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Sample GSM8498561 Query DataSets for GSM8498561
Status Public on Oct 02, 2024
Title Sirt6 cKO NP tissue 3
Sample type RNA
 
Source name Sirt6 cKO NP
Organism Mus musculus
Characteristics tissue: Nucleus Pulposus
genotype: Sirt6 cKO
age: 24 months
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.
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.
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).
 
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.
Scan protocol Array scanning was performed on an Affymetrix GeneChip Scanner 3000 7G using Command Console Software (Affymetrix)
Description Gene expression data from RNA of 24 months old mice
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.
 
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

Data table header descriptions
ID_REF
VALUE Quantification
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
AFFX-BkGr-GC03_st 4.3901 0.787849
AFFX-BkGr-GC04_st 4.61419 0.962967
AFFX-BkGr-GC05_st 4.78299 0.990811
AFFX-BkGr-GC06_st 4.81851 0.995303
AFFX-BkGr-GC07_st 4.69051 0.990363
AFFX-BkGr-GC08_st 4.4804 0.990693
AFFX-BkGr-GC09_st 4.21777 0.98378
AFFX-BkGr-GC10_st 4.23462 0.972095
AFFX-BkGr-GC11_st 3.9649 0.959304
AFFX-BkGr-GC12_st 3.93597 0.916819
AFFX-BkGr-GC13_st 3.70886 0.942265
AFFX-BkGr-GC14_st 3.56105 0.938778
AFFX-BkGr-GC15_st 3.42761 0.94941
AFFX-BkGr-GC16_st 3.51677 0.931807
AFFX-BkGr-GC17_st 3.52878 0.916386
AFFX-BkGr-GC18_st 3.66149 0.901544
AFFX-BkGr-GC19_st 4.21529 0.809059
AFFX-BkGr-GC20_st 4.36143 0.796006
AFFX-BkGr-GC21_st 4.28297 0.778272
AFFX-BkGr-GC22_st 4.34971 0.758585

Total number of rows: 28846

Table truncated, full table size 1020 Kbytes.




Supplementary file Size Download File type/resource
GSM8498561_23.CEL.gz 914.4 Kb (ftp)(http) CEL
GSM8498561_23_Clariom_S_Mouse_.sst-rma-gene-full.chp.gz 313.7 Kb (ftp)(http) CHP

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