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Sample GSM4696362 Query DataSets for GSM4696362
Status Public on Aug 11, 2021
Title 12-0094 Macula Retina
Sample type SRA
 
Source name Macula Retina
Organism Homo sapiens
Characteristics age: 86
Sex: F
disease state: geographic atrophy
Extracted molecule total RNA
Extraction protocol Donor eyes were obtained from non-diabetic Caucasians at a death-to-preservation interval of <6h. Eyes were stored in RNA later before extraction of RNA. For each eye we dissected macula and periphery from retina and RPE/choroid/sclera resulting in 4 samples per eye. RNA was extracted using the ALLPrep DNA/RNA Mini Kit (Qiagen). All RNA had an RNA integrity number of ≥8.
Strand specific RNA library was prepared from 100 ng total RNA using the Encore Complete RNA-Seq library kit (Nugen Technologies, San Carlos, CA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing RNA-seq data was aligned to the hg38 reference genome using GSNAP (v. ) with default options. Required a mapping quality scofe of ≥30 for each read. Quality control analysis of the aligned data was performed using program RNA-SeQC.
Transcripts were assembled using Cufflinks (v. ). A gene was considered differentially expressed if the false discovery rate (FDR) -adjusted p-value is <0.05.
Genome_build: hg38
Supplementary_files_format_and_content: cxb
 
Submission date Jul 27, 2020
Last update date Aug 11, 2021
Contact name Dwight Edward Stambolian
E-mail(s) stamboli@pennmedicine.upenn.edu
Phone 2158980305
Organization name University of Pennsylvania
Department Opthalmalogy
Lab Stellar-Chance 313
Street address 422 Curie Blvd.
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL11154
Series (1)
GSE155154 Human AMD
Relations
BioSample SAMN15650252
SRA SRX8829887

Supplementary file Size Download File type/resource
GSM4696362_12-0094-MR_abundances.cxb.gz 17.3 Mb (ftp)(http) CXB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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