|
Status |
Public on Oct 29, 2019 |
Title |
Left-atrium-adult-sample1 |
Sample type |
SRA |
|
|
Source name |
atrial free wall whole tissue
|
Organism |
Homo sapiens |
Characteristics |
age: Adult
|
Treatment protocol |
NA
|
Growth protocol |
Human adult and fetal atrial free wall tissue was obtained in strict accordance with the tissue regulation of the George Washington University and LUMC
|
Extracted molecule |
total RNA |
Extraction protocol |
Whole tissue: Total RNA was isolated from the atrial tissue using Trizol according to the manufacturer’s protocol (Sigma Aldrich), DNaseI treated and further purified using Nucleospin RNeasy MinElute Kit (Qiagen). PCM-1 samples: nuclei were extracted from snapfrozen samples, and stained with PCM-1 rabbit polyclonal antibody (Sigma) for FACS of specifically cardiomyocyte nuclei. Adult tissue: NuGEN's Ovation RNA-seq V2 kit. Fetal: Truseq Stranded Total RNA Library Preparation Kit (Illumina, Part# 15031048 Rev. E)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
LA-adult-1
|
Data processing |
Reads were mapped to hg19 build of the human transcriptome using STAR (Dobin et al. 2013). Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014). Genome_build: hg19 Supplementary_files_format_and_content: Atria-RNA-seq-counts.xlsx (Excel file with normalized (DESeq2) count data per gene & differential expression analysis).
|
|
|
Submission date |
Mar 05, 2019 |
Last update date |
Oct 29, 2019 |
Contact name |
Vincent M. Christoffels |
E-mail(s) |
v.m.christoffels@amsterdamumc.nl
|
Phone |
0205667821
|
Organization name |
Amsterdam UMC
|
Department |
Medical Biology
|
Lab |
Vincent Christoffels
|
Street address |
Meibergdreef 15 K2-159
|
City |
Amsterdam |
State/province |
N/A (NA) |
ZIP/Postal code |
1105 AZ |
Country |
Netherlands |
|
|
Platform ID |
GPL20301 |
Series (1) |
GSE127856 |
Identification of Atrial Fibrillation associated genes and functional non-coding variants |
|
Relations |
BioSample |
SAMN11055556 |
SRA |
SRX5465774 |