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| Status |
Public on Aug 22, 2023 |
| Title |
Min6 cells, Snd1 KO3 |
| Sample type |
SRA |
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| Source name |
Min6
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| Organism |
Mus musculus |
| Characteristics |
cell line: Min6
cell type: Mouse insulinoma cell line
genotype: Snd1 KO
treatment: CRISPR/Cas9 targeting exon 2
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction from Snd1 KO MIN6 cells was carried out following the manufacturer's instructions (Zymo Research, D7001)
One hundred nanograms of RNA from Control and Snd1 KO cell lines with RNA integrity numbers ≥ 7.0 was used for library following cDNA preparation (Takara) with the Nextera XT DNA Library Prep Kit (Illumina, Inc.). Each library was quantified, and quality accessed by Qubit and Agilent Bioanalyzer with average size of the library insert ~300-400 basepairs.
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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 mm10UCSC 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: the .tab files are the Transcripts Per Million (TPM) reads for each designated gene in the mRNA-seq dataset
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| Submission date |
Aug 16, 2023 |
| Last update date |
Aug 22, 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 (1) |
| GSE240993 |
Dynamic regulation of pancreatic β cell function and gene expression by the SND1 coregulator in vitro |
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| Relations |
| BioSample |
SAMN37007564 |
| SRA |
SRX21383140 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7713459_Snd1_KO3_L008_R1_001_preprocessed_tpm.tab.gz |
379.1 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
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