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Status |
Public on May 31, 2023 |
Title |
Chd4KO_4_Chd-666 |
Sample type |
SRA |
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Source name |
Pancreatic beta cells
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Organism |
Mus musculus |
Characteristics |
tissue: Pancreatic beta cells cell type: beta cell genotype: Chd4KO
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Nov 07, 2022 |
Last update date |
May 31, 2023 |
Contact name |
Jason Spaeth |
E-mail(s) |
jspaeth@iu.edu
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Phone |
3172748986
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Organization name |
Indiana University
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Department |
Pediatrics
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Lab |
MS2021
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Street address |
635 Barnhill Dr.
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City |
Indianapolis |
State/province |
IN |
ZIP/Postal code |
46202 |
Country |
USA |
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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. |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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