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| Status |
Public on Apr 14, 2023 |
| Title |
Crushed optic nerves, replicate 3 from hibernators |
| Sample type |
SRA |
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| Source name |
Crushed optic nerves
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| Organism |
Ictidomys tridecemlineatus |
| Characteristics |
Stage: hibernators
tissue: Crushed optic nerves
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| Extracted molecule |
total RNA |
| Extraction protocol |
Enucleated eyes were dissected to form posterior segment eye cups, which were then fixed in 4% paraformaldehyde in phosphate buffered saline(PBS) for 2–4 h at 4°C. Eyecups were either processed for vibratome sectioning (100um-thick sections, VT1000; Leica) or dissected to form retinal flat mounts. Flat-mounted retinas or retinal sections were blocked overnight in blocking buffer containing 6% normal donkey serum and 0.5% TritonX-100 in PBS at room temperature.
GS retinas and optic nerve tissue were collected and lysed in TRIzol (Thermo Fisher, Waltham, MA), total RNA was isolated and purified with miRNeasy kit (Qiagen, Hilden, Germany). TruSeq Stranded mRNA Library Prep Kit was used to generate the sequencing libraries (Illumina, San Diego, CA) following the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
566H3
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| Data processing |
[basecalling and demultiplex] The raw base call (.bcl) files were converted to demultiplexed fastq files with Bcl2fastq v2.19.1
[Trimming] For all fastq files, the adapters and low-quality reads ending with quality score<20 were trimmed using Cutadapt (v1.8.1). Reads with length<20 after trimming were also discarded
[alignment] The trimmed reads mapping to squirrel rRNA and tRNA reference were further removed. Remaining reads were aligned to the squirrel genome (Ensembl spetri2)[1] using Tophat2 (v2.1.1)
[featurecount] For quantification of gene expression, only the unique alignments to exon regions were counted using featureCounts program (v1.6.0)
Genome_build: Ensembl spetri2
Supplementary_files_format_and_content: gene counts
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| Submission date |
Apr 14, 2020 |
| Last update date |
Apr 14, 2023 |
| Contact name |
Yizhao Luan |
| E-mail(s) |
luanyz_leo@163.com
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| Organization name |
Sun Yat-sen university
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| Department |
Zhongshan Ophthalmic Center
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| Street address |
Xianlie South Rd. 54, Yuexiu Dist
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510060 |
| Country |
China |
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| Platform ID |
GPL22974 |
| Series (1) |
| GSE148651 |
Transcriptomic changes of optic nerves under crush during hibernation stage |
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| Relations |
| BioSample |
SAMN14596578 |
| SRA |
SRX8114709 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4476139_566H3-htseq-counts.tsv.gz |
91.2 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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