|
| Status |
Public on May 01, 2023 |
| Title |
IC β Hltf KO Index 18 OtC0456 |
| Sample type |
SRA |
| |
|
| Source name |
pancreas
|
| Organism |
Mus musculus |
| Characteristics |
tissue: pancreas
strain: C57Bl/6J
genotype: beta cell specific Hltf-/-
developmental stage: newborn
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pancreata were perfused in situ with RNAlater using a 1 CC syringe and a 26g ½ needle, and snap frozen prior to rRNA-depletion.
cDNA was generated from rRNA-depleted samples [3 biological replicates for control and 3 biological replicates for rIPCre fl/fl (beta cell-specific Hltf-deleted)] 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 genomic assembly mm10 and analyzed using the platform provided by DNAnexus, Inc.
Comparison of expression level (fpkm_tracking) and differential isoform expression (fpkm_tracking)
Exon quantification was performed to show the relative expression of all known Hltf isoforms
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of RPKM values for each gene; RPKM values for alternative splicing
|
| |
|
| Submission date |
Sep 08, 2019 |
| Last update date |
May 01, 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 |
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 |
SAMN12713454 |
| SRA |
SRX6816391 |
