|
Status |
Public on Oct 10, 2022 |
Title |
P9-A06 |
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: 3675
|
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 |
SAMN13156764 |
SRA |
SRX7071669 |