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Sample GSM4144099 Query DataSets for GSM4144099
Status Public on Oct 10, 2022
Title P9-F09
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: 3712
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 SAMN13156870
SRA SRX7071730

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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