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| Status |
Public on May 10, 2024 |
| Title |
C57BL/6J, Aged mouse3, RPE/choroid, 20-24 months |
| Sample type |
SRA |
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| Source name |
RPE/choroid
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| Organism |
Mus musculus |
| Characteristics |
tissue: RPE/choroid
age: 22-24 months
genotype: C57BL/6J
Sex: Female
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| Growth protocol |
The mice were purchased from the Jackson Laboratory and housed under standard conditions (23±1°C, 40%–50% humidity, and ad libitum access to food and water).
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| Extracted molecule |
total RNA |
| Extraction protocol |
All mice were humanely euthanized by administering CO2 gas followed by cervical dislocation. The eyes were immediately enucleated to collect the neural retina and RPE/choroid tissues. The isolated eyes were placed in the cold petri dish under a surgical microscope. With careful precision, the anterior parts, including the cornea, lens, and iris, as well as connective tissues, muscles, and optic nerve, were excised. Radial cuts were made symmetrically in a four-leaf pattern, allowing for the careful removal of the neural retina from the mouse eyecup. The pigmented RPE/choroid layer was gently scraped from the sclera. RPE/choroid and neural retina tissues were immediately transferred to TRIzol reagent (Invitrogen 15596026, Carlsbad, CA). Subsequently, RNA purification and on-column genomic DNA digestion were conducted using the Pure Link RNA Micro Kit (Invitrogen 12183016, Carlsbad, CA).
Ribosomal RNAs were removed with the Qiagen FastSelect -rRNA HMR Kit (Human/Mouse/Rat). RNA libraries were constructed using NEXTFLEX Rapid Directional RNA-Seq Kit 2.0 (Perkin Elmer, Waltham, MA) as per manufacturer's instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
RPE_A3
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| Data processing |
Paired-end 150 bp raw reads were trimmed to eliminate Truseq adapters and bases from the 3’ end with quality scores less than 20 using cutadapt (ver 4.4). Trimmed reads were aligned to the Mus musculus (house mouse) genome assembly GRCm39 (mm39) from Genome Reference Consortium [GCA_000001635.9 GCF_000001635.27] using STAR [44].
The expression level of ENSEMBL genes was quantified using FeatureCounts. Differential expression statistics were computed using edgeR, using raw expression counts.
Assembly: GRCm39 (mm39)
Supplementary files format and content: edgeR results for all the samples
Supplementary files format and content: normalized TPM counts
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| Submission date |
Apr 08, 2024 |
| Last update date |
May 10, 2024 |
| Contact name |
Mark Ellsworth Kleinman |
| E-mail(s) |
kleinmanlab.etsu@gmail.com
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| Phone |
423-439-5969
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| Organization name |
East Tennessee State University
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| Department |
Department of Surgery
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| Lab |
Ocular Biology and Imaging Lab
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| Street address |
Quillen College of Medicine
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| City |
Johnson City |
| State/province |
Tennessee |
| ZIP/Postal code |
37614 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE263427 |
Deciphering age-related transcriptomic changes in mouse retinal pigment epithelium |
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| Relations |
| BioSample |
SAMN40873733 |
| SRA |
SRX24188314 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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