|
| Status |
Public on Oct 29, 2019 |
| Title |
Left-atrium-PCM-1-adult-sample2 |
| Sample type |
SRA |
| |
|
| Source name |
atrial PCM-1 sorted nuclei
|
| 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-PCM-1-adult-2
|
| 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 |
SAMN11055557 |
| SRA |
SRX5465785 |
