title: Ammonium Exposure (30 min.)

description: Ammonium Exposure (30 min.)

scan_protocol: Scan Power : 100 PMT Volts : 499 Pixel Size : 5 Laser on time : 20190 Laser Power : 9.75 Scan Date : 2007-12-01 Scan Temperature : 29.10 Scan Time : 13:35:12 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1560, 3880
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 30 minutes
Compound Based Treatment : 0.5 M NH4Cl
Growth Condition : 25C YPD


title: 8D A1 vs. Mixed Reference

status: Public on Jan 24 2010

type: RNA

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

country: USA

institute: University of Washington

description: 8D A1 Kan-/lys

hyb_protocol: reference URL : http://genomics.princeton.edu/caudylab/Yeast_RNA_Prep_and_Labeling_070925.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-22 Scan Time : 16:27:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.1.0.10
Datafile type : GenePix Results 3
Image Origin : 0, 0
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

molecule: total RNA

organism: Saccharomyces bayanus

source_name: Mixed Reference

extract_protocol:
Extracted molecule : RNA
Extraction method : acid phenol extraction

treatment_protocol: Growth Condition : mixed

tag: species

value: S. bayanus

tag: strain name

value: mixed

source_name: 8D A1

treatment_protocol: Growth Condition : 25C YPD midlog

value: 8D A1

tag: genotype

value: Kan-/lys

tag: sex/mating type

value: MATa/alpha


title: galactose Acy732 30 min

description: galactose Acy732 30 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-19 Scan Time : 10:57:33 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 0, 0
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: sb common reference

label_protocol: reference URL : http://genomics.princeton.edu/caudylab/Yeast_RNA_Prep_and_Labeling_070925.pdf

source_name: galactose Acy732 30 min

treatment_protocol:
Time : 30 minutes
Growth Condition : 25C YNB + 2% galactose

value: prototroph 670.20del:KanMX

value: MATalpha


title: galactose Acy703 110 min

description: galactose Acy703 110 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-19 Scan Time : 10:24:08 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose Acy703 110 min

treatment_protocol:
Time : 110 minutes
Growth Condition : 25C YNB + 2% galactose

value: prototroph 555.11del:KanMX

value: MATa


title: 6B A7 vs. Mixed Reference

description: Segregant 6B A7 Kan-/LYS

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-17 Scan Time : 18:38:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Mixed S. bayanus reference

source_name: 6B A7

value: 6B A7

value: Kan-/LYS


title: 8D A9 vs. Mixed Reference

description: Segregant 8D A9 Kan-/lys

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-17 Scan Time : 18:20:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 8D A9

value: 8D A9


title: 6B A6 vs. Mixed Reference

description: Segregant 6B A6 Kan-/LYS

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-17 Scan Time : 18:28:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 6B A6

value: 6B A6


title: 6B A2 vs. Mixed Reference

description: Segregant 6B A2 Kan+/lys, alpha

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-16 Scan Time : 19:26:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 6B A2

value: 6B A2

value: Kan+/lys


title: 8D A8 vs. Mixed Reference

description: Segregant 8D A8 Kan-/LYS

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-17 Scan Time : 16:57:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 8D A8

value: 8D A8


title: galactose Acy732 15 min

description: galactose Acy732 15 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-19 Scan Time : 10:48:42 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose Acy732 15 min

treatment_protocol:
Time : 15 minutes
Growth Condition : 25C YNB + 2% galactose


title: Sulfite Exposure (0 min.)

description: Sulfite Exposure (0 min.)

scan_protocol: Scan Power : 100 PMT Volts : 491 Pixel Size : 5 Laser on time : 18519 Laser Power : 8.61 Scan Date : 2007-11-21 Scan Temperature : 30.69 Scan Time : 15:16:24 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 155, 2725
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: Sulfite Exposed

treatment_protocol:
Time : 0 minutes
Compound Based Treatment : 10 mM K2S2O5
Growth Condition : 25C YPD

value: prototroph


title: galactose Acy732 0 min

description: galactose Acy732 0 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-19 Scan Time : 11:34:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: S. bayanus

source_name: galactose Acy732 0 min

treatment_protocol:
Time : 0 minutes
Growth Condition : 25C YNB + 2% galactose


title: galactose Acy703 175 min

description: galactose Acy703 175 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-19 Scan Time : 11:42:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: mixed

source_name: galactose Acy703 175 min

treatment_protocol:
Time : 175 minutes
Growth Condition : 25C YNB + 2% galactose


title: 8D A10 vs. Mixed Reference

description: 8D A10 Mat a, Kan+/lys

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-22 Scan Time : 15:02:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: galactose Acy703 65 min

description: galactose Acy703 65 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 12:52:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose Acy703 65 min

treatment_protocol:
Time : 65 minutes
Growth Condition : 25C YNB + 2% galactose


title: Acy7 day 6

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-14 Scan Time : 15:35:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.0.1.25
Datafile type : GenePix Results 3
Image Origin : 0, 0
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: pooled reference of all ACY's day 0-1

treatment_protocol: Growth Condition : mixed timepoints days 0-1 for all three aging timecourses

source_name: Acy7 day 6

treatment_protocol:
Time : 6 days
Growth Condition : 25C water


title: Ammonium Exposure (20 min.)

description: Ammonium Exposure (20 min.)

scan_protocol: Scan Power : 100 PMT Volts : 485 Pixel Size : 5 Laser on time : 19825 Laser Power : 9.22 Scan Date : 2007-11-30 Scan Temperature : 28.89 Scan Time : 18:32:00 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1200, 4160
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: Mixed Reference

source_name: Ammonium Exposed

treatment_protocol:
Time : 20 minutes
Compound Based Treatment : 0.5 M NH4Cl
Growth Condition : 25C YPD


title: Ammonium Exposure (0 min.)

description: Ammonium Exposure (0 min.)

scan_protocol: Scan Power : 100 PMT Volts : 502 Pixel Size : 5 Laser on time : 20270 Laser Power : 9.83 Scan Date : 2007-12-01 Scan Temperature : 30.48 Scan Time : 14:55:48 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1480, 4120
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 0 minutes
Compound Based Treatment : 0.5 M NH4Cl
Growth Condition : 25C YPD


title: galactose Acy703 90 min

description: galactose Acy703 90 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 13:00:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: sb common reference

source_name: galactose Acy703 90 min

treatment_protocol:
Time : 90 minutes
Growth Condition : 25C YNB + 2% galactose


title: 6B A4 vs. Mixed Reference

description: Segregant 6B A4 Kan-/lys

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-16 Scan Time : 19:34:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Mixed S. bayanus reference

source_name: 6B A4

value: 6B A4


title: 8D A2 vs. Mixed Reference

description: Segregant 8D A2 Kan-/LYS

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-16 Scan Time : 19:17:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 8D A2

value: 8D A2


title: galactose Acy703 45 min

description: galactose Acy703 45 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 12:42:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose Acy703 45 min

treatment_protocol:
Time : 45 minutes
Growth Condition : 25C YNB + 2% galactose


title: galactose Acy703 145 min

description: galactose Acy703 145 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-19 Scan Time : 10:32:19 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose Acy703 145 min

treatment_protocol:
Time : 145 minutes
Growth Condition : 25C YNB + 2% galactose


title: Ethanol Exposure (60 min.)

description: Ethanol Exposure (60 min.)

scan_protocol: Scan Power : 100 PMT Volts : 489 Pixel Size : 5 Laser on time : 18672 Laser Power : 8.69 Scan Date : 2007-11-22 Scan Temperature : 29.44 Scan Time : 14:46:30 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1280, 4080
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: Ethanol Exposed

treatment_protocol:
Time : 60 minutes
Compound Based Treatment : 5% ethanol
Growth Condition : 25C YPD


title: Acy7 exponential

description: Acy7 exponential

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-12 Scan Time : 17:56:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Pooled of Dby's day 0-1

source_name: Acy7 exponential


title: Ammonium Exposure (10 min.)

description: Ammonium Exposure (10 min.)

scan_protocol: Scan Power : 100 PMT Volts : 505 Pixel Size : 5 Laser on time : 19976 Laser Power : 9.72 Scan Date : 2007-11-30 Scan Temperature : 30.94 Scan Time : 21:05:04 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1760, 3640
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol: Growth Condition : mixed

treatment_protocol:
Time : 10 minutes
Compound Based Treatment : 0.5 M NH4Cl
Growth Condition : 25C YPD


title: 8D A3 vs. Mixed Reference

description: Segregant 8D A3 Kan+/lys, alpha

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-16 Scan Time : 19:43:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 8D A3

treatment_protocol: Growth Condition : 25C YPD midlog

value: 8D A3


title: Ethanol Exposure (30 min.)

description: Ethanol Exposure (30 min.)

scan_protocol: Scan Power : 100 PMT Volts : 473 Pixel Size : 5 Laser on time : 18637 Laser Power : 8.55 Scan Date : 2007-11-22 Scan Temperature : 28.59 Scan Time : 14:10:24 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1280, 3600
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 30 minutes
Compound Based Treatment : 5% ethanol
Growth Condition : 25C YPD


title: Acy4 1 day new

description: 2nd upload

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-08 Scan Time : 17:12:31 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: ACY4 1 day after resuspension in water

treatment_protocol:
Time : 1 day
Growth Condition : 25C water

value: lys2 ura3


title: galactose Acy703 30 min

description: galactose Acy703 30 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 12:33:31 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose Acy703 30 min

treatment_protocol:
Time : 30 minutes
Growth Condition : 25C YNB + 2% galactose


title: galactose Acy703 0 min

description: galactose Acy703 0 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 12:14:14 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose Acy703 0 min

treatment_protocol:
Time : 0 minutes
Growth Condition : 25C YNB + 2% galactose


title: 6B A1 vs. Mixed Reference

description: 6B A1 Kan+/lys, alpha

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-16 Scan Time : 19:51:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 6B A1 at log phase

value: 6B A1

value: MATalpha


title: ACY4 4hrs new

description: reuploaded

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-08 Scan Time : 16:48:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: pooled reference of all ACY's day 0-1

source_name: ACY4 4hrs after resuspension in water

treatment_protocol:
Time : 4 hours
Growth Condition : 25C water


title: Ethanol Exposure (10 min.)

description: Ethanol Exposure (10 min.)

scan_protocol: Scan Power : 100 PMT Volts : 472 Pixel Size : 5 Laser on time : 18599 Laser Power : 8.70 Scan Date : 2007-11-21 Scan Temperature : 30.63 Scan Time : 16:35:54 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1440, 3400
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: Mixed Reference

treatment_protocol:
Time : 10 minutes
Compound Based Treatment : 5% ethanol
Growth Condition : 25C YPD


title: galactose Acy703 15 min

description: galactose Acy703 15 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 12:23:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: sb common reference

source_name: galactose Acy703 15 min

treatment_protocol:
Time : 15 minutes
Growth Condition : 25C YNB + 2% galactose

value: prototroph 555.11del:KanMX

value: MATa


title: 8D A5 vs. Mixed Reference

description: Segregant 8D A5 Kan+/lys, a

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-16 Scan Time : 18:31:17 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Mixed S. bayanus reference

source_name: 8D A5

value: 8D A5


title: Acy7 0+2 hrs.

description: 12/4 combined samples by mistake

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-12 Scan Time : 18:23:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

treatment_protocol: Growth Condition : mixed timepoints days 0-1 for all three aging timecourses

source_name: Acy7 0+2hrs

treatment_protocol:
Time : 0 and 2 hours mixed
Growth Condition : 25C water


title: ACY4 2hrs new

description: reup

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-08 Scan Time : 17:21:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: ACY4 2hrs after resuspension in water


title: 6B A3 vs. Mixed Reference

description: Segregant 6B A3 Kan+/LYS, a

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-16 Scan Time : 18:22:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 6B A3

value: 6B A3

value: Kan+/LYS


title: Ethanol Exposure (5 min.)

description: Ethanol Exposure (5 min.)

scan_protocol: Scan Power : 100 PMT Volts : 468 Pixel Size : 5 Laser on time : 18563 Laser Power : 8.66 Scan Date : 2007-11-21 Scan Temperature : 30.75 Scan Time : 16:00:59 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1280, 3680
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: Ethanol Exposed

treatment_protocol:
Time : 5 minutes
Compound Based Treatment : 5% ethanol
Growth Condition : 25C YPD


title: Ethanol Exposure (0 min.)

description: Ethanol Exposure (0 min.)

scan_protocol: Scan Power : 100 PMT Volts : 463 Pixel Size : 5 Laser on time : 18536 Laser Power : 8.63 Scan Date : 2007-11-21 Scan Temperature : 30.75 Scan Time : 15:33:55 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Time : 0 minutes
Compound Based Treatment : 5% ethanol
Growth Condition : 25C YPD


title: galactose Acy7 145 min

description: galactose Acy7 145 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 11:55:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose Acy7 145 min


title: 6B A5 vs. Mixed Reference

description: Segregant 6B A5 Kan+/lys, alpha

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-16 Scan Time : 18:48:16 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 6B A5

value: 6B A5


title: Acy3 6 Days

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-12 Scan Time : 17:12:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Acy3 6 Days

treatment_protocol:
Time : 6 days
Growth Condition : 25C water


title: Acy3 4hrs.

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-12 Scan Time : 17:38:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Acy3 4hrs.


title: ACY4 T0

description: 12/4 RNA isolation

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-08 Scan Time : 16:56:22 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Acy4 T0 after resuspension in water

treatment_protocol:
Time : 0 minutes
Growth Condition : 25C water


title: 8D A4 vs. Mixed Reference

description: Segregant 8D A4 Kan+/lys, a

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-16 Scan Time : 18:40:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 8D A4

value: 8D A4

value: Kan+/lys


title: galactose Acy7 110 min

description: galactose Acy7 110 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 11:46:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose Acy7 110 min

treatment_protocol:
Time : 110 minutes
Growth Condition : 25C YNB + 2% galactose

value: prototroph


title: Ura Limit - 16.5 hr.

description: Uracil auxotroph grown in limiting media (4 ug/ul uracil) at 16.5 hr.

scan_protocol: Pixel Size : 5 Scan Date : 2008-05-02 Scan Time : 14:44:38 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

treatment_protocol: Growth Condition : mixed

value: S. bayanus

source_name: Uracil Auxotroph 16.5 hr.

treatment_protocol:
Time : 16.5 hours
Growth Condition : 25C YNB + 4 mg/L uracil

value: ura3 derivative of BB11


title: NRRL-Y11845 vs. Mixed Reference

description: NRRL-Y11845 grown to log phase

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-22 Scan Time : 16:00:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Mixed Reference

value: mixed

source_name: NRRL-Y11845 grown to log phase

treatment_protocol: Growth Condition : 25C YPD midlog

value: MATa/alpha


title: Acy3 2 hrs

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-14 Scan Time : 15:09:14 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: pooled reference of all ACY's day 0-1

source_name: Acy3 2hrs

treatment_protocol:
Time : 2 hours
Growth Condition : 25C water


title: Bayanus Heat Shock (25-42) 15m

description: Bayanus Heat Shock (25-42) 15m

scan_protocol: Scan Power : 100 PMT Volts : 611 Pixel Size : 5 Laser on time : 18200 Laser Power : 8.21 Scan Date : 2007-11-09 Scan Temperature : 29.74 Scan Time : 17:06:16 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1800, 3160
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: Reference

source_name: 15 min

treatment_protocol:
Time : 15 minutes
Growth Condition : 42C YPD


title: Bayanus Heat Shock (25-42) 30m

description: Bayanus Heat Shock (25-42) 30m

scan_protocol: Scan Power : 100 PMT Volts : 588 Pixel Size : 5 Laser on time : 18236 Laser Power : 8.30 Scan Date : 2007-11-09 Scan Temperature : 30.05 Scan Time : 17:41:47 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 30 min

treatment_protocol:
Time : 30 minutes
Growth Condition : 42C YPD


title: YZB5-102 vs. Mixed Reference

description: S. bayanus strain YZB5-105

scan_protocol: Pixel Size : 5 Scan Date : 2008-01-04 Scan Time : 16:00:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Mixed S. bayanus reference

source_name: YZB5-102 grown to log phase


title: galactose Acy7 65 min

description: galactose Acy7 65 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 11:28:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: sb common reference

source_name: galactose Acy7 65 min

treatment_protocol:
Time : 65 minutes
Growth Condition : 25C YNB + 2% galactose


title: ACY3 T0

description: 12/4 rna isolations

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-08 Scan Time : 17:04:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: T0 after resuspension in water


title: Ura Limit - 13.5 hr.

description: Uracil auxotroph grown in limiting media (4 ug/ul uracil) at 13.5 hr.

scan_protocol: Pixel Size : 5 Scan Date : 2008-05-02 Scan Time : 16:08:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Uracil Auxotroph 13.5 hr.

treatment_protocol:
Time : 13.5 hours
Growth Condition : 25C YNB + 4 mg/L uracil


title: galactose Acy7 45 min

description: galactose Acy7 45 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 11:19:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose Acy7 45 min

treatment_protocol:
Time : 45 minutes
Growth Condition : 25C YNB + 2% galactose


title: Bayanus Heat Shock (25-42) 5m

description: Bayanus Heat Shock (25-42) 5m

scan_protocol: Scan Power : 100 PMT Volts : 609 Pixel Size : 5 Laser on time : 18180 Laser Power : 8.17 Scan Date : 2007-11-09 Scan Temperature : 29.20 Scan Time : 16:46:10 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1040, 2680
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: 5 min

treatment_protocol:
Time : 5 minutes
Growth Condition : 42C YPD


title: galactose Acy7 90 min

description: galactose Acy7 90 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 11:36:46 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose Acy7 90 min

treatment_protocol:
Time : 90 minutes
Growth Condition : 25C YNB + 2% galactose


title: Bayanus Heat Shock (25-42) 0m

description: Bayanus Heat Shock (25-42) 0m

scan_protocol: Scan Power : 100 PMT Volts : 513 Pixel Size : 5 Laser on time : 18161 Laser Power : 8.11 Scan Date : 2007-11-09 Scan Temperature : 28.74 Scan Time : 16:26:13 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 920, 3760
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: 0 min

treatment_protocol:
Time : 0 minutes
Growth Condition : 42C YPD


title: galactose Acy7 30 min

description: galactose Acy7 30 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 11:10:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose Acy7 30 min

treatment_protocol:
Time : 30 minutes
Growth Condition : 25C YNB + 2% galactose


title: Acy3 exponential

description: Acy3 exponential

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-14 Scan Time : 15:17:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

treatment_protocol: Growth Condition : mixed timepoints days 0-1 for all three aging timecourses

source_name: ACY3 exponential


title: Heat shock 45' (25-37)

description: Heat shock S. bayanus 37 degrees

scan_protocol: Pixel Size : 5 Scan Date : 2006-09-21 Scan Time : 17:39:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Common reference

source_name: 45' heat shock

treatment_protocol:
Time : 45 minutes
Growth Condition : 37C YPD


title: Ura Limit - 11 hr.

description: Uracil auxotroph grown in limiting media (2 ug/ul uracil) at 11 hr.

scan_protocol: Pixel Size : 5 Scan Date : 2008-05-02 Scan Time : 16:00:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Uracil Auxotroph 11 hr.

treatment_protocol:
Time : 11 hours
Growth Condition : 25C YNB + 4 mg/L uracil


title: Heat Shock 30' (25-37)

description: Heat Shock 30' (25-37)

scan_protocol: Scan Power : 100 PMT Volts : 625 Pixel Size : 5 Laser on time : 3846 Laser Power : 3.43 Scan Date : 2006-09-21 Scan Temperature : 31.42 Scan Time : 16:22:39 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.0.1.25
Datafile type : GenePix Results 3
Image Origin : 960, 6200
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: Pooled Reference

source_name: Experimental

treatment_protocol:
Time : 30 minutes
Growth Condition : 37C YPD


title: galactose Acy7 15 min

description: galactose Acy7 15 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 11:01:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

treatment_protocol: Growth Condition : mixed

source_name: galactose Acy7 15 min

treatment_protocol:
Time : 15 minutes
Growth Condition : 25C YNB + 2% galactose


title: galactose Acy7 0 min

description: galactose Acy7 0 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 10:52:32 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose Acy7 0 min

treatment_protocol:
Time : 0 minutes
Growth Condition : 25C YNB + 2% galactose


title: Bayanus Heat Shock (25-37) 15min

description: S. bayanus heat shock from 25-37 degrees, 15 minute time point

scan_protocol: Scan Power : 100 PMT Volts : 537 Pixel Size : 5 Laser on time : 17374 Laser Power : 7.63 Scan Date : 2007-10-24 Scan Temperature : 30.02 Scan Time : 15:27:56 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 800, 4000
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: Reference

treatment_protocol:
Time : 15 minutes
Growth Condition : 37C YPD


title: Bayanus Heat Shock (25-37) 60min

description: S. bayanus heat shock from 25 to 37 degrees, 60 minute time point

scan_protocol: Scan Power : 100 PMT Volts : 601 Pixel Size : 5 Laser on time : 17435 Laser Power : 7.65 Scan Date : 2007-10-24 Scan Temperature : 30.23 Scan Time : 16:29:27 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1000, 3600
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 60 minutes
Growth Condition : 37C YPD


title: Bayanus Heat Shock (25-37) 30min

description: S. bayanus heat shock from 25-37 degrees, 30 minute time point

scan_protocol: Scan Power : 100 PMT Volts : 503 Pixel Size : 5 Laser on time : 17404 Laser Power : 7.61 Scan Date : 2007-10-24 Scan Temperature : 30.14 Scan Time : 15:58:05 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 880, 3320
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.


title: Tryp Limit - 16.5 hr.

description: Tryptophan auxotroph grown in limiting media (2 ug/ul tryptophan) at 16.5 hr.

scan_protocol: Pixel Size : 5 Scan Date : 2008-05-02 Scan Time : 15:44:17 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.1.0.10
Datafile type : GenePix Results 3
Image Origin : 0, 0
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: Mixed S. bayanus reference

source_name: Tryptophan Auxotroph 16.5 hr.

treatment_protocol:
Time : 16.5 hours
Growth Condition : 25C YNB + 2 mg/L tryptophan


title: heat shock 15' (25-37)

description: heat shock 15' (25-37)

scan_protocol: Pixel Size : 5 Scan Date : 2006-09-21 Scan Time : 17:55:29 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Pooled reference

source_name: Experimental at 15'


title: Tryp Limit - 19 hr.

description: Tryptophan auxotroph grown in limiting media (2 ug/ul tryptophan) at 19 hr.

scan_protocol: Pixel Size : 5 Scan Date : 2008-05-02 Scan Time : 15:52:14 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Tryptophan Auxotroph 19 hr.

treatment_protocol:
Time : 19 hours
Growth Condition : 25C YNB + 2 mg/L tryptophan


title: ACY678 60 min

description: ACY678 60 min

scan_protocol: Pixel Size : 5 Scan Date : 2009-03-31 Scan Time : 11:22:33 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 0, 0
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: sb common reference

source_name: ACY678 60 min galactose, grown in raffinose

treatment_protocol:
Time : 60 minutes
Growth Condition : 25C YNB + 2% galactose

value: prototroph 670.20del:KanMX


title: Bayanus Heat Shock (25-37) 0min

description: 25-37 degree heat shock of S. bayanus. 0 minutes time point.

scan_protocol: Scan Power : 100 PMT Volts : 546 Pixel Size : 5 Laser on time : 17312 Laser Power : 7.52 Scan Date : 2007-10-24 Scan Temperature : 29.35 Scan Time : 14:27:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 320, 3600
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 0 minutes
Growth Condition : 37C YPD


title: ACY678 30 min

description: ACY678 30 min

scan_protocol: Pixel Size : 5 Scan Date : 2009-03-31 Scan Time : 11:13:05 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: ACY678 30 min galactose, grown in raffinose


title: Tryp Limit - 13.5 hr.

description: Tryptophan auxotroph grown in limiting media (2 ug/ul tryptophan) at 13.5 hr.

scan_protocol: Pixel Size : 5 Scan Date : 2008-05-02 Scan Time : 15:10:24 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Tryptophan Auxotroph 13.5 hr.

treatment_protocol:
Time : 13.5 hours
Growth Condition : 25C YNB + 2 mg/L tryptophan


title: Heat Shock 0' (25-37)

description: Performed with S. bayanus

scan_protocol: Scan Power : 100 PMT Volts : 616 Pixel Size : 5 Laser on time : 3735 Laser Power : 3.26 Scan Date : 2006-09-21 Scan Temperature : 29.74 Scan Time : 14:30:40 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.0.1.25
Datafile type : GenePix Results 3
Image Origin : 1360, 5720
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.


title: Bayanus Heat Shock (25-37) 5min

description: S. bayanus 25-37 degree heat shock. 5 minute time point.

scan_protocol: Scan Power : 100 PMT Volts : 520 Pixel Size : 5 Laser on time : 17345 Laser Power : 7.60 Scan Date : 2007-10-24 Scan Temperature : 29.71 Scan Time : 14:59:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 320, 3360
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 5 minutes
Growth Condition : 37C YPD


title: Heat Shock 5' (25-37)

description: Heat Shock 5' (25-37)

scan_protocol: Pixel Size : 5 Scan Date : 2006-09-21 Scan Time : 19:59:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.0.1.25
Datafile type : GenePix Results 3
Image Origin : 0, 0
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.


title: Lys Limit - 16.5 hr.

description: Lysine limitation, 16.5 hours

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-22 Scan Time : 14:53:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Mixed Reference

source_name: Lysine limited cells at 16.5 hours

treatment_protocol:
Time : 16.5 hours
Growth Condition : 25C YNB + 6 mg/L lysine


title: Tryp Limit - 11 hr.

description: Tryptophan auxotroph grown in limiting media (2 ug/ul tryptophan) at 11 hr.  Norm same with Sb only

scan_protocol: Pixel Size : 5 Scan Date : 2008-05-02 Scan Time : 15:00:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Tryptophan Auxotroph 11 hr.

treatment_protocol:
Time : 11 hours
Growth Condition : 25C YNB + 2 mg/L tryptophan


title: ACY678 0 min

description: ACY678 0 min

scan_protocol: Pixel Size : 5 Scan Date : 2009-03-31 Scan Time : 11:04:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: ACY678 0 min galactose, grown in raffinose


title: ACY331 60 min

description: ACY331 60 min

scan_protocol: Pixel Size : 5 Scan Date : 2009-03-31 Scan Time : 10:55:17 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: ACY331 60 min galactose, grown in raffinose


title: Bacteroides thetaiotaomicron-Input

status: Public on Sep 16 2009

type: SRA

city: St. Louis

first: Andrew

middle: L

last: Goodman

state: MO

address: Campus Box 8510, 4444 Forest Park Ave

department: Center for Genome Sciences

institute: Washington University School of Medicine

description: Transposon-adjacent DNA isolated by insertion sequencing (INSeq)

library_source: genomic

data_processing: Raw reads were parsed by barcode if necessary. Reads were then mapped and quantified using the MapSAM custom software package (processed_data.txt files). The format for these processed_data.txt files is as follows: Column 1 = Full 32bp sequence used for mapping insertion location; Column 2 = trimmed read sequence from tag 5' of insertion location; Column 3 = trimmed read sequence from tag 3' of insertion location; Column 4 = non-normalized read count for 5' tag; Column 5 = non-normalized read count for 3' tag; Column 6 = insertion coordinate (for "T" of "TA" dinucleotide insertion site); Column 7 = GenBank ID for reference sequence.

molecule: genomic DNA

organism: Bacteroides thetaiotaomicron

source_name: INSeq DNA

extract_protocol: Genomic DNA was purified, digested with MmeI, and separated by PAGE. Transposon-sized fragments were extracted from the gel and ligated to a double-stranded DNA adapter bearing a 3’-NN overhang. PAGE-purified adapter-ligated library molecules were PCR amplified for 18 cycles using a transposon-specific and an adapter-specific primer. The 125bp product was purified by PAGE and sequenced using an Illumina Genome Analyzer as described in the user’s manual. Sequence images were converted into raw reads using Illumina software with default settings.

tag: environment

value: Initial plated population

tag: defined microbiota

value: In vitro

tag: mouse genotype

tag: barcode


title: ACY331 30 min

description: ACY331 30 min

scan_protocol: Pixel Size : 5 Scan Date : 2009-03-31 Scan Time : 10:46:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: ACY331 30 min galactose, grown in raffinose

treatment_protocol:
Time : 30 minutes
Growth Condition : 25C YNB + 2% galactose


title: Bayanus Heat Shock (17-30) 60m

description: Bayanus Heat Shock (17-30) 60m

scan_protocol: Scan Power : 100 PMT Volts : 551 Pixel Size : 5 Laser on time : 18142 Laser Power : 8.23 Scan Date : 2007-11-08 Scan Temperature : 31.12 Scan Time : 17:38:41 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1720, 3440
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: Reference

source_name: 60 min

treatment_protocol:
Time : 60 minutes
Growth Condition : 30C YPD

value: MATalpha


title: Lys Limit - 15 hr.

description: Lysine limitation in S. bayanus, 15 hours  norm same with Sb genes only

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-22 Scan Time : 15:28:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Lysine limited cells at 15 hours

treatment_protocol:
Time : 15 hours
Growth Condition : 25C YNB + 6 mg/L lysine


title: Bayanus Heat Shock (17-30) 30m

description: Bayanus Heat Shock (17-30) 30m

scan_protocol: Scan Power : 100 PMT Volts : 556 Pixel Size : 5 Laser on time : 18115 Laser Power : 8.21 Scan Date : 2007-11-08 Scan Temperature : 30.90 Scan Time : 17:12:04 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 880, 3600
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: 30 min

treatment_protocol:
Time : 30 minutes
Growth Condition : 30C YPD


title: Bayanus Heat Shock (17-30) 5m

description: Bayanus Heat Shock (17-30) 5m

scan_protocol: Scan Power : 100 PMT Volts : 570 Pixel Size : 5 Laser on time : 17976 Laser Power : 7.97 Scan Date : 2007-11-08 Scan Temperature : 29.41 Scan Time : 14:52:11 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 880, 2280
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol: Growth Condition : mixed

source_name: 5 min

treatment_protocol:
Time : 5 minutes
Growth Condition : 30C YPD


title: Lys Limit - 18 hr.

description: Lysine limitation in S. bayanus, 18 hours

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-22 Scan Time : 16:19:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Lysine limited cells at 18 hours

treatment_protocol:
Time : 18 hours
Growth Condition : 25C YNB + 6 mg/L lysine


title: ACY331 0 min

description: ACY331 0 min

scan_protocol: Pixel Size : 5 Scan Date : 2009-03-31 Scan Time : 10:36:53 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: sb common reference

source_name: ACY331 0 min galactose, grown in raffinose

treatment_protocol:
Time : 0 minutes
Growth Condition : 25C YNB + 2% galactose


title: Lys Limit - 13.5 hr.

description: Lysine limitation in S. bayanus, 13.5 hours

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-22 Scan Time : 15:20:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Lysine limited cells at 13.5 hours

treatment_protocol:
Time : 13.5 hours
Growth Condition : 25C YNB + 6 mg/L lysine


title: 6B A10 vs. Mixed Reference

description: Segregant 6B A10 Kan-/LYS

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-17 Scan Time : 18:02:22 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Mixed S. bayanus reference

treatment_protocol: Growth Condition : 25C YPD midlog

value: Kan-/LYS


title: Acy7 1day

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-12 Scan Time : 18:14:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: pooled reference of all ACY's day 0-1

treatment_protocol: Growth Condition : mixed timepoints days 0-1 for all three aging timecourses

source_name: Acy7 1 day

treatment_protocol:
Time : 1 day
Growth Condition : 25C water

value: MATa


title: Bayanus Heat Shock (17-30) 15m

description: Bayanus Heat Shock (17-30) 15m

scan_protocol: Scan Power : 100 PMT Volts : 570 Pixel Size : 5 Laser on time : 18093 Laser Power : 8.19 Scan Date : 2007-11-08 Scan Temperature : 30.78 Scan Time : 16:50:01 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1480, 3240
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: 15 min

treatment_protocol:
Time : 15 minutes
Growth Condition : 30C YPD


title: Ring_H3K9ac

status: Public on May 18 2009

type: genomic

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

description: 261161 probes were extracted from the array and used for the analysis. Bi-weight mean used for scaling (based on full array) = Bi-weight mean = -1.877719

hyb_protocol: Equal amounts of the Cy-labeled test sample (Cy5) and reference sample (Cy3) were combined and dried down by vacuum centrifugation.  The sample was rehydrated in 39 µl of NimbleGen Hybridization Buffer (NimbleGen Systems Inc.), denatured at 95°C for 5 min and then cooled to 42°C.  Hybridization was carried out for 18 hours at 42°C.  The arrays were washed using NimbleGen Wash Buffer System (NimbleGen Systems Inc.) and immediately dried down by centrifugation

scan_protocol: Arrays were scanned at 5 m resolution using the GenePix4000B scanner (Axon Instruments). Data was extracted from scanned images using NimbleScan 2.1 extraction software (NimbleGen Systems Inc.), which allows for automated grid alignment, extraction and generation of data files.

data_processing: Log2 ratios were computed for each sample pair and scaled using the Tukey bi-weight mean, using NimbleScan Version 2.1 software or newer versions(NimbleGen Systems Inc).  Log2 ratios  were plotted to generate a graphical representation of enrichment mapped to chromosome location.

organism: Plasmodium falciparum

source_name: Ring_H3K9ac ChIP DNA

label_protocol: Each DNA sample (1 ug) was denatured at 98°C in the presence of 1 O.D. of 5’-Cy3 or Cy5 labeled random heptamers (TriLink Biotechnologies) in 62.5 mM Tris-HCl, pH 7.5, 6.25 mM MgCl2 and 0.0875% ß-mercaptoethanol. The denatured sample was chilled on ice, and then incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix (6 mM each in TE; Invitrogen) for 2 h at 37°C.  Reactions were terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water. Five- to ten-fold amplification was typically achieved.

growth_protocol: NF54 parasites in red blood cells, cultured using a semi-automated system in the presence of 10% human serum.  Cultures were synchonized by sequential use of at least 2 rounds of 5% Sorbitol and 63% Percoll.

extract_protocol: Crosslinked chromatin was prepared by adding 1% formaldehyde to the culture for 5 min followed by addition of glycine to 0.125M final concentration. After saponin lysis, nuclei were isolated by homogenization in 10mM Tris at pH 8.0, 3.0mM MgCl2, 0.2% NP-40, collected on a 0.25M sucrose-buffer cushion and suspended in SDS buffer (1% SDS, 50mM Tris pH 8.0, 10mM EDTA, protease inhibitors). Chromatin was sheared by sonication in a Bioruptor UCD-200 (Diagenode) for 10 min at 30s intervals, power setting high, to a size of 200-500 bp. Chromatin samples were processed immediatly. ChIP was performed as described elsewhere3. Quantitative PCR was performed in MyIQ sequence detector (Biorad) using primer sets described on supporting information SI Table 2. PCR products were cloned and sequenced to confirm their identities.

tag: strain

tag: cell type

value: Rings 14h-18h post-infection

tag: chip antibody

source_name: Input DNA from NF54 parasites

value: none, input DNA


title: Schizont_cDNA

type: mixed

description: 261161 probes were extracted from the array and used for the analysis. Bi-weight mean used for scaling (based on full array) = Bi-weight mean = -1.972527

extract_protocol: RNA Extraction QIAGEN

value: Mature schizonts ~4h pre-egress

source_name: Sonicated gDNA from NF54 very early Ring parasites

extract_protocol: Standar genomic DNA extraction


title: H4K16ac Kc GFP RNAi replicate #1

status: Public on Jun 10 2009

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

description: by Nimblegen, see Alekseyenko et al. 2006

hyb_protocol: [Supplied by Nimblegen] DNA Microarray Hybridization. In a new Eppendorf tube, 2.5 ug of Cy5-labeled chromatin immunoprecipitation (ChIP) DNA is mixed with 2.5 ug of Cy3-labeled genomic DNA and 36 ug of human Cot-1 DNA (Invitrogen; catalogue no. 15279-011). Sodium acetate(1/10 vol of 3 M) is added to the tube along with 2 vol of ethanol. After ethanol precipitation, the DNA is dissolved in 22.4 ul of hybridization buffer 1 (2.2× SSC/0.22% SDS). The mixture can be heated for 10 min at 37°C to facilitate the DNA to dissolve. Then 20 ul of hybridization buffer 2 (70% formamide/3× SSC/14.3% dextran sulfate) is added to the mixture, and the tube is first heated at 95°C for 5 min to denature DNA, then incubated at 42°C for 2 min. At this step, 4 ul of yeast tRNA (Sigma; catalogue no. R9001 at 10 ug/ul) and 3 ul of 2% BSA are added to the mixture, which is then spotted to a DNA microarray slide that has been incubated with the prehybridization solution for 40 min at 42°C. A 25-mm × 60-mm cover slip is then gently placed on top of the sample, and the hybridization is carried on in a hybridization chamber (Corning; catalogue no. 07-200-271) at 60°C overnight in a water bath. After the hybridization, the microarray slide is washed once with washing buffer 1 (2× SSC/0.1% SDS) at 60°C for 5 min in a glass slide staining dish. This is followed by a wash with buffer 2 (0.2× SSC/0.1% SDS) for 10 min at room temperature and three times with buffer 3 (0.2× SSC) at room temperature. The slide is then dried by a brief spinning at 1,000 × g in a table-top centrifuge.

scan_protocol: [Supplied by Nimblegen] Microarray Scanning and Initial Analysis. The microarray slides are scanned using GenePix 4000B scanner from Axon Instruments (Foster City, CA), and each microarray image is first analyzed with the image analysis software GENEPIX PRO 3.0 to derive the Cy3 and Cy5 fluorescent intensity and background noise for all the spots on the array. The intensities for both Cy3 and Cy5 channels are first adjusted by subtracting the background intensity of each spot by using the formula channel channel I - B , where channel represents either Cy5 or Cy3. The intensities are further adjusted by subtracting the median intensity of all the blank spots on the array. If any of these values was lower than 10, it was then raised to 10. Intensity Normalization: The normalization factor is calculated based on the intensities of spots that are considered good (more than 65% of pixels have intensities higher than the background intensity plus 1 SD). The median of the intensity ratios, I635/I532 is then used to adjust the Cy3 channel intensity to the same level as that of the Cy5 channel.

data_processing: Dye-specific bias was identified from the average intensity vs. log-ratio plot (i.e. MA plot) and a combination of rotation and a robust curve-fitting is used to correct the problem (Peng et al., 2007).

organism: Drosophila melanogaster

source_name: H4K16ac Kc GFP RNAi replicate #1

label_protocol: [Supplied by Nimblegen] Labeling of Amplified DNA. In a colored Eppendorf tube, 200 ng of DNA from the previous step is mixed with 20 ul of 2.5× random primer solution (BioPrime kit, Invitrogen; catalogue no. 18094-011) and dH2O in a final volume of 42.5 ul. The mixture is boiled for 5 min and then cooled on ice for 5 min. Subsequently, 5 ul of 10× low dCTP mixture (2.5 mM each for dATP, dTTP, and dGTP, and 0.6 mM for dCTP), 1.5 ul of Cy5-dCTP (Amersham; catalogue no. PA55021) or Cy3-dCTP (Amersham; catalogue no. PA53021), and 40 units of Klenow DNA polymerase are added to tube. The tube is incubated at 37°C for 2 h. After the reaction, the labeled DNA is purified using the Qiagen PCR kit (Qiagen; catalogue no. 28106).

extract_protocol: [Supplied by Nimblegen] After reversal of crosslinks, proteins in the DNA sample are removed by incubation with 120 ul of proteinase K solution (2% glycogen/5% 20 mg/ml proteinase K stock solution/TE buffer) for 2 h at 37°C. The sample is then extracted twice with phenol (Sigma; catalogue no. P-4557), once with 24:1 chloroform/isoamyl alcohol (Sigma; catalogue no. C-0549). The sample is adjusted to 200 mM NaCl. After ethanol precipitation, the DNA is dissolved in 30 ul of TE buffer containing 10 ug of DNase-free RNase A (Sigma; catalogue no. 6513) and incubated for 2 h at 37°C. The DNA at this step can be further purified with Qiagen PCR kit (Qiagen, Valencia, CA; catalogue no. 28106).

tag: IP with anti-H4K16ac from Upstate

tag: in Kc cell after GFP RNAi

source_name: Input DNA

tag: Input DNA


title: Schizont_H3K4me3

description: 261161 probes were extracted from the array and used for the analysis. Bi-weight mean used for scaling (based on full array) = Bi-weight mean = -1.125916

source_name: Schizont_H3K4me3 ChIP DNA


title: H4K16ac in SL2  replicate #1

source_name: H4K16ac in SL2  replicate #1

tag: IP with anti-K16ac SERO417

extract_protocol: [Supplied by Nimblegen]After reversal of crosslinks, proteins in the DNA sample are removed by incubation with 120 ul of proteinase K solution (2% glycogen/5% 20 mg/ml proteinase K stock solution/TE buffer) for 2 h at 37°C. The sample is then extracted twice with phenol (Sigma; catalogue no. P-4557), once with 24:1 chloroform/isoamyl alcohol (Sigma; catalogue no. C-0549). The sample is adjusted to 200 mM NaCl. After ethanol precipitation, the DNA is dissolved in 30 ul of TE buffer containing 10 ug of DNase-free RNase A (Sigma; catalogue no. 6513) and incubated for 2 h at 37°C. The DNA at this step can be further purified with Qiagen PCR kit (Qiagen, Valencia, CA; catalogue no. 28106).


title: Schizont_H3K9ac

description: 261161 probes were extracted from the array and used for the analysis. Bi-weight mean used for scaling (based on full array) = Bi-weight mean = -0.962037

source_name: Schizont_H3K9ac ChIP DNA


title: galactose Acy7 175 min

description: galactose Acy7 175 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-18 Scan Time : 12:05:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose Acy7 175 min

treatment_protocol:
Time : 175 minutes
Growth Condition : 25C YNB + 2% galactose


title: Schizont_H3

description: 261161 probes were extracted from the array and used for the analysis. Bi-weight mean used for scaling (based on full array) = Bi-weight mean = -1.403946

source_name: Schizont_H3 ChIP DNA


title: Ring_H3K4me3

description: 261161 probes were extracted from the array and used for the analysis. Bi-weight mean used for scaling (based on full array) = Bi-weight mean = -1.638289

source_name: Ring_H3K4me3 ChIP DNA


title: H4K16ac male larvae wt replicate #1

source_name: H4K16ac male larvae wt replicate #1

tag: IP with anti-H4K16ac from Serotec (AHP417)


title: Ring_H3

description: 261161 probes were extracted from the array and used for the analysis. Bi-weight mean used for scaling (based on full array) = Bi-weight mean = -1.215961

source_name: Ring_H3 ChIP DNA


title: H4K16ac female larvae wt replicate #1

source_name: H4K16ac female larvae wt replicate #1

extract_protocol: After reversal of crosslinks, proteins in the DNA sample are removed by incubation with 120 ul of proteinase K solution (2% glycogen/5% 20 mg/ml proteinase K stock solution/TE buffer) for 2 h at 37°C. The sample is then extracted twice with phenol (Sigma; catalogue no. P-4557), once with 24:1 chloroform/isoamyl alcohol (Sigma; catalogue no. C-0549). The sample is adjusted to 200 mM NaCl. After ethanol precipitation, the DNA is dissolved in 30 ul of TE buffer containing 10 ug of DNase-free RNase A (Sigma; catalogue no. 6513) and incubated for 2 h at 37°C. The DNA at this step can be further purified with Qiagen PCR kit (Qiagen, Valencia, CA; catalogue no. 28106).


title: H4K16ac Kc GFP RNAi replicate #2

source_name: H4K16ac Kc GFP RNAi replicate #2


title: MSL - Solexa

status: Public on Aug 22 2008

description: MSL ChIP

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: The tag sequences were determined using standard Solexa pipeline. The sequences were aligned to dm1 usign blat, and a set of informative tags was chosen (see manuscript for details)

label: not applicable

source_name: MSL3-TAP (Clone8)

label_protocol: not applicable

extract_protocol: not applicable

tag: MSL


title: 89877_H3

data_processing: Log2 ratios were computed for each sample pair and scaled using the Tukey bi-weight mean , using NimbleScan Version 2.1 software or newer versions(NimbleGen Systems Inc).  Log2 ratios  were plotted to generate a graphical representation of enrichment mapped to chromosome location.

source_name: H3 ChIP DNA

growth_protocol: NF54 parasites in red blood cells, cultured using a semi-automated system in the presence of 10% human serum.

extract_protocol: Crosslinked chromatin was prepared by adding 1% formaldehyde to the culture for 5 min followed by addition of glycine to 0.125M final concentration. After saponin lysis, nuclei were isolated by homogenization in 10mM Tris at pH 8.0, 3.0mM MgCl2, 0.2% NP-40, collected on a 0.25M sucrose-buffer cushion and suspended in SDS buffer (1% SDS, 50mM Tris pH 8.0, 10mM EDTA, protease inhibitors). Chromatin was sheared by sonication in a Bioruptor UCD-200 (Diagenode) for 10 min at 30s intervals, power setting high, to a size of 300-800 bp. Chromatin samples were frozen and stored at -80°C. ChIP was performed as described elsewhere3. Quantitative PCR was performed in MyIQ sequence detector (Biorad) using primer sets described on supporting information SI Table 2. PCR products were cloned and sequenced to confirm their identities.  For native ChIP, fresh nuclei were collected and washed in MNase digestion buffer (50mM Tris pH 7.4, 4mM MgCl2 1mM CaCl2). 15ng/l chromatin were digested with 0,5U MNase (Worthington) for 10 min at 37C. Reactions were stopped by adding 10mM EDTA followed by centrifugation at 13k for 5 min. Chromatin was extracted subsequently in 10mM Tris pH 7.4, 1mM EDTA and 1mM Tris pH 7.4, 0.2mM EDTA. Supernatants were pooled and diluted twice to 50mM NaCl, 20mM Tris pH7.4, 5mM EDTA, 0.5% Triton-X100, 0.05% SDS. ChIP was performed immediately and washed with 400 l of 50mM Tris pH 7.5, 10mM EDTA, 0.5% Triton X-100, 0.05% SDS,  with subsequent 100 to 150 and 250mM NaCl . Detergents were excluded from the last wash.

value: Asexual stages 10%rings, 10% trophos and schizonts

tag: extract protocol

value: X-L sonicated ChIP


title: 89272_H3


title: 89876_H3K4me3

source_name: H3K4me3 ChIP DNA


title: INPUT - Solexa

description: input

tag: input


title: H4K16ac male larvae wt replicate #2

source_name: H4K16ac male larvae wt replicate #2

tag: IP


title: H4K16ac female larvae wt replicate #2

source_name: H4K16ac female larvae wt replicate #2


title: 77620_H3K9ac

source_name: H3K9ac ChIP DNA

source_name: Input DNA from NF54 parasites


title: Ethanol Exposure (20 min.)

description: Ethanol Exposure (20 min.)

scan_protocol: Scan Power : 100 PMT Volts : 463 Pixel Size : 5 Laser on time : 18617 Laser Power : 8.72 Scan Date : 2007-11-21 Scan Temperature : 30.60 Scan Time : 16:53:40 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1440, 4000
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: Mixed Reference

tag: species

tag: strain name

source_name: Ethanol Exposed

treatment_protocol:
Time : 20 minutes
Compound Based Treatment : 5% ethanol
Growth Condition : 25C YPD

tag: genotype

tag: sex/mating type


title: 79483_H3K4me3


title: 96461_H3K9ac


title: 4944702_H3K9me3

source_name: H3K9me3 ChIP DNA

value: Native ChIP


title: 96481_H3


title: Ring_cDNA

description: 261161 probes were extracted from the array and used for the analysis. Bi-weight mean used for scaling (based on full array) = Bi-weight mean = -0.8171795

source_name: Sonicated gDNA from NF54 very early Ring parasites


title: H4K16ac in SL2  replicate #2

source_name: H4K16ac in SL2  replicate #2

source_name: Input DNA


title: Illumina G6

status: Public on Aug 21 2008

city: Canberra

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

description: Total RNA was provided to the Illumina Inc.

library_source: transcriptomic

data_processing: Custom Perl scripts were used for trimming, sorting, collating and other transformations of the data.  Sequences less than 18bp in length were removed.  Sequences were compared to known Oryza Sativa micro RNAs from miRBase 9.0.  BLAST was used to match the small RNAs to the Oryza Sativa genome (TIGR Rice Annotation Release 5.0), using a word size of 7, e-value cut-off of 1000 and no query sequence filtering.  Coordinates of perfect matches, or those with a single mismatch if no perfect matches, were retained.  Annotation was added to all recorded genome matches, but here only annotation for those with a single hit to the genome are shown.  Read numbers were scaled to tags per million from the total number of reads for each sample (46879, 55391, 21697, 11866, 3428861, 3412945 total reads for Samples GSM278532-GSM278535, GSM278571-GSM278572, respectively).

organism: Oryza sativa

source_name: developing grains

growth_protocol: Rice plants that were used for sample collection were grown in a controlled glasshouse at 25±3oC with 16 hours of lights

extract_protocol: Total RNA was extracted from approximately 1.5g of shoots and roots of 7 day-old seedlings, and 1-5 and 6-10 DAF de-husked rice grains. Tissues were ground into fine power in the presence of liquid nitrogen and processed using RNA extraction buffer (0.1M NaCl, 2% SDS, 50mM Tris/HCl, 10mM EDTA and 20mM beta-mercaptoethanol) and an equal volume of phenol/chloroform/isoamyl alcohol (25:24:1). The aqueous fraction was subsequently extracted two times using an equal volume of phenol/chloroform/isoamyl alcohol (25:24:1) and chloroform. Total RNA was then precipitated using LiCl (2M final concentration) overnight at -20oC.  Low molecular weight (LMW) RNA was precipitated from the supernatant with an equal volume of isoproponol in the presence of 0.1% SDS at -20oC for 2 days. The precipitated LMW RNA was resuspended in DEPC-treated H2O. Approximately 150µg of LMW RNA was then mixed with a trace amount of 5'- 32P-labeled RNA markers (18 and 25nt) and size fractionated on a 15% polyacrylamide and 8M urea gel. The gel fragment spanning the 18-25nt RNA markers was excised. The excised gel was crushed into fine pieces and RNA eluted overnight in 0.3M NaCl at 4oC with gentle shaking.

treatment_protocol: No treatment was applied to the biological material before sample collection

tag: source

value: 6-10 days after fertilization grains, cv Nipponbare


title: 116550_cDNA

source_name: RNA asexual stages

tag: strain

value: none (RNA)

value: RNA Extraction Trizol


title: 454 Shoots

description: Small RNAs were ligated to a 3' adaptor that has a blocked 3' terminus by introduction of a O-C3 linker, and a 5' RNA/DNA adaptor, respectively. Small RNAs were then reverse transcribed and further PCR amplified to get amplicons for sequencing.

source_name: shoots

value: 7 days old seedlings, cv Nipponbare


title: 454 G6


title: Illumina G1

value: 1-5 days after fertilization grains, cv Nipponbare


title: 89274_H3K9ac

tag: cell type


title: MSL3-TAP (Embryo) SYD62A mutant replicate #2

status: Public on Nov 19 2008

scan_protocol: [Supplied by Nimblegen] Microarray Scanning and Initial Analysis. The microarray slides are scanned using GenePix 4000B scanner from Axon Instruments (Foster City, CA), and each microarray image is first analyzed with the image analysis software GENEPIX PRO 3.0 to derive the Cy3 and Cy5 fluorescent intensity and background noise for all the spots on the array. The intensities for both Cy3 and Cy5 channels are first adjusted by subtracting the background intensity of each spot by using the formula channel channel I - B , where channel represents either Cy5 or Cy3. The intensities are further adjusted by subtracting the median intensity of all the blank spots on the array. If any of these values was lower than 10, it was then raised to 10.  Intensity Normalization:  The normalization factor is calculated based on the intensities of spots that are considered good (more than 65% of pixels have intensities higher than the background intensity plus 1 SD). The median of the intensity ratios, I635/I532 is then used to adjust the Cy3 channel intensity to the same level as that of the Cy5 channel.

tag: IgG beads were used for embryonic mutant cells (MSL3TAP tag)


title: 454 Roots

source_name: roots


title: MSL3-TAP (Embryo) SYD62A mutant replicate #1


title: Nodal diffuse large B cell lymphoma replicate 4

status: Public on May 10 2008

description: Fresh frozen samples from immunocompetent patients

hyb_protocol: The labeled samples were hybridized in Agilent microarray chambers (G2534A) at 60°C for 17 hours

scan_protocol: Images were scanned using Confocal laser scanner and quantified using Imagene software (version 6)

data_processing: Data was background subtracted and lowess normalized using GeneSpring (version 7.2) software

label: Alexa Fluor 555

organism: Homo sapiens

source_name: nodal diffuse large B cell lymphoma

label_protocol: Amplified RNA (aRNA) preparations were labeled either with Alexa Fluor 555 (lymphoma sample) or Alexa Fluor 647 (reference RNA) from Invitrogen

extract_protocol: Total RNA was extracted from the dissected lymphoma tissue using a kit from QIAGEN (Rneasy mini kit). The mRNA was amplified with RiboAmp HS RNA Amplification Kit

tag: Tissue

value: lymph node

label: Alexa Fluor 647

source_name: Stratagene Universal human RNA

tag: reference


title: Nodal diffuse large B cell lymphoma replicate 5


title: Nodal diffuse large B cell lymphoma replicate 3


title: MSL3-TAP (Embryo) M1S mutant replicate #2

tag: Input DNA


title: Nodal diffuse large B cell lymphoma replicate 9


title: Nodal diffuse large B cell lymphoma replicate 6


title: Nodal diffuse large B cell lymphoma replicate 10


title: Nodal diffuse large B cell lymphoma replicate 8


title: Nodal diffuse large B cell lymphoma replicate 11


title: Nodal diffuse large B cell lymphoma replicate 7


title: MSL3-TAP (Embryo) wt replicate #2

source_name: MSL3-TAP (Embryo) wt replicate #2

tag: IgG beads were used for wild type embryonic cells (MSL3TAP tag)


title: Nodal diffuse large B cell lymphoma replicate 2


title: Nodal diffuse large B cell lymphoma replicate 1


title: MSL3-TAP (Embryo) M1S mutant replicate #1


title: Extranodal diffuse large B cell lymphoma replicate 19

source_name: extranodal diffuse large B cell lymphoma

value: adenoid


title: MSL3-TAP (Embryo) wt replicate #1

source_name: MSL3-TAP (Embryo) wt replicate #1

tag: IgG beads were used for embryonic wild type cells (MSL3TAP tag)


title: Extranodal diffuse large B cell lymphoma replicate 18

value: tonsil


title: Extranodal diffuse large B cell lymphoma replicate 13

value: testes


title: Extranodal diffuse large B cell lymphoma replicate 14

value: spleen


title: Extranodal diffuse large B cell lymphoma replicate 16


title: Extranodal diffuse large B cell lymphoma replicate 15


title: Extranodal diffuse large B cell lymphoma replicate 11

value: ovary


title: MSL3-TAP (Embryos) replicate #2

source_name: MSL3-TAP (Embryos) replicate #2

tag: Independent experiment with dye order switched compared to replicate#1


title: MSL3-TAP (Clone8) replicate #2

source_name: MSL3-TAP (Clone8) replicate #2

tag: Independent experiment with the dye order switched compared to replicate #1


title: Extranodal diffuse large B cell lymphoma replicate 17


title: MSL3 mutant (Male Embryo) anti-MSL2 replicate#2

tag: MSL3 mutant (Male Embryo) anti-MSL2


title: Extranodal diffuse large B cell lymphoma replicate 9

value: liver


title: Extranodal diffuse large B cell lymphoma replicate 6

value: bone


title: Extranodal diffuse large B cell lymphoma replicate 7


title: Extranodal diffuse large B cell lymphoma replicate 10

value: thyroid


title: MSL3-TAP (Clone8) replicate #1

source_name: MSL3-TAP (Clone8) replicate #1

tag: IgG beads were used for Clone8 wild type cells (MSL3TAP tag)


title: Extranodal diffuse large B cell lymphoma replicate 2

value: stomach


title: Extranodal diffuse large B cell lymphoma replicate 4


title: Extranodal diffuse large B cell lymphoma replicate 3

value: epidural


title: Extranodal diffuse large B cell lymphoma replicate 8

value: pericardial


title: Extranodal diffuse large B cell lymphoma replicate 5

value: pleural


title: Primary central nervous system lymphoma replicate 13

source_name: Primary central nervous system lymphoma

value: brain


title: Primary central nervous system lymphoma replicate 7


title: Primary central nervous system lymphoma replicate 10


title: MSL3 mutant (Male Embryo) anti-MSL2 replicate#1

treatment_protocol: by Nimblegen, see Alekseyenko et al. 2006


title: Primary central nervous system lymphoma replicate 5


title: Primary central nervous system lymphoma replicate 12


title: Extranodal diffuse large B cell lymphoma replicate 12


title: Primary central nervous system lymphoma replicate 8


title: Primary central nervous system lymphoma replicate 11


title: Primary central nervous system lymphoma replicate 4


title: Primary central nervous system lymphoma replicate 9


title: Primary central nervous system lymphoma replicate 1


title: Primary central nervous system lymphoma replicate 6


title: Primary central nervous system lymphoma replicate 2


title: Primary central nervous system lymphoma replicate 3


title: MSL3-TAP (Embryos) replicate #1

source_name: MSL3-TAP (Embryos) replicate #1

tag: MSL3-TAP (Embryos) replicate #1


title: 454 G1


title: MSL3-TAP (Embryos) replicate #1 (mock control)

status: Public on Aug 01 2007

tag: IgG beads were used for wild type embryos (untag, negative control)


title: Extranodal diffuse large B cell lymphoma replicate 1

value: skin


title: H3K4me2 (SL2) replicate#2

status: Public on Sep 20 2007

description: no additional information

source_name: H3K4me2 (SL2) replicate#2

tag: H3K4me2 (SL2) replicate#2


title: MSL3-TAP (Embryos) replicate #2 (mock control)

tag: Independent experiment with dye order switched compared to replicate #1


title: MSL3-TAP (Clone8) replicate #1 (mock control)


title: H3 (SL2) replicate#1

description: no additional information

tag: H3 (SL2) replicate#1


title: MSL3-TAP larvae superspreading replicate#2

description: no additional information

tag: MSL3-TAP male larvae mutant for both roX1 and roX2 on the X chromosome, and containing a roX2 transgene inserted at position 26D8-9 (near the CG9537 gene) on chromosome 2L.


title: MSL3-TAP larvae superspreading (X+3R) replicates#2

description: no additional information


title: H3K36me3 (Cl8) replicate#1

description: no additional information

tag: H3K36me3 (Cl8) replicate#1


title: H3K36me3 (SL2) replicate#1

description: no additional information

source_name: H3K36me3 from Drosophila S2 cells

tag: H3K36me3 from Drosophila S2 cells


title: MSL3-TAP (Clone8) replicate #2 (mock control)

source_name: Input DNA


title: H3K4me2 (Cl8) replicate#1

description: no additional information

source_name: H3K4me2 (Cl8) replicate#1

tag: H3K4me2 (Cl8) replicate#1


title: H3K4me2 (SL2) replicate#1

description: no additional information

source_name: H3K4me2 (SL2)

tag: H3K4me2 (SL2)


title: H3K36me3 (Cl8) replicate#2

description: no additional information

source_name: H3K36me3 (Cl8) replicate#2

tag: H3K36me3 (Cl8) replicate#2

tag: Input DNA


title: H3K4me2 (Cl8) replicate#2

description: no additional information

source_name: H3K4me2 (Cl8) replicate#2

tag: H3K4me2 (Cl8) replicate#2


title: MSL3-TAP larvae superspreading (X+3R) replicates#1

description: no additional information

tag: MSL3-TAP male larvae mutant for both roX1 and roX2 on the X chromosome, and containing a roX2 transgene inserted at position 26D8-9 (near the CG9537 gene) on chromosome 2L


title: MSL3-TAP larvae superspreading replicate#1

description: no additional information

source_name: MSL3-TAP larvae superspreading


title: MSL3-TAP (SL2) dye-swap replicate #1

source_name: MSL3-TAP (SL2) dye-swap replicate #1

tag: MSL3-TAP (SL2) dye-swap replicate #1


title: MSL3-TAP (SL2) replicate #2 (mock control)

tag: IgG beads were used for SL2 wild type cells (untag, negative control)


title: H3 (Cl8) replicate#1

description: no additional information

source_name: H3 (Cl8) replicate#1

tag: H3 (Cl8) replicate#1


title: H3 (SL2) replicate#2

description: no additional information

tag: H3 (SL2) replicate#2


title: MSL3-TAP (SL2) replicate #1 (mock control)


title: H3 (Cl8) replicate#2

description: no additional information

source_name: H3 (Cl8) replicate#2

tag: H3 (Cl8) replicate#2


title: MSL3-TAP (SL2) replicate #2

source_name: MSL3-TAP (SL2) replicate #2

tag: IgG beads were used for SL2 wild type cells (MSL3-TAP tag)


title: H3K36me3 (SL2) replicate#2

description: no additional information


title: MSL3-TAP (SL2) dye-swap replicate #1 (mock control)


title: MSL3-TAP (SL2) replicate #1

source_name: IP MSL3-TAP: (SL2) replicate #1

tag: IP MSL3-TAP in male cell line SL2


title: H3 (SL2) replicate#3

description: no additional information

source_name: H3 (SL2) replicate#3

tag: H3 (SL2) replicate#3


title: H3K36me3 (SL2) replicate#3

description: no additional information

tag: H3K36me3 (SL2) replicate#3


title: MSL3-TAP larvae wildtype

description: no additional information

source_name: MSL3-TAP larvae wildtype

tag: MSL3-TAP larvae wildtype