|
| Status |
Public on Feb 27, 2018 |
| Title |
Vector1 |
| Sample type |
SRA |
| |
|
| Source name |
vector control
|
| Organism |
Mus musculus |
| Characteristics |
strain background: CD-1
genotype/variation: Empty vector transfected
|
| Treatment protocol |
GFP negative fraction containing Schwann cells and mesenchymal cells was cultured and transfected with Ascl1 and NeuroD1 vectors for inducing neurons, or Empty vectors as control.
|
| Growth protocol |
Tau-GFP P1 spiral ganglia were dissected and sorted. GFP positive fraction was collected as endogenous primary auditory neurons.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Single Cell RNA Purification Kit (NORGEN, #51800). RNA library preparation was performed using a two-pronged approach: (1) Two ng of input RNA was converted to double stranded cDNA using Clontech SMARTer Ultra Low Input RNA Kit v3: (2) one ng of double stranded cDNA was used as input material for the illumina’s Nextera XT library preparation kit
RNA libraries were prepared for sequencing following Clonthech and Illumina's recommended protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
VC1
Vector1_S69
|
| Data processing |
bcl2fastq v2.17 was used for both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
FASTQ files were mapped to mm10 genome by HISAT2 protocol (Kim et al., 2015) (Pertea et al., 2016)
Expression data were normalized by the transcripts per million reads (TPM) method (Wagner et al., 2012)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Nov 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yutaka Amemiya |
| E-mail(s) |
yamemiya@sri.utoronto.ca
|
| Organization name |
Sunnybrook Research Institute
|
| Lab |
Genomics Core Facility
|
| Street address |
2075 Bayview Ave.
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M4N3M5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE107461 |
Direct reprogramming of spiral ganglion non-neuronal cells into neurons: Towards ameliorating sensorineural hearing loss by gene therapy |
|
| Relations |
| BioSample |
SAMN08107444 |
| SRA |
SRX3427434 |
