NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE8726 Query DataSets for GSE8726
Status Public on Aug 06, 2008
Title Expression Data from Sod2-/- and Sod2+/+ Mouse Erythroblasts.
Organism Mus musculus
Experiment type Expression profiling by array
Summary The mitochondrial superoxide dismutase (SOD2) is a major antioxidant protein which detoxifies superoxide anion radicals generated by mitochondrial respiration (Weisiger and Fridovich, J. Biol. Chem. 1973). We designed a model of oxidative stress-induced anemia caused by SOD2-deficiency (Friedman et al. J. Exp. Med. 2001). Our previous work showed that mice reconstituted with SOD2-deficient hematopoietic stem cells develop an anemia with striking similarity to human sideroblastic anemia (SA) (Friedman et al. Blood 2004; Martin et al. Exp Hematol 2005). Our overall goal was to define early events in the pathogenesis of SOD2-deficiency SA and, in particular, to identify genes involved in the response of erythroid progenitors to oxidative stress. We compared gene expression of sorted TER-119+ CD71+ erythroblasts from SOD2-/- ('KO') versus Sod2+/+ ('WT') hematopoietic stem cell recipients using cDNA microarrays.
Samples used in this study were re-hybridized with GLYCOv2 oligonucleotide arrays. GLYCOv2 oligonucleotide arrays are custom Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA) designed for the Functional Glycomics Gateway, collaboration between the Consortium for Functional Glycomics (CFG, http://www.functionalglycomics.org/) and Nature Publishing Group. A complete description of the array can be found at http://www.functionalglycomics.org/static/consortium/resources/resourcecoree.shtml . Hybridization results and quality control details can be found at https://www.functionalglycomics.org/glycomics/publicdata/microarray.jsp , by clicking on the ‘Raw Data’ icon link for microarray experiment ‘Jeff Friedman 1: Sod2 KO anemic mice’. Briefly but importantly, one Sod2-/- sample, which was prepared separately, and whose GAPDH 3'/5' ratio was off range, was legitimately removed from the analysis of the GLYCOv2 and 430 2.0 arrays.
Keywords: Genotype comparison, genetic modification
 
Overall design We sorted Sod2-/- and Sod2+/+ size-matched mouse erythroblasts based on the expression of two developmental surface markers, CD71 and TER-119. Total RNA from 4 biological replicates per genotype were extracted and hybridized on 8 Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). After quality controls (see scan protocol), analysis was performed with GeneSifter (VizX Labs, Seattle, WA) using 4 Sod2+/+ (control samples, WT) and 3 Sod2-/- (KO) replicates.
 
Contributor(s) Martin FM, Gilmartin TJ, Friedman JS
Citation(s) 21326867
Submission date Aug 08, 2007
Last update date Aug 19, 2019
Contact name Florent M. MARTIN
E-mail(s) florent@scripps.edu
Phone +1 (858) 784-9218
Fax +1 (858) 784-2131
URL http://www.scripps.edu/
Organization name The Scripps Research Institute
Department Department of Molecular and Experimental Medicine
Lab Dr Jeffrey S. Friedman Laboratory
Street address 10550 North Torrey Pines Road, MEM-151
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (1)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
Samples (7)
GSM216494 Erythroblast_SOD2+/+_repWT17
GSM216495 Erythroblast_SOD2+/+_repWT29
GSM216496 Erythroblast_SOD2+/+_repWT33
Relations
BioProject PRJNA101979

Averaged data (+/- SEM) by groups header descriptions
ID_REF
mean 1 mean of Sod2+/+ erythroblast samples; log transformed
mean 2 mean of Sod2-/- erythroblast samples; log transformed
SEM 1 standard error of the mean; Sod2+/+ erythroblast samples
SEM 2 standard error of the mean; Sod2-/- erythroblast samples
Gene Identifier
Gene Title

Data table
ID_REF mean 1 mean 2 SEM 1 SEM 2 Gene Identifier Gene Title
1420499_at 7.74862 10.663 0.237451 0.12531 NM_008102 GTP cyclohydrolase 1
1448724_at 6.86432 9.01935 0.490204 0.58319 NM_009895 Cytokine inducible SH2-containing protein
1426065_a_at 5.56694 7.5815 0.809173 0.140796 BC012955 Tribbles homolog 3 (Drosophila)
1429692_s_at 4.9848 6.99039 0.110598 0.323079 BB698398 GTP cyclohydrolase 1
1455084_x_at 7.34018 9.2159 0.641515 0.240273 BB758291 RIKEN cDNA 2700043D08 gene
1426423_at 6.97947 8.79804 0.535788 0.242311 BM222403 Serine hydroxymethyltransferase 2 (mitochondrial)
1448364_at 5.63609 7.37579 0.130504 0.395486 U95826 Cyclin G2
1419254_at 9.04845 10.7757 0.321075 0.323938 BG076333 Methylenetetrahydrofolate dehydrogenase (NAD+ dependent), methenyltetrahydrofolate cyclohydrolase
1449401_at 4.02193 5.72678 0.115769 1.30958 NM_007574 Complement component 1, q subcomponent, C chain
1452318_a_at 3.70074 5.40473 0.116276 0.582176 M12573 Heat shock protein 1B
1425225_at 6.61051 8.28139 0.122408 1.382 BC027310 Fc receptor, IgG, low affinity IV
1425927_a_at 6.62419 8.24594 0.543806 0.206675 AF375476 Activating transcription factor 5
1419253_at 8.91596 10.5284 0.271904 0.31021 BG076333 Methylenetetrahydrofolate dehydrogenase (NAD+ dependent), methenyltetrahydrofolate cyclohydrolase
1437726_x_at 4.00277 5.54771 0.045168 1.40818 BB111335 Complement component 1, q subcomponent, beta polypeptide
1456225_x_at 6.63552 8.15369 0.632557 0.171525 BB508622 Tribbles homolog 3 (Drosophila)
1427127_x_at 3.66656 5.18225 0.107312 0.482675 M12573 Heat shock protein 1B
1429701_at 6.29674 7.78984 0.097618 0.234425 AK010362 RIKEN cDNA 2410003J06 gene
1450464_at 4.98299 6.43184 0.06989 0.161596 NM_007893 E4F transcription factor 1
1449424_at 7.1789 8.62292 0.165304 0.345255 NM_013738 Pleckstrin 2
1423006_at 8.20809 9.63028 0.203939 0.396286 NM_008842 Proviral integration site 1

Total number of rows: 45101

Table truncated, full table size 3889 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE8726_RAW.tar 41.5 Mb (http)(custom) TAR (of CEL, EXP)
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap