|
| Status |
Public on Feb 28, 2020 |
| Title |
AP6 [Lmb2] |
| Sample type |
SRA |
| |
|
| Source name |
Freshly isolated heart cell
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: Postnatal days 19
cell type: single cardiomyocytes
group: mAG-hGem positive
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ventricular cardiac cells were dissociated by enzymatic digestion from Azami green geminin (mAG-Geminin) transgenic mice and sorted by FACS. Following cell lysis, mRNA was reverse transcribed into 1st strand cDNA. Single cell cDNA was subjected to quality control using PCR for the cardiomyocytespecific marker, troponin T2 (Tnnt2). Potential contamination from non-cardiomyocytes (i.e. cardiac fibroblasts and endothelial cells) was detected by PCR for platelet derived growth factor receptor ß (Pdgfrb).Single cells showing Tnnt2 positive and Pdgfrb negative were considered as confirmed cardiomyocytes.
library preparation using the Illumina TruSeq RNA sample preparation kit according to the manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalling- CASAVA 1.8.2
trimReads.py (https://github.com/safisher/ngs/blob/master/trimReads.py) - adaptor trimming, low quality base masking, polyA/T trimming
alignment to reference genome - STAR 2.4.0j (--outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 30 --outFilterMismatchNmax 100 --outFilterMismatchNoverLmax 0.3 --outFilterMatchNminOverLread 0.4)
Quantification- Uniquely mapped reads quantifed with HTSeq v0.6.1p1 (--mode=intersection-strict --stranded=no --type=exon --idattr=gene_id)
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq gene counts
|
| |
|
| Submission date |
Dec 20, 2017 |
| Last update date |
Feb 28, 2020 |
| Contact name |
Junhyong Kim |
| Organization name |
University of Pennsylvania
|
| Department |
Biology
|
| Lab |
Junhyong Kim
|
| Street address |
433 S University Avenue
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE108360 |
Lamin B2 controls nuclear envelope permeability and regulates cardiomyocyte regeneration |
|
| Relations |
| BioSample |
SAMN08214496 |
| SRA |
SRX3490205 |
