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Series GSE11821 Query DataSets for GSE11821
Status Public on Jun 19, 2008
Title Expression data from Igf-1 -/- and Igf-1+/+ mouse cochleas
Organism Mus musculus
Experiment type Expression profiling by array
Summary Different mutations in the gene encoding humans IGF-I cause intrauterine growth retardation, postnatal growth failure, microcephaly, mental retardation, bilateral sensorineural deafness and multiple dysmorphic features. Insight into the role of IGFs in inner ear cochlear ganglion neurogenesis has come from the study of genetically modified mice. Postnatal cochlear development is severely impaired in mice Igf1-/-, which develop smaller cochlea and cochlear ganglia, an immature tectorial membrane and they display a significant decrease in the number and size of auditory neurons.
We used microarrays to define the genetic signatures of Igf-1 +/+ and Igf-1-/- mouse cochea and identify the differentially expressed genes.

Keywords: comparison between WT and KO
 
Overall design Cochleae from two E18.5 were isolated from both Igf-1+/+ wild type and Igf-1-/- null mice and pooled to obtain RNA. Heterozygous male and female with a genetic background C57BL/6J were mated to obtain embryos 18.5 days post coitus (E18.5). Three independent pools were used. Cochlear tissues included the otic capsule but not vestibular tissues.
 
Contributor(s) Sánchez-Calderón H, Milo M, Rodríguez de la Rosa L, Pichel JR, Holley M, Varela-Nieto1 I
Citation(s) 20111592, 23034329, 26235979
Submission date Jun 18, 2008
Last update date May 04, 2018
Contact name Marta Milo
E-mail(s) m.milo@sheffield.ac.uk
Organization name University of Sheffield
Department Biomedical Science
Street address Western Bank
City Sheffield
State/province South Yorkshire
ZIP/Postal code S10 2TN
Country United Kingdom
 
Platforms (1)
GPL8321 [Mouse430A_2] Affymetrix Mouse Genome 430A 2.0 Array
Samples (2)
GSM298803 Coch_4_1+_+
GSM298804 Coch_4_2-_-
Relations
BioProject PRJNA105917

Differential Expression - Full Table header descriptions
ID_REF
Coch_4_1+_+
Coch_4_2-_-
Chch -/- Std
Coch_4_1+_+ Std
LRM
LRStd
PPLR
Gene Symbol
Gene Symbol

Data table
ID_REF Coch_4_1+_+ Coch_4_2-_- Chch -/- Std Coch_4_1+_+ Std LRM LRStd PPLR Gene Symbol Gene Symbol
1417943_at 0 4.843479167 2.062013932 0.570077546 4.843479167 2.139366697 0.990217376 guanine nucleotide binding protein (G protein), gamma 4 subunit Gng4
1450466_at 0.806038251 5.306325848 1.799620198 0.474630135 4.500287597 1.861157334 0.992197067 RIKEN cDNA B230310J22 gene B230310J22Rik
1420252_at 0.569005464 4.766724051 1.617046849 0.410728197 4.197718588 1.668393887 0.99406564 --- ---
1421886_at 0 4.178836589 2.07486739 0.566542069 4.178836589 2.150824168 0.98935049 Son of sevenless homolog 1 (Drosophila) Sos1
1421182_at 0.092786362 4.229313941 1.947952398 0.66288918 4.136527579 2.057654152 0.97780093 C-type lectin domain family 1, member b Clec1b
1427217_at 0 4.101874354 1.847603923 0.51290194 4.101874354 1.917474552 0.98966437 zinc finger protein 455 Zfp455
1449227_at 0.764822799 4.790255786 1.977933402 0.680947391 4.025432987 2.091867561 0.972843069 cholesterol 25-hydroxylase Ch25h
1449986_at 0 4.023441383 2.568627214 0.75979069 4.023441383 2.678642876 0.980760465 RIKEN cDNA 2310034C09 gene 2310034C09Rik
1423340_at 0.433332317 4.323906836 1.64124054 0.547067753 3.890574518 1.730015502 0.987739516 transcription factor AP-2 beta Tcfap2b
1427553_at 0.146847491 4.009806992 1.929449038 0.781951527 3.862959501 2.081879387 0.968238677 Mus musculus, clone IMAGE:4190185 ---
1451686_x_at 0.855939312 4.676510513 2.127846629 0.877323688 3.820571201 2.301614244 0.951538034 amelogenin X chromosome Amelx
1434324_x_at 0.258898478 4.076696339 2.33793544 1.049267259 3.817797861 2.562597101 0.931863673 eukaryotic translation initiation factor 3, subunit 3 (gamma) Eif3s3
1421243_at 0 3.784836897 2.080450668 0.905813577 3.784836897 2.269090835 0.955469147 ring finger protein 144 Rnf144
1453117_at 0.31557393 3.946765941 2.515188025 1.297287173 3.631192011 2.830039719 0.900269501 surfeit gene 2 Surf2
1427999_at 0 3.625765568 2.311312386 0.88274298 3.625765568 2.47414634 0.961994155 small nuclear RNA activating complex, polypeptide 5 Snapc5
1432043_at 0.338014692 3.953010376 1.51015552 0.516672198 3.614995683 1.59609519 0.988240586 smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans) Smu1
1420018_s_at 0 3.613933438 1.733395684 0.638752962 3.613933438 1.847340235 0.978040508 tetraspanin 8 Tspan8
1448532_at 0 3.593991206 1.68077959 0.482184511 3.593991206 1.748577116 0.992635934 prolactin-like protein C 2 Prlpc2
1432432_a_at 0.461115996 4.049946325 1.823683148 0.732896371 3.588830329 1.965440743 0.966072399 RAB3C, member RAS oncogene family Rab3c
1419891_s_at 0.453055326 4.030408002 1.581684544 0.558882025 3.577352675 1.677520526 0.983518101 expressed sequence C77545 C77545

Total number of rows: 22690

Table truncated, full table size 3095 Kbytes.




Differential Expression - 0.95 cut-off with Fold-Change > 1 header descriptions
ID_REF
Coch_4_1+_+
Coch_4_2-_-
Chch -/- Std
Coch_4_1+_+ Std
LRM
LRStd
PPLR
Gene Symbol
Gene Symbol

Data table
ID_REF Coch_4_1+_+ Coch_4_2-_- Chch -/- Std Coch_4_1+_+ Std LRM LRStd PPLR Gene Symbol Gene Symbol
1452535_at 1.756378831 3.724979297 1.539362837 0.953302584 1.968600466 1.810641809 0.86153441 Anti-CD4 immunoglobulin heavy chain (VH2-DQ52-JH3 region) ---
1427576_at 0 1.904492911 2.129813388 1.384862438 1.904492911 2.540462367 0.834465949 Monoclonal antiidiotypic antibody IgK (hypervariable region) mRNA ---
1427828_at 2.290200166 4.088297565 1.359759779 0.868068846 1.798097399 1.613223536 0.867488858 Murine retrovirus readthrough RNA sequence ---
1452558_at 1.29065016 2.839938285 1.391641334 0.967384041 1.549288124 1.694844384 0.819672634 T-cell receptor gamma-chain mRNA, complete cds, clone MNG7 ---
1425446_at 3.708838037 4.882838852 0.721794125 0.452305617 1.174000815 0.851802284 0.915937725 MRNA similar to RIKEN cDNA 5830413C03 gene (cDNA clone MGC:7065 IMAGE:3156775) ---
1427766_at 0 1.13126887 3.472916144 1.804742541 1.13126887 3.913852601 0.895674502 T-cell receptor alpha chain (TCRA) ---
1439028_at 1.875736463 3.11820818 1.852119532 1.446517254 1.242471718 2.35005509 0.701492856 Ubiquitin-fold modifier 1 (Ufm1), mRNA 1810045K17Rik
1449703_at 0.56020504 2.565698778 2.079317873 1.441525307 2.005493739 2.530130042 0.786007522 Zinc finger, AN1-type domain 2A (Zfand2a), mRNA AA407930
1420155_at 0.849276166 2.379988527 1.736272699 1.294228628 1.530712361 2.165564736 0.760167701 expressed sequence AA408954 AA408954
1419327_at 0.417645192 3.169723735 2.149630026 1.264054658 2.752078543 2.493740849 0.865115449 expressed sequence AA415817 AA415817
1449748_at 0 2.410814262 1.726146754 1.012674618 2.410814262 2.001272719 0.894893983 expressed sequence AA517023 AA517023
1449658_at 0.460651624 2.998043467 1.898939429 1.097347499 2.537391843 2.193203704 0.876350328 expressed sequence AA536748 AA536748
1419797_at 0.132303967 2.656971931 1.565273979 0.861086371 2.524667964 1.786491637 0.921201371 expressed sequence AA672641 AA672641
1456525_at 1.857468251 4.770851599 1.507028281 0.651698069 2.913383349 1.641902742 0.962001048 EST AA881470 AA881470
1451116_at 0.031976523 2.492343639 2.507347626 1.670136358 2.460367116 3.012664531 0.792942844 acetoacetyl-CoA synthetase Aacs
1448813_at 1.543751694 3.038105481 1.847679105 1.371870539 1.494353787 2.301292431 0.741945253 arylacetamide deacetylase (esterase) Aadac
1451869_at 4.24912493 5.255256144 0.48554633 0.305402839 1.006131213 0.573607995 0.96028815 ATP-binding cassette, sub-family A (ABC1), member 3 Abca3
1416263_at 3.960926162 5.208864261 0.961323331 0.621508301 1.247938099 1.144733644 0.862177755 ATP-binding cassette, sub-family B (MDR/TAP), member 9 Abcb9
1450109_s_at 2.248038939 3.633352304 1.052814005 0.713862491 1.385313365 1.272012965 0.861938873 ATP-binding cassette, sub-family C (CFTR/MRP), member 2 Abcc2
1435683_a_at 4.383403632 5.760495195 1.264547598 0.849568071 1.377091563 1.523432484 0.816986392 ATP-binding cassette, sub-family C (CFTR/MRP), member 5 Abcc5

Total number of rows: 1227

Table truncated, full table size 173 Kbytes.




Differential Expression - 0.05 cut-off with Fold-Change > -1 header descriptions
ID_REF
Coch_4_1+_+
Coch_4_2-_-
Chch -/- Std
Coch_4_1+_+ Std
LRM
LRStd
PPLR
Gene Symbol
Gene Symbol

Data table
ID_REF Coch_4_1+_+ Coch_4_2-_- Chch -/- Std Coch_4_1+_+ Std LRM LRStd PPLR Gene Symbol Gene Symbol
1459725_s_at 5.472516591 0 0.520425216 2.466232896 -5.472516591 2.520545001 0.009827398 demilune cell and parotid protein /// cDNA sequence BC005655 Dcpp /// BC005655
1452543_a_at 6.448075097 1.15008982 0.442843372 2.070431463 -5.297985277 2.117261603 0.006169782 secretoglobin, family 1A, member 1 (uteroglobin) Scgb1a1
1449428_at 5.004855874 0 0.729255386 2.4882834 -5.004855874 2.592945757 0.022887645 claudin 18 Cldn18
1416645_a_at 5.422481805 1.184942857 0.273268381 1.478852055 -4.237538948 1.503887965 0.00241828 alpha fetoprotein Afp
1422334_a_at 5.5472773 1.440319138 0.537594951 1.843089531 -4.106958162 1.919892536 0.016211338 surfactant associated protein A1 Sftpa1
1449015_at 5.008907756 1.000450067 0.608338874 1.876625212 -4.008457689 1.972764145 0.021081936 resistin like alpha Retnla
1420428_at 5.266849597 1.534846325 0.634752196 1.817155518 -3.732003271 1.924828441 0.026258232 advanced glycosylation end product-specific receptor Ager
1420672_at 4.430580689 0.721989272 0.680236576 1.860122671 -3.708591417 1.980600452 0.030571625 potassium voltage-gated channel, Isk-related subfamily, member 1 Kcne1
1425218_a_at 8.395054095 4.76099863 0.270594645 1.073752405 -3.634055465 1.107323661 0.000515667 secretoglobin, family 3A, member 2 Scgb3a2
1424963_at 3.623350194 0 0.399622457 2.119244592 -3.623350194 2.156593552 0.0054287 retinitis pigmentosa 1 homolog (human) Rp1h
1421734_at 4.523067108 0.979058034 0.662814756 1.75850698 -3.544009074 1.879273849 0.029658285 interleukin 8 receptor, beta Il8rb
1422010_at 3.503108308 0 1.149916714 2.381770897 -3.503108308 2.644832897 0.091209715 toll-like receptor 7 Tlr7
1420894_at 4.44751615 0.958110572 0.347288948 1.366258077 -3.489405579 1.409705908 0.006656737 transforming growth factor, beta receptor I Tgfbr1
1418639_at 10.94387807 7.471719016 0.164000922 0.45567287 -3.472159049 0.484287174 3.76E-13 surfactant associated protein C Sftpc
1432027_a_at 3.66342861 0.207916585 1.199595265 2.391768262 -3.455512025 2.675739939 0.098278525 TBC1 domain family, member 14 Tbc1d14
1421705_at 4.293570579 0.88241299 0.350651554 1.36799071 -3.411157589 1.412216377 0.007857591 sodium channel, voltage-gated, type III, alpha Scn3a
1449071_at 3.397741168 0 0.915116028 2.101504497 -3.397741168 2.292107872 0.055015322 myosin, light polypeptide 7, regulatory Myl7
1455957_x_at 3.388106675 0 0.543354801 2.089877151 -3.388106675 2.159356604 0.011848933 CEA-related cell adhesion molecule 11 Ceacam11
1426134_at 3.381356673 0 0.81306325 2.287889942 -3.381356673 2.428067593 0.037854561 triadin Trdn
1449081_at 4.71810084 1.339608807 0.742166725 1.830728859 -3.378492033 1.975444154 0.043610357 carboxylesterase 3 Ces3

Total number of rows: 911

Table truncated, full table size 126 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
GSE11821_RAW.tar 4.2 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
Processed data are available on Series record
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