|
| Status |
Public on Oct 10, 2022 |
| Title |
P9-E08 |
| Sample type |
SRA |
| |
|
| Source name |
inner ear
|
| Organism |
Mus musculus |
| Characteristics |
organ: inner ear
tissue: Endolymphatic sac
age: E14.5
genotype: Sox9Y440X/+ endolymphatic sacs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction from dissociated cells was done according to Smartseq2 protocol (Picelli et al., 2014)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
number of genes expressed: 3432
|
| Data processing |
The fastq read-pairs were aligned to mouse reference genome (mm10) using the HISAT2 aligner
The resulting SAM files were sorted and re-formatted as BAM files using SAMTOOLS (0.1.18)
The BAM files were quantified to mouse gene model by GENCODE (v19) using Cufflinks and HTSeq-count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample for all genes
|
| |
|
| Submission date |
Oct 30, 2019 |
| Last update date |
Oct 10, 2022 |
| Contact name |
Peikai Chen |
| E-mail(s) |
pkchen1@hku.hk
|
| Phone |
852-258315217
|
| Organization name |
The University of Hong Kong
|
| Department |
Faculty of Medicine
|
| Street address |
Sassoon Road 5
|
| City |
Pok Fu Lam |
| ZIP/Postal code |
10000 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE139587 |
SOX9 and SOX10 control fluid homeostasis in the inner ear for hearing through independent and cooperative mechanisms (scRNA-seq: batch2) |
|
| Relations |
| BioSample |
SAMN13156834 |
| SRA |
SRX7071718 |
