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Sample GSM3475306 Query DataSets for GSM3475306
Status Public on Mar 06, 2019
Title perfused_BMEC
Sample type SRA
 
Source name IMR90-4 iPSC-derived blood-brain barrier endothelium
Organism Homo sapiens
Characteristics culture condition: perfused
days in channel: 14
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 SAMN10432064
SRA SRX5012156

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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