NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7663604 Query DataSets for GSM7663604
Status Public on Feb 26, 2024
Title E10.5 otocyst wild type replicate 1
Sample type SRA
 
Source name E10.5 otocyst
Organism Mus musculus
Characteristics tissue: E10.5 otocyst
genotype: WT
Treatment protocol N/A
Growth protocol Timed pregnancies were established to generate litters of embryos, with the morning of seminal plug detection marking E0.5. The day of birth was defined as Postnatal day 0 (P0).
Extracted molecule total RNA
Extraction protocol Otocysts were collected from E10.5 embryos in ice-cold PBS and RNALater (Ambion AM7021). RNA was isolated from pairs of otocysts from three embryos of each genotype (WT, Chd7Gt/+, Sox2CreER/+ and Chd7Gt/+;Sox2CreER/+) using the RNAqueous Micro Scale RNA Isolation kit according to the manufacturer’s instructions (Ambion AM1931, Austin, TX).
Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions (NEB E7760, Ipswich, MA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Libraries were subjected to 151-bp paired-end sequencing on an Illumina NovaSeq machine following the manufacturer’s protocol (Illumina, San Diego, CA).
Bcl2fastq2 Conversion software was used to create de-multiplexed FastQ files (Illumina).
Sequencing reads were trimmed with Cutadapt v2.3 (2) and read quality was assessed using FastQC v0.11.8 (3).
Reads were aligned to the mouse reference genome GRCm38 (ENSEMBL) with STAR v2.7.8a (4) and RSEM v1.3.3 was used to assign count estimates to aligned genes (5).
Quality control metrics from this pipeline were integrated and evaluated using multiQC v1.7 (6)
Assembly: mm9
Supplementary files format and content: tab-delimited text file contains raw counts for each sample
 
Submission date Jul 26, 2023
Last update date Feb 26, 2024
Contact name Donna Martin
E-mail(s) donnamm@umich.edu
Organization name University of Michigan
Street address 1150 Medical Center Dr
City Ann Arbor
ZIP/Postal code 48109
Country USA
 
Platform ID GPL24247
Series (2)
GSE239361 CHD7 and SOX2 Act in a Common Gene Regulatory Network During Mammalian Semicircular Canal and Cochlear Development (RNA-Seq)
GSE239363 CHD7 and SOX2 Act in a Common Gene Regulatory Network During Mammalian Semicircular Canal and Cochlear Development
Relations
BioSample SAMN36718194
SRA SRX21166571

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