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Sample GSM8191514 Query DataSets for GSM8191514
Status Public on May 10, 2024
Title C57BL/6J, Aged mouse3, RPE/choroid, 20-24 months
Sample type SRA
Source name RPE/choroid
Organism Mus musculus
Characteristics tissue: RPE/choroid
age: 22-24 months
genotype: C57BL/6J
Sex: Female
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).
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.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description RPE_A3
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
Submission date Apr 08, 2024
Last update date May 10, 2024
Contact name Mark Ellsworth Kleinman
Phone 423-439-5969
Organization name East Tennessee State University
Department Department of Surgery
Lab Ocular Biology and Imaging Lab
Street address Quillen College of Medicine
City Johnson City
State/province Tennessee
ZIP/Postal code 37614
Country USA
Platform ID GPL24247
Series (1)
GSE263427 Deciphering age-related transcriptomic changes in mouse retinal pigment epithelium
BioSample SAMN40873733
SRA SRX24188314

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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