title: WT_vs_mutTRXB1

hyb_protocol: Agilent hybridization  protocol v 4.1

scan_protocol: Scanning protocol" Using the Scan Array  Express microarray  scanner. 1.Turn on the scanner and  the computer (in this order) 2.Login: scanner 3.Double click the  'ScanArray Express' icon 4.Switch on lasers 1 and 3  at least 15 minutes prior to  scanning arrays 5.Click the 'File' button This is to prevent you from  accidentally turning off the  laser after the 15 minutes  warming-up phase 6.Insert the slide with the  array-side up and the label  towards the outside. On  Agilent slides the array side  is the side  with the label that has the  word "Agilent" on it 7.Press 'Scan | Prescan' 8.Put resolution at 50  m,  select both labels used,  and set PMT values for  both channels at for  instance 40% (Agilent  arrays) 9.Press 'Start' 10.Press 'Palette,' 'Green'  as soon as projection of  the image has started (first  dye), select the red colour  as soon as  scanning of the second  layer (second dye) has  started 11.Adjust PMT values to  balance signals obtained  for both channels. If  necessary do a few  low-resolution scans to  obtain a  optimal balance 12.Click the 'Scan' button  again 13.Select frame for high  resolution scan, adjust  resolution (to 10  m) and  scan the array for both  dyes 14.Press 'File | Save' to  save the files, 'Save all'  saves both dye layers "Create a new folder for  each array "'Save all' saves the  signals from both layers in  individual files 15.Switch off the lasers  and the scanner.

label_protocol:
cDNA synthesis and , Labeling Protocol 1.4
Annealing Annealing Mix
x µl	 RNA preparation (=10  µg)
y µl	 nuclease-free water
1 µl	 Random Nonamers
11 µl	 TOTAL
1.mix Annealing  Mix in a 200 µl PCR  tube gently by pipetting  up and down
2.incubate for  5’ 70°C
3.cool at room  temperature for 10’  (annealing)
4.spin down the  mixture to the bottom of  the tube
5.place on ice  Reverse transcription
Reverse Transcription  Mix
4 µl	5x  buffer
2 µl	0.1  M DTT
1 µl	 dNTP-mix
1 µl	 AA-dUTP
1 µl  	 TMIII (keep only briefly  outside  20°C)
20 µl	 TOTAL
1.Mix by very  gently by pipetting up  and down.
2.Incubate for 3  hrs at 42°C (in  PCR-machine)
3.Cool on ice  for immediate  purification or place at   20°C for storage  Degradation of mRNA
1.Add 2 µl 2,5  M NaOH
2.Mix (vortex)  and spin down
3.Incubate for  15 min. at 37°C
4.Add 10 µl 2 M  HEPES free acid
5.Mix (vortex)  and spin down
6.Ready for  purification or store at   20°C
 Labelling of cDNA with  cyanine dyes  Purification of amino  allyl-modified cDNA Followed Ge Healthcare  kit "Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA and  Aminoallyl-aRNA" code  RPN5661
Labelling of amino  allyl-modified cDNA with  CyDye
1.Add the  amino allyl modified  cDNA (in 0.1 M sodium  bicarbonate) directly into  one aliquot of CyDye  NHS Ester.  Resuspend the ester  completely by pipetting  several times and  transfer the solution to  an amber 1.5 ml tube
2.Incubate at  room temperature, in the  dark for 60 to 90  minutes
3.Add 15 µl 4 M  Hydroxylamine to each  coupling reaction
4.Mix by stirring  and incubate at room  temperature, in the dark,  for 15 minutes
5.Proceed  directly to purification of  CyDye-labelled cDNA  following Ge Healthcare kit "Amersham CyDye (Cy3/Cy5)Reactive Dye Protocols for Post Labelling Aminoallyl-cDNA and Aminoallyl-aRNA" product code RPN5661

extract_protocol:
Extraction RNA version ,1.3,
Collecting cells" Quenching Buffer 66.7 mM HEPES (pH  6.5) 60%Methanol
Extraction Mixture
500 µll  phenol/Chloroform
30 µl10% SDS -30 µl3 M NaAc (pH 5.2)
500 mg glass-beads  (75-150 µm)
400 µlTE buffer  Prepare in a screw-cap  tube
1.For each sample  prepare a tube with  Extraction Mixture
2.Harvest cells and  quench them  immediately in  Quenching Buffer. Add  4 volumes of Quenching  Buffer ( 40°C) to 1  volume of  cell culture 3.Mix and store the  sample at -40°C
4.Centrifuge cells at  -20  C at 9000 rpm for 10  minutes (Centrifuge  RC5B)
5.Discard the  supernatant; keep the  cell pellet cooled and  work quickly to prevent  condensation of water.  Transfer the pellet  with a pre-cooled  spatula to a screw-crap  tube with Extraction  Mixture
6.Mix the cell pellet  thoroughly with  Extraction Mixture by  shaking by hand
7.Freeze the tube  immediately in liquid  nitrogen
8.Break cells in the  Savant FastPrep  FP120. Three times 40  seconds at speed 4.0  (cool cells between  steps if necessary)
9.Centrifuge for 5  minutes at 4°C in an  Eppendorf centrifuge at  10.000 rpm
10.Transfer 500 µl of  the supernatant to a  new tube. Add 400 µl  chloroform (chloroform  should be cooled at  4°C)
11.Centrifuge for 2  minutes in an Eppendorf  centrifuge at full speed  (4°C) 5.Continue with the  "High Pure RNA  Isolation Kit" from  Roche (order # 1 828  665) 6.Incubate for 60  minutes with DnaseI,  elute with 50 µl elution  buffer 7.Store the RNA in at  least 2 aliquots, one of  20 µl (for concentration  and quality analysis and  labelling) and one  back-up  of 30 µl at  80°C

tag: L. plantarum WCFS1

tag: Lactobacillus plantarum NZ7608 (trxB1 disruption).


title: 13281301 - C11-24h-WT vs C16-24h-mutant

status: Public on Aug 09 2007

type: RNA

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

country: France

institute: INRA

description: Identification of Arabidopsis genes regulataed by Erwinia amylovora and of a subset of Arabiddopsis genes regulated by the type three secretion system of Erwinia amylovora

hyb_protocol: C16-24h-mutant Cy5 / C11-24h-WT Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: leaf - media	soil	 hygrometry	70%	 temperature	21degreeC	 light	8h light(900 lux)/16h dark

treatment_protocol: Name:Ea-mutant-24h - biotic stress - biotic stress,erwinia amylovora:time 24hour . infiltration of Arabidopsis leaves with Erwinia amylovora TTSS mutant CFBP6023; harvest 24 hours post infiltration

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):boyes

treatment_protocol: Name:Ea-WT-24h - biotic stress - biotic stress,erwinia amylovora:time 24hour . infiltration of Arabidopsis leaves with water; harvest 24 hours post infiltration this is the water control : effect of infiltration


title: WT+perox_vs_WT

city: Wageningen

first: L.

middle: Mariela

last: Serrano

address: Nieuwe Kanaal 9A

country: Netherlands

institute: TI Food and Nutrition

hyb_protocol: Hybridization version 4.1 Agilent hybridization  protocol v 4.1

scan_protocol: Scanning protocol" Using the Scan Array  Express microarray  scanner. 1.Turn on the scanner and  the computer (in this order) 2.Login: scanner 3.Double click the  'ScanArray Express' icon 4.Switch on lasers 1 and 3  at least 15 minutes prior to  scanning arrays 5.Click the 'File' button This is to prevent you from  accidentally turning off the  laser after the 15 minutes  warming-up phase 6.Insert the slide with the  array-side up and the label  towards the outside. On  Agilent slides the array side  is the side  with the label that has the  word "Agilent" on it 7.Press 'Scan | Prescan' 8.Put resolution at 50  m,  select both labels used,  and set PMT values for  both channels at for  instance 40% (Agilent  arrays) 9.Press 'Start' 10.Press 'Palette,' 'Green'  as soon as projection of  the image has started (first  dye), select the red colour  as soon as  scanning of the second  layer (second dye) has  started 11.Adjust PMT values to  balance signals obtained  for both channels. If  necessary do a few  low-resolution scans to  obtain a  optimal balance 12.Click the 'Scan' button  again 13.Select frame for high  resolution scan, adjust  resolution (to 10  m) and  scan the array for both  dyes 14.Press 'File | Save' to  save the files, 'Save all'  saves both dye layers "Create a new folder for  each array "'Save all' saves the  signals from both layers in  individual files 15.Switch off the lasers

data_processing:
Data Processing 1.- Background correction  2.-Normalization lowess.
VALUE column reports log2 (test/ref) ratios.

organism: Lactiplantibacillus plantarum

label_protocol: cDNA synthesis and , Labeling Protocol 1.4"  Annealing Annealing Mix 	x µl	 RNA preparation (=10  µg) 	y µl	 nuclease-free water 	1 µl	 Random Nonamers 	11 µl	 TOTAL  1.	mix Annealing  Mix in a 200 µl PCR  tube gently by pipetting  up and down 2.	incubate for  5’ 70°C 3.	cool at room  temperature for 10’  (annealing) 4.	spin down the  mixture to the bottom of  the tube 5.	place on ice  Reverse transcription  Reverse Transcription  Mix 	4 µl	5x  buffer 	2 µl	0.1  M DTT 	1 µl	 dNTP-mix 	1 µl	 AA-dUTP 	1 µl  	 TMIII (keep only briefly  outside  20°C) 	20 µl	 TOTAL  1.	Mix by very  gently by pipetting up  and down (vigorous  pipetting will denature  the enzyme!) 2.	Incubate for 3  hrs at 42°C (in  PCR-machine) 3.	Cool on ice  for immediate  purification or place at   20°C for storage  Degradation of mRNA 1.	Add 2 µl 2,5  M NaOH 2.	Mix (vortex)  and spin down 3.	Incubate for  15 min. at 37°C 4.	Add 10 µl 2 M  HEPES free acid 5.	Mix (vortex)  and spin down 6.	Ready for  purification or store at   20°C    Labelling of cDNA with  cyanine dyes  Purification of amino  allyl-modified cDNA Followed Ge Healthcare  kit "Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA and  Aminoallyl-aRNA" code  RPN5661  Labelling of amino  allyl-modified cDNA with  CyDye 1.	Add the  amino allyl modified  cDNA (in 0.1 M sodium  bicarbonate) directly into  one aliquot of CyDye  NHS Ester.  Resuspend the ester  completely by pipetting  several times and  transfer the solution to  an amber 1.5 ml tube 2.	Incubate at  room temperature, in the  dark for 60 to 90  minutes 3.	Add 15 µl 4 M  Hydroxylamine to each  coupling reaction 4.	Mix by stirring  and incubate at room  temperature, in the dark,  for 15 minutes 5.	Proceed  directly to purification of  CyDye-labelled cDNA  Followed Ge Healthcare kit "Amersham CyDye (Cy3/Cy5)Reactive Dye Protocols for Post Labelling Aminoallyl-cDNA and Aminoallyl-aRNA" code RPN5661

extract_protocol: Extraction RNA version ,1.3, Collecting cells" Quenching Buffer 66.7 mM	HEPES (pH  6.5) 60%Methanol Extraction Mixture -500 µll  phenol/Chloroform -30 µl10% SDS -30 µl3 M NaAc (pH 5.2) -500 mg glass-beads  (75-150 µm) -400 µlTE buffer  Prepare in a screw-cap  tube  1.For each sample  prepare a tube with  Extraction Mixture 2.Harvest cells and  quench them  immediately in  Quenching Buffer. Add  4 volumes of Quenching  Buffer ( 40°C) to 1  volume of  cell culture 3.Mix and store the  sample at -40°C 4.Centrifuge cells at  -20  C at 9000 rpm for 10  minutes (Centrifuge  RC5B) 5.Discard the  supernatant; keep the  cell pellet cooled and  work quickly to prevent  condensation of water.  Transfer the pellet  with a pre-cooled  spatula to a screw-crap  tube with Extraction  Mixture 6.Mix the cell pellet  thoroughly with  Extraction Mixture by  shaking by hand 7.Freeze the tube  immediately in liquid  nitrogen 8.Break cells in the  Savant FastPrep  FP120. Three times 40  seconds at speed 4.0  (cool cells between  steps if necessary) 9.Centrifuge for 5  minutes at 4°C in an  Eppendorf centrifuge at  10.000 rpm 10.Transfer 500 µl of  the supernatant to a  new tube. Add 400 µl  chloroform (chloroform  should be cooled at  4°C) 11.Centrifuge for 2  minutes in an Eppendorf  centrifuge at full speed  (4°C) 5.Continue with the  "High Pure RNA  Isolation Kit" from  Roche (order # 1 828  665) 6.Incubate for 60  minutes with DnaseI,  elute with 50 µl elution  buffer 7.Store the RNA in at  least 2 aliquots, one of  20 µl (for concentration  and quality analysis and  labelling) and one  back-up  of 30 µl at  80°C

tag: Lactobacillus plantarum WCFS1+ 3.5 mM hydrogen peroxide

tag: Lactobacillus plantarum WCFS1


title: P3_AS_HepG2_sRW_C73_T1

status: Public on Aug 10 2007

city: Santa Clara

first: Thomas

middle: R

last: Gingeras

state: CA

address: 3380 Central Expressway

country: USA

institute: Affymetrix, Inc.

description: See publication for details

hyb_protocol: See publication for details

scan_protocol: See publication for details

data_processing: See publication for details

label: biotin

organism: Homo sapiens

source_name: Whole-cell short RNA from HepG2 cell line

label_protocol: See publication for details

extract_protocol: Whole-cell short RNA protocol - see publication for details

tag: See publication for details


title: 13281277 - B04-06h-water vs B09-06h-WT

hyb_protocol: B09-06h-WT Cy5 / B04-06h-water Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:Ea-WT-06h - biotic stress - biotic stress,erwinia amylovora:time 6hour . infiltration of Arabidopsis leaves with Ea WT; harvest 6 hours post infiltration

treatment_protocol: Name:Water-06h - abiotic stress - abiotic stress,water:time 6hour . infiltration of Arabidopsis leaves with water; harvest 6 hours post infiltration this is the water control : effect of infiltration


title: 13281300 - C16-24h-mutant vs C11-24h-WT

hyb_protocol: C11-24h-WT Cy5 / C16-24h-mutant Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13281276 - B09-06h-WT vs B04-06h-water

hyb_protocol: B04-06h-water Cy5 / B09-06h-WT Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: P3_S_HeLa_sRW_C84_T1

description: See publication for details

source_name: Whole-cell short RNA from HeLa cell line


title: P3_AS_HeLa_sRW_C73_T1

description: See publication for details

source_name: Whole cell RNA from HeLa cell line


title: transfected HEK cells; siGFP versus mock 1a

city: Heidelberg

first: Cordula

last: Tschuch

address: Neuenheimer Feld 580

country: Germany

institute: DKFZ

description: Experiment 1a

hyb_protocol: Purified, dye-labeled cDAN was mixed with Ultra-Hyb buffer (Ambion), agitated for 60min at 60°, then for 10min at 70°C on a thermo mixer and subsequently applied to pre-heated microarrays mounted in a GeneTAC Hybridisation Station. After hybridization slides were washed sequential.

scan_protocol: Microarrays were scanned at 5 mm resolution and variable PMT voltage to abtain maximal signal intensities with <0.1% probe saturation, a count ratio of 0.8-1.2 (Cy5/Cy3) and maximal congruence of histogram curves, using a GenePix 4000B microarray scanner.

data_processing: Dta summaries on the spot intensities are provided by GenePix Pro, Version 5.1, using local background correction. This includes the mean and the median pixel intensities at each scan wavelength for both feature and background pixels.

source_name: Total RNA from siGFP transfected HEK cells labeled with Cyanine-3

label_protocol: Samples were labeled with fluorochrome by the Klenow fragment using the Bioprime Kit (Invitrogen, Karlsruhe, Germany).

growth_protocol: Cells were grown in an incubator with 95% relative air humidity and 5% CO2 in the adequate medium supplemented with 10% FCS, L-glutamine and antibiotics.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Cells were transfected using the transfection reagent Effentene according to the manufacturer's protocoll.

tag: HEK cell line (CRL-1573)

source_name: Total RNA from mock transfected HEK cells labeled with Cyanine-5


title: 13281295 - C06-24h-water vs C11-24h-WT

hyb_protocol: C11-24h-WT Cy5 / C06-24h-water Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:Water-24h - abiotic stress - abiotic stress,water:time 6hour . infiltration of Arabidopsis leaves with water; harvest 24 hours post infiltration this is the water control : effect of infiltration


title: P3_S_HepG2_sRW_C84_T1

description: See publication for details


title: 13279355 - C11-24h-WT vs C06-24h-water

hyb_protocol: C06-24h-water Cy5 / C11-24h-WT Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13281279 - B09-06h-WT vs B14-06h-mutant

hyb_protocol: B14-06h-mutant Cy5 / B09-06h-WT Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:Ea-mutant-06h - biotic stress - biotic stress,erwinia amylovora:time 6hour . infiltration of Arabidopsis leaves with Erwinia amylovora TTSS mutant CFBP6023; harvest 6 hours post infiltration


title: 13279352 - C09-06h-WT vs C14-06h-mutant

hyb_protocol: C14-06h-mutant Cy5 / C09-06h-WT Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: P3_AS_HeLa_sRW_C84_T1

description: See publication for details


title: 13256897 - B14-06h-mutant vs B09-06h-WT

hyb_protocol: B09-06h-WT Cy5 / B14-06h-mutant Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13256485 - C09-06h-WT vs C04-06h-water

hyb_protocol: C04-06h-water Cy5 / C09-06h-WT Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13001222 - Co-Pool2 vs Kis-Pool2

description: Transcription profiling of NtKIS overexpressing lines

hyb_protocol: Kis-Pool2 Cy5 / Co-Pool2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: whole plant - Media : MS1/2 hygrometry : 90% Temperature : 22 Light : 16h

treatment_protocol: no treatment

tag: Arabidopsis thaliana (columbia)  - harvest date:19-01-05


title: 13256487 - C04-06h-water vs C09-06h-WT

hyb_protocol: C09-06h-WT Cy5 / C04-06h-water Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Comparison between ST52 and ST22. Growth conditions iron-sufficient (50 uM FeCl3). Rep 5

city: Stanford

first: SMD

last: Staff

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description: Biological replicate 6 of 6. Comparison between ST52 (H37Rv ideR::aph, attB::ideR) and ST22 (H37Rv ideR::aph). Growth conditions iron-sufficient (50 uM FeCl3)

hyb_protocol: The quality of cDNA labeling was monitored by quantitatively measuring the intensities of Cy3- and Cy5-labeled samples hybridized to the MTB genomic positive control spots.

scan_protocol: Microarrays were scanned using a GenePix 4000 A (Axon Instruments). The intensities of the two dyes at each spot were quantified using SCANALYZE (M. Eisen; http://rana.lbl.gov/EisenSoftware.htm).

data_processing: The intensities of the two dyes at each spot were quantified using SCANALYZE, written by M. Eisen at Stanford University and available at http://rana.stanford.edu/software. Data processing value is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm). The overall reproducibility, both biological and technical, of the microarray experiments was evaluated using the Significance Analysis of Microarrays (SAM) program. Six DNA microarray experiments, which compared identical RNAs on the same array, were compared to six microarray experiments on three biological sample sets for each condition. The SAM algorithm was set for two-class unpaired analysis with 500 permutations and K-nearest imputer for missing data. Significantly regulated genes were selected by adjusting the delta value to give a false discovery rate below 1%. In each data set, all genes regulated 1.5-fold and greater were determined to be significant with a false discovery rate of less than 1%, indicating a high degree of reproducibility.

organism: Mycobacterium tuberculosis

source_name: Cell culture grew in iron-sufficient (50 uM FeCl3)

label_protocol:
All steps in the MTB DNA microarray gene expression analysis were performed as described. Briefly:
1. Bring 0.5-5 µg RNA (Typically 3 µg) to 11 µl and add 2 µl (~2 mg/ml) random hexamers.
2. Heat 10 min at 65C (or 2 min at 98C), snap cool on ice. 10 rxns 20 rxns.
3. Add 11µl 5.0 µl 5X First-Strand buffer (51) (102) 2.5 µl 100 mM DTT (25.5) (51) 2.0 µl dNTP (5 mM A,G,C and 0.2 mM T) (20.5) (41) 1.5 µl Cy3 or Cy5 (Typically use Cy5 for sample that should change) (15.3) (30.6) Then add 1.2-1.8 µl Stratascript or 0.8-1.2 µl Superscript II RTase.
4. Incubate 10m at 25C followed by 90m at 42C in PCR machine.

growth_protocol: Escherichia coli JM109 was routinely used in DNA-cloning procedures. M. tuberculosis strain H37Rv (American Type Culture Collection) was maintained in Middlebrook 7H9 broth or on 7H10 agar (Difco) supplemented with 0.2% glycerol, 0.05% Tween 80, and 10% albumin-dextrose-NaCl complex (ADN). When media with defined amounts of iron were needed, 7H9 and 7H10 were prepared omitting ferric ammonium citrate. We refer to these media as reconstituted 7H9 (r7H9) or r7H10. These media were subsequently supplemented with the desired amount of iron in the form of FeCl3. Minimal medium (MM) was also used to grow cultures under defined iron conditions for the determination of mycobactin, growth curves (MM agar), and RNA extraction (MM broth). This medium contained 0.5% (wt/vol) asparagine, 0.5% (wt/vol) KH2PO4, 2% glycerol, 0.5 mg of ZnCl2/liter, 0.1 mg of MnSO4/liter, and 40 mg of MgSO4/liter. It was supplemented with the desired concentrations of FeCl3, and in the case of the broth, 0.05% Tween 80 and 10% ADN were included. Where indicated, antibiotics were included at the following concentrations: kanamycin, 20  ug/ml; streptomycin, 20 ug/ml; and hygromycin, 150 ug/ml.

extract_protocol: Cells were disrupted by three 30-sec pulses in a BioSpec Products bead beater. After 5 min at room temperature, samples were centrifuged at 13,000 x g for 45 sec, and the supernatants were extracted with 300 ul of chloroformyisoamyl alcohol (24:1) and precipitated with isopropyl alcohol. Samples were incubated 10 min to overnight at 4 C and centrifuged for 10 min at 4 C. The RNA pellets were washed with 1 ml of 75% ethanol, centrifuged at 13,000 x g for 5 min, and air-dried. After suspension of the RNA pellets in 90 ul of water, 10 ul of DNase I 10x buffer and 4 units of DNase I (Ambion, Austin, TX) were added and the samples were incubated for 30 min. Final purification of RNA was by RNeasy column (Qiagen, Chatsworth, CA).

treatment_protocol: Frozen cell pellets were suspended in 1 ml of Trizol reagent (GIBCOy BRL) and transferred to 2-ml screw-cap tubes containing 0.4-ml of 0.1-mm diameter zirconiaysilica beads (BioSpec Products, Bartlesville, OK).

tag: ST22 (H37Rv ideR::aph)

label_protocol: same as channel 1

tag: ST52 (H37Rv ideR::aph, attB::ideR)


title: 12961305 - C5 vs WT

description: CDT1 is a protein of the pre-replication complex, and accumulates during the G1-S transition, thus play a major role in S-phase entry

hyb_protocol: WT  Cy5 / C5 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 650V,laser power 100%

source_name: WT

growth_protocol: aerial - 16h photoperiod

tag: Arabidopsis thaliana (wassilewskija)  - dev.stage (Boyes et al. Plant Cell 2001):boyes

tag: Arabidopsis thaliana (wassilewskija)  mutant (CDT1) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13001220 - Co-Pool1 vs Kis-Pool1

hyb_protocol: Kis-Pool1 Cy5 / Co-Pool1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 12961161 - C3 vs WT

hyb_protocol: WT  Cy5 / C3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 680V,laser power 100%

tag: Arabidopsis thaliana (wassilewskija)  mutant (cdt1) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 12949732 - WT  vs C5

hyb_protocol: C5 Cy5 / WT  Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Comparison between ST52 and ST22. Growth conditions iron-sufficient (50 uM FeCl3). Rep 4

description: Biological replicate 5 of 6. Comparison between ST52 (H37Rv ideR::aph, attB::ideR) and ST22 (H37Rv ideR::aph). Growth conditions iron-sufficient (50 uM FeCl3)


title: 12961163 - WT  vs C3

hyb_protocol: C3 Cy5 / WT  Cy3 : 30pmol.


title: Comparison between ST52 and ST22. Growth conditions iron-sufficient (50 uM FeCl3). Rep 3

description: Biological replicate 4 of 6. Comparison between ST52 (H37Rv ideR::aph, attB::ideR) and ST22 (H37Rv ideR::aph). Growth conditions iron-sufficient (50 uM FeCl3)


title: 12961160 - WT  vs C2

hyb_protocol: C2 Cy5 / WT  Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 12961159 - C2 vs WT

hyb_protocol: WT  Cy5 / C2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Comparison between ST52 and ST22. Growth conditions iron-sufficient (50 uM FeCl3). Rep 1

description: Biological replicate 2 of 6. Comparison between ST52 (H37Rv ideR::aph, attB::ideR) and ST22 (H37Rv ideR::aph). Growth conditions iron-sufficient (50 uM FeCl3)


title: Comparison between ST52 and ST22. Growth conditions iron-sufficient (50 uM FeCl3).

description: Biological replicate 1 of 6. Comparison between ST52 (H37Rv ideR::aph, attB::ideR) and ST22 (H37Rv ideR::aph). Growth conditions iron-sufficient (50 uM FeCl3)


title: Comparison between ST22 and H37Rv. Growth conditions iron-sufficient (50 uM FeCl3). Rep 5

description: Biological replicate 6 of 6. Comparison between ST22 (H37Rv ideR::aph) and H37Rv (wild_type). Growth conditions iron-sufficient (50 uM FeCl3)

tag: H37Rv (wild_type)


title: Comparison between ST52 and ST22. Growth conditions iron-sufficient (50 uM FeCl3). Rep 2

description: Biological replicate 3 of 6. Comparison between ST52 (H37Rv ideR::aph, attB::ideR) and ST22 (H37Rv ideR::aph). Growth conditions iron-sufficient (50 uM FeCl3)


title: 13001221 - Kis-Pool2 vs Co-Pool2

hyb_protocol: Co-Pool2 Cy5 / Kis-Pool2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Bee_worker/drone_antennae_rep1

city: Urbana

first: Hugh

last: Robertson

state: IL

address: 505 S. Goodwin Ave.

department: Entomology

institute: University of Illinois at Urbana-Champaign

hyb_protocol: Microarray slides were prepared for prehybridization by passing them array-side down twice over steam from a beaker of boiling water and dried briefly on a warm adjustable-temperature block. The oligonucleotides were cross-linked to the array in a Stratalinker (Stratagene) set at 6000 ujoules (x 1000).  Excess oligonucleotides were removed by washing the microarray slide quickly in 0.2% SDS and agitating vigorously for 2 minutes, then washing 2X in molecular biology-grade water (Eppendorf). Slides were transferred to Coplin jars containing prehybridization buffer (20% formamide, 5X Denhardt’s, 6X SSC, 0.1%SDS, 25ug/mL tRNA) in a 42°C waterbath for 1 hour with occasional shaking.  Slides were washed in molecular biology-grade water 5X, followed by one wash in isopropanol, and spun dry in a ChipMate (Tomy).  Slides were placed in Corning hybridization chambers with a LifterSlip (Eerie Scientific) positioned over the area of the spotted oligonucleotides. For each pair of Cy5/Cy3 probes to be hybridized together, one dried probe was suspended in 15 uL nuclease-free water and then transferred to the second probe for suspension.  The probes were heated to 95°C for 2-3 min, chilled on ice for 5 min and kept at room temperature.  To each labeled probe pair, 15 uL of pre-warmed (50°C) 2X hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) was added and the entire volume pipetted under the Lifterslip edge.  A drop of hybridization solution was placed in each chamber well for humidity.  Chambers were incubated in a light-proof hybridization oven at 42°C overnight. Microarray slides were transferred to a Coplin jar containing Wash 1 (1X SSC, 0.2% SDS) at 42°C for 8 minutes with agitation.  The slides were agitated in Wash 2 (0.1X SSC, 0.2% SDS) for 8 min at room temperature followed by two successive washes in Wash 3 (0.1X SSC) for 8 min at room temperature. The slides were spun dry and stored in a dark container until scanning.

scan_protocol: Microarray slides were scanned on an Axon 4000B Scanner using GenePix v6.0 software.  Arrays were scanned using 33% power and manually-adjusted PMT values to achieve an overall count ratio of 1.0 from both channels.

data_processing: Analysis was performed using SAS software v.9.1 (SAS Institute Inc., Cary, North Carolina).  Spots that were flagged “bad” or “not found” in GenePix, as well as buffer-only and blank spots were removed.  Median background signal intensity values were subtracted from median foreground signal intensity values, negative values were set to 1.0.  A low-intensity filter was applied that removed spots where the background-subtracted intensity in both channels was less than the overall average array background intensity for each channel.  Additionally, any spot saturated (>65,535 pixels) in both channels was also excluded.  Background-subtracted intensity values were log2-transformed and then normalized within array using loess (local regression) transformation, a correction for intensity-dependent effects.  Normalization for common mean and variance between microarrays was achieved by scaling and centering the loess-transformed values.  Outliers were removed by excluding spots that were +/- 3 SD from the dataset mean. Using a mixed model ANOVA, gene-specific normalized observations were modeled as the fixed effect of sex and the random effects of biological replicate nested in sex and technical replicate nested in biological replicate.

organism: Apis mellifera

label_protocol: For each reverse transcription reaction, 20 ug of total RNA was suspended in 18.5 uL nuclease-free water containing 2 ug oligo-dT16 primer (Operon) and denatured for 10 min at 70°C. A cocktail containing 6.0 uL 5X first strand buffer (Invitrogen), 3.0 uL 0.1M DTT, 0.6 uL 50X amino-allyl dNTP mix (25mM each dATP, dCTP, dGTP, 15mM dTTP, 10mM amino-allyl-dUTP (Sigma)), 2.0 uL Superscript III (Invitrogen, 200U/uL), and 0.5 uL RNase inhibitor (Fisher, 40U/uL) was added to each reaction and incubated overnight at 46°C in a hybridization oven.  RNA was hydrolyzed by adding 10 uL 1M NaOH and 10 uL 0.5M EDTA with a 15 min incubation at 65°C followed by neutralized with 10 uL 1M HCl.  The 1st cDNA was purified using the Qiagen Qiaquick PCR purification kit, following manufacturer’s instructions with substitutions for the wash buffer (phosphate wash buffer: 5mM KPO4, pH 8.0, 80% EtOH) and elution buffer (phosphate elution buffer: 4mM KPO4, pH8.5).  1st cDNA was eluted from the column twice using 30 ul phosphate elution buffer and dried completely in a SpeedVac. Single-use CyDye label (Cy5, GE Healthcare) was suspended in 9 uL fresh 0.1M Na2CO3 pH 9.0 and transferred to the cDNA pellet for suspension. Labeling reactions were incubated 1 hour in complete darkness.  The pH of the labeling reaction was adjusted with 35 uL 3M NaOAc pH5.2.  The labeled-cDNA was purified using the Qiagen Qiaquick PCR purification kit following manufacturer’s instructions and eluted twice using 40ul elution buffer.  The entire sample was analyzed on a spectrophotometer at 260 nm, 320 nm, 550 nm, 650 nm, and 750 nm to calculate pmoles of cDNA synthesized and label incorporation.  Labeled probes were then dried to completion in a SpeedVac and stored at -20°C until hybridization.

extract_protocol: Total RNA was isolated using an RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Whole antennae from worker bees collected at the hive entrance were dissected in pools of 50 sets of antennae.

tag: Bee_worker(female) antennae

label_protocol: For each reverse transcription reaction, 20 ug of total RNA was suspended in 18.5 uL nuclease-free water containing 2 ug oligo-dT16 primer (Operon) and denatured for 10 min at 70°C. A cocktail containing 6.0 uL 5X first strand buffer (Invitrogen), 3.0 uL 0.1M DTT, 0.6 uL 50X amino-allyl dNTP mix (25mM each dATP, dCTP, dGTP, 15mM dTTP, 10mM amino-allyl-dUTP (Sigma)), 2.0 uL Superscript III (Invitrogen, 200U/uL), and 0.5 uL RNase inhibitor (Fisher, 40U/uL) was added to each reaction and incubated overnight at 46°C in a hybridization oven.  RNA was hydrolyzed by adding 10 uL 1M NaOH and 10 uL 0.5M EDTA with a 15 min incubation at 65°C followed by neutralized with 10 uL 1M HCl.  The 1st cDNA was purified using the Qiagen Qiaquick PCR purification kit, following manufacturer’s instructions with substitutions for the wash buffer (phosphate wash buffer: 5mM KPO4, pH 8.0, 80% EtOH) and elution buffer (phosphate elution buffer: 4mM KPO4, pH8.5).  1st cDNA was eluted from the column twice using 30 ul phosphate elution buffer and dried completely in a SpeedVac. Single-use CyDye label (Cy3, GE Healthcare) was suspended in 9 uL fresh 0.1M Na2CO3 pH 9.0 and transferred to the cDNA pellet for suspension. Labeling reactions were incubated 1 hour in complete darkness.  The pH of the labeling reaction was adjusted with 35 uL 3M NaOAc pH5.2.  The labeled-cDNA was purified using the Qiagen Qiaquick PCR purification kit following manufacturer’s instructions and eluted twice using 40ul elution buffer.  The entire sample was analyzed on a spectrophotometer at 260 nm, 320 nm, 550 nm, 650 nm, and 750 nm to calculate pmoles of cDNA synthesized and label incorporation.  Labeled probes were then dried to completion in a SpeedVac and stored at -20°C until hybridization.

treatment_protocol: Whole antennae from drone bees collected at the hive entrance were dissected in pools of 50 sets of antennae.

tag: Bee_drone(male) antennae


title: Bee_worker/drone_antennae_rep2


title: Comparison between ST22 and H37Rv. Growth conditions iron-sufficient (50 uM FeCl3). Rep 4

description: Biological replicate 5 of 6. Comparison between ST22 (H37Rv ideR::aph) and H37Rv (wild_type). Growth conditions iron-sufficient (50 uM FeCl3)


title: Comparison between ST22 and H37Rv. Growth conditions iron-sufficient (50 uM FeCl3). Rep 3

description: Biological replicate 4 of 6. Comparison between ST22 (H37Rv ideR::aph) and H37Rv (wild_type). Growth conditions iron-sufficient (50 uM FeCl3)


title: Comparison between ST22 and H37Rv. Growth conditions iron-sufficient (50 uM FeCl3). Rep 2

description: Biological replicate 3 of 6. Comparison between ST22 (H37Rv ideR::aph) and H37Rv (wild_type). Growth conditions iron-sufficient (50 uM FeCl3)


title: Comparison between ST22 and H37Rv. Growth conditions iron-sufficient (50 uM FeCl3). Rep 1

description: Biological replicate 2 of 6. Comparison between ST22 (H37Rv ideR::aph) and H37Rv (wild_type). Growth conditions iron-sufficient (50 uM FeCl3)


title: Comparison between ST22 and H37Rv. Growth conditions iron-sufficient (50 uM FeCl3)

description: Biological replicate 1 of 6. Comparison between ST22 (H37Rv ideR::aph) and H37Rv (wild_type). Growth conditions iron-sufficient (50 uM FeCl3)


title: 13001219 - Kis-Pool1 vs Co-Pool1

hyb_protocol: Co-Pool1 Cy5 / Kis-Pool1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Comparison between iron-sufficient (50 uM FeCl3) and iron-deficient (2 uM FeCl3) grew conditions. Rep 5

description: Biological replicate 6 of 6. Comparison between iron-sufficient (50 uM FeCl3) and iron-deficient (2 uM FeCl3) grew conditions. Strain H37Rv.

source_name: Cell culture grew in iron-deficient (2 uM FeCl3)


title: Comparison between iron-sufficient (50 uM FeCl3) and iron-deficient (2 uM FeCl3) grew conditions. Rep 3

description: Biological replicate 4 of 6. Comparison between iron-sufficient (50 uM FeCl3) and iron-deficient (2 uM FeCl3) grew conditions. Strain H37Rv.


title: Comparison between iron-sufficient (50 uM FeCl3) and iron-deficient (2 uM FeCl3) grew conditions. Rep 2

description: Biological replicate 3 of 6. Comparison between iron-sufficient (50 uM FeCl3) and iron-deficient (2 uM FeCl3) grew conditions. Strain H37Rv.


title: Comparison between iron-sufficient (50 uM FeCl3) and iron-deficient (2 uM FeCl3) grew conditions. Rep 1

description: Biological replicate 2 of 6. Comparison between iron-sufficient (50 uM FeCl3) and iron-deficient (2 uM FeCl3) grew conditions. Strain H37Rv.


description: Biological replicate 1 of 6. Comparison between iron-sufficient (50 uM FeCl3) and iron-deficient (2 uM FeCl3) grew conditions. Strain H37Rv.


title: Comparison between iron-sufficient (50 uM FeCl3) and iron-deficient (2 uM FeCl3) grew conditions. Rep 4

description: Biological replicate 5 of 6. Comparison between iron-sufficient (50 uM FeCl3) and iron-deficient (2 uM FeCl3) grew conditions. Strain H37Rv.


title: 13281283 - B11-24h-WT vs B16-24h-mutant

description: Identification of Arabidopsis genes regulataed by Erwinia amylovora and of a subset of Arabiddopsis genes regulated by the type three secretion system of Erwinia amylovora

hyb_protocol: B16-24h-mutant Cy5 / B11-24h-WT Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: NA12745 growth 1

status: Public on Aug 08 2007

city: Montreal

first: Tony

last: Kwan

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

description: Probeset expression data from NA12745 growth 1

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16-20 hr at 45C on GeneChip Human Exon 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Affymetrix Power Tools package using Affymetrix default analysis settings and sketch quantile as normalization method.

source_name: CEU NA12745 Biological growth 1

label_protocol: Biotinlabelled target for the microarray experiment were prepared using 1 ug of total RNA. The RNA was subjected to a rRNA removal procedure with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen) and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix).

growth_protocol: Cells were grown at 37°C and 5% CO2 in RPMI 1640 medium supplemented with 15% heat-inactivated fetal bovine serum, 2 mM L-glutamine and penicillin/streptomycin

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were harvested at a density of 0.8-1.1 x 10e6 cells/mL. Cells were then resuspended and lysed in TRIzol reagent

tag: Gender

value: female, Cell-type:lymphoblasts

tag: Coriell cell line repository identifier:GM12745


title: NA12751 growth 2

description: Probeset expression data from NA12751 growth 2

source_name: CEU NA12751 Biological growth 2

tag: Coriell cell line repository identifier:GM12751


title: NA12751 growth 1

description: Probeset expression data from NA12751 growth 1

source_name: CEU NA12751 Biological growth 1


title: NA12744 growth 1

description: Probeset expression data from NA12744 growth 1

source_name: CEU NA12744 Biological growth 1

tag: Coriell cell line repository identifier:GM12744


title: NA12743 growth 1

description: Probeset expression data from NA12743 growth 1

source_name: CEU NA12743 Biological growth 1

tag: Coriell cell line repository identifier:GM12743


title: NA12746 growth 1

description: Probeset expression data from NA12746 growth 1

source_name: CEU NA12746 Biological growth 1

value: male, Cell-type:lymphoblasts

tag: Coriell cell line repository identifier:GM12746


title: NA12742 growth 1

description: Probeset expression data from NA12742 growth 1

source_name: CEU NA12742 Biological growth 1

tag: Coriell cell line repository identifier:GM12742


title: NA12751 growth 3

description: Probeset expression data from NA12751 growth 3

source_name: CEU NA12751 Biological growth 3


title: NA12750 growth 3

description: Probeset expression data from NA12750 growth 3

source_name: CEU NA12750 Biological growth 3

tag: Coriell cell line repository identifier:GM12750


title: NA12740 growth 1

description: Probeset expression data from NA12740 growth 1

source_name: CEU NA12740 Biological growth 1

tag: Coriell cell line repository identifier:GM12740


title: NA12747 growth 1

description: Probeset expression data from NA12747 growth 1

source_name: CEU NA12747 Biological growth 1

tag: Coriell cell line repository identifier:GM12747


title: NA12740 growth 2

description: Probeset expression data from NA12740 growth 2

source_name: CEU NA12740 Biological growth 2


title: NA12748 growth 1

description: Probeset expression data from NA12748 growth 1

source_name: CEU NA12748 Biological growth 1

tag: Coriell cell line repository identifier:GM12748


title: NA12750 growth 1

description: Probeset expression data from NA12750 growth 1

source_name: CEU NA12750 Biological growth 1


title: NA12741 growth 1

description: Probeset expression data from NA12741 growth 1

source_name: CEU NA12741 Biological growth 1

tag: Coriell cell line repository identifier:GM12741


title: NA12740 growth 3

description: Probeset expression data from NA12740 growth 3

source_name: CEU NA12740 Biological growth 3


title: NA12739 growth 1

description: Probeset expression data from NA12739 growth 1

source_name: CEU NA12739 Biological growth 1

tag: Coriell cell line repository identifier:GM12739


title: NA12739 growth 2

description: Probeset expression data from NA12739 growth 2

source_name: CEU NA12739 Biological growth 2


title: NA12739 growth 3

description: Probeset expression data from NA12739 growth 3

source_name: CEU NA12739 Biological growth 3


title: DvH_240min._1000_ppm_Oxygen_set330

type: mixed

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Oxygen. This sample was treated with 1000 ppm Oxygen.  Treatment time point = 240 min.

hyb_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J. 2005.  Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

scan_protocol: ImaGene software

data_processing: See Methods in: S. R. Chhabra, Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T. C. Hazen, J. D. Wall, J. Zhou, A.  . Arkin, and A. K. Singh, Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough, J Bacteriol. 2006 March; 188(5): 1817-1828. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16484192

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 240min. 1000 ppm Oxygen

growth_protocol: Desulfovibrio vulgaris Hildenborough (ATCC 29579) was grown in a defined lactate (60 mM)/sulfate (50 mM) medium, LS4D at 30°C in 1L bottle fitted with a gas tight apparatus used for sparging. Humidified gas was used to sparge D. vulgaris cultures in gas tight 1L bottles. The sparge rate was 200 ml/min.

treatment_protocol: 240min. 1000 ppm Oxygen.

tag: str. Hildenborough

molecule: genomic DNA

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, genomic DNA.


title: NA12749 growth 1

description: Probeset expression data from NA12749 growth 1

source_name: CEU NA12749 Biological growth 1

tag: Coriell cell line repository identifier:GM12749


title: NA12750 growth 2

description: Probeset expression data from NA12750 growth 2

source_name: CEU NA12750 Biological growth 2


title: Pax5-deficient progenitor cell tumors vs wt pro-B-cells 20MM108

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohr-Gasse 7

country: Austria

institute: Research Institute of Molecular Pathology

hyb_protocol: For hybridisation protocol, see Schebesta et al., Immunity 2002

scan_protocol: Images were quantified using GenePix Pro 4.1.1.4

data_processing: Print tip LOESS normalized, background subtracted. VALUE data obtained from log2 of processed Red signal/processed Green signal. Pre-processing using marray package from BioConductor

organism: Mus musculus

source_name: in vitro cultured WT pro-B cells

label_protocol: RNA amolified as described in Bouchard et al., Development 2005; for labeling protocol, see Schebesta et al., Immunity 2002: 5mg of total RNA were used

growth_protocol: Pro-B cells were cultured on irradiated ST2 cells in IL-7-containing Iscove's modified Dulbecco's medium supplemented with 50 microM beta-mercaptoethanol, 1 mM glutamine, 1mM penicillin, 1mM streptomycin, 2% heat-inactivated fetal calf serum and 0.03% (w/v) primatone.

extract_protocol: Total RNA extracted using Trizol following manufacturer's protocol

tag: WT +/+ #5 pro-B-cells

tag: Age

value: 2 weeks

tag: Tissue

value: Bone marrow

tag: Strain

tag: Pax5Flox/Flox CD19-cre lymphoma cell #1

growth_protocol: Tumor cells were cultured on irradiated ST2 cells in IL-7-, SCF-, and Flt3L-containing Iscove's modified Dulbecco's medium supplemented with 50 microM beta-mercaptoethanol, 1 mM glutamine, 1mM penicillin, 1mM streptomycin, 2% heat-inactivated fetal calf serum and 0.03% (w/v) primatone.

value: C57BL/6/129 mixed Pax5Flox/Flox CD19-cre

value: about 8 months

value: Lymph node


title: Pax5-deficient progenitor cell tumors vs wt pro-B-cells 20MM123

tag: Pax5Flox/Flox CD19-cre lymphoma cell #2


title: DvH_120min._1000_ppm_Oxygen_set319

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Oxygen. This sample was treated with 1000 ppm Oxygen.  Treatment time point = 120 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 120min. 1000 ppm Oxygen

label_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J.  2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

treatment_protocol: 120min. 1000 ppm Oxygen.


title: DvH_60min._1000_ppm_Oxygen_set329

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Oxygen. This sample was treated with 1000 ppm Oxygen.  Treatment time point = 60 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 60min. 1000 ppm Oxygen

extract_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J.  2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

treatment_protocol: 60min. 1000 ppm Oxygen.


title: Pax5-deficient progenitor cell tumors vs wt pro-B-cells 20MM124

tag: Pax5Flox/Flox CD19-cre lymphoma cell '#3


title: control lean rat A6

status: Public on Aug 07 2007

city: Indianapolis

first: Dan

last: Li

state: IN

address: Lilly Corporate Center

institute: Eli Lilly & Company

description: Gene expression data from epididymal fat tissues.

hyb_protocol: Following fragmentation, 5 microg of cRNA were hybridized on R230_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

organism: Rattus norvegicus

source_name: epididymal fat

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Animals were maintained on a 12:12-hour light-dark photoperiod (light on 10:00 PM).

treatment_protocol: Epididymal fat tissues were isolated and placed on ice in the Trizol solution

tag: Long Evans, 16-26 weeks, control lean group


title: Native pulp

city: Oulu

first: Virve

last: Pääkkönen

address: Aapistie 3

department: Institute of Dentistry

country: Finland

institute: University of Oulu

scan_protocol: HP GeneArray Scanner was used

data_processing: The expression data was analyzed using Affymetrix GeneChip Operating Software version 1.1.1. Signal intensities of all probe sets were scaled to the target value of 500.

source_name: Native human pulp tissue

label_protocol: Experimental procedures for GeneChip (Affymetrix, Santa Clara, CA, USA) were performed according to the Affymetrix GeneChip Expression Analysis Technical Manual. In essence, using 10 µg of total RNA as template double-stranded DNA was synthesized by means of the Superscript Choice System (Gibco BRL Life Technologies, Rockville, MD, USA) and T7-(dT)24 primer. The DNA was purified using GeneChip Sample Cleanup Module (Qiagen, Valencia, CA, USA). In vitro transcription was performed to produce biotin labeled cRNA using a BioArray HighYield RNA Transcription Labeling Kit (Enzo Diagnostics, Farmingdale, NY, USA) according to the manufacturer’s instructions. Biotinylated cRNA was cleaned with an GeneChip Sample Cleanup Module (Qiagen), fragmented to 35 to 200 nt, and and hybridized to the array After being washed, the array was stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR, USA). Staining signal was amplified by biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA, USA) and second staining with streptavidin-phycoerythrin,

extract_protocol: Trizol-protocol

tag: Native pulp tissue of healthy third molars of young patients


title: 18 day male embryonic heart (H21)

city: Uppsala

first: judith

last: mank

address: Norbyvägen 18D

department: evolutionary biology

country: Sweden

institute: uppsala university

description: See Ellegren et al. in Press

hyb_protocol: affymetrix protocol

scan_protocol: affymetix protocol

data_processing:
All pre-processing and statistical analysis of microarray data was performed in R version 2.4.1 using Bioconductor packages release 1.9 . The CEL files were processed using GCRMA30, a background adjustment method taking into account the GC content of probes when assessing non-specific binding, followed by quantile normalization and median-polish summarization of probe intensities into probe set intensities. A linear model was fitted to the log2 of the expression levels based on all probe sets and considering sex and tissue as a combined factor using the Lim,ma package. After pre-processing and linear model fitting the probe sets were filtered on expression; an expression threshold was set on both average expression level and absent/present calls from the R implementation of the Affymetrix MAS 5.0 algorithm. Only probe sets with average expression over a defined threshold and present in more than half of the samples within at least one tissue-sex combination were considered as significantly expressed. This resulted in 15,398 probe sets for heart, 16,846 for brain and 17,438 for gonads, and these probe sets composed the reference for analysis of differently expressed genes between the sexes.
Annotation of probe sets. Annotations for the probe sets were extracted from Ensembl (www.ensembl.org) via biomRt in R. The Ensembl mapping of probe sets is based on alignments of individual probes to the chicken genome version 2.1 (WASHUC2 May 2006) and covers 21,885 of the 37,693 chicken-specific probe sets, which is close to the total number of protein-coding genes in the chicken genome identified by Ensembl. Several transcripts are represented by more than one probe set; the 21,885 probe sets with annotation corresponds to 14,414 unique transcripts. The genomic location for probe sets was taken from Ensembl. Gene ontology (GO) terms were available from the Gene Ontology Annotation Database (http://www.ebi.ac.uk/GOA/) for 18,239 of the 21,885 chicken probe sets with Ensembl annotation. To get a broader overview of the GO terms assigned to genes, the terms were traced back to the ancestral term at different levels in each of the gene ontology classes biological process, molecular function and cellular component. These limited sets of terms where then used to test for over- and under representation among biased genes.

organism: Gallus gallus

source_name: heart tissue, excised day 18

label_protocol: affyemtrix protocol

extract_protocol: Heart, left gonads and diencephalon from each of four male and four female embryos were homogenized by syringe and needle followed by use of the Homogenizer system (Invitrogen, Carlsbad, CA, USA). RNA was extracted from heart and brain homogenates with the PureLink Micro-to-Midi Total RNA Purification System (Invitrogen), and RNA was then DNase treated with a DNA-free kit (Ambion, Austin, TX, USA). Due to limited amounts of available tissue, gonad RNA extraction was performed with an RNeasy Micro Kit (Qiagen, Hilden, Germany) with integrated DNase treatment. RNA concentration was measured with ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and RNA quality was evaluated using the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc, Palo Alto, CA). Two micrograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA). Affymetrix GeneChip® expression arrays (Human Genome U133 Plus 2.0 Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA), the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G. In total, 24 hybridizations were made (4 individuals x 3 tissues x 2 sexes), however, three samples failed to meet Affymetrix quality control criteria and were removed from further analysis (heart and brain from one male, and gonads from one female).

treatment_protocol: Samples were decapitated at day 18, and tissue was extracted

tag: white leghorn


title: 18 day male embryonic heart (H16)

description: See Ellegren et al. in Press


title: 18 day female embryonic heart (H2)

description: See Ellegren et al. in Press


title: control lean rat A8


title: control lean rat A7


title: Diet Induced Obese rat C7

tag: Long Evans, 16-26 weeks, DIO (diet induced obese) group


title: control lean rat A3


title: 18 day female embryonic heart (H12)

description: See Ellegren et al. in Press


title: 18 day male embryonic gonad (G9)

description: See Ellegren et al. in Press

source_name: gallus gallus day 18 embryonic gonad


title: 18 day male embryonic gonad (G19)

description: See Ellegren et al. in Press


title: control lean rat A2


title: 18 day female embryonic heart (H20)

description: See Ellegren et al. in Press


title: 18 day male embryonic gonad (G21)

description: See Ellegren et al. in Press


title: Diet Induced Obese rat C5


title: 18 day female embryonic heart (H10)

description: See Ellegren et al. in Press


title: Diet Induced Obese rat C8


title: control lean rat A4


title: P3_S_HeLa_sRW_C73_T1

description: See publication for details

hyb_protocol: See publication for details

source_name: Whole-cell short RNA from HeLa cell line

tag: See publication for details


title: control lean rat A5


title: 18 day male embryonic gonad (G16)

description: See Ellegren et al. in Press


title: 13279347 - C14-06h-mutant vs C09-06h-WT

description: Identification of Arabidopsis genes regulataed by Erwinia amylovora and of a subset of Arabiddopsis genes regulated by the type three secretion system of Erwinia amylovora

hyb_protocol: C09-06h-WT Cy5 / C14-06h-mutant Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: control lean rat A1


title: Diet Induced Obese rat C3


title: 18 day female embryonic gonad (G20)

description: See Ellegren et al. in Press


title: 18 day female embryonic gonad (G2)

description: See Ellegren et al. in Press


title: Diet Induced Obese rat C2


title: GBM_1043_14629-14597

city: Santa Barbara

first: Tsunglin

last: Liu

address: R5157, BIO II, UCSB

institute: Neuroscience Research Institute

description: All RNA samples had a 28S/18S ratio over 1.5 with no evidence of degradation.  All scanned images were visually inspected for surface defects.  Quality Control assessment of array data was performed using GCOS v1.4 (Affymetrix, Santa Clara, Ca) and Array Assist v5.0 build 30237 (Stratagene, La Jolla, Ca).  Hybridization and Poly-A controls were within expected parameters, and 3'/5' ratios for actin and GAPDH were below 3 (mean Beta Actin 3'/5' = 1.53 and mean GAPDH 3'/5' = 1.02).  GCOS v1.4 Expression Reports also revealed expected Call percentages (Present: 48% to 62%; Absent: 36% to 49%; Marginal: 1.5% to 1.9%).   All arrays were within 1.5 fold of each other in overall intensity.

hyb_protocol: Aliquots of each sample were hybridized to U133A oligonucleotide microarray using standard Affymetrix protocols.

scan_protocol: The chips were scanned using the GeneArray scanner (Affymetrix) using standard Affymetrix protocols.

data_processing: The CEL files generated by the Affymetrix Microarray Suite (MAS 5.0) were converted into DCP files using the DNA-Chip Analyzer (dCHIP 1.3).

source_name: tumor tissue GBM, patient tag 1043, experiment 14629-14597

label_protocol: cRNA probes were generated using standard Affymetrix protocols.

extract_protocol: Total RNA was isolated from tumor samples using a TRIzol reagent (Invitrogen Life Technologies, Carlsbad, CA) and was followed by a cleanup on a RNeasy column (Qiagen, Hilden, Germany).

tag: Tumor tissue

value: high grade glioblastoma


title: gliosarcoma_631_6958-6955

source_name: tumor tissue gliosarcoma, patient tag 631, experiment 6958-6955

value: high grade gliosarcoma


title: GBM_1354_4782-4767

source_name: tumor tissue GBM, patient tag 1354, experiment 4782-4767


title: 18 day female embryonic gonad (G12)

description: See Ellegren et al. in Press


title: GBM_1507_34705-34696

source_name: tumor tissue GBM, patient tag 1507, experiment 34705-34696


title: GBM_931_4776-4764

source_name: tumor tissue GBM, patient tag 931, experiment 4776-4764


title: Diet Induced Obese rat C6


title: AMG_1326_34703-34695

source_name: tumor tissue AMG, patient tag 1326, experiment 34704-34695

value: low grade anaplastic mixed glioma


title: 18 day male embryonic brain (B19)

description: See Ellegren et al. in Press

data_processing:
All pre-processing and statistical analysis of microarray data was performed in R version 2.4.1 using Bioconductor packages release 1.9 . The CEL files were processed using GCRMA30, a background adjustment method taking into account the GC content of probes when assessing non-specific binding, followed by quantile normalization and median-polish summarization of probe intensities into probe set intensities. A linear model was fitted to the log2 of the expression levels based on all probe sets and considering sex and tissue as a combined factor using the Lim,ma package. After pre-processing and linear model fitting the probe sets were filtered on expression; an expression threshold was set on both average expression level and absent/present calls from the R implementation of the Affymetrix MAS 5.0 algorithm. Only probe sets with average expression over a defined threshold and present in more than half of the samples within at least one tissue-sex combination were considered as significantly expressed. This resulted in 15,398 probe sets for heart, 16,846 for brain and 17,438 for gonads, and these probe sets composed the reference for analysis of differently expressed genes between the sexes.
Annotation of probe sets. Annotations for the probe sets were extracted from Ensembl (www.ensembl.org) via biomRt in R. The Ensembl mapping of probe sets is based on alignments of individual probes to the chicken genome version 2.1 (WASHUC2 May 2006) and covers 21,885 of the 37,693 chicken-specific probe sets, which is close to the total number of protein-coding genes in the chicken genome identified by Ensembl. Several transcripts are represented by more than one probe set; the 21,885 probe sets with annotation corresponds to 14,414 unique transcripts. The genomic location for probe sets was taken from Ensembl. Gene ontology (GO) terms were available from the Gene Ontology Annotation Database for 18,239 of the 21,885 chicken probe sets with Ensembl annotation. To get a broader overview of the GO terms assigned to genes, the terms were traced back to the ancestral term at different levels in each of the gene ontology classes biological process, molecular function and cellular component. These limited sets of terms where then used to test for over- and under representation among biased genes.

source_name: Gallus gallus 18 day embryo brain

extract_protocol: Heart, left gonads and diencephalon from each of four male and four female embryos were homogenized by syringe and needle followed by use of the Homogenizer system (Invitrogen, Carlsbad, CA, USA). RNA was extracted from heart and brain homogenates with the PureLink Micro-to-Midi Total RNA Purification System (Invitrogen), and RNA was then DNase treated with a DNA-free kit (Ambion, Austin, TX, USA). Due to limited amounts of available tissue, gonad RNA extraction was performed with an RNeasy Micro Kit (Qiagen, Hilden, Germany) with integrated DNase treatment. RNA concentration was measured with ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and RNA quality was evaluated using the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc, Palo Alto, CA). Two micrograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA). Affymetrix GeneChip® expression arrays (Chicken Genome Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA), the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G. In total, 24 hybridizations were made (4 individuals x 3 tissues x 2 sexes), however, three samples failed to meet Affymetrix quality control criteria and were removed from further analysis (heart and brain from one male, and gonads from one female).

tag: white leghorn embryos


title: Diet Induced Obese rat C1


title: oligodendroglioma_IC_26342-26338

source_name: tumor tissue oligodendroglioma, patient tag IC, experiment 26342-26338

value: low grade oligodendroglioma


title: 18 day female embryonic brain (B12)

description: See Ellegren et al. in Press


title: 18 day female embryonic brain (B10)

description: See Ellegren et al. in Press


title: 18 day male embryonic brain (B16)

description: See Ellegren et al. in Press


title: 18 day female embryonic brain (B2)

description: See Ellegren et al. in Press


title: GBM_1745_6948-6920

source_name: tumro tissue GBM, patient tag 1745, experiment 6948-6920


title: 18 day male embryonic brain (B21)

description: See Ellegren et al. in Press


title: 18 day female embryonic brain (B20)

description: See Ellegren et al. in Press


title: AMG_1649_34707-34697

source_name: tumor tissue AMG, patient tag 1649, experiment 34707-34697


title: gliosarcoma_762_26300-26291

source_name: tumor tissue gliosarcoma, patient tag 762, experiment 26300-26291


title: GBM_932_15432-15410

source_name: tumor tissue GBM, patient tag 932, experiment 15432-15410


title: DND41 day 3 1uM MRK-003

status: Public on Aug 06 2007

city: Rahway

first: Olivia

last: Fong

state: NJ

department: Molecular Profiling

institute: Merck & Co.

description: T-ALL cell line

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: DND41 day 3 DMSO

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

growth_protocol: T-ALL cell lines were plated at a density of 5e4-1.5e5 cells per ml (depending on doubling time) and were treated with 1uM MRK-003 for 3 days.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: T-ALL cell line

source_name: DND41 day 3 1uM MRK-003


title: GBM/gliosarcoma_KH_24016-24007

source_name: tumor tissue GBM/gliosarcoma, patient tag KH, experiment 24016-24007

value: high grade glioblastoma/gliosarcoma


title: Supt7 day 3 1uM MRK-003

description: T-ALL cell line

source_name: Supt7 day 3 DMSO

source_name: Supt7 day 3 1uM MRK-003

growth_protocol:
T-ALL cell lines were plated at a density of 5e4-1.5e5 cells per ml (depending on doubling time) and were treated with 1uM MRK-003 for 3 days.
T-ALL cell lines were plated at a density of 5e4-1.5e5 cells per ml (depending on doubling time) and were treated with 1uM MRK-003 for 3 days.


title: Hsb2 day 3 1uM MRK-003

description: T-ALL cell line

source_name: Hsb2 day 3 DMSO

treatment_protocol: T-ALL cell lines were plated at a density of 5e4-1.5e5 cells per ml (depending on doubling time) and were treated with 1uM MRK-003 for 3 days.

source_name: Hsb2 day 3 1uM MRK-003


title: Loucy day 3 1uM MRK-003

description: T-ALL cell line

source_name: Loucy day 3 DMSO

source_name: Loucy day 3 1uM MRK-003


title: Be13 day 3  1uM MRK-003

description: T-ALL cell line

source_name: Be13 day 3  DMSO

source_name: Be13 day 3  1uM MRK-003


title: Exposed to Diamide 5 mM sigH mutant rep2

status: Public on Aug 04 2007

description: Biological replicate 3 of 6. Cell culture exposed to Diamide 5 mM for 60 minutes. sigH mutant

hyb_protocol: The quality of cDNA labeling was monitored by quantitatively measuring the intensities of Cy3- and Cy5-labeled samples hybridized to the MTB genomic positive control spots.

data_processing: The overall reproducibility of the microarray experiments was evaluated using the Signifi-cance Analysis of Microarrays (SAM) program.  The SAM algorithm was set for two-class unpaired analysis with 500 permutations and K-nearest imputer for missing data. Significantly regulated genes were selected by adjusting the delta value to give a false discovery rate below 1%. In each data set, all genes regulated 1.5-fold and greater were determined to be significant with a false discovery rate of less than 1%, indicating a high degree of reproducibility.

source_name: Cell culture untreated

label_protocol: All steps in the MTB DNA microarray gene expression analysis were performed as described. Controls for array quality were printed onto each slide and included a dilution series of MTB genomic DNA (positive control) and salmon sperm DNA (negative control). Additionally, DNA prelabeled with the cyanine dyes Cy3 or Cy5 were printed to ascertain whether spot-to-spot carryover contamination had occurred during the printing step.

growth_protocol: All the experiments were performed with M. tuberculosis H37Rv and its derivatives obtained during this study. Bacteria were grown in either Middlebrook 7H9 (liquid medium) or 7H10 (solid medium; Difco) both supplemented with ADN, 0.2% glycerol and 0.05% Tween 80. Liquid cultures were grown in roller bottles at 37 C. Plates were incubated at 37 C in sealed plastic bags. Escherichia coli strain JM109 was grown in Luria broth (LB; Difco) at 37 C in shaking cultures. When required, antibiotics were added at the following concentrations: kanamycin, 20 ug/ml for M. tuberculosis or 50 ug/ml for E. coli; hygromycin, 150 ug/ml for M. tuberculosis or 50 ug/ml for E. coli; ampicillin, 100 ug/ml; streptomycin, 20 ug/ml. Sucrose selection was performed on 7H10 plates with 8% sucrose.

extract_protocol:
RNA extraction for RTÐPCR experiments was performed as described previously. Briefly, bacteria were thawed on ice, broken with zirconia beads
(Biospec Products), extracted twice with phenolÐchloroformÐ isoamyl alcohol (25:24:1) and then precipitated in ethanol. To remove the chromosomal DNA, samples were treated twice with TRI reagent (Molecular Research Center) according to the manufacturerÕs instructions. RNA extraction for microarray experiments was performed using the following protocol: the frozen cell pellets were suspended in 1ml of Trizol reagent (Gibco BRL) and transferred to 2ml screw cap tubes containing 0.5 ml of 0.1-mm-diameter zirconia/silica beads (BioSpec Products). Cells were disrupted by two 30 s pulses in a BioSpec Products bead beater. After a 5 min incubation at room temperature, samples were centrifuged at maximum speed for 45 s, and the supernatants were transferred to 2ml Heavy Phase Lock Gel I tubes (Eppendorf) containing 300 ul of chloroformÐisoamyl alcohol (24:1), inverted rapidly for 15 s and incubated 2 min. The samples were centrifuged for 5 min, and the aqueous phase was added to 270 ul of isopropanol. After the addition of 270 ul of 0.8M Na citrate-1.2M NaCl, samples were incubated overnight at 4 C and centrifuged for 10 min at 4 C. The RNA pellets were washed with 1ml of 75% ethanol, centrifuged for 5 min and air dried. After suspension of the RNA pellets in 90 ul of water, 10 ul of DNase I 10x  buffer and 4 units of DNase I (Ambion) were added, and the samples were incubated for 30 min. Final purification of RNA used an RNeasy column (Qiagen).

tag: sigH mutant (H37Rv sigH::hyg)


title: Exposed to Diamide 5 mM sigH mutant rep1

description: Biological replicate 2 of 6. Cell culture exposed to Diamide 5 mM for 60 minutes. sigH mutant


title: Exposed to Diamide 5 mM sigH mutant rep4

description: Biological replicate 5 of 6. Cell culture exposed to Diamide 5 mM for 60 minutes. sigH mutant


title: Exposed to Diamide 5 mM sigH mutant rep3

description: Biological replicate 4 of 6. Cell culture exposed to Diamide 5 mM for 60 minutes. sigH mutant


title: Exposed to Diamide 5 mM sigH mutant rep5

description: Biological replicate 6 of 6. Cell culture exposed to Diamide 5 mM for 60 minutes. sigH mutant


title: Exposed to Diamide 5 mM sigH mutant

description: Biological replicate 1 of 6. Cell culture exposed to Diamide 5 mM for 60 minutes. sigH mutant


title: Exposed to Diamide 5 mM H37Rv (wild type) rep3

description: Biological replicate 4 of 6. Cell culture exposed to Diamide 5 mM for 60 minutes. H37Rv (wild type)

tag: H37Rv (wild type)


title: Exposed to Diamide 5 mM H37Rv (wild type) rep4

description: Biological replicate 5 of 6. Cell culture exposed to Diamide 5 mM for 60 minutes. H37Rv (wild type)


title: Exposed to Diamide 5 mM H37Rv (wild type) rep2

description: Biological replicate 3 of 6. Cell culture exposed to Diamide 5 mM for 60 minutes. H37Rv (wild type)


title: Exposed to Diamide 5 mM H37Rv (wild type) rep5

description: Biological replicate 6 of 6. Cell culture exposed to Diamide 5 mM for 60 minutes. H37Rv (wild type)


title: CEM day 3 1uM MRK-003

description: T-ALL cell line

source_name: CEM day 3 DMSO

source_name: CEM day 3 1uM MRK-003


title: Comparison between H37Rv (wild type) and sigH mutant rep2

description: Biological replicate 3 of 3. Comparison between H37Rv (wild type) and sigH mutant. Cell culture untreated.


title: RPMI 8402 day 3 1uM MRK-003

description: T-ALL cell line

source_name: RPMI 8402 day 3 DMSO

source_name: RPMI 8402 day 3 1uM MRK-003


title: DU528 day 3 1uM MRK-003

description: T-ALL cell line

source_name: DU528 day 3 DMSO

source_name: DU528 day 3 1uM MRK-003


title: Comparison between H37Rv (wild type) and sigH mutant rep1

description: Biological replicate 2 of 3. Comparison between H37Rv (wild type) and sigH mutant. Cell culture untreated.


title: PF382 day 3 1uM MRK-003

description: T-ALL cell line

source_name: PF382 day 3 DMSO

source_name: PF382 day 3 1uM MRK-003


title: Supt13 day 3 1uM MRK-003

description: T-ALL cell line

source_name: Supt13 day 3 DMSO

source_name: Supt13 day 3 1uM MRK-003


title: MOLT 4 day 3 1uM MRK-003

description: T-ALL cell line

source_name: MOLT 4 day 3 DMSO

source_name: MOLT 4 day 3 1uM MRK-003


description: Biological replicate 1 of 3. Comparison between H37Rv (wild type) and sigH mutant. Cell culture untreated.


title: Molt16 day 3 1uM MRK-003

description: T-ALL cell line

source_name: Molt16 day 3 DMSO

source_name: Molt16 day 3 1uM MRK-003


title: SUPT 11 day 3 1uM MRK-003

description: T-ALL cell line

source_name: SUPT 11 day 3 DMSO

source_name: SUPT 11 day 3 1uM MRK-003


title: Tall1 day 3 1uM MRK-003

description: T-ALL cell line

source_name: Tall1 day 3 DMSO

source_name: Tall1 day 3 1uM MRK-003


title: Jurkat day 3 1uM MRK-003

description: T-ALL cell line

source_name: Jurkat day 3 DMSO

source_name: Jurkat day 3 1uM MRK-003


title: Molt13 day 3 1uM MRK-003

description: T-ALL cell line

source_name: Molt13 day 3 DMSO

source_name: Molt13 day 3 1uM MRK-003


title: 18 day male embryonic heart (H19)

description: See Ellegren et al. in Press

source_name: heart tissue, excised day 18