NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6718852 Query DataSets for GSM6718852
Status Public on May 31, 2023
Title Chd4KO_4_Chd-666
Sample type SRA
 
Source name Pancreatic beta cells
Organism Mus musculus
Characteristics tissue: Pancreatic beta cells
cell type: beta cell
genotype: Chd4KO
Extracted molecule total RNA
Extraction protocol RNA was isolated from FACS-purified β cells using the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher). The DNAse treated RNA was analyzed on an Agilent 2100 Bioanalyzer. Only samples with an RNA Integrity Number above 8.0 were used for cDNA synthesis and library preparation.
cDNA was first synthesized using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech Laboratories, Inc.). A dual indexed cDNA library was then prepared using Nextera XT DNA Library Prep Kit (Illumina, Inc.). Each library was quantified, and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled in equal molarity. The average size of the library insert was approximately 300-400 bp
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The generated FASTQ files were processed and interpreted using the Genialis visual informatics platform (https://www.genialis.com). Sequence quality checks were performed on raw and trimmed reads with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), and Trimmomatic was used to trim adapters and filter out poor quality reads. Trimmed reads were then mapped to the mm10 UCSC reference genome using the HISAT2 aligner. Gene expression levels were quantified with HTSeq-count, and differential gene expression analyses performed with DESeq2. Poorly expressed genes, which have expression count summed over all samples below 10, were filtered out from the differential expression analysis input matrix.
Assembly: mm10
Supplementary files format and content: preprocessed_tpm
 
Submission date Nov 07, 2022
Last update date May 31, 2023
Contact name Jason Spaeth
E-mail(s) jspaeth@iu.edu
Phone 3172748986
Organization name Indiana University
Department Pediatrics
Lab MS2021
Street address 635 Barnhill Dr.
City Indianapolis
State/province IN
ZIP/Postal code 46202
Country USA
 
Platform ID GPL24247
Series (2)
GSE217445 The Chd4 helicase regulates chromatin accessibility and gene expression critical for β-cell function in vivo [RNA-seq]
GSE217446 The Chd4 helicase regulates chromatin accessibility and gene expression critical for β-cell function in vivo.
Relations
BioSample SAMN31643067
SRA SRX18193397

Supplementary file Size Download File type/resource
GSM6718852_Chd4KO_4_Chd-666_S23_L001_R1_001_preprocessed_tpm.tab.gz 406.1 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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