|
| Status |
Public on Jan 16, 2023 |
| Title |
P4 Shox2-Cre/+; R26 tdTomato/+ mouse SAN scRNA-seq library |
| Sample type |
SRA |
| |
|
| Source name |
scRNA-seq library
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
tissue: heart/SAN
Stage: P4
|
| Treatment protocol |
Microdissected SAN was minced, digested, and single cell suspension was prepared using the Pierce Cardiomyocyte Isolation Kit as stated in Methods section
|
| Growth protocol |
Hearts from neonatal P4 mice were dissected out, Cre+ hearts were selected based on tdTomato fluorescence expression, and SAN region was strictly microdissected guided by fluorescence reporter expression
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cell suspension was washed with 1X PBS (0.04% BSA) before 10x Genomics procedure. The concentration of single cell suspension was adjusted to about 500 to 1000 cells/µL and was loaded on the 10x Genomics’ Chromium™ system (10x Genomics, Pleasanton, CA) with the aim of 6000 to 10000 cells per channel (Chromium™ Single Cell 3' Library & Gel Bead Kit v2, catalog number 120237).
scRNA-Seq libraries were constructed following the manufacturer’s instructions (Zheng et al., 2017).
Library was sequenced using Illumina NextSeq 500/550 sequencing systems (Illumina, San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Binary base call (BCL) files generated were demultiplexed and converted to standard FASTQ files using the mkfastq function from Cell Ranger pipeline (version 3.1.0).
The demultiplexed reads were merged and processed using the Salmon Alevin with default parametersexcept for --forceCells=10000 to generate the expression matrix. The reference and gene annotation were downloaded from GENCODE website (GRCm38.p6/mm10).
Technical artifacts (ambient RNA and random barcode swapping) were eliminated using CellBender with default parameters except for --expected-cells=6000, --total-droplets-included 10000 and --epocs=200.
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI count matrices representing gene expression values (comma-separated) were generated as described above. Each column represents a single cell, each row represents a single gene.
|
| |
|
| Submission date |
Jun 30, 2020 |
| Last update date |
Jan 16, 2023 |
| Contact name |
Nikhil V Munshi |
| E-mail(s) |
Nikhil.Munshi@UTSouthwestern.edu
|
| Phone |
2146484001
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Internal Medicine-Cardiology
|
| Lab |
NB10224
|
| Street address |
6000 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE153536 |
The cis-Regulatory Landscape of Cardiac Rhythm |
|
| Relations |
| BioSample |
SAMN15403414 |
| SRA |
SRX8639228 |
