|
| Status |
Public on Aug 11, 2022 |
| Title |
Day 15 RNA-seq KO 2 |
| 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: Dpy30-KO
|
| 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_D15.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) |
[email protected]
|
| 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 |
SAMN20721361 |
| SRA |
SRX11725649 |
