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Sample GSM995550 Query DataSets for GSM995550
Status Public on Jul 30, 2013
Title HRN2
Sample type SRA
 
Source name retina
Organism Homo sapiens
Characteristics disease status: normal
tissue: retina
Extracted molecule total RNA
Extraction protocol Normal human retina total RNA was purchased from Biochain. RNA-Seq libraries were prepared from 5 μg total RNA following a modified Illumina mRNA-Seq protocol (Illumina). Briefly, mRNA was purified using oligo-dT beads (Invitrogen). The purified mRNA was then fragmented for 2 minutes at 94°C on a thermalcycler with the addition of 2 μl of 10X fragmentation buffer (1 mM ZnCl2, 1 mM Tris-HCl, pH 7.0). The reaction was stopped with the addition of 4 μl of 100 mM EDTA, pH 8.0. First strand cDNA was synthesized using SuperScript II reagents following manufacturers instructions (Invitrogen). The remaining steps: second strand cDNA synthesis, end-repair, monoadenylation, and adapter ligation were performed following Illumina’s mRNA-Seq protocol. All reagents, excluding paired-end adapters, were purchased from New England Biolabs. Paired-end adapters and PCR primers were purchased from Illumina. cDNA libraries were size selected using a 2% agarose gel and fragments between 300-350 bp were selected. Size selected samples were then PCR amplified using 15 cycles. cDNA library quantity and quality were determined using DNA 1000 chips on a Bioanalyzer 2100 (Agilent)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description supplier: Biochain
Data processing fastq files generated using CASAVA v1.8
The fastq files were first concatenated, and alignment and post-processing of the fastq was performed using the RNA-Seq Unified Mapper v1.10 using default parameters
novel splicing was determined by parsing the junctions_high-quality.bed (output from RUM post-processing) using custom scripts.
Genome_build: hg19
 
Submission date Aug 31, 2012
Last update date May 15, 2019
Contact name Eric Pierce
E-mail(s) eric_pierce@meei.harvard.edu
URL http://www.masseyeandear.org/research/ophthalmology/laboratories/oculargenomics/
Organization name Massachusetts Eye and Ear Infirmary
Department Ophthalmology
Lab Ocular Genomics Institute
Street address 243 Charles Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platform ID GPL11154
Series (1)
GSE40524 Unprecedented alternative splicing and 3 Mb of novel transcribed sequence leads to significant transcript diversity in the transcriptome of the human retina
Relations
SRA SRX181607
BioSample SAMN01141800

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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