|
Status |
Public on Mar 06, 2019 |
Title |
static_BMEC |
Sample type |
SRA |
|
|
Source name |
IMR90-4 iPSC-derived blood-brain barrier endothelium
|
Organism |
Homo sapiens |
Characteristics |
culture condition: static days in channel: 1
|
Treatment protocol |
Brain endothelium was cultured for 1 day under static conditions or 14 days under perfused conditions.
|
Growth protocol |
iPSC-derived blood-brain barrier endothelium was seeded into channels in gelatin hydrogels.
|
Extracted molecule |
total RNA |
Extraction protocol |
Endothelium was removed from channels using trypsin, and total RNA was isolated using Direct-zol RNA MiniPrep Plus Kit (Zymo Research) with DNase I treatment following manufacturer's instructions. Samples were submitted to Vanderbilt Technologies for Advanced Genomics (VANTAGE) for library preparation. cDNA libraries were prepared using a stranded mRNA (poly-A-selected) kit.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
Sequences were aligned to the human transcriptome using HISAT2 (version 1.2.0-OSX_x86_64). A list of known splice sites was generated using the UCSC Table Browser and hisat2_extract_splice_sites.py. Alignments were assembled using StringTie (version 1.3.4d.OSX_x86_64). FPKM values were extracted using Ballgown. Genome_build: GRCh38 Supplementary_files_format_and_content: CSV file contains transcript coverage and FPKM values for both samples.
|
|
|
Submission date |
Nov 15, 2018 |
Last update date |
Mar 06, 2019 |
Contact name |
Ethan Lippmann |
E-mail(s) |
ethan.s.lippmann@vanderbilt.edu
|
Organization name |
Vanderbilt University
|
Department |
Chemical and Biomolecular Engineering
|
Lab |
Lippmann Lab
|
Street address |
2400 Highland Ave, Room 303
|
City |
Nashville |
State/province |
TN |
ZIP/Postal code |
37212 |
Country |
USA |
|
|
Platform ID |
GPL24676 |
Series (1) |
GSE122588 |
iPSC-Derived Brain Endothelium Exhibits Stable, Long-Term Barrier Function in Perfused Hydrogel Scaffolds |
|
Relations |
BioSample |
SAMN10432065 |
SRA |
SRX5012155 |