NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5792388 Query DataSets for GSM5792388
Status Public on Apr 20, 2023
Title Six1-KO rep1
Sample type SRA
 
Source name otic vesicle E10.5
Organism Mus musculus
Characteristics strain: C57BL/6
developmental stage: E10.5 mouse embryo
tissue: otic vesicle
genotype: Six1-KO
Extracted molecule total RNA
Extraction protocol E10.5 mouse embryos were obtained and the otic vesicles were removed with dissection tweezers. Total RNA from pools of vesicles (3 pools with 6 vesicles each for each genotype) was obtained using the Rneasy Micro Kit (Qiagen). Residual DNA was removed using the Turbo DNA Free Kit (Thermofisher). 10-30 ng of total RNA were used per sample for library preparation.
Libraries were constructed using the QuantSeq 3' mRNA-Seq Library Prep Kit (Illumina), following the manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description otic vesicles from E10.5 Six1-/- mouse embryo
Data processing Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina HiSeq Control Software.
Conversion of BCL files to FASTQ format was performed with the bcl2fastq Software (Illumina).
Reads were aligned, counted, and mapped using BlueBee’s STAR-aligner, HTSeq-count, and RSEQC.
Differential gene expression analysis was performed with DESeq2 within Bluebee (Lexogen QuantSeq DE)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file includes normalised counts for each sample.
 
Submission date Jan 09, 2022
Last update date Apr 20, 2023
Contact name Ignacio Palmero
E-mail(s) ipalmero@iib.uam.es
Organization name CSIC
Street address Arturo Duperier, 4.
City Madrid
State/province Madrid
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL17021
Series (1)
GSE193334 Gene expression profiling of Six1-null developing inner ear.
Relations
BioSample SAMN24777267
SRA SRX13688170

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap