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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 10, 2021 |
| Title |
Lens Fibers from Male Young Mice, 0 Hours post surgery, rep 2 |
| Sample type |
SRA |
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| Source name |
LFC
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| Organism |
Mus musculus |
| Characteristics |
cell type: Lens fiber cells (LFC)
age: 3 Months
Sex: Male
injury_status: 0H
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| Extracted molecule |
total RNA |
| Extraction protocol |
Lens epithelial cell RNA was harvested using the RNeasy Mini Kit (50) from Qiagen (Cat No./ID: 74104), and lens fiber cell RNA isolated using the SV Total RNA Isolation System (Promega- Catalog number- Z3100).
SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian v2 (Takara Bio USA, Inc., Mountain View, CA, USA).
Paired end 100 nucleotide reads, ribosomal depletion.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
YF_2M_S74
All0H_AF0vYF0_ExactTestQVL_Differential_Expression.xlsx
All0H_YF0vYE0_ExactTestQVL_Differential_Expression.xlsx
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| Data processing |
Reads were trimmed for quality, adaptor content, and to remove a kit specific trinucleotide sequence using the software "TrimGalore!" with the following parameters: --length 85 --paired --clip_R2 3 --phred33
Trimmed reads were aligned using Hisat2 with the following parameters: -p8 --verbose --dta --fr --phred33
Aligned reads were sorted by position using samtools sort.
Aligned reads were quantified using Htseq-Count with the following parameters: -i gene_id -r pos -f bam -s reverse -m union --type exon
Gene level counts were analyzed for differential expression using the edgeR.
Genome_build: GRCm38, GTF File: Mouse Ensembl version 101
Supplementary_files_format_and_content: *_GeneCount.txt: Htseq-count, Tab Separated, Column 1: Ensembl Gene ID, Column 2: Count.
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| Submission date |
Feb 11, 2021 |
| Last update date |
Apr 26, 2024 |
| Contact name |
Melinda K. Duncan |
| E-mail(s) |
duncanm@udel.edu
|
| Phone |
3028310533
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| Organization name |
University of Delaware
|
| Department |
Biological Sciences
|
| Lab |
Vertebrate Development
|
| 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) |
| GSE166619 |
The influence of sex and age on the lens injury response |
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| Relations |
| BioSample |
SAMN17866527 |
| SRA |
SRX10077016 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5076543_YF_2M_S74_GeneCount.txt.gz |
175.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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