|
| Status |
Public on May 28, 2021 |
| Title |
RAGP neuronal cell [PR1643_744.G.2] |
| Sample type |
SRA |
| |
|
| Source name |
RAGP of pig heart
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Yucatan minipig
gender: Female
tissue: Right atrial ganglionic plexus (RAGP)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single neuronal clusters were collected using Laser Capture Microdissection (LCM) from Right Atrial Ganglionic Plexus (RAGP) of the pig heart.
RNA libraries were prepared using Smart-3Seq protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
PR1643_744.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt
|
| Data processing |
Single cell scale RNA-seq libraries from SMART-3Seq protocol were sequenced using an Illumina.
Raw sequencing data (Illumina sequencer’s base call files (BCLs)) was converted to fastq files using the Illumina bcl2fastq program.
The reads from Fastq files were trimmed to remove poly A tail and G overhang and the 5 base umi was extracted.
The trimmed reads were aligned, using STAR-2.7.2a (Dobin et al. 2013) to the Sus scrofa reference genome sequence version Sus_scrofa.Sscrofa11.1.fasta, available in the Ensembl database. Sus_scrofa.Sscrofa11.1.95.gtf was used as a reference transcriptome. Aligned files from reads from 4 lanes are merged by MergeSamfiles from picard.
Feature count algorithm, Subread R (featureCounts) package (Liao et al. 2013) was used to count genomic features genes and exons. A digital gene expression matrix was created from this data.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: PR1643-142-samples-raw-gene-counts.txt: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: PR1643-normalized-gene-counts.txt: Matrix table with normalized counts.
|
| |
|
| Submission date |
Jul 09, 2020 |
| Last update date |
May 28, 2021 |
| Contact name |
Rajanikanth Vadigepalli |
| E-mail(s) |
Rajanikanth.Vadigepalli@jefferson.edu
|
| Phone |
2159550576
|
| Organization name |
Jefferson University
|
| Department |
Pathology
|
| Lab |
Daniel Baugh Institute
|
| Street address |
1020 Locust St, 314C
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19107 |
| Country |
USA |
| |
|
| Platform ID |
GPL20983 |
| Series (2) |
| GSE154119 |
A Single Neuron Scale Molecular Phenotype Map of the Right Atrial Ganglionic Plexus in the Pig Heart |
| GSE154411 |
A spatially-tracked single cell transcriptomics map of neuronal networks in the intrinsic cardiac nervous system |
|
| Relations |
| BioSample |
SAMN15495213 |
| SRA |
SRX8700624 |
