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| Status |
Public on Aug 19, 2021 |
| Title |
goat optic nerve OD #1 1 |
| Sample type |
SRA |
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| Source name |
optic nerve
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| Organism |
Capra hircus |
| Characteristics |
tissue: right retrobulbar optic nerve
tissue: optic nerve
breed: Saanen dairy goat
treatment: uninjured
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| Treatment protocol |
Left pre-chiasmatic optic nerve was crushed one day before collected samples.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of each sample was extracted following the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
RNA libraries were prepared for sequencing using standard illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ARS1 (Capra hicus) genome using Tophat2 software
Cufflinks are used for assemble transcripts and remap and quantity gene-expression level which is estimate by FPKM value.
Genome_build: ARS1
Supplementary_files_format_and_content: tab-delimited text files include raw counts and FPKM values for each Sample.
Supplementary_files_format_and_content: known_lncRNA.result.txt (includes our known lncRNA)
Supplementary_files_format_and_content: LncRNA.fa (contains the sequences of unknown genes)
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| Submission date |
Aug 16, 2021 |
| Last update date |
Aug 19, 2021 |
| Contact name |
Yu Zhonghao |
| E-mail(s) |
yuzhonghao0101@gmail.com
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| Phone |
19817563122
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| Organization name |
The Eye Hospital, School of Ophthalmology & Optometry
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| Street address |
270 Xueyuan West Road
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| City |
Wenzhou City |
| State/province |
Zhejiang Province, China |
| ZIP/Postal code |
325000 |
| Country |
China |
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| Platform ID |
GPL27106 |
| Series (1) |
| GSE182164 |
RNA seq of the retina and optic nerve from goats 1 day after pre-chiasmatic optic nerve crush injury |
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| Relations |
| SRA |
SRX11765074 |
| BioSample |
SAMN20834979 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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