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| Status |
Public on Dec 15, 2021 |
| Title |
WT 0 hr PCS rep3 |
| Sample type |
SRA |
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| Source name |
Lens
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| Organism |
Mus musculus |
| Characteristics |
time point: 0 hr
surgery: cataract surgery
strain: C57BL/6
tissue: Lens capsule and attached LECscataract surgery
age: Adult 2 month old
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
By using an in vivo mouse model of cataract surgery, fiber cells were removed from wild type (WT) and β8 integrin conditional knockout (β8ITGcKO) lenses via a central corneal incision, leaving behind the lens capsule and attached LECs. Samples were harvested at 0 hour and 24 hours PCS, flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit (50) from Qiagen (Cat No./ID: 74104).
RNA libraries were prepared for sequencing using standard Clonthech protocols for SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
WT 0 hr PCS rep3
WT0vsBT80.txt
WT0vsBT80.txt
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| Data processing |
Analysis was performed by DNA Link USA, Inc
Sequence quality was assessed using FASTQC
Sequences were trimmed 5' 8bp and 3' 2bp and filtered 35bp minimum length after trimming using Cutadapt v 1.12
Trimmed reads were aligned to the reference genome using Tophat v2.1.0
Pairwise differential expression analysis was performed using Cuffdiff v2.2.1
Genome_build: Mus musculus mm10 (UCSC downlad GRCm38 and gff from NCBI/RefSeq GRCm38.p5 vertion)
Supplementary_files_format_and_content: tab-delimited w/ the following columns: test_id, gene_id, gene locus, sample_1, sample_2, status, Sample1_Rep_1, Sample1_Rep_2, Sample1_Rep_3, Sample1_AVE, Sample2_Rep_1, Sample2_Rep_2, Sample2_Rep_3, Sample2_AVE, value_1, value_2, log2(fold_change), test_stat, p_value, q_value, significant
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| Submission date |
Feb 18, 2020 |
| Last update date |
Dec 15, 2021 |
| Contact name |
Melinda K. Duncan |
| E-mail(s) |
duncanm@udel.edu
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| Phone |
3028310533
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| Organization name |
University of Delaware
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| Department |
Biological Sciences
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| Lab |
Vertebrate Development
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| Street address |
327 Wolf Hall
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| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19716 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE145492 |
Lens epithelial cell transcriptome reprogramming at 24 hours post cataract surgery (PCS) in wild type (WT) and β8 integrin Conditional Knockout (β8ITGcKO) mice. |
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| Relations |
| BioSample |
SAMN14127776 |
| SRA |
SRX7740998 |
| 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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