|
| Status |
Public on Jun 30, 2023 |
| Title |
9M WT, NP 6 |
| Sample type |
RNA |
| |
|
| Source name |
Nucleus pulposus from 9-month-old wildtype mice
|
| Organism |
Mus musculus |
| Characteristics |
tissue: nucleus pulposus
genotype: Glut1f/f (WT)
age: 9-month-old
|
| Treatment protocol |
GLUT1f/f and K19Cre; GLUT1f/f Mice were injected 3 days in a row with 100ug/gbw Tamoxifen at 3-months-old
|
| Growth protocol |
GLUT1f/f and K19Cre; GLUT1f/f Mice were aged to 9-months-old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NP tissues were scooped into RNAlater and processed using Qiagen RNeasy Mini Kit
|
| Label |
biotin
|
| Label protocol |
Fragmented biotin labeled cDNA (from 100 ng of RNA) was synthesized using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).
|
| |
|
| Hybridization protocol |
Gene chips, Mouse Clariom S were hybridized with 2.5 μg fragmented and biotin-labeled cDNA in 100 μl of hybridization cocktail. Arrays were washed and stained with GeneChip hybridization wash & stain kit using Gene chip Fluidic Station 450.
|
| Scan protocol |
Chips were scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software. Quality Control of the experiment was performed by Expression Console Software v 1.4.1.
|
| Data processing |
Chp files were generated by sst-rma normalization from Affymetrix .cel file using Expression Console Software. Experimental group was compared with control group by using Transcriptome array console 4.0 and DEGs with a Fold Change ±2, p-value or FDR<0.05. PANTHER tool was used to compute enriched pathways in DEGs that are altered with a Fold Change ±2, p-value <0.05.
Tukey's Bi-weight average of exon intensity of all the samples in a condition; log2(Expression).
|
| |
|
| Submission date |
Jul 18, 2022 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Shira N Johnston |
| E-mail(s) |
snj007@students.jefferson.edu
|
| Organization name |
Thomas Jefferson University
|
| Street address |
1025 Walnut St., Suite 511 College Bldg.
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19107 |
| Country |
USA |
| |
|
| Platform ID |
GPL23038 |
| Series (1) |
| GSE208396 |
GLUT1 is redundant in hypoxic and glycolytic nucleus pulposus cells of the intervertebral disc |
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