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Status |
Public on Oct 02, 2024 |
Title |
Sirt6 cKO NP tissue 4 |
Sample type |
RNA |
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Source name |
Sirt6 cKO NP
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Organism |
Mus musculus |
Characteristics |
tissue: Nucleus Pulposus genotype: Sirt6 cKO age: 24 months
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Growth protocol |
Sirt6 fl/fl or Sirt6 cKO mice were obtained and intevertebral discs were processed for RNA transcriptomic analysis at 24 months-of-age.
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Extracted molecule |
total RNA |
Extraction protocol |
NP and AF tissues were micro-dissected from caudal and lumbar intervertebral discs of four Sirt6fl/fl and four Sirt6cKO mice at 24 months of age and immediately placed in RNAlater® Reagent (INVITROGEN). Tissues were homogenized with a Pellet Pestle Motor (Sigma Aldrich, Z359971) and RNA was extracted from tissue lysates using RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.
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Label |
biotin
|
Label protocol |
Single-stranded cDNA was generated, then fragmented and biotin-labeled using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).
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Hybridization protocol |
Affymetrix Gene chips, Mouse Clariom S, were hybridized with 2.5 μg fragmented and biotin-labeled cDNA in 100 μl of hybridization cocktail.
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Scan protocol |
Array scanning was performed on an Affymetrix GeneChip Scanner 3000 7G using Command Console Software (Affymetrix)
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Description |
Gene expression data from RNA of 24 months old mice
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Data processing |
Raw data were processed and .CHP files were generated by sst-rma normalization from Affymetrix .CEL files, and quality control of the expeirment was performed in Transcriptome Analysis Console (TAC) v4.0.2 (Affymetrix). The experimental group was compared to the control group in the TAC, including all probe sets where at least 50% of the samples had a DABG (detected above background) p < 0.05.
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Submission date |
Sep 05, 2024 |
Last update date |
Oct 02, 2024 |
Contact name |
Makarand V Risbud |
E-mail(s) |
pranay1130@gmail.com
|
Phone |
215-955-1063
|
Organization name |
Thomas Jefferson University
|
Street address |
1025 Walnut St.
|
City |
Philadelphia |
ZIP/Postal code |
19107 |
Country |
USA |
|
|
Platform ID |
GPL23038 |
Series (1) |
GSE276439 |
SIRT6 loss causes intervertebral disc degeneration in mice by dysregulating senescence and SASP status |
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