|
| 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 |
