NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4133272 Query DataSets for GSM4133272
Status Public on Aug 12, 2020
Title HUVEC AD-HIES2_TNF
Sample type SRA
 
Source name Umbilical Cord
Organism Homo sapiens
Characteristics isolated cells: HUVEC
treatment: TNFa 50ng/ml for 8h
genotype/variation: AD-HIES STAT3 mutation
Treatment protocol For RNA isolation, HUVECs were seeded on 6 well plates at density of 250,000 cells per well. In 48 hours, when cells reached confluence, media was changed to fresh one with or without 50ng/ml TNFα for 8h and total RNA was extracted for RNA-Seq analysis.
Growth protocol The cords were shipped overnight from hospitals in PBS supplemented with Penicillin-Streptomycin (No. 15140122, ThermoFisher Scientific). Umbilical veins were washed 3 times with PBS supplemented with Penicillin-Streptomycin and Amphotericin B (No. 400-104, Gemini Bio-Products, West Sacramento, CA) and then filled with collagenase, type II (No.17101-015, ThermoFisher Scientific) at 0.2% in PBS and the ends were closed. The cords were placed in 37C incubator for 20 min. The cells were pelleted from the collagenase suspension, resuspended in endothelial cell culture media (EBM Basal Medium (No.CC-3121, Lonza) supplemented with EGM-2 SingleQuots Kit (No.CC-4176, Lonza)), Penicillin-Streptomycin and Amphotericin B and plated on fibronectin (No. F2006, Sigma) coated T25 flask. The media was changed next day, and cells were routinely cultured on 10 cm fibronectin coated dishes.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol Reagent (No. 15596026, ThermoFisher Scientific).
One mg of total RNA was used as input for library preparation using the TruSeqRNA Sample Preparation Kit v2 (Illumina) according to manufacturer’s instructions. Sequencing libraries were quantitated by qPCR on a LightCycler 480 Instrument II (Roche) and assessed for size distribution and absence of adapter dimers using a Fragment Analyzer (AATI). Libraries were pooled for multiplexing and sequencing was performed on the Illumina HiSeq 3000 Sequencing System with run parameters at paired-end 75bp read length for >25 million paired-end reads per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description HUVEC_RNA-seq.txt
Data processing RNA-seq data quality was assessed using FastQC
Reads obtained for each sample were aligned to the hg19 human reference genome using Tophat2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include total counts values for all samples
 
Submission date Oct 21, 2019
Last update date Aug 12, 2020
Contact name Manfred Boehm
Organization name NHLBI
Street address 9000 Rockbille Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL21290
Series (2)
GSE139188 Gene expression analysis in endothelial cells derived from patients with Autosomal-dominant hyper-IgE syndrome (AD-HIES)
GSE139365 Gene expression analysis in primary cells derived from patients with Autosomal-dominant hyper-IgE syndrome (AD-HIES)
Relations
BioSample SAMN13071237

Supplementary data files not provided
Raw data not provided for this record
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap