title: Sample NA18594


title: Sample NA18623

status: Public on Jul 27 2009

type: genomic

city: San Diego

last: Illumina Inc.

state: CA

address: 9885 Towne Centre Drive

country: USA

institute: Illumina Inc.

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

label_protocol: standard Illumina protocol

extract_protocol: standard Illumina protocol

tag: sample


title: Sample NA18987


title: Sample NA18633


title: Sample NA18622


title: Sample NA18621


title: Sample NA18573


title: Sample NA18970


title: Sample NA18995


title: Sample NA18980


title: Sample NA18976


title: Sample NA18978


title: Sample NA18967


title: Sample NA18571


title: Sample NA18620


title: Sample NA18570


title: Sample NA18612


title: Sample NA18566


title: Sample NA18563


title: Sample NA18975


title: Sample NA18973


title: Sample NA18965


title: Sample NA18611


title: Sample NA18555


title: Sample NA18564


title: Sample NA18961


title: Sample NA18960


title: Sample NA18959


title: Sample NA18953


title: Sample NA18969


title: Sample NA18964


title: Sample NA18608


title: Sample NA18552


title: Sample NA18968


title: Sample NA18547


title: Sample NA18609


title: Sample NA18972


title: Sample NA18550


title: Sample NA18572


title: Sample NA18966


title: Sample NA18956


title: Sample NA18945


title: Sample NA18952


title: Sample NA18949


title: Sample NA18542


title: Sample NA18948


title: Sample NA18605


title: Sample NA18603


title: Sample NA18537


title: Sample NA18562


title: Sample NA18944


title: Sample NA18947


title: Sample NA18942


title: Sample NA18943


title: Sample NA18951


title: Sample NA18529


title: Sample NA18558


title: Sample NA18524


title: Sample NA18545


title: Sample NA18561


title: Sample NA18940


title: Sample NA18532


title: Sample NA12043


title: Sample NA18526


title: Sample NA12740


title: Sample NA18540


title: Sample NA12264


title: Sample NA12864


title: Sample NA12717


title: Sample NA12752


title: Sample NA10839


title: Sample NA12815


title: Sample NA12751


title: Sample NA11882


title: Sample NA12146


title: Sample NA12891


title: Sample NA11994


title: Sample NA06994


title: Sample NA10860


title: Sample NA12873


title: Sample NA12812


title: Sample NA12750


title: Sample NA12057


title: Sample NA11831


title: Sample NA10835


title: Sample NA07348


title: Sample NA10855


title: Sample NA11881


title: Sample NA12003


title: Sample NA12760


title: Sample NA10838


title: Sample NA10830


title: Sample NA11830


title: Sample NA12761


title: Sample NA06985


title: Sample NA11993


title: Sample NA11995


title: Sample NA12865


title: Sample NA12249


title: Sample NA12802


title: Sample NA11840


title: Sample NA06991


title: Sample NA12874


title: Sample NA12813


title: Sample NA12716


title: Sample NA12878


title: Sample NA12155


title: Sample NA10856


title: Sample NA12872


title: Sample NA11832


title: Sample NA12801


title: Sample NA12762


title: Sample NA07000


title: Sample NA12239


title: Sample NA07019


title: Sample NA12248


title: Sample NA12154


title: Sample NA10854


title: Sample NA10846


title: Sample NA12144


title: Sample NA06993


title: Sample NA12763


title: Sample NA12145


title: Sample NA07048


title: Sample NA07357


title: Sample NA07022


title: Sample NA10831


title: Sample NA12044


title: Sample NA11829


title: Sample NA11992


title: Sample NA07029


title: Sample NA12892


title: Sample NA07345


title: Sample NA12006


title: Sample NA10857


title: Sample NA12004


title: Sample NA12056


title: Sample NA07056


title: Sample NA12156


title: Sample NA12875


title: Sample NA12234


title: Sample NA10851


title: Sample NA10861


title: Sample NA07034


title: Sample NA12814


title: Sample NA10847


title: Sample NA10863


title: Sample NA11839


title: Sample NA07055


title: Sample NA10859


title: Sample NA12707


title: Sample NA19239


title: Sample NA19210


title: Sample NA19208


title: Sample NA19211


title: Sample NA19221


title: Sample NA19222


title: Sample NA19240


title: Sample NA19206


title: Sample NA19209


title: Sample NA12005


title: Sample NA19204


title: Sample NA19207


title: Sample NA19205


title: Sample NA19202


title: Sample NA12753


title: Sample NA19200


title: Sample NA19203


title: Sample NA19173


title: Sample NA19192


title: Sample NA19193


title: Sample NA19194


title: Sample NA19161


title: Sample NA19160


title: Sample NA19152


title: Sample NA19172


title: Sample NA19145


title: Sample NA19171


title: Sample NA19154


title: Sample NA19153


title: Sample NA19140


title: Sample NA19139


title: Sample NA19142


title: Sample NA19141


title: Sample NA19129


title: Sample NA19201


title: Sample NA19138


title: Sample NA19128


title: Sample NA19119


title: Sample NA19120


title: Sample NA19116


title: Sample NA19144


title: Sample NA19143


title: Sample NA19100


title: Sample NA19094


title: Sample NA18913


title: Sample NA18912


title: Sample NA19093


title: Sample NA19102


title: Sample NA19103


title: Sample NA18872


title: Sample NA18871


title: Sample NA18870


title: Sample NA18862


title: Sample NA19101


title: Sample NA18856


title: Sample NA19099


title: Sample NA18860


title: Sample NA18859


title: Sample NA18854


title: Sample NA19092


title: Sample NA18855


title: Sample NA18852


title: Sample NA18521


title: Sample NA18857


title: Sample NA18517


title: Sample NA18853


title: Sample NA18516


title: Sample NA18507


title: Sample NA18515


title: Sample NA18506


title: Sample NA18863


title: Sample NA18861


title: Sample NA18505


title: Sample NA18504


title: Sample NA18503


title: Sample NA18508


title: Sample NA18502


title: Sample NA18500


title: Sample NA19012


title: Sample NA19005


title: Sample NA18997


title: Sample NA19003


title: Sample NA18501


title: Sample NA18999


title: Sample NA18991


title: Sample NA18990


title: Sample NA18987


title: Sample NA19007


title: Sample NA18980


title: Sample NA18981


title: Sample NA18975


title: Sample NA18978


title: Sample NA18973


title: Sample NA18992


title: Sample NA18971


title: Sample NA18974


title: Sample NA18969


title: Sample NA18972


title: Sample NA18968


title: Sample NA18966


title: Sample NA18965


title: Sample NA18967


title: Sample NA18952


title: Sample NA18953


title: Sample NA18960


title: Sample NA18964


title: Sample NA18959


title: Sample NA18947


title: Sample NA18956


title: Sample NA18943


title: Sample NA18945


title: Sample NA18944


title: Sample NA18951


title: Sample NA18942


title: Sample NA18637


title: Sample NA18624


title: Sample NA18635


title: Sample NA18632


title: Sample NA18623


title: Sample NA18633


title: Sample NA18961


title: Sample NA18622


title: Sample NA18611


title: Sample NA18609


title: Sample NA18612


title: Sample NA18621


title: Sample NA18608


title: Sample NA18948


title: Sample NA18603


title: Sample NA18594


title: Sample NA18577


title: Sample NA18573


title: Sample NA18605


title: Sample NA18582


title: Sample NA18620


title: Sample NA18566


title: Sample NA18593


title: Sample NA18572


title: Sample NA18562


title: Sample NA18561


title: Sample NA18564


title: Sample NA18563


title: Sample NA18570


title: Sample NA18552


title: Sample NA18542


title: Sample NA18545


title: Sample NA18550


title: Sample NA18547


title: Sample NA18537


title: Sample NA18529


title: Sample NA12891


title: Sample NA18532


title: Sample NA18524


title: Sample NA12878


title: Sample NA12875


title: Sample NA18571


title: Sample NA12864


title: Sample NA18592


title: Sample NA12874


title: Sample NA12814


title: Sample NA12892


title: Sample NA12802


title: Sample NA12873


title: Sample NA12813


title: Sample NA12815


title: Sample NA12812


title: Sample NA12872


title: Sample NA12801


title: Sample NA12763


title: Sample NA12760


title: Sample NA12761


title: Sample NA12762


title: Sample NA12753


title: Sample NA12751


title: Sample NA12717


title: Sample NA12750


title: Sample NA12264


title: Sample NA12716


title: Sample NA12154


title: Sample NA12249


title: Sample NA12155


title: Sample NA12145


title: Sample NA12144


title: Sample NA12146


title: Sample NA12057


title: Sample NA12003


title: Sample NA11995


title: Sample NA12043


title: Sample NA11994


title: Sample NA12004


title: Sample NA12006


title: Sample NA11992


title: Sample NA11881


title: Sample NA11882


title: Sample NA12005


title: Sample NA11840


title: Sample NA11829


title: Sample NA11830


title: Sample NA11993


title: Sample NA11832


title: Sample NA12234


title: Sample NA10861


title: Sample NA10863


title: Sample NA10857


title: Sample NA10855


title: Sample NA10859


title: Sample NA10847


title: Sample NA12044


title: Sample NA10838


title: Sample NA10831


title: Sample NA10851


title: Sample NA10835


title: Sample NA07348


title: Sample NA10839


title: Sample NA07357


title: Sample NA07034


title: Sample NA07022


title: Sample NA07029


title: Sample NA07056


title: Sample NA07019


title: Sample NA10830


title: Sample NA06994


title: Sample NA06991


title: Sample NA06993


title: Sample NA19239


title: Sample NA19194


title: Sample NA19238


title: Sample NA06985


title: Sample NA19240


title: Sample NA19173


title: Sample NA07048


title: Sample NA19172


title: Sample NA19193


title: Sample NA19192


title: Sample NA19145


title: Sample NA19159


title: Sample NA19171


title: Sample NA19141


title: Sample NA07000


title: Sample NA19143


title: Sample NA19144


title: Sample NA19142


title: Sample NA19137


title: Sample NA19140


title: Sample NA19161


title: Sample NA19120


title: Sample NA19138


title: Sample NA19139


title: Sample NA19116


title: Sample NA19119


title: Sample NA18994


title: Sample NA19160


title: Sample NA19092


title: Sample NA18992


title: Sample NA18999


title: Sample NA19003


title: Sample NA18978


title: Sample NA19093


title: Sample NA18972


title: Sample NA18971


title: Sample NA18968


title: Sample NA18960


title: Sample NA18987


title: Sample NA18965


title: Sample NA18949


title: Sample NA18953


title: Sample NA18952


title: Sample NA18856


title: Sample NA18854


title: Sample NA18951


title: Sample NA19094


title: Sample NA18855


title: Sample NA18944


title: Sample NA18853


title: Sample NA18852


title: Sample NA18609


title: Sample NA18612


title: Sample NA18576


title: Sample NA18593


title: Sample NA18857


title: Sample NA18547


title: Sample NA18558


title: Sample NA18608


title: Sample NA18517


title: Sample NA18516


title: Sample NA18550


title: Sample NA18529


title: Sample NA18542


title: Sample NA18577


title: Sample NA18515


title: Sample NA12892


title: Sample NA12875


title: Sample NA12891


title: Sample NA12865


title: Sample NA12813


title: Sample NA18537


title: Sample NA12878


title: Sample NA12801


title: Sample NA12812


title: Sample NA12750


title: Sample NA12874


title: Sample NA12239


title: Sample NA12740


title: Sample NA12249


title: Sample NA12248


title: Sample NA12234


title: Sample NA12044


title: Sample NA12154


title: Sample NA12264


title: Sample NA11995


title: Sample NA11992


title: Sample NA12057


title: Sample NA11993


title: Sample NA12056


title: Sample NA12043


title: Sample NA10861


title: Sample NA11881


title: Sample NA10863


title: Sample NA11994


title: Sample NA11882


title: Sample NA12236


title: Sample NA12751


title: Sample NA10859


title: Sample NA12146


title: Sample NA10835


title: Sample NA10847


title: Sample NA10830


title: Sample NA10860


title: Sample NA07357


title: Sample NA07348


title: Sample NA06994


title: Sample NA06985


title: Sample NA19239


title: Sample NA19240


title: Sample NA19222


title: Sample NA07000


title: Sample NA07029


title: Sample NA19221


title: Sample NA10851


title: Sample NA19211


title: Sample NA19210


title: Sample NA19209


title: Sample NA06993


title: Sample NA19203


title: Sample NA19208


title: Sample NA19205


title: Sample NA19206


title: Sample NA19201


title: Sample NA19200


title: Sample NA07345


title: Sample NA10857


title: Sample NA19238


title: Sample NA19202


title: Sample NA19194


title: Sample NA19223


title: Sample NA19207


title: Sample NA19193


title: Sample NA19144


title: Sample NA19154


title: Sample NA19153


title: Sample NA19159


title: Sample NA19143


title: Sample NA19141


title: Sample NA19171


title: Sample NA19152


title: Sample NA19161


title: Sample NA19142


title: Sample NA19137


title: Sample NA19128


title: Sample NA19204


title: Sample NA19139


title: Sample NA19131


title: Sample NA19160


title: Sample NA19145


title: Sample NA19192


title: Sample NA19173


title: Sample NA19138


title: Sample NA19172


title: Sample NA19130


title: Sample NA19140


title: Sample NA19127


title: Sample NA19129


title: Sample NA19132


title: Sample NA19099


title: Sample NA19102


title: Sample NA19092


title: Sample NA19093


title: Sample NA19119


title: Sample NA19103


title: Sample NA19094


title: Sample NA19120


title: Sample NA18870


title: Sample NA19116


title: Sample NA19101


title: Sample NA18872


title: Sample NA18863


title: Sample NA18860


title: Sample NA18859


title: Sample NA19098


title: Sample NA18914


title: Sample NA18912


title: Sample NA19100


title: Sample NA18871


title: Sample NA18858


title: Sample NA18862


title: Sample NA18861


title: Sample NA18913


title: Sample NA18855


title: Sample NA18857


title: Sample NA18856


title: Sample NA18853


title: Sample NA18523


title: Sample NA18852


title: Sample NA18516


title: Sample NA18854


title: Sample NA18515


title: Sample NA18503


title: Sample NA18521


title: Sample NA18517


title: Sample NA18508


title: Sample NA18522


title: Sample NA18500


title: Sample NA18506


title: Sample NA18505


title: Sample NA18999


title: Sample NA18507


title: Sample NA18502


title: Sample NA19012


title: Sample NA18995


title: Sample NA18997


title: Sample NA18504


title: Sample NA19007


title: Sample NA19000


title: Sample NA19005


title: Sample NA18991


title: Sample NA19003


title: Sample NA18981


title: Sample NA18501


title: Sample NA18998


title: Sample NA18972


title: Sample NA18971


title: Sample NA18994


title: Sample NA18987


title: Sample NA18974


title: Sample NA18990


title: Sample NA18980


title: Sample NA18978


title: Sample NA18969


title: Sample NA18973


title: Sample NA18975


title: Sample NA18976


title: Sample NA18961


title: Sample NA18965


title: Sample NA18959


title: Sample NA18960


title: Sample NA18953


title: Sample NA18970


title: Sample NA18968


title: Sample NA18967


title: Sample NA18966


title: Sample NA18964


title: Sample NA18992


title: Sample NA18947


title: Sample NA18952


title: Sample NA18944


title: Sample NA18945


title: Sample NA18949


title: Sample NA18948


title: Sample NA18951


title: Sample NA18940


title: Sample NA18633


title: Sample NA18635


title: Sample NA18942


title: Sample NA18956


title: Sample NA18943


title: Sample NA18636


title: Sample NA18612


title: Sample NA18621


title: Sample NA18611


title: Sample NA18637


title: Sample NA18632


title: Sample NA18623


title: Sample NA18603


title: Sample NA18594


title: Sample NA18620


title: Sample NA18605


title: Sample NA18582


title: Sample NA18622


title: Sample NA18609


title: Sample NA18593


title: Sample NA18592


title: Sample NA18624


title: Sample NA18577


title: Sample NA18572


title: Sample NA18579


title: Sample NA18563


title: Sample NA18571


title: Sample NA18550


title: Sample NA18608


title: Sample NA18576


title: Sample NA18555


title: Sample NA18570


title: Sample NA18573


title: Sample NA18566


title: Sample NA18564


title: Sample NA18562


title: Sample NA18552


title: Sample NA18532


title: Sample NA18558


title: Sample NA18561


title: Sample NA18537


title: Sample NA18545


title: Sample NA18547


title: Sample NA12891


title: Sample NA12875


title: Sample NA18529


title: Sample NA18526


title: Sample NA18542


title: Sample NA12892


title: Sample NA18524


title: Sample NA12872


title: Sample NA12813


title: Sample NA12864


title: Sample NA12814


title: Sample NA12812


title: Sample NA12873


title: Sample NA12878


title: Sample NA12815


title: Sample NA12760


title: Sample NA12753


title: Sample NA12865


title: Sample NA12801


title: Sample NA12752


title: Sample NA12761


title: Sample NA12802


title: Sample NA12763


title: Sample NA12762


title: Sample NA12874


title: Sample NA12717


title: Sample NA12234


title: Sample NA12740


title: Sample NA12751


title: Sample NA12750


title: Sample NA12249


title: Sample NA12248


title: Sample NA12239


title: Sample NA12236


title: Sample NA12264


title: Sample NA12144


title: Sample NA12145


title: Sample NA12005


title: Sample NA12044


title: Sample NA12716


title: Sample NA12155


title: Sample NA12004


title: Sample NA12156


title: Sample NA12006


title: Sample NA12146


title: Sample NA11995


title: Sample NA12056


title: Sample NA12003


title: Sample NA11882


title: Sample NA12154


title: Sample NA11881


title: Sample NA11832


title: Sample NA11993


title: Sample NA11831


title: Sample NA11994


title: Sample NA11840


title: Sample NA12057


title: Sample NA10863


title: Sample NA12043


title: Sample NA10860


title: Sample NA11839


title: Sample NA11829


title: Sample NA10861


title: Sample NA10856


title: Sample NA10857


title: Sample NA10859


title: Sample NA10855


title: Sample NA11992


title: Sample NA10851


title: Sample NA11830


title: Sample NA10846


title: Sample NA10847


title: Sample NA07357


title: Sample NA07348


title: Sample NA10839


title: Sample NA07034


title: Sample NA07055


title: Sample NA10830


title: Sample NA10835


title: Sample NA10831


title: Sample NA10838


title: Sample NA06994


title: Sample NA07029


title: Sample NA06985


title: Sample NA07048


title: Sample NA19239


title: Sample NA19240


title: Sample NA07056


title: Sample NA07019


title: Sample NA19238


title: Sample NA19223


title: Sample NA06993


title: Sample NA19221


title: Sample NA19211


title: Sample NA07345


title: Sample NA07000


title: Sample NA19222


title: Sample NA19208


title: Sample NA07022


title: Sample NA19210


title: Sample NA06991


title: Sample NA19193


title: Sample NA19201


title: Sample NA19207


title: Sample NA19209


title: Sample NA19202


title: Sample NA19206


title: Sample NA19200


title: Sample NA19154


title: Sample NA19194


title: Sample NA19203


title: Sample NA19192


title: Sample NA19145


title: Sample NA19152


title: Sample NA19171


title: Sample NA19161


title: Sample NA19173


title: Sample NA19172


title: Sample NA19204


title: Sample NA19205


title: Sample NA19144


title: Sample NA19143


title: Sample NA19142


title: Sample NA19160


title: Sample NA19153


title: Sample NA19159


title: Sample NA19140


title: Sample NA19141


title: Sample NA19130


title: Sample NA19139


title: Sample NA19137


title: Sample NA19138


title: Sample NA19128


title: Sample NA19120


title: Sample NA19129


title: Sample NA19119


title: Sample NA19116


title: Sample NA19100


title: Sample NA19132


title: Sample NA19101


title: Sample NA19099


title: Sample NA19131


title: Sample NA18914


title: Sample NA19127


title: Sample NA18912


title: Sample NA18913


title: Sample NA19098


title: Sample NA19093


title: Sample NA18860


title: Sample NA18871


title: Sample NA18862


title: Sample NA18870


title: Sample NA18863


title: Sample NA19102


title: Sample NA18856


title: Sample NA18859


title: Sample NA18861


title: Sample NA18857


title: Sample NA19092


title: Sample NA18854


title: Sample NA19103


title: Sample NA18855


title: Sample NA18522


title: Sample NA18852


title: Sample NA18523


title: Sample NA18872


title: Sample NA19094


title: Sample NA18521


title: Sample NA18517


title: Sample NA18516


title: Sample NA18508


title: Sample NA18504


title: Sample NA18858


title: Sample NA18502


title: Sample NA18507


title: Sample NA18515


title: Sample NA18506


title: Sample NA18505


title: Sample NA19007


title: Sample NA18503


title: Sample NA19003


title: Sample NA19005


title: Sample NA19012


title: Sample NA18501


title: Sample NA19000


title: Sample NA18500


title: Sample NA18998


title: Sample NA18995


title: Sample NA18999


title: Sample NA18997


title: Sample NA18994


title: Sample NA18853


title: Sample NA18992


title: Sample NA18990


title: Sample NA18991


title: Sample NA18987


title: Sample NA18975


title: Sample NA18980


title: Sample NA18974


title: Sample NA18976


title: Sample NA18981


title: Sample NA18973


title: Sample NA18969


title: Sample NA18978


title: Sample NA18972


title: Sample NA18967


title: Sample NA18966


title: Sample NA18961


title: Sample NA18965


title: Sample NA18960


title: Sample NA18968


title: Sample NA18953


title: Sample NA18964


title: Sample NA18959


title: Sample NA18971


title: Sample NA18948


title: Sample NA18952


title: Sample NA18951


title: Sample NA18949


title: Sample NA18970


title: Sample NA18945


title: Sample NA18947


title: Sample NA18956


title: Sample NA18636


title: Sample NA18942


title: Sample NA18940


title: Sample NA18944


title: Sample NA18637


title: Sample NA18635


title: Sample NA18620


title: Sample NA18633


title: Sample NA18623


title: Sample NA18632


title: Sample NA18622


title: Sample NA18624


title: Sample NA18612


title: Sample NA18609


title: Sample NA18621


title: Sample NA18605


title: Sample NA18593


title: Sample NA18608


title: Sample NA18582


title: Sample NA18943


title: Sample NA18594


title: Sample NA18579


title: Sample NA18592


title: Sample NA18576


title: Sample NA18577


title: Sample NA18603


title: Sample NA18573


title: Sample NA18611


title: Sample NA18564


title: Sample NA18572


title: Sample NA18562


title: Sample NA18571


title: Sample NA18566


title: Sample NA18552


title: Sample NA18570


title: Sample NA18558


title: Sample NA18555


title: Sample NA18563


title: Sample NA18547


title: Sample NA18532


title: Sample NA18537


title: Sample NA18529


title: Sample NA18550


title: Sample NA18542


title: Sample NA18545


title: Sample NA12892


title: Sample NA18526


title: Sample NA15510


title: Sample NA12875


title: Sample NA12891


title: Sample NA12878


title: Sample NA18524


title: Sample NA12874


title: Sample NA12873


title: Sample NA12864


title: Sample NA12865


title: Sample NA12872


title: Sample NA12814


title: Sample NA18561


title: Sample NA12763


title: Sample NA12813


title: Sample NA12812


title: Sample NA12802


title: Sample NA12760


title: Sample NA12762


title: Sample NA12752


title: Sample NA12815


title: Sample NA12751


title: Sample NA12716


title: Sample NA12750


title: Sample NA12740


title: Sample NA12801


title: Sample NA12248


title: Sample NA12717


title: Sample NA12239


title: Sample NA12707


title: Sample NA12264


title: Sample NA12154


title: Sample NA12249


title: Sample NA12156


title: Sample NA12155


title: Sample NA12146


title: Sample NA12761


title: Sample NA12056


title: Sample NA12044


title: Sample NA12144


title: Sample NA12057


title: Sample NA12145


title: Sample NA12004


title: Sample NA12753


title: Sample NA12234


title: Sample NA12005


title: Sample NA11995


title: Sample NA12003


title: Sample NA11881


title: Sample NA11992


title: Sample NA11994


title: Sample NA12006


title: Sample NA11993


title: Sample NA11882


title: Sample NA11840


title: Sample NA11839


title: Sample NA11831


title: Sample NA11830


title: Sample NA10855


title: Sample NA10859


title: Sample NA12043


title: Sample NA10861


title: Sample NA10860


title: Sample NA10856


title: Sample NA10851


title: Sample NA11829


title: Sample NA10847


title: Sample NA10838


title: Sample NA10835


title: Sample NA10839


title: Sample NA10857


title: Sample NA10830


title: Sample NA10846


title: Sample NA10831


title: Sample NA11832


title: Sample NA07357


title: Sample NA07345


title: Sample NA07348


title: Sample NA07048


title: Sample NA07029


title: Sample NA07022


title: Sample NA07034


title: Sample NA07019


title: Sample NA07055


title: Sample NA07000


title: Sample NA06985


title: Sample NA19240


title: Sample NA06994


title: Sample NA19222


title: Sample NA19209


title: Sample NA07056


title: Sample NA19208


title: Sample NA19239


title: Sample NA19221


title: Sample NA19207


title: Sample NA19204


title: Sample NA19210


title: Sample NA06991


title: Sample NA19203


title: Sample NA19206


title: Sample NA19205


title: Sample NA19211


title: Sample NA19202


title: Sample NA10863


title: Sample NA19192


title: Sample NA19193


title: Sample NA19173


title: Sample NA19154


title: Sample NA19145


title: Sample NA19142


title: Sample NA19161


title: Sample NA19153


title: Sample NA19152


title: Sample NA19143


title: Sample NA06993


title: Sample NA19200


title: Sample NA19144


title: Sample NA19140


title: Sample NA19194


title: Sample NA19138


title: Sample NA19129


title: Sample NA19120


title: Sample NA19128


title: Sample NA19171


title: Sample NA19116


title: Sample NA19201


title: Sample NA19139


title: Sample NA19119


title: Sample NA19160


title: Sample NA19100


title: Sample NA19103


title: Sample NA19102


title: Sample NA19101


title: Sample NA19141


title: Sample NA19092


title: Sample NA19094


title: Sample NA19099


title: Sample NA18912


title: Sample NA19093


title: Sample NA18863


title: Sample NA18870


title: Sample NA18862


title: Sample NA18861


title: Sample NA18857


title: Sample NA18860


title: Sample NA18856


title: Sample NA18859


title: Sample NA18913


title: Sample NA18872


title: Sample NA18854


title: Sample NA18871


title: Sample NA18855


title: Sample NA18521


title: Sample NA18853


title: Sample NA18852


title: Sample NA18516


title: Sample NA18517


title: Sample NA18503


title: Sample NA18504


title: Sample NA18506


title: Sample NA18515


title: Sample NA18502


title: Sample NA18505


title: Sample NA18507


title: Sample NA18508


title: Sample NA19003


title: Sample NA19007


title: Sample NA18999


title: Sample NA18500


title: Sample NA19005


title: Sample NA18992


title: Sample NA18997


title: Sample NA18978


title: Sample NA18501


title: Sample NA19012


title: Sample NA18990


title: Sample NA18972


title: Sample NA18991


title: Sample NA18987


title: Sample NA18981


title: Sample NA18980


title: Sample NA18974


title: Sample NA18967


title: Sample NA18966


title: Sample NA18969


title: Sample NA18973


title: Sample NA18968


title: Sample NA18975


title: Sample NA18964


title: Sample NA18971


title: Sample NA18965


title: Sample NA18961


title: Sample NA18953


title: Sample NA18945


title: Sample NA18959


title: Sample NA18943


title: Sample NA18951


title: Sample NA18637


title: Sample NA18952


title: Sample NA18948


title: Sample NA18944


title: Sample NA18956


title: Sample NA18633


title: Sample NA18947


title: Sample NA18623


title: Sample NA18942


title: Sample NA18632


title: Sample NA18612


title: Sample NA18624


title: Sample NA18622


title: Sample NA18635


title: Sample NA18621


title: Sample NA18620


title: Sample NA18611


title: Sample NA18605


title: Sample NA18608


title: Sample NA18960


title: Sample NA18609


title: Sample NA18603


title: Sample NA18592


title: Sample NA18593


title: Sample NA18582


title: Sample NA18594


title: Sample NA18577


title: Sample NA18562


title: Sample NA18563


title: Sample NA18571


title: Sample NA18566


title: Sample NA18573


title: Sample NA18572


title: Sample NA18542


title: Sample NA18537


title: Sample NA18552


title: Sample NA18561


title: Sample NA12892


title: Sample NA18532


title: Sample NA18547


title: Sample NA18545


title: Sample NA18550


title: Sample NA18564


title: Sample NA18529


title: Sample NA12874


title: Sample NA18524


title: Sample NA18570


title: Sample NA12872


title: Sample NA12813


title: Sample NA12815


title: Sample NA12891


title: Sample NA12878


title: Sample NA12875


title: Sample NA12864


title: Sample NA12814


title: Sample NA12812


title: Sample NA12761


title: Sample NA12762


title: Sample NA12763


title: Sample NA12802


title: Sample NA12753


title: Sample NA12801


title: Sample NA12717


title: Sample NA12750


title: Sample NA12716


title: Sample NA12264


title: Sample NA12760


title: Sample NA12154


title: Sample NA12249


title: Sample NA12751


title: Sample NA12144


title: Sample NA12057


title: Sample NA12234


title: Sample NA12155


title: Sample NA12146


title: Sample NA12145


title: Sample NA12004


title: (129S1xB6) F1 XY gonad L1

status: Public on Oct 30 2009

type: RNA

city: Bar Harbor

first: Steven

middle: C

last: Munger

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Reference sample includes 4 pairs of e11.5 XY gonads, 3 pairs of e11.5 XX gonads, 4 e11.5 XY whole embryos, and 2 e11.5 XX whole embryos.

hyb_protocol: To each array, 900ng each of Cy5-labeled experimental and Cy3-labeled reference cRNA were co-hybridized at 65C for 17h according to Syed and Threadgill 2006.

scan_protocol: Microarrays were scanned using an Agilent scanner, and raw data were collected using feature extraction software (Agilent).

data_processing: Probe level data were imported into BRB-ArrayTools software (version 3.7.0), and normalized using the Lowess smoother function.

molecule: total RNA

organism: Mus musculus

source_name: e11.5 XY mouse gonads (1 pair)

label_protocol: 200-450ng total RNA from each sample was amplified into cRNA using the Low RNA Input Linear Amplification kit (Agilent) and labeled with 1.5uL Cy5-CTP according to protocols established by Agilent and modified by us (see Syed and Threadgill 2006).

growth_protocol: C57BL/6J (stock# 000664) and 129S1/SvImJ (stock# 002448) mice were obtained from The Jackson Laboratory. Timed matings were established, embryos were collected from pregnant mothers at embryonic day 11.5 (e11.5), where e0.5 is defined as noon on the day a mating plug was detected. Embryos were staged more precisely by counting tail somites distal to the hindlimbs according to Hacker et al (1995). Embryos that fell within a 17-21 tail somite window were included in this study.

extract_protocol: Total RNA isolated from e11.5 XY gonads (separated from mesonephroi) using Trizol reagent according to standard protocols optimized in lab. Glycogen was added (10ug) as a carrier molecule to improve RNA yield.

treatment_protocol: Gonads were dissected away from mesonephroi in sterile PBS and stored in RNAlater RNA stabilization solution (Ambion) at -80C.

tag: tissue

value: gonad

tag: sex

value: XY

tag: developmental stage

tag: strain

source_name: pooled gonads and whole mouse embryos e11.5

value: gonads and whole embryos

value: pooled XY and XX samples

value: Sox9-ECFP(C57BL/6J) x CD-1


title: Sample NA12003


title: Sample NA12006


title: Sample NA12005


title: Sample NA12044


title: Sample NA11994


title: Sample NA12043


title: Sample NA19172


title: Sample NA11840


title: Sample NA11882


title: Sample NA11995


title: Sample NA11832


title: Sample NA11993


title: Sample NA11830


title: Sample NA12873


title: Sample NA11829


title: Sample NA11992


title: Sample NA10857


title: Sample NA10861


title: Sample NA10859


title: Sample NA10851


title: Sample NA10847


title: Sample NA10839


title: Sample NA10838


title: Sample NA11881


title: Sample NA10835


title: Sample NA10855


title: Sample NA07348


title: Sample NA10830


title: Sample NA07056


title: Sample NA07357


title: Sample NA06985


title: Sample NA07048


title: Sample NA07029


title: Sample NA07022


title: Sample NA07000


title: Sample NA06994


title: Sample NA10863


title: Sample NA19239


title: Sample NA06991


title: Sample NA10831


title: Sample NA19222


title: Sample NA06993


title: Sample NA19208


title: Sample NA19211


title: Sample NA19205


title: Sample NA19209


title: Sample NA07019


title: Sample NA19238


title: Sample NA19221


title: Sample NA19240


title: Sample NA19206


title: Sample NA19204


title: Sample NA07034


title: Sample NA19203


title: Sample NA19200


title: Sample NA19193


title: Sample NA19223


title: Sample NA19202


title: Sample NA19201


title: Sample NA19207


title: Sample NA19161


title: Sample NA19194


title: Sample NA19192


title: Sample NA19171


title: Sample NA19173


title: Sample NA19172


title: Sample NA19210


title: Sample NA19152


title: Sample NA19154


title: Sample NA19159


title: Sample NA19145


title: Sample NA19142


title: Sample NA19160


title: Sample NA19140


title: Sample NA19153


title: Sample NA19131


title: Sample NA19144


title: Sample NA19130


title: Sample NA19132


title: Sample NA19137


title: Sample NA19139


title: Sample NA19120


title: Sample NA19116


title: Sample NA19127


title: Sample NA19138


title: Sample NA19129


title: Sample NA19103


title: Sample NA19128


title: Sample NA19143


title: Sample NA19098


title: Sample NA19101


title: Sample NA19099


title: Sample NA19100


title: Sample NA19141


title: Sample NA19093


title: Sample NA19092


title: Sample NA19102


title: Sample NA18913


title: Sample NA18914


title: Sample NA19094


title: Sample NA18871


title: Sample NA18912


title: Sample NA18870


title: Sample NA18862


title: Sample NA18860


title: Sample NA19119


title: Sample NA18856


title: Sample NA18863


title: Sample NA18854


title: Sample NA18853


title: Sample NA18859


title: Sample NA18522


title: Sample NA18858


title: Sample NA18857


title: Sample NA18861


title: Sample NA18521


title: Sample NA18852


title: Sample NA18504


title: Sample NA18515


title: Sample NA18872


title: Sample NA18508


title: Sample NA18502


title: Sample NA18506


title: Sample NA18501


title: Sample NA18855


title: Sample NA18516


title: Sample NA18500


title: Sample NA18998


title: Sample NA18505


title: Sample NA19005


title: Sample NA19003


title: Sample NA19012


title: Sample NA19000


title: Sample NA18523


title: Sample NA18997


title: Sample NA18981


title: Sample NA18991


title: Sample NA18503


title: Sample NA18987


title: Sample NA18980


title: Sample NA19007


title: Sample NA18994


title: Sample NA18507


title: Sample NA18517


title: Sample NA18975


title: Sample NA18992


title: Sample NA18995


title: Sample NA18990


title: Sample NA18974


title: Sample NA18973


title: Sample NA18971


title: Sample NA18966


title: Sample NA18999


title: Sample NA18964


title: Sample NA18972


title: Sample NA18969


title: Sample NA18968


title: Sample NA18965


title: Sample NA18976


title: Sample NA18959


title: Sample NA18978


title: Sample NA18951


title: Sample NA18943


title: Sample NA18949


title: Sample NA18944


title: Sample NA18970


title: Sample NA18942


title: Sample NA18967


title: Sample NA18961


title: Sample NA18960


title: Sample NA18952


title: Sample NA18632


title: Sample NA18624


title: Sample NA18947


title: Sample NA18945


title: Sample NA18953


title: Sample NA18940


title: Sample NA18605


title: Sample NA18636


title: Sample NA18603


title: Sample NA18594


title: Sample NA18579


title: Sample NA18948


title: Sample NA18593


title: Sample NA18576


title: Sample NA18635


title: Sample NA18956


title: Sample NA18623


title: Sample NA18633


title: Sample NA18622


title: Sample NA18621


title: Sample NA18611


title: Sample NA18620


title: Sample NA18637


title: Sample NA18612


title: Sample NA18609


title: Sample NA18608


title: Sample NA18555


title: Sample NA18563


title: Sample NA18550


title: Sample NA18572


title: Sample NA18571


title: Sample NA18537


title: Sample NA18545


title: Sample NA18529


title: Sample NA18552


title: Sample NA18532


title: Sample NA18592


title: Sample NA15510


title: Sample NA18582


title: Sample NA12872


title: Sample NA18577


title: Sample NA12865


title: Sample NA12815


title: Sample NA12814


title: Sample NA18573


title: Sample NA12801


title: Sample NA18570


title: Sample NA18558


title: Sample NA18564


title: Sample NA18561


title: Sample NA18547


title: Sample NA18566


title: Sample NA18562


title: Sample NA12760


title: Sample NA12751


title: Sample NA12750


title: Sample NA12892


title: Sample NA18526


title: Sample NA18542


title: Sample NA12740


title: Sample NA12873


title: Sample NA12707


title: Sample NA12874


title: Sample NA12875


title: Sample NA18524


title: Sample NA12878


title: Sample NA12864


title: Sample NA12264


title: Sample NA12891


title: Sample NA12249


title: Sample NA12812


title: Sample NA12813


title: Sample NA12802


title: Sample NA12763


title: Sample NA12762


title: Sample NA12156


title: Sample NA12753


title: Sample NA12761


title: Sample NA12752


title: Sample NA12056


title: Sample NA12144


title: Sample NA12145


title: Sample NA12716


title: Sample NA12248


title: Sample NA12717


title: Sample NA12154


title: Sample NA12234


title: Sample NA12146


title: Sample NA12043


title: Sample NA12155


title: Sample NA12005


title: Sample NA12004


title: Sample NA12006


title: Sample NA12057


title: Sample NA12239


title: Sample NA12044


title: Sample NA12003


title: Sample NA11995


title: Sample NA11994


title: Sample NA11993


title: Sample NA11992


title: Autistic_AU1443

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
4107

hyb_protocol: The two differentially labeled probes (Cy3 vs Cy5) were mixed and dried. 1X hybridization buffer (50% formamide, 5X SSC, and 0.1% SDS), as well as Human COT1-DNA (Life Technologies) and Poly(A)-DNA (Pharmacia), were added. Each sample was hybridized on a TIGR40K cDNA microarray overnight. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an GenePix 4000B scanner. Images were quantified using TIGR Spotfinder.

data_processing: The intensity data was normalized and filtered using Lowess normalization and standard deviation regularization within Midas software and analyzed using MeV, which are open-access software programs for DNA microarray analyses. Significant differentially expressed genes were identified using the Significance Analysis of Microarrays (SAM) module within MeV for both 2-class and 4-class analyses, with a maximum false discovery rate (FDR) of 5%.

source_name: LCL derived from autistic sibling

label_protocol: 10 ug of total RNA were primed with 2 ul of Random Hexamer Primers (3 mg/mL) at 70°C for 10 min, then reversed transcribed at 42°C overnight in the presence of 400 U SuperScript II RTase (Invitrogen), and 1.2 ul of 25X aminoallyl-dNTP mix (Ambion). 4.5 ul of the appropriate NHS-ester Cy dye (AmershamPharmacia) in DMSO was added to aa-cDNA.

extract_protocol: Total RNA was isolated from LCL using the TRIzol (Invitrogen) isolation method according to the manufacturer’s protocols.

tag: disease

value: autistic

tag: cell type

value: lymphoblastoid

tag: sample type

value: test

tag: agre id

source_name: Strategene Universal Reference Human RNA

value: reference


title: Sample NA11881


title: Autistic_AU1234

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
4360


title: Autistic_AU1244

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
3650


title: Control_AU1443

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
4109

source_name: LCL derived from nonautistic sibling

value: nonautistic


title: Autistic_AU1181

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
3913


title: Sample NA11882


title: Control_AU1327

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
3299


title: Sample NA11839


title: Control_AU1244

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
3649


title: Control_AU1234

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
4359


title: Sample NA11840


title: Autistic_AU1065

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
2769


title: Sample NA11832


title: Control_AU0939

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
2590


title: Sample NA11831


title: Control_AU1065

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
2772


title: Autistic_AU0939

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
2591


title: Autistic_AU0777

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
2044


title: Control_AU1181

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
3914


title: Control_AU0777

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
2022


title: Autistic_AU1327

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
3301


title: Autistic_AU0808

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
2020


title: Sample NA10863


title: Sample NA11830


title: Sample NA10861


title: Control_AU0808

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
2019


title: Sample NA11829


title: Sample NA10859


title: Sample NA10860


title: Sample NA10856


title: Sample NA10857


title: Sample NA10851


title: Sample NA10855


title: Sample NA10846


title: Sample NA10847


title: Autistic_AU0555

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
802


title: Sample NA10838


title: Control_AU0465

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
781


title: Autistic_AU0465

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
785


title: Autistic_AU0388

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
777


title: Autistic_AU0325_b

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
366

source_name: LCL derived from autistic sibling, MZ twin

tag: zygosity

value: MZ twin


title: Sample NA10835


title: Sample NA10839


title: Sample NA10831


title: Autistic_AU0108

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
737


title: Control_AU0388

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
779


title: Sample NA07357


title: Autistic_AU0227_b

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
356


title: Sample NA10830


title: Control_AU0555

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
3168


title: Control_AU0325

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
365


title: Autistic_AU0227_a

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
355


title: Autistic_AU0145_b

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
489

source_name: LCL derived from autistic sibling, triplet, DZ twin

value: triplet, DZ twin


title: Autistic_AU0325_a

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
364


title: Sample NA07345


title: Sample NA07348


title: Sample NA07055


title: Sample NA07056


title: Control_AU0108

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
735


title: Sample NA07048


title: Autistic_AU0145_a

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
488


title: Autistic_AU1059_b

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
3144


title: Control_AU1059

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
3143


title: Control_AU0227

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
354


title: Autistic_AU1059_a

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
3141


title: Sample NA07022


title: Sample NA07019


title: Control_AU0145

description:
Lymphoblastoid cell line derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE).
487

source_name: LCL derived from nonautistic sibling, triplet

value: triplet


title: Sample NA07034


title: Sample NA07029


title: Sample NA07000


title: Sample NA06994


title: Sample NA19222

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH


title: Sample NA06985


title: Sample NA19211


title: Sample NA19239


title: Sample NA19238


title: Sample NA19240


title: Sample NA06991


title: Sample NA19223


title: det2-1 replica 1

city: Valencia

first: David

last: Alabadi

state: Valencia

address: Av de los Naranjos s/n, Campus UPV, Edificio 8E

department: Biologia del Desarrollo

country: Spain

institute: Instituto de Biologia Molecular y Celular de Plantas (CSIC-UPV)

description: det2-1 seedlings transferred to 29ºC labelled with Cy5 (replica 1) and compared with det2-1 control seedlings kept at 20ºC labelled with Cy3 (replica 1)

hyb_protocol: DNA onto slides was rehydrated by placing the slide upside-down over a water bath at 60°C for 10 s, and snap dry onto a heat block at 65°C. Rehydratation was repeated 3 times. DNA was immobilized by UV light by exposing the slides DNA-side-up to 65 mJ in a UV cross-linker (Stratagene). Slides were then washed twice in 0.1% SDS and 4 times in water, 2 min each wash at RT, and finally dipped in 96% ethanol for 1 min and dried by centrifugation at 2000 rpm 1 min at RT. Slides were prehybridized for 30 min at 42°C with 100 µL of prehybridization solution (6x SSC (Sigma), 1% BSA (Sigma) and 0.5% SDS (Sigma)), under a 60x22 mm coverslip LifterSlip (Erie Scientific) in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were rinsed 5 times in H2O in a slide rack at RT and dried by centrifugation at 2000 rpm 1 min at RT. Slides were hybridized immediately.  Both coupled aa-aRNA (Cy3 and Cy5) were mixed and fragmented in the presence of 20 µg of tRNA (Ambion) and 20 µg of poly(A) (Roche) using the RNA fragmentation Reagent (Ambion) as described by the manufacturer, in a final volume of 10 µL. Fragmented aa-aRNA was used directly in the hybridization mix, which contains 50 µL deionized formamide (Sigma), 30 µL 20x SSC, 5 µL 100x Denhardt´s solution (Sigma), and 5 µL 10% SDS in a final volume of 100 µL. Hybridization mixture was denatured at 95 °C for 5 min, spun briefly, and applied by capillarity between a pre-treated slide (see above) and a 60x42 mm coverslip LifterSlip. Slides were incubated o/n at 37°C in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were washed sequentially once in 1x SSC 0.1% SDS 5 min at 30°C; once in 0.2x SSC 0.1% SDS 5 min at 30°C; twice in 0.1x SSC 2 min each at 30°C; and finally 0.01x SSC 10 sec at RT. Slides were dried by centrifugation at 2000 rpm 1 min at RT.

scan_protocol: Hybridized microarray slides were scanned at 532-nm for the Cy3 and 635-nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA), at 10-mm resolution and 100% laser power.

data_processing: Spot intensities were quantified using GenePix Pro 6.0 microarray-analysis software (Axon Molecular Devices, Sunnyvale CA). Spots with a net intensity in both channels lower than the median signal background plus twice standard deviations were removed as low signal spots.  Data were normalized by median global intensity using the GenePix Pro 6.0 software. VALUEs for wt-REP2, wt-REP3, pac-REP2, pac-REP3, npa-REP2, npa-REP3, det2-REP2 and det2-REP3 have been dye-swap corrected.

organism: Arabidopsis thaliana

source_name: det2-1 seedlings transferred to 29ºC

label_protocol: RNA was amplified using the MessageAmp II aRNA Amplification kit (Ambion), basically as described by the manufacturer. 5-(3-aminoallyl)-UTP (aa-UTP) (Ambion) was incorporated into the amplified RNA (aRNA) at ratio 1:1 with UTP. After purification 7.5 µg of aminoallyl-aRNA (aa-aRNA) were used in a coupling reaction with either fluorescent Cy3 or Cy5 as reactive N-hydroxyl succinimidal dyes (NHS-dyes) (Amersham Pharmacia Biotech, Piscataway, NJ). For this, each aliquot of Cy3 or Cy5 were dissolved in 20 µL of DMSO and used in four coupling reactions. aa-aRNA was dissolved in 15 µL of freshly-made 0.1 M NaCO3 pH 9.0, and mixed with 5 µl of either Cy-3 or Cy-5 dye. Coupling was allowed for 1 h at RT in the dark. Reaction was stopped with 35 µL of 100 mM sodium acetate pH 5.2 and incubated 5 min in the dark. Fluorescent aa-aRNA was purified using a MegaClear purification column (Ambion) as described by the manufacturer. Coupled aa-aRNA (250-300 pmol Cy dye in 5-7 µg aa-aRNA) was dried in a speedvac and dissolved in 2.5 µL of filtered water.

growth_protocol: Wild type Arabidopsis seeds were surface sterilized and sown on sterile filter papers, deposited on half-strength MS media plus 1% sucrose and stratified for 7 days at 4ºC in darkness.  det2-1 mutant seeds were sown directly on the MS media and stratified like the wild types. Duplicate plates were prepared for each case. Germination of all seeds was induced by placing plates at 20ºC and under white fluorescent light (150 mmol m-2 s-1) for 24h. Next, wild type seeds on filter papers were transferred to treatment plates containing either 1 mM paclobutrazol (PAC), 100 mM NPA or mock solution. All plates were kept for three additional days at 20ºC under constant, white fluorescent light (20 mmol m-2 s-1).

extract_protocol: Total RNA was extracted from frozen, 4-day-old whole seedlings, using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: One plate per sample category was transferred to 29ºC under continuous, white fluorescent light (20 mmol m-2 s-1) for 2h; control plates were kept at 20ºC under the same lighting regime.

tag: 4-day-old det2-1 seedlings transferred to 29ºC

source_name: det2-1 control seedlings kept at 20ºC

tag: 4-day-old det2-1 control seedlings kept at 20ºC


title: Sample NA19221


title: Sample NA19210


title: Sample NA06993


title: Wild type NPA-treated replica 2

description: NPA-treated, wild type seedlings transferred to 29ºC labelled with Cy3 (replica 2) compared with NPA-treated, wild type control seedlings kept at 20ºC labelled with Cy5 (replica 2)

tag: 4-day-old NPA-treated, wild type control seedlings kept at 20ºC

tag: 4-day-old NPA-treated, wild type seedlings transferred to 29ºC


title: Wild type PAC-treated replica 3

description: PAC-treated, wild type seedlings transferred to 29ºC labelled with Cy3 (replica 3), compared to PAC-treated, wild type control seedlings kept at 20ºC labelled with Cy5 (replica 3)

tag: 4-day-old PAC-treated, wild type control seedlings kept at 20ºC

tag: 4-day-old PAC-treated, wild type seedlings transferred to 29ºC


title: Sample NA19208


title: Sample NA19207


title: Sample NA19209


title: det2-1 replica 3

description: det2-1 seedlings transferred to 29ºC labelled with Cy3 (replica 3) and compared with det2-1 control seedlings kept at 20ºC labelled with Cy5 (replica 3)


title: det2-1 replica 2

description: det2-1 seedlings transferred to 29ºC labelled with Cy3 (replica 2) and compared with det2-1 control seedlings kept at 20ºC labelled with Cy5 (replica 2)


title: Wild type PAC-treated replica 1

description: PAC-treated, wild type seedlings transferred to 29ºC labelled with Cy5 (replica 1), compared to PAC-treated, wild type control seedlings kept at 20ºC labelled with Cy3 (replica 1)


title: Wild type NPA-treated replica 1

description: NPA-treated, wild type seedlings transferred to 29ºC labelled with Cy5 (replica 1) compared with NPA-treated, wild type control seedlings kept at 20ºC labelled with Cy3 (replica 1)


title: Wild type NPA-treated replica 3

description: NPA-treated, wild type seedlings transferred to 29ºC labelled with Cy3 (replica 3) compared with NPA-treated, wild type control seedlings kept at 20ºC labelled with Cy5 (replica 3)


title: Sample NA19204


title: Wild type mock treated replica 2

description: Mock-treated, wild type seedlings transferred to 29ºC, labelled with Cy3 (replica 2), compared with mock-treated, wild type control seedlings kept at 20ºC labelled with Cy5 (replica 2)

source_name: Mock-treated, wild type control seedlings kept at 20ºC

tag: 4-day-old mock-treated, wild type control seedlings kept at 20ºC

tag: 4-day-old mock-treated, wild type seedlings transferred to 29ºC


title: Wild type PAC-treated replica 2

description: PAC-treated, wild type seedlings transferred to 29ºC labelled with Cy3 (replica 2), compared to PAC-treated, wild type control seedlings kept at 20ºC labelled with Cy5 (replica 2)


title: Wild type mock treated replica 3

description: Mock-treated, wild type seedlings transferred to 29ºC, labelled with Cy3 (replica 3), compared with mock-treated, wild type control seedlings kept at 20ºC labelled with Cy5 (replica 3)


title: Sample NA19192

tag: sample


title: Sample NA19201


title: Sample NA19200


title: Sample NA19205


title: Sample NA19193


title: Sample NA19203


title: Sample NA19202


title: Sample NA19173


title: Sample NA19160


title: Sample NA19194


title: Sample NA19171


title: Sample NA19172


title: Sample NA19152


title: Sample NA19161


title: Wild type mock treated replica 1

description: Mock-treated, wild type seedlings transferred to 29ºC labelled with Cy5 (replica 1), compared with mock-treated, wild type control seedlings kept at 20ºC labelled with Cy3 (replica1)


title: Sample NA19144


title: Sample NA19153


title: Sample NA19206


title: Sample NA19141


title: Sample NA19145


title: Sample NA19142


title: Sample NA19132


title: Sample NA19129


title: Sample NA19140


title: Sample NA19139


title: Sample NA19159


title: Sample NA19154


title: Sample NA19130


title: Sample NA19102


title: Sample NA19131


title: Sample NA19143


title: Sample NA19137


title: Sample NA19116


title: Sample NA19138


title: Sample NA19239


title: Sample NA19100


title: Sample NA19127


title: Sample NA19119


title: Sample NA19103


title: Sample NA19098


title: Sample NA19240


title: Sample NA19194


title: Sample NA19101


title: Sample NA19128


title: Sample NA19238_R


title: Sample NA19099


title: Sample NA19238


title: Sample NA19193


title: Sample NA19094


title: Sample NA18914


title: Sample NA19171


title: Sample NA19172


title: Sample NA18913


title: Sample NA19093


title: Sample NA19173


title: Sample NA18871


title: Sample NA19144


title: Sample NA19092


title: Sample NA18870


title: Sample NA19159


title: Sample NA19145


title: Sample NA19192


title: Sample NA18872


title: Sample NA18862


title: Sample NA19143


title: Sample NA18863


title: Sample NA18861


title: Sample NA19142


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title: Sample NA18860


title: Sample NA19160


title: Sample NA19140


title: Sample NA18912


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title: Sample NA19211


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title: Sample NA19137


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title: Sample NA18516


title: Sample NA18968


title: Sample NA19139


title: Sample NA19116


title: Sample NA18953


title: Sample NA19132


title: Sample NA19103


title: Sample NA18951_R


title: Sample NA19005


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title: Sample NA19098


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title: Sample NA18854


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title: Sample NA18913


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title: Sample NA18994


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title: Sample NA18961


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title: Sample NA12878


title: Sample NA18987


title: Sample NA12875


title: Sample NA18981


title: Sample NA18960


title: Sample NA12892


title: Sample NA12874


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title: Sample NA12812


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title: Sample NA18948


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title: Sample NA12249


title: Sample NA18961


title: Sample NA18944


title: Sample NA18951


title: Sample NA12248_R2


title: Sample NA18967


title: Sample NA12248_R


title: Sample NA18948


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title: Sample NA18940


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title: Sample NA12154


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title: Sample NA18608


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title: Sample NA18594


title: Sample NA18605


title: Sample NA11995


title: Sample NA11993_R


title: Sample NA19240


title: Sample NA18582


title: Sample NA11994


title: Sample NA19239


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title: Sample NA18592


title: Sample NA18609


title: Sample NA18611


title: Sample NA11993


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title: Sample NA18620


title: Sample NA18576


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title: Sample NA18608


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title: Sample NA19238


title: Sample NA18579


title: Sample NA18605


title: Sample NA10863


title: Sample NA18572


title: Sample NA11882


title: Sample NA18594


title: Sample NA10861


title: Sample NA19192


title: Sample NA10860


title: Sample NA19173


title: Sample NA10859


title: Sample NA18592


title: Sample NA18593


title: Sample NA19161


title: Sample NA19172


title: Sample NA18577


title: Sample NA18582


title: Sample NA18566


title: Sample NA10857


title: Sample NA18579


title: Sample NA10851


title: Sample NA19171


title: Sample NA18571


title: Sample NA18572


title: Sample NA18564


title: Sample NA18558


title: Sample NA18573


title: Sample NA10847


title: Sample NA18576


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title: Sample NA18570


title: Sample NA10835


title: Sample NA10830


title: Sample NA19145


title: Sample NA19159


title: Sample NA18561


title: Sample NA07345


title: Sample NA07348


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title: Sample NA07357


title: Sample NA19144


title: Sample NA18564


title: Sample NA18571


title: Sample NA19143


title: Sample NA18562


title: Sample NA18552


title: Sample NA19140


title: Sample NA18555


title: Sample NA18563


title: Sample NA18566


title: Sample NA06994


title: Sample NA19138


title: Sample NA06993_R


title: Sample NA18561


title: Sample NA18537


title: Sample NA07029


title: Sample NA18550


title: Sample NA18532


title: Sample NA06993


title: Sample NA18547


title: Sample NA07000


title: Sample NA18545


title: Sample NA18542


title: Sample NA19119


title: Sample NA19141


title: Sample NA19137


title: Sample NA19139


title: Sample NA18524


title: Sample NA18558


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title: Sample NA19120


title: Sample NA19129


title: Sample NA06991


title: Sample NA06985


title: Sample NA18552


title: Sample NA12878


title: ST486_NT2 (gcrma)

city: New York

first: Mariano

middle: Javier

last: Alvarez

state: NY

address: 1130 St. Nicholas ave.

department: Systems Biology

institute: Columbia University

description: Lentiviral-mediated expression of non-target control shRNA in ST486 Burkitt's lymphoma cells for 24h. 5 ug of total RNA were hybridized in Affymetrix U95Av2 expression arrays.

hyb_protocol: According to Affymetrix 701025 rev 6

scan_protocol: The arrays were processed on a Gene Chip Fluidics Station 450 and scanned on a Affymetrix GeneChip Scanner (Santa Clara, CA).

data_processing: Normalization and summarization by gcrma implemented in gcrma package / bioconductor (www.bioconductor.org), using fast parameter set to FALSE

label: biotin

source_name: ST486 Burkitt's lymphoma cells transduced with NT control shRNA lentivirus-vector for 24h

label_protocol: Affymetrix one cycle cDNA synthesis protocol (Affymetrix 701025 Rev 6)

extract_protocol: TRIZOL followed by RNAeasy (Qiagen) columns cleanup

tag: transduction

value: non-target control shRNA (Sigma SHC002)

tag: time


title: Sample NA18526


title: Sample NA19116


title: Sample NA18540


title: Sample NA19003


title: Sample NA12875


title: ST486_NT3 (gcrma)


title: Sample NA12892


title: Sample NA18545


title: ST486_NT1 (gcrma)


title: Sample NA12891


title: Sample NA18555


title: Sample NA18537


title: Sample NA18532


title: Sample NA18529


title: ST486_MYB1 (gcrma)

description: Lentiviral-mediated expression of MYB shRNA in ST486 Burkitt's lymphoma cells for 24h. 5 ug of total RNA were hybridized in Affymetrix U95Av2 expression arrays.

source_name: ST486 Burkitt's lymphoma cells transduced with MYB shRNA lentivirus-vector for 24h

value: MYB shRNA (Sigma TRCN0000040062)


title: ST486_MYB2 (gcrma)


title: Sample NA18542


title: Sample NA18992


title: ST486_MYB3 (gcrma)


title: Sample NA12872


title: Sample NA19093


title: ST486_Fox3 (gcrma)

description: Lentiviral-mediated expression of FOXM1 shRNA in ST486 Burkitt's lymphoma cells for 24h. 5 ug of total RNA were hybridized in Affymetrix U95Av2 expression arrays.

source_name: ST486 Burkitt's lymphoma cells transduced with FOXM1 shRNA lentivirus-vector for 24h

value: FOXM1 shRNA (Sigma TRCN0000015546)


title: Sample NA12865


title: Sample NA19092


title: ST486_Fox2 (gcrma)


title: Sample NA12864


title: Sample NA18978


title: Sample NA12874


title: Sample NA18999


title: Sample NA18526


title: Sample NA12891


title: Sample NA12814


title: Sample NA12878


title: Sample NA18524


title: Sample NA18968


title: Sample NA12873


title: ST486_Fox1 (gcrma)


title: Sample NA18987


title: Sample NA12875


title: Sample NA18994


title: Sample NA12802


title: ST486_MYB3 (MAS5)

data_processing: Normalization and summarization by MAS5 implemented in affy package / bioconductor (www.bioconductor.org), and log2 transformation


title: ST486_NT3 (MAS5)


title: ST486_MYB2 (MAS5)


title: ST486_NT2 (MAS5)


title: Sample NA12815


title: Sample NA12892


title: Sample NA18971


title: Sample NA18972


title: Sample NA18952


title: Sample NA12813


title: Sample NA12812


title: Sample NA12874


title: Sample NA18965


title: ST486_NT1 (MAS5)


title: Sample NA12762


title: Sample NA18960


title: Sample NA12873


title: Sample NA12801


title: ST486_Fox2 (MAS5)


title: Sample NA18953


title: ST486_MYB1 (MAS5)


title: Sample NA12865


title: Sample NA12872


title: Sample NA12763


title: Sample NA12864


title: Sample NA12752


title: ST486_Fox3 (MAS5)


title: Sample NA12761


title: Sample NA18951


title: Sample NA12802


title: Sample NA12760


title: Sample NA18949


title: Sample NA12814


title: Sample NA12753


title: Sample NA12812


title: Sample NA18857


title: Sample NA18944


title: Sample NA12751


title: Sample NA12813


title: ST486_Fox1 (MAS5)


title: Sample NA18856


title: Sample NA12801


title: Sample NA18852


title: Sample NA12740


title: Sample NA18854


title: Sample NA12717


title: Sample NA12762


title: Sample NA12264


title: Sample NA12716


title: Sample NA18853


title: Sample NA12248


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title: Sample NA12752


title: Sample NA12761


title: Sample NA12236


title: Sample NA12760


title: Sample NA18593


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title: Sample NA18608


title: Sample NA12750


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title: Sample NA12239


title: Sample NA18577


title: Sample NA12717


title: Sample NA12156


title: Sample NA18558


title: Sample NA12249


title: Sample NA12154


title: Sample NA12155


title: Sample NA12707


title: Sample NA18576


title: Sample NA18555


title: Sample NA12146


title: Sample NA12248


title: Sample NA18547


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title: Sample NA12057


title: Sample NA18542


title: Sample NA12750


title: Sample NA18550


title: Sample NA12239


title: Sample NA18537


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title: Sample NA12056


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title: Sample NA12043


title: Sample NA12044


title: Sample NA12144


title: Sample NA18529


title: Sample NA12156


title: Sample NA18517


title: Sample NA12155


title: Sample NA12005


title: Sample NA12154


title: Sample NA12146


title: Sample NA12006


title: Sample NA18516


title: Sample NA12892


title: Sample NA12003


title: Sample NA12004


title: Sample NA12891


title: Sample NA12145


title: Sample NA11994


title: Sample NA12878


title: Sample NA12875


title: Sample NA18515


title: Sample NA12057


title: Sample NA12874


title: Sample NA12044


title: Sample NA12056


title: Sample NA11993


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title: Sample NA11992


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title: Sample NA12813


title: Sample NA12003


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title: Sample NA12750


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title: Sample NA11994


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title: Sample NA11993


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title: Sample NA11992


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title: Sample NA12801


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title: Sample NA10861


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title: Sample NA12239


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title: Sample NA11840


title: Sample NA12156


title: Sample NA10863


title: Sample NA11830


title: Sample NA11831


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title: Sample NA12056


title: Sample NA12146


title: Sample NA12248


title: Sample NA10847


title: Sample NA10846


title: Sample NA10831


title: Sample NA12057


title: Sample NA10861


title: Sample NA12154


title: Sample NA10839


title: Sample NA10860


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title: Sample NA10854


title: Sample NA12043


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title: Sample NA10838


title: Sample NA10857


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title: Sample NA10847


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title: Sample NA07055


title: Sample NA11992


title: Sample NA11994


title: Sample NA07048


title: Sample NA10855


title: Sample NA11993


title: Sample NA10846


title: Sample NA07348


title: Sample NA10851


title: Sample NA10839


title: Sample NA10860


title: Sample NA07029


title: Sample NA10863


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title: Sample NA07022


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title: Sample NA10859


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title: Sample NA07055


title: Sample NA06991


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title: Sample NA07345


title: Sample NA07048


title: Sample NA07034


title: Sample NA07029


title: Sample NA07022


title: S.0.5

city: Philadelphia

first: Louise

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

description: ear tissue from mouse

hyb_protocol: Illumina Hyb protocol

scan_protocol: Illumina scan protocol

data_processing:
1. The raw data of the spot density was extracted from Illumina BeadStudio software.
2. Check samples outlier.
3. Filter out genes that had poor detection in all samples ( detection p-value>0.05 in all samples) or genes that have at least <1.2 fold change between at least 2 samples
4. Quantile normalization for the filtering data.
5. Apply one-way ANOVA on the quantile normalization data to find out the significant gene data.

source_name: S.0.  normal ear tissue from the mouse strain SM/J

label_protocol:
Pipette 2 mL Block E1 buffer + streptavidin-Cy3 into fresh Wash Tray(s).
Transfer the BeadChip, face up into Wash Tray(s) on rocker.
Place cover on tray and rock at medium speed for 10 minutes.

extract_protocol: Total RNA was extracted using Trizol according to manufacturer's protocol (Invitrogen).

tag: tissue

value: ear tissue

tag: strain

value: SM/J


title: S.7.2

description: ear tissue from mouse from around the injury site, 7 days post-injury

source_name: S.7.  SM/J ear tissue from around the injury site, 7 days post-injury

tag: stress

value: ear punch

value: 7 days post-injury


title: L.7.3

source_name: L.7.  LG/J ear tissue from around the injury site, 7 days post-injury

value: LG/J


title: S.7.3


title: S.0.2

description: ear tissue from mouse


title: L.7.1


title: L.0.1

description: ear tissue from mouse

source_name: L.0.  normal ear tissue from the mouse strain LG/J


title: S.0.4

description: ear tissue from mouse


title: L.0.4

description: ear tissue from mouse


title: Right atria dnPI3K-Mst1 1650

status: Public on Jul 25 2009

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

description: Gene expression data from heart atria

hyb_protocol: Following fragmentation, 15 ug of cRNA were processed through second-cycle single stranded cDNA, fragmented and labelled cDNA were then hybridized for 16 hr at 45C on Affymetrix Mouse Gene 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Gene arrays were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Gene array data is processd by Expression Console software in which mean probeset signals for all probesets are analysed. A receiver operating curve (ROC) is generated by thrseholding the computed value for the probesets. PLIER signals that pass this QC control is used for subsequent analysis.

source_name: RNA from mouse heart atria, dnPI3K-Mst1

label_protocol: Fragmented and biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA for Affymetrix Mouse Gene 1.0 ST arrays

growth_protocol: The mice were on a standard chow diet, and were kept in temperature controlled cages (21 - 23 degree celcius) and maintained a 12 hour light/dark cycle

extract_protocol: Heart was homogenized individually using motar and pestle in liquid nitrogen. Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen).

treatment_protocol: Transgenics models dnPI3k, Mst1 and dnPI3K-Mst1 were made accordingly.

tag: male C57BL/6/FVB/N


title: Left atria dnPI3K-Mst1 1650

description: Gene expression data from heart atria


title: L.7.2


title: Left atria dnPI3K-Mst1 1649

description: Gene expression data from heart atria


title: Right atria dnPI3K-Mst1 1647

description: Gene expression data from heart atria


title: Left atria dnPI3K-Mst1 1509

description: Gene expression data from heart atria


title: L.0.3

description: ear tissue from mouse


title: Right atria dnPI3K 1660

description: Gene expression data from heart atria

source_name: RNA from mouse heart atria, dnPI3K


title: Right atria dnPI3K-Mst1 1649

description: Gene expression data from heart atria


title: Right atria dnPI3K-Mst1 1509

description: Gene expression data from heart atria


title: Left atria dnPI3K-Mst1 1647

description: Gene expression data from heart atria


title: Left atria dnPI3K 1660

description: Gene expression data from heart atria


title: S.7.1


title: Left atria dnPI3K 3241

description: Gene expression data from heart atria


title: Right atria dnPI3K 3241

description: Gene expression data from heart atria


title: Left atria dnPI3K 1648

description: Gene expression data from heart atria


title: ancestor versus CV115

city: Missoula

first: Frank

last: Rosenzweig

state: MT

address: 32 Campus Drive, HS 104

department: Division of Biological Sciences

institute: University of Montana

description: evolved strains were isolated after 770 generations in a glucose limited chemostat (Davis minimal medium, 0.0125% glucose, dilution rate = 0.2/hr.)

hyb_protocol: Hybridization was performed using protocols developed at the J. Craig Venter Institute (http://pfgrc.tigr.org/protocols/protocols.shtml) with the following modifications: Slides were blocked (using 5X SSC, 0.1% SDS, 1% Roche Blocking Reagent) prior to hybridization as described (http://www.genomics.princeton.edu/dunham/MDhomemadeDNA.pdf) (Roche Applied Science, Mannheim, Germany).

scan_protocol: Hybridized arrays were scanned using an Axon 4000B scanner and software package GenePix  5.0 (Molecular Devices, Sunnyvale, CA).

data_processing: a-CGH images were processed using a combination of GenePix Pro 5.0, the TIGR TM4 software suite available at (www.tm4.org), and Microsoft Excel. Image analysis and spot filtering was done in GenePix and a-CGH spots were considered acceptable if they: (1) passed the default flag conditions imposed by the software during spot finding; (2) had an intensity:background ratio >1.5 and overall intensity >350 in the reference channel; and (3) had an intensity:background ratio >1.0 in the experimental channel.  Ratios were normalized using total intensity normalization and replicate spots were averaged using TIGR MIDAS software.

organism: Escherichia coli K-12

source_name: evolved strain CV115

label_protocol: CGH was performed using protocols developed at the J. Craig Venter Institute (http://pfgrc.tigr.org/protocols/protocols.shtml) with the following modifications. 5 μg of genomic DNA was sonicated to an average fragment length of 2-5 kb using a Branson Digital Sonifier at 11% amplitude for 1.1 seconds and a final concentration of 0.5 mM, and 1:1 aa-dUTP:dTTP labeling mixture was used in the Klenow reaction.

extract_protocol: Genomic DNA was extracted from cells grown in batch culture using a modification of methods described by Syn and Swarup [92]. Subsequent to DNA precipitation, spun pellets were re-suspended in 1XTE (10 mM Tris, 1 mM EDTA, pH 8.0) containing 50μg/mL DNAse-free RNAse A and incubated at 37°C for 30 minutes. Samples were re-extracted once with phenol:chloroform (3:1), once with phenol:chloroform (1:1) and twice with chloroform and then precipitated with EtOH using standard techniques. Following re-precipitation, the DNA was dissolved in TE.

tag: parent strain

tag: growth medium

value: Luria broth

source_name: ancestor JA122

tag: ancestor strain


title: ancestor versus CV103

source_name: evolved strain CV103


title: ancestor versus CV101

source_name: evolved strain CV101


title: ancestor versus CV116

source_name: evolved strain CV116


title: Right atria dnPI3K 1648

description: Gene expression data from heart atria


title: ancestor versus consortium, biological replicate 3, hybridization 2

data_processing: Total intensity normalized, background subtracted data obtained from log2 of processed experimental signal/processed reference signal. TIGR TM4 software suite was used.

source_name: consortium 3

label_protocol: Samples were labeled following the protocol developed at the J. Craig Venter Institute (http://pfgrc.tigr.org/protocols/protocols.shtml) with the following modifications:  20 μg of total RNA was reverse transcribed using 9 μg of random hexamer and 0.83 mM 1:1 aa-dUTP:dTTP labeling mixture.

extract_protocol: Total RNA was extracted using an SDS lysis/ hot phenol method developed by the Dunham lab http://www.genomics.princeton.edu/dunham/MDyeastRNA.htm. Briefly, frozen filters were mixed with 4 mL lysis solution (10 mM EDTA, 0.5% SDS, 10 mM Tris pH 7.4) and vortexed to remove cells. An equal volume of acid phenol (pH 4.5) was added and the mixture was incubated at 65°C for 1 hour with frequent mixing. The entire extraction was transferred to a phase-lock gel tube (5Prime Inc., Gaithersburg, MD) and centrifuged according to the manufacturer’s instructions. The aqueous layer was extracted twice more with chloroform:isoamyl alcohol (24:1) and precipitated with ethanol. Pellets were dried and dissolved in RNase free water, treated with 0.1U/µl RQ1 RNase-free DNase at 37°C for 1 hour (Promega, Madison WI), then further purified using the Qiagen RNeasy Mini kit. RNA quality was assessed on agarose denaturing gels as well as using a Bioanalyzer (Agilent Technologies) and quantified spectrophotometrically

value: Davis minimal medium with 0.0125% glucose

tag: culture condition

value: chemostat, dilution rate=0.2/hr.

source_name: ancestral strain JA122, monoculture

tag: ancestral strain

value: chemostat, dilution rate = 0.2/hr


title: ancestor versus consortium, biological replicate 2, hybridization 2

source_name: consortium 2


title: ancestor versus consortium, biological replicate 2, hybridization 1


title: ancestor versus consortium, biological replicate 3, hybridization 1


title: Right atria Ntg 1834

description: Gene expression data from heart atria

source_name: RNA from mouse heart atria, Ntg


title: ancestor versus CV116 biological replicate 3, sample B, hybridization 1

source_name: evolved strain CV116, monoculture


title: Right atria dnPI3K 1507

description: Gene expression data from heart atria


title: Left atria dnPI3K 1507

description: Gene expression data from heart atria


title: ech52-meso95B

city: Nantes

first: Raluca

last: TEUSAN

address: 1, rue gaston veil

country: France

institute: INSERM U915

hyb_protocol: Each individual Cy3-labeled sample was mixed with an equal amount of Cy5-labeled reference sample (1 µg each), fragmented using the RNA Fragmentation Reagents (Ambion), vacuum dried and dissolved in 42 µL hybridization solution (5X Denhardt, 3.5X SSC, 0.3% SDS, 0.5 µg/µL Yeast tRNA (Life Technologies), 0.5 µg/µL polyA RNA (Sigma), 50% formamide, H2O). Denaturation was achieved by heating at 98°C for 2 min and was immediately followed by a preannealing step at 37°C for 30 min. Hereafter, 40 µL of each sample were pipetted onto the chips. Hybridization was performed at 42°C for 17 h using a Glass Array Hybridization Cassette (Telechem). At the end, the chips were washed in the following washing solutions (2X SSC, 0.1% SDS; 1X SSC; 0.2X SSC; 0.05X SSC) and dried by centrifugation (3 min, 1200 rpm).

scan_protocol: Hybridized arrays were scanned by fluorescence confocal microscopy (ScanArray Express, Perkin-Elmer). Fluorescence signal measurements were obtained separately for each fluorochrome at 10 µm/pixel resolution.

data_processing: Hybridization and background signals were measured using GenePix Pro 5.0 image analysis software (Axon Instruments). Technical biases were corrected by a Lowess normalization using a channel-by-channel procedure. For each microarray, Cy3 and Cy5 signal intensities were individually normalized to the median profile of all Cy3 or Cy5 signal intensities (values below background were filtered out).

source_name: mesothelioma cell line

label_protocol: Amino allyl RNA (aRNA) were generated using the Amino Allyl MessageAmp II aRNA AmplificationKit (Ambion) according to manufacturer's recommandations, and were subsequently labeled using Cy3 Post-labeling Reactive Dye Pack (Amersham).

growth_protocol: All cell lines were were maintained in complete medium composed of RPMI 1640 supplemented with 10% heat inactivated FCS, 100 IU/mL penicillin, 0.1 mg/mL streptomycin and 2 mM L-glutamine and cultured at 37°C in a 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated and treated with DNAse I using the RNAse-Free DNAse Set and the RNeasy Mini Kit (Qiagen).

tag: cell type

value: cells isolated from pleural effusion

tag: tumor histology

value: epithelioid mesothelioma

tag: age

value: 58-year old woman

source_name: reference sample

tag: rna pool

value: comprised of equal quantities of RNA from all samples


title: ech54-meso122

value: 73 years old

tag: gender

value: male


title: ech53-meso96

value: 68 years old


title: Left atria Ntg 1662

description: Gene expression data from heart atria


title: Left atria Ntg 1834

description: Gene expression data from heart atria


title: ech51-meso56

value: 79 years old


title: Right atria Ntg 1662

description: Gene expression data from heart atria


title: ech48-meso37

value: 65 years old


title: ancestor versus consortium, biological replicate 1, hybridization 2

source_name: consortium 1


title: ancestor versus consortium, biological replicate 1, hybridization 1


title: Right atria Ntg 1657

description: Gene expression data from heart atria


title: Left atria Ntg 1657

description: Gene expression data from heart atria


title: ancestor versus CV116 biological replicate 3, sample A, hybridization 2


title: ancestor versus CV115 biological replicate 3, sample B, hybridization 1

source_name: evolved strain CV115, monoculture


title: ancestor versus CV116 biological replicate 3, sample A, hybridization 1


title: ech46-meso34

value: 77-year old woman


title: ech49-meso47

value: 83 years old


title: ech47-meso36

value: 74 years old


title: Right atria Ntg 1301

description: Gene expression data from heart atria


title: ech44-meso30

value: 78 years old


title: ancestor versus CV115 biological replicate 3, sample A, hybridization 1


title: Left atria Ntg 1301

description: Gene expression data from heart atria


title: ech40-ADK72

source_name: adenocarcinoma cell line

value: pleural metastasis from adenocarcinoma of the lung (TITF-1 positive)

value: 60 years old


title: ech41-ADK117

value: 86 years old


title: Right atria Mst1 1840

description: Gene expression data from heart atria

source_name: RNA from mouse heart atria, Mst1


title: ech45-meso31

value: sarcomatoid mesothelioma

value: 51 years old


title: ech43-meso13

value: cells isolated from pleural effusion

value: epithelioid mesothelioma

value: 81 years old


title: ancestor versus CV115 biological replicate 3, sample A, hybridization 2

value: Davis minimal medium with 0.0125% glucose

value: chemostat, dilution rate=0.2/hr.

value: chemostat, dilution rate = 0.2/hr


title: ech39-ADK60

value: 68-year old woman

value: comprised of equal quantities of RNA from all samples


title: ech42-meso11

value: male


title: ancestor versus CV103 biological replicate 3, sample B, hybridization 1

source_name: evolved strain CV103, monoculture


title: ancestor versus CV103 biological replicate 3, sample A, hybridization 2


title: ancestor versus CV103 biological replicate 3, sample A, hybridization 1


title: Right atria Mst1 1839

description: Gene expression data from heart atria


title: ech34-meso95B

value: 58-year old woman


title: ech37-MeT-5A

source_name: SV40 transformed mesothelial cells

value: MeT-5A cell line (CRL-9444)


title: ech32-meso52

value: 65-year old woman


title: ancestor versus CV101 biological replicate 3, sample B, hybridization 1

source_name: evolved strain CV101, monoculture


title: ech28-meso34

value: 77-year old woman


title: ech36-meso122

value: 73 years old


title: ech29-meso36

value: 74 years old


title: Left atria Mst1 1840

description: Gene expression data from heart atria


title: ech50-meso52


title: ancestor versus CV101 biological replicate 3, sample A, hybridization 2


title: Left atria Mst1 1466

description: Gene expression data from heart atria


title: ech35-meso96

value: 68 years old


title: Right atria Mst1 1838

description: Gene expression data from heart atria


title: ech33-meso56

value: 79 years old


title: ancestor versus CV101 biological replicate 3, sample A, hybridization 1


title: ech27-meso31

value: cells isolated from pleural effusion

value: sarcomatoid mesothelioma

value: 51 years old


title: Right atria Mst1 1466

description: Gene expression data from heart atria


title: ech30-meso37

value: epithelioid mesothelioma

value: 65 years old


title: ech26-meso30

value: 78 years old


title: ancestor versus CV116 biological replicate 2, sample B, hybridization 1

value: Davis minimal medium with 0.0125% glucose

value: chemostat, dilution rate=0.2/hr.

value: chemostat, dilution rate = 0.2/hr


title: ech31-meso47

value: 83 years old

value: male

value: comprised of equal quantities of RNA from all samples


title: ancestor versus CV116 biological replicate 2, sample A, hybridization 2


title: ancestor versus CV116 biological replicate 2, sample A, hybridization 1


title: ancestor versus CV115 biological replicate 2, sample B, hybridization 1


title: ech20-ADK3

value: pleural metastasis from adenocarcinoma probably from lung origin

value: 64 years old


title: ech25-meso13

value: 81 years old


title: Left atria Mst1 1838

description: Gene expression data from heart atria


title: ech21-ADK60

value: pleural metastasis from adenocarcinoma of the lung (TITF-1 positive)

value: 68-year old woman


title: ech18-meso122

value: cells isolated from pleural effusion

value: 73 years old


title: ech19-Met5A

value: MeT-5A cell line (CRL-9444)


title: ech38-ADK3


title: ancestor versus CV115 biological replicate 2, sample A, hybridization 2


title: ech24-meso11

value: epithelioid mesothelioma


title: ech22-ADK72

value: 60 years old


title: Left atria Mst1 1839

description: Gene expression data from heart atria


title: yucatananse Fiber 2 DPA (58060)

city: Athens

first: Alan

middle: R

last: Gingle

state: GA

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

institute: University of Georgia

description: yucatananse Fiber 2 DPA (58060)

hyb_protocol: Hybridization by NimbleGen

scan_protocol: Scanning by NimbleGen

data_processing: The procedure for spot detection was performed by NimbleGen.  All values of the 42,429 genes with 7 redundant probes per gene were median polished with Tukey's biweight prior to performing a standard mixed linear model (LM) analysis of the data for expression differences between each fiber developmental stage within and between accessions of G. barbadense.

organism: Gossypium hirsutum

source_name: Fiber 2 DPA

label_protocol: Labelling by NimbleGen

extract_protocol: Hot-borate / Li precipitation method("Wilkins and Smart, 1996")

tag: genome

tag: polyploid level

tag: tissue & age

value: Fiber 2 DPA

tag: soil type

value: Bessey Mix

tag: soil mix

value: "50% Canadian Spagum Peat :40% Coarse Perlite :10% Mineral Soil (""Iowa Dirt"")"

tag: date planted

tag: planting location

value: "Pohl Conservatory, Bessey Hall, Ames, IA"

tag: average temperature (c)

value: 80 daytime - 70 nighttime

tag: day light regime

value: ambient daylight

tag: light sources

value: sun and 10 hour day sodium supplemental lighting

tag: night duration

value: natural

tag: age at harvest

value: 20 weeks

tag: developmental stage at harvest

value: Mature plant

tag: harvest time(hours after daybreak)

tag: harvested tissue type

value: Fiber

tag: number of plants harvested


title: yucatananse Fiber 2 DPA (58058)

description: yucatananse Fiber 2 DPA (58058)


title: ech14-meso52

tag: cell type

tag: tumor histology

tag: age

value: 65-year old woman

tag: rna pool

value: comprised of equal quantities of RNA from all samples


title: ancestor versus CV103 biological replicate 2, sample A, hybridization 2

tag: parent strain

tag: growth medium

value: Davis minimal medium with 0.0125% glucose

tag: culture condition

value: chemostat, dilution rate=0.2/hr.

tag: ancestral strain

value: chemostat, dilution rate = 0.2/hr


title: ancestor versus CV115 biological replicate 2, sample A, hybridization 1


title: TM1 Fiber 2 DPA (58057)

description: TM1 Fiber 2 DPA (58057)

tag: genome

tag: polyploid level

tag: tissue & age

tag: soil type

tag: soil mix

tag: date planted

tag: planting location

tag: average temperature (c)


title: ech12-meso37

value: cells isolated from pleural effusion

value: epithelioid mesothelioma

value: 65 years old

tag: gender

value: male


title: ancestor versus CV103 biological replicate 2, sample B, hybridization 1


title: ech10-meso34

tag: cell type

value: 77-year old woman


title: ech15-meso56

tag: tumor histology

value: 79 years old


title: yucatananse Fiber 2 DPA (58059)

description: yucatananse Fiber 2 DPA (58059)

value: Fiber 2 DPA

value: Bessey Mix

value: "50% Canadian Spagum Peat :40% Coarse Perlite :10% Mineral Soil (""Iowa Dirt"")"

value: "Pohl Conservatory, Bessey Hall, Ames, IA"

value: 80 daytime - 70 nighttime

tag: day light regime

value: ambient daylight

tag: light sources

tag: night duration

tag: age at harvest

tag: developmental stage at harvest

tag: harvest time(hours after daybreak)

tag: harvested tissue type

tag: number of plants harvested


title: TM1 Fiber 2 DPA (58056)

description: TM1 Fiber 2 DPA (58056)

tag: genome

tag: polyploid level

tag: tissue & age

value: sun and 10 hour day sodium supplemental lighting

value: natural

value: 20 weeks

value: Mature plant

value: Fiber


title: ech17-meso96

value: cells isolated from pleural effusion

tag: age

value: 68 years old

tag: rna pool

value: comprised of equal quantities of RNA from all samples


title: ech13'-meso47

value: epithelioid mesothelioma

value: 83 years old

value: male


title: ech23-ADK117

value: pleural metastasis from adenocarcinoma of the lung (TITF-1 positive)

value: 86 years old


title: ech16-meso95B

value: 58-year old woman


title: ancestor versus CV101 biological replicate 2, sample B, hybridization 1

tag: parent strain

tag: growth medium

value: Davis minimal medium with 0.0125% glucose

tag: culture condition

value: chemostat, dilution rate=0.2/hr.

tag: ancestral strain

value: chemostat, dilution rate = 0.2/hr


title: ech6-meso11

tag: cell type

tag: tumor histology

value: 78 years old

tag: gender


title: ech11-meso36

value: 74 years old


title: ancestor versus CV101 biological replicate 2, sample A, hybridization 2


title: TM1 Fiber 2 DPA (58055)

description: TM1 Fiber 2 DPA (58055)

value: Fiber 2 DPA

tag: soil type

value: Bessey Mix

tag: soil mix

value: "50% Canadian Spagum Peat :40% Coarse Perlite :10% Mineral Soil (""Iowa Dirt"")"

tag: date planted

tag: planting location

value: "Pohl Conservatory, Bessey Hall, Ames, IA"

tag: average temperature (c)

value: 80 daytime - 70 nighttime

tag: day light regime

value: ambient daylight

tag: light sources

value: sun and 10 hour day sodium supplemental lighting

tag: night duration

value: natural

tag: age at harvest

value: 20 weeks


title: A2 and D5 Fiber 2 DPA (58061)

description: A2 and D5 Fiber 2 DPA (58061)

organism:
Gossypium arboreum
Gossypium raimondii

tag: genome

value: A-genome and D-genome physical mixture

tag: polyploid level:

tag: tissue & age

tag: developmental stage at harvest

value: Mature plant

tag: harvest time(hours after daybreak)

tag: harvested tissue type

value: Fiber

tag: number of plants harvested


title: ancestor versus CV103 biological replicate 2, sample A, hybridization 1

tag: parent strain

tag: growth medium

value: Davis minimal medium with 0.0125% glucose

tag: culture condition

tag: ancestral strain


title: ech8'-meso30

tag: cell type

value: cells isolated from pleural effusion

tag: tumor histology

value: epithelioid mesothelioma

tag: age

tag: gender

value: male

tag: rna pool

value: comprised of equal quantities of RNA from all samples


title: ech5-ADK117

value: pleural metastasis from adenocarcinoma of the lung (TITF-1 positive)

value: 86 years old


title: ech9-meso31

value: sarcomatoid mesothelioma

value: 51 years old