|
| Status |
Public on Mar 12, 2019 |
| Title |
OHC_159 |
| Sample type |
SRA |
| |
|
| Source name |
Cochlea
|
| Organism |
Mus musculus |
| Characteristics |
age: p15
background: C3HeB/FeJ
cell type: OHC
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Individual cells were dissociated from mouse cochlear tissue using a collagenase digestion and gentle tituration. Cells were then isolated using pulled glass micropipettes, washed to remove extracellular contaminants and re-isolated.
Single cell reverse transciption and PCR amplification was performed using Smartseq2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Single-Cell SmartSeq2 Illumina
|
| Data processing |
For Illumina data processing begin with R1.gz and R2.gz paired end read files for each sample. Process each sample individually.
Perform Kallisto pseudoalignment to the mm10 transcriptome to generate gene expression .tsv file for each sample.
Perform Star alignment to the mm10 genome to generate .sam output for each cell.
Use samtools view to convert the .sam file to .bam format
Use samtools sort tool to sort the .bam file
Corresponding publication includes extensive discussion of mRNA transcript structure and splicing. Transcript structure features are visualized using .bam files. The .bam files can be regenerated using the provided raw data files (fastq).
Genome_build: mm10
Supplementary_files_format_and_content: Output files are in .tsv format.
|
| |
|
| Submission date |
May 08, 2018 |
| Last update date |
Mar 12, 2019 |
| Contact name |
Paul T Ranum |
| E-mail(s) |
ranump@chop.edu
|
| Phone |
1 (651) 398-6455
|
| Organization name |
The Children's Hospital of Philadelphia
|
| Department |
Center for Cellular and Molecular Therapy
|
| Lab |
Davidson Lab
|
| Street address |
3501 Civic Center Blvd.
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE114157 |
Insights into the Biology of Hearing and Deafness Revealed by Single-Cell RNA Sequencing |
|
| Relations |
| BioSample |
SAMN09089938 |
| SRA |
SRX4090764 |
