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| Status |
Public on Jul 08, 2020 |
| Title |
FNcKO 48 hr PCS rep 3 |
| Sample type |
SRA |
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| Source name |
Lens
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| Organism |
Mus musculus |
| Characteristics |
strain: Mixed (C57BL/6, 129, FVB/N)
tissue: Lens capsule and attached LECs
age: Adult 2 month old
genotype: Fibronectin conditional knockout
time point: 48hr
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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 Fibronectin conditional knockout (FNcKO) lenses via a central corneal incision, leaving behind the lens capsule and attached LECs. Samples were harvested at 0 hour and 48 hours PCS, flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit (50) from Qiagen (Cat No./ID: 74104). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols for Stradeded TruSeq Library Preparation Kit for the Illumina HiSeq 2500
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
FNcKO 48 hr PCS rep3
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| Data processing |
Analysis was performed by the University of Delaware Bioinformatics Core Facility using a modified MAPRseq pipeline implemented on the BioMix compute cluster at the Center for Bioinformatics and Computational Biology/Delaware Biotechnology Institute
Sequence quality was assessed using FASTQC
Sequences were end-trimmed (Q30) and filtered (no ambiguous nucleotides, 35bp minimum length after trimming) using Trim Galore (v0.4.4)
Trimmed reads were aligned to the reference genome using Tophat v2.1.0
Mapping quality was assessed using RSeQC v2.3.7 and metrics extracted from BedTools v2.17 and SamTools v1.4
Feature counts were extracted using HtSeq v0.6.1p1
Pairwise differential expression analysis was performed on features with >1 cpm in at least 2 samples using EdgeR v 3.16.5
Genome_build: Mus musculus mm10 (UCSC tophat version as downloaded May 2017)
Supplementary_files_format_and_content: tab-delimited w/ the following columns: "Chr" (Chromosome), "GeneID" (Gene Symbol), GeneCount (Read Count), RPKM
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| Submission date |
May 02, 2019 |
| Last update date |
Jul 08, 2020 |
| 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 |
GPL17021 |
| Series (1) |
| GSE119879 |
Lens epithelial cell transcriptome reprogramming at 48 hours post cataract surgery (PCS) in wild type (WT) and Fibronectin Conditional Knockout (FNcKO) mice |
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| Relations |
| BioSample |
SAMN11565731 |
| SRA |
SRX5782051 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3744995_S15.tab.txt.gz |
553.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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