|
| Status |
Public on May 01, 2023 |
| Title |
ID β Hltf KO Index601_OtC7517 |
| Sample type |
SRA |
| |
|
| Source name |
Newborn pancreas
|
| Organism |
Mus musculus |
| Characteristics |
tissue: pancreas
strain: C57Bl/6J
genotype: immunodeficient (ID) beta cell specific Hltf-/- mouse
developmental stage: newborn
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Because pancreata are ribonuclease-rich, trunks of decapitated newborn mice were perfused in situ with RNAlater by insertion of a 20g-1-inch needle attached to a 5 ml syringe into the abdomen via the crural (posterior) attachment of the diaphragm . RNA stabilization occurred concomitant with the initial stretching of the pancreas. Pancreata were stored in RNA later at -70C until total RNA was isolated. RNA integrity and purity were assessed (Agilent Bioanalyzer) for 10 samples, i.e. 3 from β Hltf KO IC mice with low (<15 mg/dL) blood sugar, 3 from Hltf +/+ controls, and 4 from β Hltf KO ID mice.
cDNA was generated from Ribo-Zero Plus rRNA-depleted samples and subjected to Illumina library preparation.
Libraries were sequenced utilizing Illumina sequencing technology.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
rRNA depleted
|
| Data processing |
Paired-end 100 nucleotide reads were aligned to reference mouse genome C57BL/6J (GRCm38/mm10) and analyzed using the platform provided by DNAnexus, Inc. (Mountain View, CA) to generate three-way transcriptomic (RNAseq) analyses of whole pancreata from β Hltf KO IC and ID newborn mice, and wild type (Hltf +/+) controls.
Comparison of expression level (fpkm_tracking) and differential isoform expression (fpkm_tracking).
The analysis included alternative splicing analysis in control (Hltf +/+) pancreata.
Exon quantification was performed to show the relative expression of all known Hltf isoforms.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text files of RPKM values for each gene; RPKM values for alternative splicing.
|
| |
|
| Submission date |
Dec 09, 2022 |
| Last update date |
May 02, 2023 |
| Contact name |
Beverly S Chilton |
| E-mail(s) |
[email protected]
|
| 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 |
GPL17021 |
| 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 |
SAMN32134232 |
| SRA |
SRX18631079 |
