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| Status |
Public on Feb 14, 2024 |
| Title |
ASC, bio rep4 |
| Sample type |
SRA |
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| Source name |
lens capsule
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| Organism |
Mus musculus |
| Characteristics |
tissue: lens capsule
strain: C57BL/6
age: six to eight weeks
genotype: WT
treatment: injury-induced ASC
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| Treatment protocol |
A small incision was made at the center of the anterior capsule by vertically inserting a 26-gauge hypodermic needle through the cornea. The depth of insertion reached a quarter of the blade's length
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| Growth protocol |
Adult C57BL/6 mice aged six to eight weeks were utilized to create the injury-induced ASC model
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Trizol reagent.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
ASC_rep_4
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| Data processing |
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through fastp software.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Supplementary files format and content: xls file includes raw counts for each sample
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| Submission date |
Oct 15, 2023 |
| Last update date |
Feb 14, 2024 |
| Contact name |
Fanying Jiang |
| E-mail(s) |
jiangfy3@mail2.sysu.edu.cn
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| Phone |
+8615521187291
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| Organization name |
Zhongshan Ophthalmic Center, Sun Yat-Sen University
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| Street address |
No. 7, Jinsui Road
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| City |
Guangzhou |
| ZIP/Postal code |
510060 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE245411 |
Smurf1 modulates Smad signaling pathway in fibrotic cataract formation [mouse_ASC] |
| GSE245412 |
Smurf1 modulates Smad signaling pathway in fibrotic cataract formation |
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| Relations |
| BioSample |
SAMN37819315 |
| SRA |
SRX22094272 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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