 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 30, 2024 |
| Title |
WT Control - A3907 |
| Sample type |
SRA |
| |
|
| Source name |
Bone
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone
Sex: Female
age: 11-weeks
strain: C57BL6/N
genotype: WT
disease state: Control
duration of_disease: 0-weeks
|
| Treatment protocol |
To induce type 1 diabetes (T1D), WT and Sarm1-KO mice were fasted overnight prior to i.p. injection with 100 mg/kg streptozotocin (STZ, Sigma S0130) made fresh in saline and used within 5-minutes of reconstitution. Food was returned to the cage one hour after STZ injection. Control mice received saline only. Fasting, injection, and re-feeding was repeated on Day 2. Blood glucose was measured on Day 3 with a standard glucometer by using a lancet to obtain a drop of blood from the vein at the tip of the tail (Bayer Contour). STZ was administered again on Day 4 following the same procedure if fed blood glucose levels did not reach 300 mg/dL.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For extraction of bone RNA samples, tibia and femur from one hind limb were cleaned with gauze to remove soft tissue, epiphyses were removed to expose the marrow cavity, and bones were placed into a 0.5 mL tube with an 18-gauge needle hole in the bottom nested in a 1.5 mL tube. Marrow was separated by centrifugation at 1000*g for 1 min. The marrow-depleted bone was placed into a RINO 1.5 mL Screw Cap tube (MidSci) with stainless steel beads and 1 mL TRIzol. Bones were snipped with dissection scissors into fragments before bullet homogenization for 5 min. Samples in TRIzol were further incubated at RT for 5 min for complete digestion before extraction with chloroform and PureLink RNA Mini Kit (Invitrogen 12183025) according to manufacturer instructions. RNA was eluted in 30 µL RNase free water and stored at -80 ˚C until use.
Approximately 1 µg of RNA was submitted for RNAseq by BGI Tech Global where polyA mRNA was enriched by oligo dT, fragmented, and reverse transcribed using random N6-primed RT followed by second-strand cDNA synthesis with dUTP. The synthesized cDNA underwent end-repair and 3’ adenylation, prior to adaptor ligation to the ends of the fragments. The dUTP-marked strand was selectively degraded by Uracil-DNA-Glycolase and the remaining strand was PCR-amplified to generate a cDNA library suitable for sequencing on a DNBSEQ platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
The DNBSEQ platform was used to perform paired-end 100 bp sequence reads, generating an average of 4.56G Gb per sample.
Sequencing data was filtered using SOAPnuke, a filtering algorithm that removes reads containing the adaptor, reads with N content >5%, and reads with base quality score <15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads.
After filtering, HISAT and Bowtie2 were used to align clean reads to the Mus musculus reference genome version GCF_000001635.26_GRCm38.p6 with an average mapping ratio of 97.7% and 80.2%, respectively --> read counts.
Read counts were normalized per sample to generate TPM values
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes normalized TPM counts for each Sample
|
| |
|
| Submission date |
Dec 30, 2023 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Erica L Scheller |
| Organization name |
Washington University
|
| Street address |
660 S Euclid Ave
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL28457 |
| Series (1) |
| GSE252292 |
Sarm1 knockout prevents type 1 diabetic bone disease in females independent of neuropathy |
|
| Supplementary data files not provided |
| Raw data are available in SRA |
|
|
|
|
 |
