|
| Status |
Public on Jun 03, 2023 |
| Title |
A_ID β Hltf-KO |
| Sample type |
SRA |
| |
|
| Source name |
pancreas
|
| Organism |
Mus musculus |
| Characteristics |
tissue: pancreas
cell type: whole tissue
genotype: C57Bl/6J
genotype: Beta Hltf-KO
|
| Treatment protocol |
Abdominal tissue sections (5 µm) from IC and ID β Hltf KO newborn mice were processed with the RNeasy FFPE kit for DV200 analysis. Replicate sections from IC and ID β Hltf KO newborn mice were placed within fiducial frames of capture areas A,B and C,D respectively, on Visium GEX slide V11D13-089-A1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Visium for FFPE uses RNA-templated ligation (RTL) probes targeting the whole transcriptome.
Spatially barcoded, ligated products were released from the slide, and harvested for qPCR with KAPA SYBR Fast qPCR master mix. Sample index sets were selected to distinguish each of the 4 samples in a multiplexed sequencing run. Samples were amplified using Ilumina-compatible indexing primers,
Visium Mouse Transcriptome Probe Set v1.0
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
short-read sequencing (Illumina NovaSeq) of barcoded libraries by Genewiz single index
data analysis of tissue images and sequencing files in FASTQ format with Space Ranger
space ranger aggr pipeline aggregated data from replicate samples and from replicate regions
read 2 sequences were mapped against the reference mouse genome C57BL/6J (GRCm38/mm10) and read 1 sequences were used for UMI filtering to obtain spatial information
Spaceranger count combined a brightfield microscope slide image and FASTQ files from spaceranger mkfastq and performed alignment, tissue detection, fiducial detection, barcode/UMI counting, and prepared a full resolution slide image for visualization in Loupe Browser.
Assembly: The pipeline used the Visium spatial barcodes to generate feature-spot matrices, determine clusters, and perform gene expression analyses. The pipeline used a probe aligner algorithm for FFPE tissues.
Supplementary files format and content: Scalefactors, JSON
Supplementary files format and content: Images, PNG
|
| |
|
| Submission date |
Jun 02, 2023 |
| Last update date |
Jun 04, 2023 |
| Contact name |
Beverly S Chilton |
| E-mail(s) |
beverly.chilton@ttuhsc.edu
|
| Phone |
806-743-2709
|
| Organization name |
Texas Tech University HSC
|
| Department |
Cell Biology & Biochemistry
|
| Lab |
5B136 & 137
|
| Street address |
3601 4th St-MS6540
|
| City |
Lubbock |
| State/province |
TX |
| ZIP/Postal code |
79430 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE137060 |
Helicase-like transcription factor (Hltf)-deletion activates Hmgb1-Rage axis and granzyme A-mediated killing of pancreatic β cells resulting in neonatal lethality |
|
| Relations |
| BioSample |
SAMN35570730 |
| SRA |
SRX20578940 |
