|
| Status |
Public on Jun 01, 2019 |
| Title |
βDKO_sorted_1 |
| Sample type |
SRA |
| |
|
| Source name |
Flow-Sorted islet β cells
|
| Organism |
Mus musculus |
| Characteristics |
age: 7 Weeks
strain: Mixed (C57BL/6J; 129SV)
cell type: Flow-Sorted islet beta cells
genotype: BetaDKO
|
| Growth protocol |
Isolated islets from Tamoxifen treated Control (MIP-CreERT;Brg1f/+;Brm+/-;R26LSL-tdTomato/+; ) or βDKO (MIP-CreERT; Brg1f/f; Brm-/-; R26LSLtdTomato/+) animals were dispersed into a single cell suspension (Accumax, Sigma A7089), stained with DAPI, and sorted by fluorescence activated cell sorting.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from FACS-purified β cells using the Maxwell 16 LEV simplyRNA Tissue Kit (Promega-TM351), then DNAse treated and analyzed on an Agilent 2100 Bioanalyzer. Only samples with an RNA Integrity Number above 8.0 were used for cDNA synthesis and library preparation
|
| |
|
| 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
Genome_build: mm10
Supplementary_files_format_and_content: Processed Data File is presented as Transcripts per Million (TPM) and contains triplicates for Control and bDKO RNA-Sequencing datasets
|
| |
|
| Submission date |
Mar 27, 2019 |
| Last update date |
Jun 03, 2019 |
| 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 (1) |
| GSE128945 |
The Pdx1 bound Swi/Snf chromatin remodeling complex regulates pancreatic progenitor cell proliferation and mature islet β cell function |
|
| Relations |
| BioSample |
SAMN11267032 |
| SRA |
SRX5582911 |
