|
| Status |
Public on Jan 01, 2018 |
| Title |
347P1 |
| Sample type |
SRA |
| |
|
| Source name |
Pooled laser capture microdissected endoneurial microvessels from cryopreserved sural nerve (donor 4)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Sural nerve
passage number: Not applicable
age: 51
Sex: Male
|
| Growth protocol |
Primary endoneurial endothelial cells were isolated from sciatic nerves via endoneurial stripping, enzymatic digestion and density centrifugation. Primary endoneurial endothelial cells (1 x 10^6 per 75 cm2 flask) were grown to confluence in specialized pHEndEC growth medium on rat tail collagen-coated Corning CellBIND flasks and RNA extracted using TRIzol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Endoneurial microvessels were fluorescently detected in 20 micron thick axial cryosections of human sural nerve biopsies using UEA-1-FITC, and laser capture microdissection performed. Microvessels were stored in extraction buffer at -80oC and RNA isolated using Arcturus Pico Pure Isolation Kit (Thermo Fisher Scientific) or miRNeasy kit (Qiagen, Hilden, Germany). On-column DNase digestion was also performed to remove contaminating genomic DNA using the RNase-free DNase Set (Qiagen).
cDNA libraries were generated using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Clontech) and ribosomal cDNA was depleted prior to the final amplification step
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using bcl2fastq version 1.8.4 (for Illumina HiSeq2500) and bcl2fastq version 2.18.0.12 (for NextSeq500)
Reads were aligned to hg19 using RSEM version 1.2.31 with parameters --paired-end; --star; --estimate-rpsd; --append-names; --output-genome-bam; --star-gzipped-read-file
Genes with FPKM values > 0.1 were then further analyzed in gProfiler
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited files of FPKM and gProfiler results
|
| |
|
| Submission date |
Dec 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Eroboghene Ubogu |
| E-mail(s) |
ubogu@uab.edu
|
| Organization name |
University of Alabama at Birmingham
|
| Department |
Neurology
|
| Lab |
NIRL
|
| Street address |
1720 7th Avenue South, SC200
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294-0017 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE107574 |
The human blood-nerve barrier transcriptome |
|
| Relations |
| BioSample |
SAMN08118432 |
| SRA |
SRX3436774 |
