title: Muvar_49b49w

description:
Comparison between mutation accumulation lines 49 at the late 3rd instar larvae (blue gut) and 49 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 49, late 3rd instar larvae (blue gut)

source_name: Mutation accumulation line 49, start of pupariation (white prepupae)


title: Muvar_54w46w

status: Public on Sep 04 2005

type: RNA

city: Cambridge

first: Scott

middle: A

last: Rifkin

state: MA

address: 16 Divinity Ave

department: OEB

country: USA

institute: Harvard University

description:
Comparison between mutation accumulation lines 54 at the start of pupariation (white prepupae) and 46 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

molecule: total RNA

organism: Drosophila melanogaster

source_name: Mutation accumulation line 54, start of pupariation (white prepupae)

source_name: Mutation accumulation line 46, start of pupariation (white prepupae)


title: Muvar_67b67w

description:
Comparison between mutation accumulation lines 67 at the late 3rd instar larvae (blue gut) and 67 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 67, late 3rd instar larvae (blue gut)

source_name: Mutation accumulation line 67, start of pupariation (white prepupae)


title: Muvar_71w42w

description:
Comparison between mutation accumulation lines 71 at the start of pupariation (white prepupae) and 42 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 71, start of pupariation (white prepupae)

source_name: Mutation accumulation line 42, start of pupariation (white prepupae)


title: Muvar_71w67w

description:
Comparison between mutation accumulation lines 71 at the start of pupariation (white prepupae) and 67 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_65w46w

description:
Comparison between mutation accumulation lines 65 at the start of pupariation (white prepupae) and 46 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 65, start of pupariation (white prepupae)


title: Muvar_67w23w

description:
Comparison between mutation accumulation lines 67 at the start of pupariation (white prepupae) and 23 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 23, start of pupariation (white prepupae)


title: Muvar_42w65w

description:
Comparison between mutation accumulation lines 42 at the start of pupariation (white prepupae) and 65 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_65b65w

description:
Comparison between mutation accumulation lines 65 at the late 3rd instar larvae (blue gut) and 65 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 65, late 3rd instar larvae (blue gut)


title: Muvar_46w51w

description:
Comparison between mutation accumulation lines 46 at the start of pupariation (white prepupae) and 51 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 51, start of pupariation (white prepupae)


title: Muvar_54b54w

description:
Comparison between mutation accumulation lines 54 at the late 3rd instar larvae (blue gut) and 54 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 54, late 3rd instar larvae (blue gut)


title: Muvar_46b46w

description:
Comparison between mutation accumulation lines 46 at the late 3rd instar larvae (blue gut) and 46 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 46, late 3rd instar larvae (blue gut)


title: Muvar_46w67w

description:
Comparison between mutation accumulation lines 46 at the start of pupariation (white prepupae) and 67 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_42b42w

description:
Comparison between mutation accumulation lines 42 at the late 3rd instar larvae (blue gut) and 42 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 42, late 3rd instar larvae (blue gut)


title: Muvar_71b71w

description:
Comparison between mutation accumulation lines 71 at the late 3rd instar larvae (blue gut) and 71 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 71, late 3rd instar larvae (blue gut)


title: Muvar_18w46w

description:
Comparison between mutation accumulation lines 18 at the start of pupariation (white prepupae) and 46 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 18, start of pupariation (white prepupae)


title: Muvar_46w42w

description:
Comparison between mutation accumulation lines 46 at the start of pupariation (white prepupae) and 42 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_49w18w

description:
Comparison between mutation accumulation lines 49 at the start of pupariation (white prepupae) and 18 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_67w67b

description:
Comparison between mutation accumulation lines 67 at the start of pupariation (white prepupae) and 67 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_71b46b

description:
Comparison between mutation accumulation lines 71 at the late 3rd instar larvae (blue gut) and 46 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_71b49b

description:
Comparison between mutation accumulation lines 71 at the late 3rd instar larvae (blue gut) and 49 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 49, late 3rd instar larvae (blue gut)


title: Muvar_65w49w

description:
Comparison between mutation accumulation lines 65 at the start of pupariation (white prepupae) and 49 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 49, start of pupariation (white prepupae)


title: Muvar_59w67w

description:
Comparison between mutation accumulation lines 59 at the start of pupariation (white prepupae) and 67 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 59, start of pupariation (white prepupae)


title: Muvar_71b65b

description:
Comparison between mutation accumulation lines 71 at the late 3rd instar larvae (blue gut) and 65 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_67b46b

description:
Comparison between mutation accumulation lines 67 at the late 3rd instar larvae (blue gut) and 46 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_21b21w

description:
Comparison between mutation accumulation lines 21 at the late 3rd instar larvae (blue gut) and 21 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 21, late 3rd instar larvae (blue gut)

source_name: Mutation accumulation line 21, start of pupariation (white prepupae)


title: Muvar_18b18w

description:
Comparison between mutation accumulation lines 18 at the late 3rd instar larvae (blue gut) and 18 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 18, late 3rd instar larvae (blue gut)


title: Muvar_42w18w

description:
Comparison between mutation accumulation lines 42 at the start of pupariation (white prepupae) and 18 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_67b51b

description:
Comparison between mutation accumulation lines 67 at the late 3rd instar larvae (blue gut) and 51 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 67, late 3rd instar larvae (blue gut)

source_name: Mutation accumulation line 51, late 3rd instar larvae (blue gut)


title: Muvar_65b42b

description:
Comparison between mutation accumulation lines 65 at the late 3rd instar larvae (blue gut) and 42 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_71w54w

description:
Comparison between mutation accumulation lines 71 at the start of pupariation (white prepupae) and 54 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 71, start of pupariation (white prepupae)

source_name: Mutation accumulation line 54, start of pupariation (white prepupae)


title: Muvar_67b23b

description:
Comparison between mutation accumulation lines 67 at the late 3rd instar larvae (blue gut) and 23 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 23, late 3rd instar larvae (blue gut)


title: Muvar_71w71b

description:
Comparison between mutation accumulation lines 71 at the start of pupariation (white prepupae) and 71 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_65w65b

description:
Comparison between mutation accumulation lines 65 at the start of pupariation (white prepupae) and 65 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 65, start of pupariation (white prepupae)

source_name: Mutation accumulation line 65, late 3rd instar larvae (blue gut)


title: Muvar_67w65w

description:
Comparison between mutation accumulation lines 67 at the start of pupariation (white prepupae) and 65 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 67, start of pupariation (white prepupae)


title: Muvar_42w59w

description:
Comparison between mutation accumulation lines 42 at the start of pupariation (white prepupae) and 59 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 42, start of pupariation (white prepupae)


title: Muvar_65b18b

description:
Comparison between mutation accumulation lines 65 at the late 3rd instar larvae (blue gut) and 18 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_54b65b

description:
Comparison between mutation accumulation lines 54 at the late 3rd instar larvae (blue gut) and 65 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 54, late 3rd instar larvae (blue gut)


title: Muvar_65w71w

description:
Comparison between mutation accumulation lines 65 at the start of pupariation (white prepupae) and 71 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_54w59w

description:
Comparison between mutation accumulation lines 54 at the start of pupariation (white prepupae) and 59 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_51w59w

description:
Comparison between mutation accumulation lines 51 at the start of pupariation (white prepupae) and 59 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 51, start of pupariation (white prepupae)


title: Muvar_21w65w

description:
Comparison between mutation accumulation lines 21 at the start of pupariation (white prepupae) and 65 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_51w71w

description:
Comparison between mutation accumulation lines 51 at the start of pupariation (white prepupae) and 71 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_59w49w

description:
Comparison between mutation accumulation lines 59 at the start of pupariation (white prepupae) and 49 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_23w42w

description:
Comparison between mutation accumulation lines 23 at the start of pupariation (white prepupae) and 42 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 23, start of pupariation (white prepupae)


title: Muvar_59w59b

description:
Comparison between mutation accumulation lines 59 at the start of pupariation (white prepupae) and 59 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 59, late 3rd instar larvae (blue gut)


title: Muvar_51b71b

description:
Comparison between mutation accumulation lines 51 at the late 3rd instar larvae (blue gut) and 71 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 71, late 3rd instar larvae (blue gut)


title: Muvar_54w23w

description:
Comparison between mutation accumulation lines 54 at the start of pupariation (white prepupae) and 23 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_54w54b

description:
Comparison between mutation accumulation lines 54 at the start of pupariation (white prepupae) and 54 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_54b51b

description:
Comparison between mutation accumulation lines 54 at the late 3rd instar larvae (blue gut) and 51 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_59b42b

description:
Comparison between mutation accumulation lines 59 at the late 3rd instar larvae (blue gut) and 42 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 42, late 3rd instar larvae (blue gut)


title: Muvar_49b42b

description:
Comparison between mutation accumulation lines 49 at the late 3rd instar larvae (blue gut) and 42 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 49, late 3rd instar larvae (blue gut)


title: Muvar_54b49b

description:
Comparison between mutation accumulation lines 54 at the late 3rd instar larvae (blue gut) and 49 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_51w51b

description:
Comparison between mutation accumulation lines 51 at the start of pupariation (white prepupae) and 51 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_59w21w

description:
Comparison between mutation accumulation lines 59 at the start of pupariation (white prepupae) and 21 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 59, start of pupariation (white prepupae)

source_name: Mutation accumulation line 21, start of pupariation (white prepupae)


title: Muvar_51w23w

description:
Comparison between mutation accumulation lines 51 at the start of pupariation (white prepupae) and 23 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_51b21b

description:
Comparison between mutation accumulation lines 51 at the late 3rd instar larvae (blue gut) and 21 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 51, late 3rd instar larvae (blue gut)

source_name: Mutation accumulation line 21, late 3rd instar larvae (blue gut)


title: Muvar_23b59b

description:
Comparison between mutation accumulation lines 23 at the late 3rd instar larvae (blue gut) and 59 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_51b51w

description:
Comparison between mutation accumulation lines 51 at the late 3rd instar larvae (blue gut) and 51 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_23b71b

description:
Comparison between mutation accumulation lines 23 at the late 3rd instar larvae (blue gut) and 71 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_49w54w

description:
Comparison between mutation accumulation lines 49 at the start of pupariation (white prepupae) and 54 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 49, start of pupariation (white prepupae)

source_name: Mutation accumulation line 54, start of pupariation (white prepupae)


title: Muvar_42w42b

description:
Comparison between mutation accumulation lines 42 at the start of pupariation (white prepupae) and 42 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_49w49b

description:
Comparison between mutation accumulation lines 49 at the start of pupariation (white prepupae) and 49 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_49w51w

description:
Comparison between mutation accumulation lines 49 at the start of pupariation (white prepupae) and 51 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_46b21b

description:
Comparison between mutation accumulation lines 46 at the late 3rd instar larvae (blue gut) and 21 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 46, late 3rd instar larvae (blue gut)


title: Muvar_59b51b

description:
Comparison between mutation accumulation lines 59 at the late 3rd instar larvae (blue gut) and 51 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_46w46b

description:
Comparison between mutation accumulation lines 46 at the start of pupariation (white prepupae) and 46 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 46, start of pupariation (white prepupae)


title: Muvar_49b23b

description:
Comparison between mutation accumulation lines 49 at the late 3rd instar larvae (blue gut) and 23 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 23, late 3rd instar larvae (blue gut)


title: Muvar_51b18b

description:
Comparison between mutation accumulation lines 51 at the late 3rd instar larvae (blue gut) and 18 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 18, late 3rd instar larvae (blue gut)


title: Muvar_59b46b

description:
Comparison between mutation accumulation lines 59 at the late 3rd instar larvae (blue gut) and 46 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_65b23b

description:
Comparison between mutation accumulation lines 65 at the late 3rd instar larvae (blue gut) and 23 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 65, late 3rd instar larvae (blue gut)


title: Muvar_42b54b

description:
Comparison between mutation accumulation lines 42 at the late 3rd instar larvae (blue gut) and 54 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 54, late 3rd instar larvae (blue gut)


title: Muvar_49b21b

description:
Comparison between mutation accumulation lines 49 at the late 3rd instar larvae (blue gut) and 21 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_46b54b

description:
Comparison between mutation accumulation lines 46 at the late 3rd instar larvae (blue gut) and 54 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_21w54w

description:
Comparison between mutation accumulation lines 21 at the start of pupariation (white prepupae) and 54 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_18w21w

description:
Comparison between mutation accumulation lines 18 at the start of pupariation (white prepupae) and 21 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 18, start of pupariation (white prepupae)


title: Muvar_46b18b

description:
Comparison between mutation accumulation lines 46 at the late 3rd instar larvae (blue gut) and 18 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_23w21w

description:
Comparison between mutation accumulation lines 23 at the start of pupariation (white prepupae) and 21 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 23, start of pupariation (white prepupae)


title: Muvar_42b71b

description:
Comparison between mutation accumulation lines 42 at the late 3rd instar larvae (blue gut) and 71 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 71, late 3rd instar larvae (blue gut)


title: Muvar_42b67b

description:
Comparison between mutation accumulation lines 42 at the late 3rd instar larvae (blue gut) and 67 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 42, late 3rd instar larvae (blue gut)

source_name: Mutation accumulation line 67, late 3rd instar larvae (blue gut)


title: Chicken pituitary gland, post-hatch day 3, replicate 2 vs pituitary reference pool (embryonic day 17,post-hatch day 3)

status: Public on Sep 02 2005

city: College Park

first: Tom

middle: Eric

last: Porter

state: MD

address: Building #142

department: Animal and Avian Sciences

institute: University of Maryland

hyb_protocol: The microarray was hybridized overnight at 42 C with Cy3-labeled post-hatch day 3 cDNA and an aliquot of the Cy5-labeled reference pool cDNA using microarray hybridization buffer (Amersham Biosciences).  Slides were washed in increasing stringency using salt sodium citrate.

scan_protocol: The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

data_processing: The two images from each slide were processed with Spotfinder version 2.2.4 (The Institute for Genomic Research, Rockville, MD) using the following settings:  Otsu thresholding algorithm (minimum spot size 3 and maximum spot size 25); keep flagged values; keep raw data; and quality control filter set so 50% cutoff equals background plus 1 standard deviation.  Data were normalized using Microarray Data Analysis System (MIDAS) version 2.18 (The Institute for Genomic Research).  In MIDAS, channel A and B flags and channel A and B background checking were used, and the signal-to-noise threshold was set at 3.0.  Data from the Cy3 channel were first Lowess (LocFit) normalized by pin (block) using a smoothing parameter of 0.33 with Cy5 as the reference and then sujected to standard deviation regularization first by pin (block) then by slide with Cy5 as the reference.  A cross file cutoff of 25% was used, so that at least 4 of the 16 slides for a given spot had to pass quality control checks.  The data from each spot on each slide were then expressed as log2-ratio, or log2(normalized Cy3/raw Cy5), which is given in the data table below.   Log2-ratios for the spots were statistically analyzed by one-way analysis of variance using Statistical Analysis Systems version 8.02 (SAS Institute, Cary, NC) to identify cDNAs that were differentially expressed on at least one of the developmental ages (n = 4; P < 0.05), and a fold-change of > 1.6 was used as a filter for false positives.

organism: Gallus gallus

label_protocol: 1 microgram amplified antisense RNA (equivalent to 1 microgram mRNA) was converted to cDNA using random primers with the Amino Allyl cDNA Labeling Kit (Ambion), and Cy3-monoreactive NHS esters (Amersham Biosciences, Piscataway, NJ) were coupled to the cDNA.  Labeled cDNA was purified from unicorporated dye using CyScribe GFX Purification Kit (Amersham Biosciences).

growth_protocol: Fertilized chicken eggs were placed in 37.5 C humidified incubator on embryonic day 0 and killed by decapitation 2 days after hatching (typical incubation period is 21 days).  The pituitary gland from 1 post-hatch day 3 chicken was dissected, immediately frozen in liquid nitrogen, and stored at -80 C until RNA extraction.

extract_protocol: Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Valencia, CA) and was amplifed using a modification of the Eberwine Procedure (Phillips J, Eberwine JH 1996 METHODS: A Companion to Methods in Enzymology 10: 283-288). Briefly, 500 ng was reverse-transcribed using SuperScript II (Invitrogen, Carlsbad, CA) and an oligo(dT) primer containing a T7 promoter site (5'-GGCCAGTGAATTGTAATATCGACTCACTATAGGGAGGCGGT24-3'; Affymetrix, Santa Clara, CA).  Following second strand synthesis and purification, double-stranded cDNA was used as a template for in vitro transcription using the T7 MEGAscript kit (Ambion, Austin, TX) and the resulting amplified antisense RNA was quantified with the Ribogreen RNA Quantitation Kit (Invitrogen, Carlsbad, CA).

source_name: Reference pool of chicken pituitary gland amplified RNA, embryonic day 17 and post-hatch day 3

label_protocol: 1 microgram amplified antisense RNA (equivalent to 1 microgram mRNA) from the pool was converted to cDNA using random primers with the Amino Allyl cDNA Labeling Kit (Ambion) and Cy5-monoreactive NHS esters (Amersham Biosciences, Piscataway, NJ) were coupled to the cDNA.  Labeled cDNA was purified from unicorporated dye using CyScribe GFX Purification Kit (Amersham Biosciences) and a pool was made of all Cy5-labeled cDNA to be split among the 16 slides in the experiment.

extract_protocol: Extraction and amplification was conducted as described for channel 1 for each of the 6 samples used in the study, and a pool was made of 2 micrograms from each sample.

tag: Chicken pituitary amplified antisense RNA, pooled from all replicates (n=3) on each of embryonic day 17 and post-hatch day 3 to be used as a reference sample (6 samples total)


title: Muvar_21w21b

description:
Comparison between mutation accumulation lines 21 at the start of pupariation (white prepupae) and 21 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 21, start of pupariation (white prepupae)


title: Chicken pituitary gland, post-hatch day 3, replicate 3 vs pituitary reference pool (embryonic day 17,post-hatch day 3)


title: Muvar_23w49w

description:
Comparison between mutation accumulation lines 23 at the start of pupariation (white prepupae) and 49 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_18w71w

description:
Comparison between mutation accumulation lines 18 at the start of pupariation (white prepupae) and 71 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 71, start of pupariation (white prepupae)


title: Chicken pituitary gland, embryonic day 17, replicate 3 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 17, replicate 3

hyb_protocol: The microarray was hybridized overnight at 42 C with Cy3-labeled embryonic day 17 cDNA and an aliquot of the Cy5-labeled reference pool cDNA using microarray hybridization buffer (Amersham Biosciences).  Slides were washed in increasing stringency using salt sodium citrate.

growth_protocol: Fertilized chicken eggs were placed in 37.5 C humidified incubator on embryonic day 0 and removed from the incubator on embryonic day 17.  Pituitary glands from 2 embryonic day 17 embryos were pooled, immediately frozen in liquid nitrogen, and stored at -80 C until RNA extraction.

source_name: Reference pool of chicken embryonic pituitary gland amplified RNA, embryonic days 10, 12, 14, and 17

extract_protocol: Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

tag: Chicken embryonic pituitary amplified antisense RNA, pooled from all replicates (n=4) on each of embryonic days 10, 12, 14, and 17 to be used as a reference sample (16 samples total)


title: Chicken pituitary gland, post-hatch day 3, replicate 1 vs pituitary reference pool (embryonic day 17,post-hatch day 3)


title: Muvar_18b49b

description:
Comparison between mutation accumulation lines 18 at the late 3rd instar larvae (blue gut) and 49 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 49, late 3rd instar larvae (blue gut)


title: Chicken pituitary gland, embryonic day 17, replicate 4 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 17, replicate 4


title: Chicken pituitary gland, embryonic day 17, replicate 3 vs pituitary reference pool (embryonic day 17,post-hatch day 3)

growth_protocol: Fertilized chicken eggs were placed in 37.5 C humidified incubator on embryonic day 0 and removed from the incubator on embryonic day 17.  The pituitary gland from 1 embryonic day 17 embryo was dissected, immediately frozen in liquid nitrogen, and stored at -80 C until RNA extraction.


title: Chicken pituitary gland, embryonic day 17, replicate 1 vs pituitary reference pool (embryonic day 17,post-hatch day 3)


title: Muvar_18b67b

description:
Comparison between mutation accumulation lines 18 at the late 3rd instar larvae (blue gut) and 67 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_23w23b

description:
Comparison between mutation accumulation lines 23 at the start of pupariation (white prepupae) and 23 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Chicken pituitary gland, embryonic day 17, replicate 2 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 17, replicate 2


title: Muvar_21b59b

description:
Comparison between mutation accumulation lines 21 at the late 3rd instar larvae (blue gut) and 59 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 21, late 3rd instar larvae (blue gut)

source_name: Mutation accumulation line 59, late 3rd instar larvae (blue gut)


title: Chicken pituitary gland, embryonic day 17, replicate 2 vs pituitary reference pool (embryonic day 17,post-hatch day 3)


title: Muvar_18b59b

description:
Comparison between mutation accumulation lines 18 at the late 3rd instar larvae (blue gut) and 59 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_18w18b

description:
Comparison between mutation accumulation lines 18 at the start of pupariation (white prepupae) and 18 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_21b65b

description:
Comparison between mutation accumulation lines 21 at the late 3rd instar larvae (blue gut) and 65 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Chicken pituitary gland, embryonic day 14, replicate 4 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 14, replicate 4

hyb_protocol: The microarray was hybridized overnight at 42 C with Cy3-labeled embryonic day 14 cDNA and an aliquot of the Cy5-labeled reference pool cDNA using microarray hybridization buffer (Amersham Biosciences).  Slides were washed in increasing stringency using salt sodium citrate.

growth_protocol: Fertilized chicken eggs were placed in 37.5 C humidified incubator on embryonic day 0 and removed from the incubator on embryonic day 14.  Pituitary glands from 4 embryonic day 14 embryos were pooled, immediately frozen in liquid nitrogen, and stored at -80 C until RNA extraction.


title: Muvar_21b67b

description:
Comparison between mutation accumulation lines 21 at the late 3rd instar larvae (blue gut) and 67 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Muvar_23b54b

description:
Comparison between mutation accumulation lines 23 at the late 3rd instar larvae (blue gut) and 54 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Chicken pituitary gland, embryonic day 14, replicate 2 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 14, replicate 2


title: Chicken pituitary gland, embryonic day 17, replicate 1 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 17, replicate 1


title: Muvar_23b23w

description:
Comparison between mutation accumulation lines 23 at the late 3rd instar larvae (blue gut) and 23 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster


title: Chicken pituitary gland, embryonic day 12, replicate 3 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 12, replicate 3

hyb_protocol: The microarray was hybridized overnight at 42 C with Cy3-labeled embryonic day 12 cDNA and an aliquot of the Cy5-labeled reference pool cDNA using microarray hybridization buffer (Amersham Biosciences).  Slides were washed in increasing stringency using salt sodium citrate.

growth_protocol: Fertilized chicken eggs were placed in 37.5 C humidified incubator on embryonic day 0 and removed from the incubator on embryonic day 12.  Pituitary glands from 8 embryonic day 12 embryos were pooled, immediately frozen in liquid nitrogen, and stored at -80 C until RNA extraction.


title: Chicken pituitary gland, embryonic day 12, replicate 4 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 12, replicate 4


title: Chicken pituitary gland, embryonic day 12, replicate 1 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 12, replicate 1


title: Chicken pituitary gland, embryonic day 14, replicate 3 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 14, replicate 3


title: Chicken pituitary gland, embryonic day 10, replicate 2 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 10, replicate 2

hyb_protocol: The microarray was hybridized overnight at 42 C with Cy3-labeled embryonic day 10 cDNA and an aliquot of the Cy5-labeled reference pool cDNA using microarray hybridization buffer (Amersham Biosciences).  Slides were washed in increasing stringency using salt sodium citrate.

growth_protocol: Fertilized chicken eggs were placed in 37.5 C humidified incubator on embryonic day 0 and removed from the incubator on embryonic day 10.  Pituitary glands from 16 embryonic day 10 embryos were pooled, immediately frozen in liquid nitrogen, and stored at -80 C until RNA extraction.


title: Chicken pituitary gland, embryonic day 10, replicate 4 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 10, replicate 4


title: Muvar_21w51w

description:
Comparison between mutation accumulation lines 21 at the start of pupariation (white prepupae) and 51 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 51, start of pupariation (white prepupae)


title: Chicken pituitary gland, embryonic day 14, replicate 1 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 14, replicate 1


title: Seedlings, small RNA MPSS sets 1 and 2 combined

type: MPSS

city: Davis

first: Blake

middle: C.

last: Meyers

state: CA

address: 451 Health Sciences Dr.

department: UC Davis Genome Center

institute: University of California - Davis

description: Seedlings were grown on media containing 1 xMS salts, 1% sucrose. 2-week-old seedlings were sprayed with water. After 2 hours, seedlings were collected and total RNA was isolated using TRIzol reagent.

data_processing: To determine the normalized abundance value for each signature in the library, we separately merged 2-step runs and 3-step runs to create a raw abundance count for each stepper. The raw abundance count for each stepper was calculated as the average from all 2-step or from all 3-step runs for a given signature. The average total number of signatures sequenced in all 2-step or for all 3-step runs was also calculated within the library. The final stage to merge the data within the steppers was to calculate the normalized abundance for each stepper. The normalized abundance is the raw abundance count divided by the average total number of signatures for both of the steppers in the library, multiplied by 250,000 to obtain a "transcripts per quarter million" or TPQ value. For each signature, only the one normalized value is used - either the 2-step or 3-step normalized value, selected based on the higher of the sum of the 2-step or 3-step data across all libraries. More details are available in Meyers et al. (2004, Genome Research 14:1641) or Lu et al. (2005).  This method was applied separately for signatures matching to tRNAs, rRNAs, snoRNAs or snRNAs. These signatures were removed from the primary set of small RNA signatures and treated as a separate set.

organism: Arabidopsis thaliana

source_name: Inflorescence tissue

tag: Ecotype


title: Human Vaginal Epithelial 1

status: Public on Sep 01 2005

city: Boston

first: Adam

middle: Mark

last: Papallo

address: 100 Morrissey Blvd.

department: Department of Physics

institute: University of Massachusetts Boston

description: Normal Human Vaginal Epithelial

data_processing: CodeLink System Software Analysis 2.2.19

organism: Homo sapiens

source_name: Normal Human Vaginal Epithelial

tag: Normal primary cell culture


title: Chicken pituitary gland, embryonic day 10, replicate 3 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 10, replicate 3


title: Human Vaginal Epithelial 2

description: Normal Human Vaginal Epithelial


title: Chicken pituitary gland, embryonic day 10, replicate 1 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 10, replicate 1


title: Seedlings, small RNA MPSS set 2

source_name: Seedlings


title: Human Uterine Microvascular Endothelial Cells 2

description: Normal Human Uterine Microvascular Endothelial Cells


title: Human Uterine Smooth Muscle Cell 3

description: Normal Human Uterine Smooth Muscle Cell

source_name: Normal Human Uterine Smooth Muscle Cell


title: Human Uterine Microvascular Endothelial Cells 1

source_name: Normal Human Uterine Microvascular Endothelial Cells


title: Human Urethra Smooth Muscle Cells 3

description: Normal Human Urethra Smooth Muscle Cells


title: Inflorescence tissues, small RNA MPSS

description: Plants were grown in soil in growth chamber with 16 hours of light for 5 weeks. Immature inflorescence was harvested ~2 hours after dark. Tissue included inflorescence meristem and early stage floral buds (up to Stage 11/12). Total RNA was isolated using TRIzol reagent.


title: Human Uterine Smooth Muscle Cell 4

description: Normal Human Uterine Smooth Muscle Cell


title: Human Ureter Smooth Muscle Cells 1

description: Normal Human Ureter Smooth Muscle Cells

source_name: Normal Human Ureter Smooth Muscle Cells


title: Human Umbilical Artery Endothelial Cell 6

description: Normal Human Umbilical Artery Endothelial Cell


title: Human Urethra Smooth Muscle Cells 2

source_name: Normal Human Urethra Smooth Muscle Cells


title: Human Umbilical Artery Endothelial Cell 5

source_name: Normal Human Umbilical Artery Endothelial Cell


title: Human Umbilical Artery Endothelial Cell 4


title: Human Saphenous Vein Endothelial Cells 1

description: Normal Human Saphenous Vein Endothelial Cells


title: Human Umbilical Artery Endothelial Cell 3


title: Human Saphenous Vein Endothelial Cells 2

source_name: Normal Human Saphenous Vein Endothelial Cells


title: Seedlings, small RNA MPSS set 1


title: Human Tibial Artery Smooth Muscle Cells 1

description: Normal Human Tibial Artery Smooth Muscle Cells


title: Human Umbilical Artery Endothelial Cell 1


title: Human Renal Epithelial 2

description: Normal Human Renal Epithelial

source_name: Normal Human Renal Epithelial


title: Human Umbilical Artery Endothelial Cell 2


title: Human Renal Vein Smooth Muscle 1

description: Normal Human Renal Vein Smooth Muscle

source_name: Normal Human Renal Vein Smooth Muscle


title: Human Renal Epithelial 3

description: Normal Human Renal Epithelial


title: Human Skeletal Muscle Stromal Cells 1

description: Normal Human Skeletal Muscle Stromal Cells


title: Human Prostate Smooth Muscle 1

description: Normal Human Prostate Smooth Muscle

source_name: Normal Human Prostate Smooth Muscle


title: Human Prostate Smooth Muscle 3

description: Normal Human Prostate Smooth Muscle


title: Human Popliteal Vein Smooth Muscle Cell 1

description: Normal Human Popliteal Vein Smooth Muscle Cell


title: Human Prostate Stromal 1

description: Normal Human Prostate Stromal

source_name: Normal Human Prostate Stromal


title: Human Prostate Smooth Muscle 2

description: Normal Human Prostate Smooth Muscle


title: Human Pulmonary Artery Smooth Muscle Cells 5

description: Normal Human Pulmonary Artery Smooth Muscle Cells


title: Human Pulmonary Artery Smooth Muscle Cells 4

source_name: Normal Human Pulmonary Artery Smooth Muscle Cells


title: Human Mammary Stromal Cells 1

description: Normal Human Mammary Stromal Cells

source_name: Normal Human Mammary Stromal Cells


title: Human Neonatal Dermal Fibroblasts Pooled 2

description: Normal Human Neonatal Dermal Fibroblasts Pooled


title: Human Pulmonary Artery Smooth Muscle Cells 2


title: Human Lung Fibroblasts 1

description: Normal Human Lung Fibroblasts

source_name: Normal Human Lung Fibroblasts


title: Human Neonatal Dermal Fibroblasts Pooled 1

source_name: Normal Human Neonatal Dermal Fibroblasts Pooled


title: Human Pulmonary Artery Smooth Muscle Cells 3


title: Human Lung Fibroblasts 2

description: Normal Human Lung Fibroblasts


title: Human Hepatic Fibroblasts 1

description: Normal Human Hepatic Fibroblasts

source_name: Normal Human Hepatic Fibroblasts


title: Human Iliaic Artery Endothelial Cells 4

description: Normal Human Iliaic Artery Endothelial Cells


title: Human Hepatic Fibroblasts 2

description: Normal Human Hepatic Fibroblasts


title: Human Lung Fibroblasts 3

description: Normal Human Lung Fibroblasts


title: Human Colon Smooth Muscle 1

description: Normal Human Colon Smooth Muscle

source_name: Normal Human Colon Smooth Muscle


title: Human Iliaic Artery Endothelial Cells 1

source_name: Normal Human Iliaic Artery Endothelial Cells


title: Human Colon Smooth Muscle 2

description: Normal Human Colon Smooth Muscle


title: Human Popliteal Artery Smooth Muscle Cells 1

description: Normal Human Popliteal Artery Smooth Muscle Cells


title: Human Hepatic Artery Smooth Muscle 1

description: Normal Human Hepatic Artery Smooth Muscle


title: Human Hepatic Vein Smooth Muscle 1

description: Normal Human Hepatic Vein Smooth Muscle

source_name: Normal Human Hepatic Vein Smooth Muscle


title: Human Iliaic Artery Endothelial Cells 3


title: Human Cardiac Stromal Cells 3

description: Normal Human Cardiac Stromal Cells

source_name: Normal Human Cardiac Stromal Cells


title: Human Cervical Ectoepithelial 2

description: Normal Human Cervical Ectoepithelial

source_name: Normal Human Cervical Ectoepithelial


title: Human Cardiac Stromal Cells 1

description: Normal Human Cardiac Stromal Cells


title: Human Cardiac Stromal Cells 2

description: Normal Human Cardiac Stromal Cells


title: Human Bladder Smooth Muscle Cells 3

description: Normal Human Bladder Smooth Muscle Cells


title: Chicken pituitary gland, embryonic day 12, replicate 2 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

description: Chicken embryonic pituitary gland, embryonic day 12, replicate 2

source_name: Reference pool of chicken embryonic pituitary gland amplified RNA, embryonic days 10, 12, 14, and 17


title: Human Cardiac Microvascular Endothelial Cells 1

description: Normal Human Cardiac Microvascular Endothelial Cells


title: Human Cervical Ectoepithelial 1

description: Normal Human Cervical Ectoepithelial


title: Fetal Kidney_day_22_treated_mother_rep9

status: Public on Aug 31 2005

city: Jerusalem

first: Yoav

middle: M

last: Smith

address: Hadassah Ein-Karem

department: Medical School

country: Israel

institute: Hebrew University

description: standard technique for comparisons of 5 normal samples to 5 samples of grows restricted fetuses

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing: MAS 5.0

label: According to Affymetrix protocol

organism: Rattus norvegicus

source_name: Fetal Kidney_day_22_treated_mother

label_protocol: According to Affymetrix protocol

growth_protocol: Mother kept on a regular diet.4 in a cage.

extract_protocol: Total RNA was extracted from the frozen tissue, using the RNA STAT-60TM Total RNA/mRNA Isolation Reagent (Tel-Test Inc., Friendswood, TX), according to the manufacturer’s instructions

treatment_protocol: Hyperinsulinemia was produced in pregnant female Wistar rats by subcutaneous implantation of a 2mm segment of a sustained release insulin implant (linplant, Linshin Canada Inc., Canada) a week before and again a week after mating. Female Wistar rats (weight, 200–280 g) were fed on a normal diet and allowed to drink tap water ad libitum. Blood pressure was measured weekly by the tail-cuff method. The experiment conducted as described in our previous investigations (Bursztyn at al., 1993; Podjarny et al., 1998; Bursztyn et al, 2003).

tag: Wistar rat 22 day of gestation


title: Human Bladder Microvascular Endothelial Cells 1

description: Normal Human Bladder Microvascular Endothelial Cells


title: Human Bladder Smooth Muscle Cells 2

source_name: Normal Human Bladder Smooth Muscle Cells


title: Fetal Kidney_day_22_treated_mother_rep7


title: Human Aortic Smooth Muscle 1

description: Normal Human Aortic Smooth Muscle

source_name: Normal Human Aortic Smooth Muscle


title: Fetal Kidney_day_22_normal_mother_rep2

source_name: Fetal Kidney_day_22_normal_mother

treatment_protocol: mother kept on regular diet . Sacrified on day 22 of gestation.Kidneys disected and snap frozen in liquid nitrogen and kept at -80 celzius


title: Fetal Kidney_day_22_treated_mother_rep8


title: Fetal Kidney_day_22_normal_mother_rep4


title: Fetal Kidney_day_22_normal_mother_rep1

extract_protocol: Total RNA was extracted from the frozen tissue, using the RNA STAT-60TM Total RNA/mRNA Isolation Reagent (Tel-Test Inc., Friendswood, TX), according to the manufacturer’s instructions.

treatment_protocol: mother kept on regular diet . Sacrified on day 22 of gestation.Kidneys disected and snap frozen in liquid nitrogen and kept at -80 celzius.


title: Fetal Kidney_day_22_treated_mother_rep10


title: Fetal Kidney_day_22_treated_mother_rep6


title: Human Bladder Smooth Muscle Cells 1


title: Fetal Kidney_day_22_normal_mother_rep3


title: clr4D_vs_wt_1

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: Schizosaccharomyces pombe cells, clr4 null versus wild type expression replicate 1

hyb_protocol: Cy3 labeled cDNA was mixed with Cy5 labeled cDNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer

scan_protocol: Slides were scanned using Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software version 7.5

data_processing: Log ratios of clr4 null over wild type were obtained by dividing normalized median Cy5 value over its corrresponding Cy3 value

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe wild type RNA

label_protocol: 15 ug total RNA were reverse-transcribed by Invitrogen Superscript Indirect cDNA Labeling System incorporating amino-allyl dUTP. Purified cDNA was covalently coupled with Cy3 mono  NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled cDNA was purified by Invitrogen SNAP column.

growth_protocol: Asynchronous growing fission yeast cells at 30 C

extract_protocol: total RNA isolated from asynchronous growing fission yeast cells at 30 C by Epicentre MasterPure Yeast RNA Purification Kit.

tag: cDNA reverse transcribed from total RNA isolated from wild type Schizosaccharomyces pombe cells

source_name: Schizosaccharomyces pombe clr4 null RNA

tag: cDNA reverse transcribed from total RNA isolated from clr4 null Schizosaccharomyces pombe cells


title: clr4D_vs_wt_2

description: Schizosaccharomyces pombe cells, clr4 null versus wild type expression replicate 2


title: Chp1_1_clr4D

type: genomic

description: Schizosaccharomyces pombe cells, Chp1 ChIP(chromatin immunoprecipitation)-on-chip, clr4 null replicate 1

hyb_protocol: 500 ng of Cy3 labeled WCE DNA was mixed with 500 ng of Cy5 labeled ChIP DNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer

data_processing: Log ratios of ChIP over WCE were obtained by dividing normalized median Cy5 value over its corrresponding Cy3 value

molecule: genomic DNA

source_name: Schizosaccharomyces pombe whole cell extract (WCE) genomic DNA

label_protocol: WCE DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy3 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked at 18C with paraformaldehyde for 30 minutes

extract_protocol: Chromatin was extracted from cross-linked cells following lysis with bead beater and sonication.  After reverse cross-linked and digested with Rnase A and proteinase K, DNA was recovered by phenol/chloroform extraction and ethanol precipitation

treatment_protocol: Schizosaccharomyces pombe cells crosslinked with paraformaldehyde

source_name: Schizosaccharomyces pombe chromatin immunoprecipitated DNA

label_protocol: ChIP DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy5 mono  NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked with paraformaldehyde at 18C for 30 minutes

tag: Chromatin DNA isolated from paraformaldehyde cross-linked clr4 null Schizosaccharomyces pombe cells and enriched for Chp1-FLAG chromatin with anti-FLAG antibody.


title: Human Spleen Smooth Muscle 1

description: Normal Human Spleen Smooth Muscle

source_name: Normal Human Spleen Smooth Muscle


title: H3K9me2_1_wt

description: Schizosaccharomyces pombe cells, H3K9me2 ChIP(chromatin immunoprecipitation)-on-chip, replicate 1

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for H3K9me2 chromatin with antibody against dimethylated histone H3 at lysine 9.


title: Chp1_2_wt

description: Schizosaccharomyces pombe cells, Chp1 ChIP(chromatin immunoprecipitation)-on-chip, replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for Chp1-FLAG chromatin with anti-FLAG antibody.


title: Rdp1_1_wt

description: Schizosaccharomyces pombe cells, Rdp1 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 1

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked with paraformadehyde at 18C for 30 minutes, followed by dimethyl adipimidate crosslinking at room temperature for 45 min.

treatment_protocol: Schizosaccharomyces pombe cells crosslinked with paraformadehyde/dimethyl adipimidate

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for Rdp1-TAP chromatin with Ig-G Sepharose.


title: Rdp1_2_wt

description: Schizosaccharomyces pombe cells, Rdp1 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells


title: Chp1_1_wt

description: Schizosaccharomyces pombe cells, Chp1 ChIP(chromatin immunoprecipitation)-on-chip, replicate 1


title: Ago1_2_wt

description: Schizosaccharomyces pombe cells, Ago1 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for Myc-Ago1 chromatin with anti-Myc antibody.


title: Swi6_1_clr4D

description: Schizosaccharomyces pombe cells, Swi6 ChIP(chromatin immunoprecipitation)-on-chip, clr4 null replicate 1

tag: Chromatin DNA isolated from paraformaldehyde cross-linked clr4 null Schizosaccharomyces pombe cells and enriched for Swi6 chromatin with anti-Swi6 antibody.


title: Ago1_1_clr4D

description: Schizosaccharomyces pombe cells, Ago1 ChIP(chromatin immunoprecipitation)-on-chip, clr4 null replicate 1

tag: Chromatin DNA isolated from paraformaldehyde cross-linked clr4 null Schizosaccharomyces pombe cells and enriched for Myc-Ago1 chromatin with anti-myc antibody.


title: Swi6_2_wt

description: Schizosaccharomyces pombe cells, Swi6 ChIP(chromatin immunoprecipitation)-on-chip, replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for Swi6 chromatin with anti-Swi6 antibody.


title: Fetal Kidney_day_22_normal_mother_rep5


title: Ago1_1_wt

description: Schizosaccharomyces pombe cells, Ago1 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 1


title: Swi6_1_wt

description: Schizosaccharomyces pombe cells, Swi6 ChIP(chromatin immunoprecipitation)-on-chip, replicate 1


title: Human Pulmonary Artery Smooth Muscle Cells 1

description: Normal Human Pulmonary Artery Smooth Muscle Cells


title: H3K4me2_2_wt

description: Schizosaccharomyces pombe cells, H3K4me2 ChIP(chromatin immunoprecipitation)-on-chip, replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for H3K4me2 chromatin with antibody against dimethylated histone H3 at lysine 4.


title: Mouse_FGFR1_E12.5_hets_vs_hom_8

status: Public on Aug 26 2005

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

country: United Kingdom

institute: Kennedy Institute of Rheumatology

description: Sample details: We analysed changes in gene expression in the dorsal telencephalon of forebrain-specific FGFR1 mutant mice. Gene expression was compared between the dorsal telencephalons of single E12.5 embryos of two genotypes: FGFR1 heterozygous (HET1,3,8) and homozygous mutants (HOM2,4,7) that were both heterozygous for the FoxG1 transcription factor, as Cre recombinase expression is driven off the endogenous FoxG1 locus in these animals (Hebert, J. M., Lin, M., Partanen, J., Rossant, J. and McConnell, S. K. (2003b). FGF signaling through FGFR1 is required for olfactory bulb morphogenesis. Development 130, 1101-11. & Hebert, J. M. and McConnell, S. K. (2000). Targeting of cre to the Foxg1 (BF-1) locus mediates loxP recombination in the telencephalon and other developing head structures. Dev Biol 222, 296-306.

hyb_protocol: See Livesey, F. J., Furukawa, T., Steffen, M. A., Church, G. M. and Cepko, C. L. (2000). Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr Biol 10, 301-10

scan_protocol: Hybridised microarrays were scanned on a GenePix 4000B microarray scanner and the resulting images were analysed with GenePix 5 array analysis software.

data_processing: log ratios were lowess normalised, and filtered to exclude (1) spots flagged as bad and (2) spots where 55% of the foreground pixels in either channel were less intense than the (background intensity + 1SD)

organism: Mus musculus

tag: See description


title: H3K4me2_1_wt

description: Schizosaccharomyces pombe cells, H3K4me2 ChIP(chromatin immunoprecipitation)-on-chip, replicate 1


title: H3K9me2_1_clr4D

description: Schizosaccharomyces pombe cells, H3K9me2 ChIP(chromatin immunoprecipitation)-on-chip, clr4 null replicate 1

tag: Chromatin DNA isolated from paraformaldehyde cross-linked clr4 null Schizosaccharomyces pombe cells and enriched for H3K9me2 chromatin with antibody against dimethylated histone H3 at lysine 9.


title: Mouse_FGFR1_E12.5_hets_vs_hom_5


title: Human Iliaic Artery Endothelial Cells 5

description: Normal Human Iliaic Artery Endothelial Cells


title: Mouse_FGFR1_E12.5_hets_vs_hom_7


title: Mouse_FGFR1_E12.5_hets_vs_hom_9


title: Mouse_FGFR1_E12.5_hets_vs_hom_3


title: Mouse_FGFR1_E12.5_hets_vs_hom_6


title: Mouse_FGFR1_E12.5_hets_vs_hom_2


title: H3K9me2_2_clr4D

description: Schizosaccharomyces pombe cells, H3K9me2 ChIP(chromatin immunoprecipitation)-on-chip, clr4 null replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked clr4 null Schizosaccharomyces pombe cells


title: Mouse_FGFR1_E12.5_hets_vs_hom_4


title: Mouse_Peg1_E12.5_mutant_vs_wildtype_6

description: Sample details: single E12.5 Peg1 mutant cortices were directely compared to single E12.5 wild type cortices. Six mutant cortices (M1,3,4,5,6,7) were compared to three wild type cortices (WT2,8,9). As Mest is an imprinted gene that is only expressed from the paternal allele, mutants were generated by crossing males carrying a LacZ-targeted allele in which exons 3-8 were removed to wild-type females, as described (Lefebvre, L., Viville, S., Barton, S. C., Ishino, F., Keverne, E. B. and Surani, M. A. (1998). Abnormal maternal behaviour and growth retardation associated with loss of the imprinted gene Mest. Nat Genet 20, 163-9.)  RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156.


title: Mouse_Peg1_E12.5_mutant_vs_wildtype_5


title: Mouse_FGFR1_E12.5_hets_vs_hom_1

description:
Sample details: We analysed changes in gene expression in the dorsal telencephalon of forebrain-specific FGFR1 mutant mice. Gene expression was compared between the dorsal telencephalons of single E12.5 embryos of two genotypes: FGFR1 heterozygous (HET1,3,8) and homozygous mutants (HOM2,4,7) that were both heterozygous for the FoxG1 transcription factor, as Cre recombinase expression is driven off the endogenous FoxG1 locus in these animals (Hebert, J. M., Lin, M., Partanen, J., Rossant, J. and McConnell, S. K. (2003b). FGF signaling through FGFR1 is required for olfactory bulb morphogenesis. Development 130, 1101-11. & Hebert, J. M. and McConnell, S. K. (2000). Targeting of cre to the Foxg1 (BF-1) locus mediates loxP recombination in the telencephalon and other developing head structures. Dev Biol 222, 296-306.
).   RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156.


title: Mouse_Peg1_E12.5_mutant_vs_wildtype_4


title: Rdp1_1_clr4D

description: Schizosaccharomyces pombe cells, Rdp1 ChIP(chromatin immunoprecipitation)-on-chip, clr4 null replicate 1

tag: Chromatin DNA isolated from paraformaldehyde cross-linked clr4 null Schizosaccharomyces pombe cells and enriched for Rdp1-TAP chromatin with Ig-G Sepharose.


title: Mouse_Peg1_E12.5_mutant_vs_wildtype_3


title: Mouse_Peg1_E12.5_mutant_vs_wildtype_2


title: Mouse_E13.5_Front_Middle_Back_17

description: Sample details: Three pools of rostral (R1-3), three pools of middle (M1-3), and three pools of caudal (C1-3) E13.5 MF1 neocortex were collected from 4 embryos. All possible 18 comparisons were carried out. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156.


title: Mouse_Peg1_E12.5_mutant_vs_wildtype_1


title: Mouse_E13.5_Front_Middle_Back_18


title: Mouse_E13.5_Front_Middle_Back_15


title: H3K9me2_2_wt

description: Schizosaccharomyces pombe cells, H3K9me2 ChIP(chromatin immunoprecipitation)-on-chip, replicate 2


title: Mouse_E13.5_Front_Middle_Back_12


title: Mouse_E13.5_Front_Middle_Back_7


title: Mouse_E13.5_Front_Middle_Back_10


title: Mouse_E13.5_Front_Middle_Back_13


title: Mouse_E13.5_Front_Middle_Back_6


title: Mouse_E13.5_Front_Middle_Back_8


title: Mouse_E13.5_Front_Middle_Back_2


title: Mouse_E13.5_Front_Middle_Back_11


title: Mouse_E13.5_Front_Middle_Back_4


title: Mouse_E13.5_Front_Middle_Back_5


title: Mouse_E13.5_Front_Middle_Back_14


title: Mouse_E13.5_Front_Middle_Back_9


title: Mouse_C57_E13.5_necortex_rostral_vs_caudal_r2_dyeswap

description: Sample details: rostral or caudal thirds of E13.5 C57 neocortex where pooled from three embryos. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156.

tag: see description


title: Mouse_E13.5_Front_Middle_Back_3


title: Mouse_C57_E13.5_necortex_rostral_vs_caudal_r3


title: Mouse_C57_E13.5_necortex_rostral_vs_caudal_r3_dyeswap


title: Mouse_E13.5_Front_Middle_Back_1


title: Mouse_C57_E13.5_necortex_rostral_vs_caudal_r1


title: Mouse_E13.5_Front_Middle_Back_16


title: Mouse_MF1_E13.5_necortex_rostral_vs_caudal_r3_dyeswap

description: Sample details: rostral or caudal thirds of E13.5 MF1 neocortex where pooled from three embryos. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156.


title: Mouse_MF1_E13.5_necortex_rostral_vs_caudal_r2_dyeswap


title: Mouse_MF1_E11.5_necortex_rostral_vs_caudal_r3_dyeswap

description: Sample details: rostral or caudal thirds of E11.5 MF1 neocortex where pooled from three embryos. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156.

data_processing: log ratios were lowess normalised, and filted to exclude (1) spots flagged as bad and (2) spots where 55% of the foreground pixels in either channel where less intense than the (background intensity + 1SD)


title: Mouse_C57_E13.5_necortex_rostral_vs_caudal_r1_dyeswap


title: ctr9 deletion

city: Denver

first: Judith

middle: A.

last: Jaehning

state: CO

address: 4200 E. 9th Avenue Campus Box B-121

department: Biochemistry and Molecular Genetics

institute: UCHSC

description: ctr9 deletion

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 4.0

label: biotin

organism: Saccharomyces cerevisiae

source_name: whole cell

label_protocol: Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Whole cell extracts were prepared from liquid cultures of a ctr9 strain grown to mid-log phase in YPD medium with 4% glucose

tag: ctr9 deletion strain


title: Mouse_MF1_E13.5_necortex_rostral_vs_caudal_r1


title: paf1 deletion 2

description: paf1 deletion

extract_protocol: Whole cell extracts were prepared from liquid cultures of a paf1 strain grown to mid-log phase in YPD medium with 4% glucose

tag: paf1 deletion strain


title: Mouse_MF1_E11.5_necortex_rostral_vs_caudal_r1_dyeswap


title: Mouse_MF1_E13.5_necortex_rostral_vs_caudal_r1_dyeswap


title: Mouse_MF1_E13.5_necortex_rostral_vs_caudal_r2


title: Mouse_MF1_E11.5_necortex_rostral_vs_caudal_r3


title: 5 Hr. Timepoint

description: TetO2-Paf1 strain grown in the presence of doxycycline for 5 hrs.

extract_protocol: Whole cell extracts were prepared from liquid cultures of TetO2-Paf1 grown to mid-log phase in the presence of doxycyclinefor 5 hrs.

tag: Tetracycline regulated-Paf1 (TetO2-Paf1) strain grown in the presence of doxycycline for 5 hrs.


title: paf1 deletion 1

description: paf1 deletion


title: Wild type 2

description: Wild type

extract_protocol: Whole cell extracts were prepared from liquid cultures of wild type strain grown to mid-log phase in YPD medium with 4% glucose

tag: Wild type


title: Mouse_C57_E11.5_necortex_rostral_vs_caudal_r2

description: Sample details: rostral or caudal thirds of E11.5 C57 neocortex where pooled from three embryos. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156.


title: Mouse_MF1_E11.5_necortex_rostral_vs_caudal_r1


title: Mouse_MF1_E11.5_necortex_rostral_vs_caudal_r2_dyeswap


title: 8 Hr. Timepoint

description: TetO2-Paf1 strain grown in the presence of doxycycline for 8 hrs.

extract_protocol: Whole cell extracts were prepared from liquid cultures of TetO2-Paf1 grown to mid-log phase in the presence of doxycyclinefor 8 hrs.

tag: Tetracycline regulated-Paf1 (TetO2-Paf1) strain grown in the presence of doxycycline for 8 hrs.


title: Wild type 1

description: Wild type


title: 6 Hr. Timepoint

description: TetO2-Paf1 strain grown in the presence of doxycycline for 6 hrs.

extract_protocol: Whole cell extracts were prepared from liquid cultures of TetO2-Paf1 grown to mid-log phase in the presence of doxycyclinefor 6 hrs.

tag: Tetracycline regulated-Paf1 (TetO2-Paf1) strain grown in the presence of doxycycline for 6 hrs.


title: 2 Hr. Timepoint

description: TetO2-Paf1 strain grown in the presence of doxycycline for 2 hrs.

extract_protocol: Whole cell extracts were prepared from liquid cultures of TetO2-Paf1 grown to mid-log phase in the presence of doxycycline for 2 hrs.

tag: Tetracycline regulated-Paf1 (TetO2-Paf1) strain grown in the presence of doxycycline for 2 hrs.


title: 0 Hr. Timepoint

description: TetO2-Paf1 strain grown in the absence of doxycycline

extract_protocol: Whole cell extracts were prepared from liquid cultures of TetO2-Paf1 grown to mid-log phase in the absence of doxycycline

tag: Tetracycline regulated-Paf1 (TetO2-Paf1) strain grown in the absence of doxycycline


title: Mouse_MF1_E13.5_necortex_rostral_vs_caudal_r3


title: 4 Hr. Timepoint

description: TetO2-Paf1 strain grown in the presence of doxycycline for 4 hrs.

extract_protocol: Whole cell extracts were prepared from liquid cultures of TetO2-Paf1 grown to mid-log phase in the presence of doxycyclinefor 4 hrs.

tag: Tetracycline regulated-Paf1 (TetO2-Paf1) strain grown in the presence of doxycycline for 4 hrs.


title: Mouse_C57_E11.5_necortex_rostral_vs_caudal_r1_dyeswap

description: Sample details: rostral or caudal thirds of E11.5 C57 neocortex where pooled from three embryos. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. "Single Step Method of RNA Isolation by Acid Guanidinium Thiocyanate-Phenol-Chloroform Extraction." Amplification and probe labelling were carried out as detailed in this paper: Livesey, F. J., Furukawa, T., Steffen, M. A., Church, G. M. and Cepko, C. L. (2000). Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr Biol 10, 301-10


title: Mouse_C57_E11.5_necortex_rostral_vs_caudal_r2_dyeswap


title: 483MM

status: Public on Aug 25 2005

city: San Diego

first: Tim

last: Jatkoe

institute: Veridex

description: Melanoma

data_processing: Affymetrix Microarray Suite version 5.0

source_name: skin

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was isolated from skin, nevus and melanoma samples according to Standard Trizol protocol or Qiagen RNeasy Mini Kit protocol.

tag: Melanoma


title: 473MM

description: Melanoma


title: 470MM

description: Melanoma


title: 484MM

description: Melanoma


title: 477MM

description: Melanoma


title: 457MM

description: Melanoma


title: Mouse_C57_E13.5_necortex_rostral_vs_caudal_r2


title: 453MM

description: Melanoma


title: 482MM

description: Melanoma


title: 456MM

description: Melanoma


title: 463MM

description: Melanoma


title: 461MM

description: Melanoma


title: Mouse_MF1_E11.5_necortex_rostral_vs_caudal_r2


title: 450MM

description: Melanoma


title: 448MM

description: Melanoma


title: 447MM

description: Melanoma


title: 446MM

description: Melanoma


title: 454MM

description: Melanoma


title: 452MM

description: Melanoma


title: 443MM

description: Melanoma


title: 449MM

description: Melanoma


title: 455MM

description: Melanoma


title: 445MM

description: Melanoma


title: OWB-R stress replicate 2

city: Riverside

first: xinping

last: cui

address: Department of Statistics, University of California, Riverside

department: Statistics

institute: University of California,Riverside

description: drought stress

data_processing: GCOS 1.2

organism: Hordeum vulgare

source_name: whole seedling

extract_protocol: Five seedlings were used for RNA extraction

tag: cv. Oregon Wolfe Barley Recessive

tag: drought stress


title: 444MM

description: Melanoma


title: 405MM

description: Melanoma


title: 407MM

description: Melanoma


title: OWB-D stress replicate 2

description: drought stress

tag: cv. Oregon Wolfe Barley Dominant


title: 409MM

description: Melanoma


title: Steptoe stress and unstress replicate 1

description: drought stress and unstressed

tag: cv. Steptoe

tag: drought stress and unstressed


title: OWB-D stress replicate 3

description: drought stress


title: OWB-D stress replicate 1

description: drought stress


title: 392MM

description: Melanoma


title: 442MM

description: Melanoma


title: Steptoe stress and unstress replicate 3

description: drought stress and unstressed


title: OWB-R stress replicate 1

description: drought stress


title: Steptoe stress and unstress replicate 2

description: drought stress and unstressed


title: Morex stress and unstress replicate 2

description: drought stress and unstressed

tag: cv. Morex


title: Morex stress and unstress replicate 1

description: drought stress and unstressed


title: Barke stress and unstress replicate 4

description: drought stress and unstressed

tag: cv. Barke


title: 478MM

description: Melanoma


title: OWB-R unstress replicate 3

description: unstressed

tag: unstressed


title: 481MM

description: Melanoma


title: 476MM

description: Melanoma


title: 511MM

description: Melanoma


title: 512MM

description: Melanoma


title: Barke stress and unstress replicate 1

description: drought stress and unstressed


title: OWB-D unstress replicate 3

description: unstressed


title: OWB-R unstress replicate 2

description: unstressed


title: 475MM

description: Melanoma


title: OWB-R unstress replicate 1

description: unstressed


title: 465MM

description: Melanoma


title: OWB-D unstress replicate 2

description: unstressed


title: OWB-D unstress replicate 1

description: unstressed


title: 466MM

description: Melanoma


title: OWB-R stress replicate 3

description: drought stress


title: 469MM

description: Melanoma


title: 472MM

description: Melanoma


title: 441MM

description: Melanoma


title: 464MM

description: Melanoma


title: 397MM

description: Melanoma


title: 459MM

description: Melanoma


title: 493MM

description: Nevus

tag: Nevus


title: 468MM

description: Melanoma


title: 440MM

description: Melanoma


title: 460MM

description: Melanoma


title: 499MM

description: Nevus


title: 498MM

description: Nevus


title: 491MM

description: Nevus


title: 489MM

description: Nevus


title: 490MM

description: Nevus


title: 495MM

description: Nevus


title: 487MM

description: Nevus


title: Bladder_BW3vsC0_Dye

city: Barcelona

first: Moises

middle: Burset

last: Albareda

state: Barcelona

address: Cartagena, 340-350

department: Molecular biology

country: Spain

institute: Fundacio Puigvert

description:
Bladder washing RNA degradation state 3.
filters to remove bad spots:
circularity>=0.4
area>=40
bg[RG]med/morph[RG]<=8
[RG]median/bg[RG]SD<=0.0045
badspot=0

data_processing: log2((Rmedian-morphR)/(Gmedian-morphG)) adjusting previously mean intensity to 400 for all arrays and channels

tag: Normal urothelium pool (4 males)

tag: Individual tumoral bladder washing (pT2 G3)


title: 509MM

description: Nevus


title: 502MM

description: Nevus


title: 501MM

description: Nevus


title: 500MM

description: Nevus


title: 497MM

description: Nevus


title: 507MM

description: Nevus


title: 508MM

description: Nevus


title: Bladder_BW3vsC0


title: 496MM

description: Nevus


title: Bladder_BW2vsC0_Dye

description:
Bladder washing RNA degradation state 2.
filters to remove bad spots:
circularity>=0.4
area>=40
bg[RG]med/morph[RG]<=8
[RG]median/bg[RG]SD<=0.0045
badspot=0


title: Bladder_BW2vsC0


title: 503MM

description: Nevus


title: Bladder_T3vsC0

description:
Tissue RNA degradation state 3

filters to remove bad spots:
circularity>=0.4
area>=40
bg[RG]med/morph[RG]<=8
[RG]median/bg[RG]SD<=0.0045
badspot=0

tag: Individual tumoral urothelium (pT2 G3)


title: 504MM

description: Nevus


title: Bladder_BW0vsC0

description:
Bladder washing intact RNA.
filters to remove bad spots:
circularity>=0.4
area>=40
bg[RG]med/morph[RG]<=8
[RG]median/bg[RG]SD<=0.0045
badspot=0


title: Bladder_BW1vsC0

description:
Bladder washing RNA degradation state 1.
filters to remove bad spots:
circularity>=0.4
area>=40
bg[RG]med/morph[RG]<=8
[RG]median/bg[RG]SD<=0.0045
badspot=0


title: Bladder_BW0vsC0_Dye


title: 432MM

description: Normal skin

tag: Normal


title: Bladder_BW1vsC0_Dye


title: 437MM

description: Normal skin


title: 431MM

description: Normal skin


title: 433MM

description: Normal skin


title: 485MM

description: Normal skin


title: Liver_D3T _Rep3

status: Public on Aug 24 2005

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description: No

hyb_protocol: Affymetrix Standard Protocol

scan_protocol: Affymetrix Standard Protocol

data_processing: Normalized with MAS5 across the 8 samples in this project; All probe sets included; No log transformation

label: Affymetrix Standard Protocl

source_name: D3T treated rat liver, snap frozen

label_protocol: Affymetrix Standard Protocol

growth_protocol: Rat AIN 76A chow (Harlan Teklad, WI)

extract_protocol: Total RNA extraction kit: Stat-60 (Tel-Test Inc, TX)

treatment_protocol: gavage with D3T (3H-1, 2-dithiole-3-thione) for 0.3 mmol/kg body weight, disolved in vehicle (saturated sucrose); 1st, 3rd and 5th day, once per day

tag: Strain

value: Fischer 344

tag: Gender

value: Male

tag: Age

tag: Tissue

value: Liver of D3T treated rat


title: Liver_D3T _Rep4

description: No


title: Bladder_T2vsC0_Dye

description:
Tissue RNA degradation state 2

filters to remove bad spots:
circularity>=0.4
area>=40
bg[RG]med/morph[RG]<=8
[RG]median/bg[RG]SD<=0.0045
badspot=0


title: Liver_D3T _Rep2

description: No


title: Liver_Control _Rep1

description: No

source_name: Control rat liver, snap frozen

treatment_protocol:
gavage with 0.2 ml vehicle (saturated sucrose);
1st, 3rd and 5th day, once per day

value: Liver of vehicle treated rat