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Sample GSM5514736 Query DataSets for GSM5514736
Status Public on Aug 11, 2022
Title Day 45 RNA-seq WT 3
Sample type SRA
 
Source name Mouse beta cells with S2 cell spike-in
Organisms Drosophila melanogaster; Mus musculus
Characteristics strain: PdxCreER mTmG
cell type: Mouse beta cells with S2 cell spike-in
genotype/variation: CTRL
Extracted molecule polyA RNA
Extraction protocol RNA-seq: FACS-enriched beta cells were pooled with a 10% spike-in of S2 cells. RNA was isolated using Trizol.
RNA libraries were prepared from 400ng of total RNA per sample using poly-A capture beads and NEBNext directional RNA-seq library prep kit for Illumina (E7760). scRNA-seq libraries were prepared using Chromium Single Cell 3’ protocol with Reagent Kit v3.1 (10X Genomics)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description processed data file: LFC_D45.csv, geneCounts.csv
Data processing Illumina NextSeq Control Software v2.2.0.4 for base calling
RNA-seq: Reads aligned to GRCm38/mm10; Gencode vM24 using STAR v2.7.3a with default settings
RNA-seq: Transcript abundance measured using Salmon v1.4.0 in alignment mode with seqBias and gcBias settings
RNA-seq: Differential gene expression determined using DESeq2
scRNA-seq: Cellranger v5.0.0 used to demultiplex and convert to fastq
scRNA-seq: barcode detection, read mapping, quality filtering and transcript counting performed with Alevin (Salmon v1.4.0). Processing steps are documented in "scRNAseq_commands.txt"
Genome_build: GRCm38/mm10; Gencode vM24
Supplementary_files_format_and_content: csv file showing KO vs WT differential gene expression metrics for RNA-seq. Output of DESeq2.
Supplementary_files_format_and_content: csv file showing gene counts for each gene in each sample for RNA-seq. Output of DESeq2.
Supplementary_files_format_and_content: matrix file for gene counts per cell for scRNA-seq. Output of Salmon Alevin.
 
Submission date Aug 12, 2021
Last update date Aug 11, 2022
Contact name Brad Hoffman
E-mail(s) brad.hoffman@ubc.ca
Organization name University of British Columbia
Street address Room A4-151 950 W28 Ave
City Vancouver
State/province BC
ZIP/Postal code V5Z 2B3
Country Canada
 
Platform ID GPL25537
Series (2)
GSE181950 H3K4 Methylation in β-cells prevents transcriptional downregulation and variance associated with type 2 diabetes [RNA-seq]
GSE181951 H3K4 Methylation in β-cells prevents transcriptional downregulation and variance associated with type 2 diabetes.
Relations
BioSample SAMN20721365
SRA SRX11725653

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

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