nerve head
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| Organism |
Felis catus |
| Characteristics |
genotype: WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the dissected ONH tissue using RNeasy Fibrous Tissue Mini Kit (Qiagen, Germantown, MD) following the manufacturer’s instructions
RNA libraries were prepared for sequencing following Illumina TruSeq® Stranded mRNA Sample Preparation Guide Rev.E
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Generated raw reads (FASTQ format) were quality-control checked by FastQC after filtering to remove adaptor sequences, low-quality reads (quality score <20) and those that did not meet filter length ( length <28) by Skewer (ver 0.1.127), a fast and sensitive adapter trimmer for llumina paired-end sequences. Mapping of trimmed reads to the Felis catus reference genome sequence (ICGSC Felis_catus_8.0/ felCat8) was performed using STAR ver 2.4.2a. Gene transcript abundances were estimated by RSEM ver 1.2.22.
Genome_build: ICGSC Felis_catus_8.0/felCat8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Feb 01, 2018 |
| Last update date |
Apr 07, 2020 |
| Contact name |
Kazuya Oikawa |
| Organization name |
University of Wisconsin-Madison
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| Street address |
1300 University Ave
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
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| Platform ID |
GPL17081 |
| Series (1) |
| GSE110019 |
Sub-region-Specific Optic Nerve Head Glial Activation in Glaucoma |
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| Relations |
| BioSample |
SAMN08452406 |
| Supplementary data files not provided |
| Raw data are available in SRA |
| Processed data are available on Series record |
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