title: H37Rv_hypoxia_7day_rep6

value: H37Rv Condition:aerobically grown

source_name: Rv_7d RNA

tag: Strain H37Rv Condition


title: H37dosR mutant_hypoxia_4hr_rep1

status: Public on Feb 20 2008

type: RNA

city: Seattle

first: Tige

last: Rustad

state: WA

address: 307 Westlake Avenue N, Suite 500

department: Pathobiology

country: USA

institute: Seattle Biomedical Research Institute

description: H37dosR mutant_hypoxia_4hr_rep1

hyb_protocol: Slides prehybed for >1 hour in prehyb buffer (5X SSC, 0.1% SDS, 1% BSA), washed 2X for 1 minute in water, 15 seconds in isopropanol, dried by centrifugation.  Probes added to slides, sealed in incubation chambers and submerged in 42 degree incubator overnight.  Arrays washed in increasingly stringent washes: 5 minutes at 42 degrees low stringency wash (0.2%SDS, 1XSSC), 10 minutes lower stringency wash (0.2%SDS, 0.1XSSC), 4 times 1 minute in 0.1XSSC, 10 seconds in 0.01XSSC.  Slides dried by centrifugation.

scan_protocol: Arrays scanned in with a GenePix4000B using GenePix 6 scanning software.  Gain adjusted during preview scan to roughly equivalence between channels with a few saturated spots.

data_processing: Data analysis conducted with Acuity 4 software package.  Spots flagged as not found were excised from the dataset.  Remaining features were lowess normalized seperately for each print tip.

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: Log phase RNA

label_protocol: Standard amino-allyl labelling protocol from TIGR.  cDNA made with Superscript III using aminoallyl dUTP.  cDNA purified using Qiaquick column from Qiagen.  Tags conjugated to reactive Cy dyes in the presence of sodium carbonate.  Excess Cy dye removed with a Qiaquick column from Qiagen.  Probes resuspended in hyb buffer (50% formamide, 5X SSC, and  0.1% SDS) and kept at room temp until added to array slides.

growth_protocol: Grown to mid log phase (OD600 0.3-0.5) in 2L roller bottles with 200-400 mL Middlebrook 7H9 media+ADC and Tween.  Diluted to an OD of 0.1 and transferred to three-armed flask.

extract_protocol: Pellets were bead beat in the presence of trizol.  Aqueus phase isolated using phase lock gel.  RNA precipitated in 50% isopropanol 50% high salt solution ((0.8M Na Citrate, 1.2M NaCl).  RNA purified using Rneasy columns from Qiagen.

treatment_protocol: 0.2% O2 (Balance N2) introduced into flask at a rate of 0.15 cfm and allowed to exit through 0.2 micron filter.  Samples (15-60mL) taken via pipette introduced into the flask while gas continued to flow.  Samples centrifuged for 5 minutes at 3000 RPM to softly pellet, superenatent decanted and pellet flash frozen in dry ice/ethanol bath.

tag: Strain

value: H37dosR mutant Condition:aerobically grown

source_name: dosR_mutant_4h RNA

tag: Strain H37dosR mutant Condition

value: 4 hour exposure to 0.2%O2


title: H37Rv_hypoxia_7day_rep1

value: 7 day exposure to 0.2%O2


title: H37Rv_hypoxia_4day_rep7

source_name: Rv_4d RNA

value: 4 day exposure to 0.2%O2


title: H37Rv_hypoxia_7day_rep7


title: H37Rv_hypoxia_7day_rep5


title: H37Rv_hypoxia_4day_rep2


title: H37Rv_hypoxia_4day_rep4


title: H37Rv_hypoxia_1day_rep9

source_name: Rv_1d RNA

value: 1 day exposure to 0.2%O2


title: H37Rv_hypoxia_4day_rep5


title: H37Rv_hypoxia_8hr_rep2

source_name: Rv_8h RNA

value: 8 hour exposure to 0.2%O2


title: NFkB target gene expression in ES cells in the absence of LIF

city: Cambridge

first: Josema

last: Torres-Ibanez

address: Tennis Court Road

country: United Kingdom

institute: Wellcome Trust Centre for Stem Cell Research

description:
Important: do not allow the membrane to dry during the detection procedure.
Carefully transfer the membrane to a container containing 20 ml of 1x blocking buffer (provided by the manufacturer) and incubate at room temperature for 15 minutes with gentle shaking.
Add 20 ul of Streptavidin-HRP conjugate (provided by the manufacturer) directly to the container containing the membrane with the 20 ml of 1x Blocking Buffer. Incubate at room temperature for 15 minutes.
Wash 3 times with 1x Washing Buffer (provided by the manufacturer) at room temperature.
Add 20 ml of 1x Detection Buffer (provided by the manufacturer) and incubate for 5 minutes at room temperature.
Incubate for 5 minutes the membrane with 2 ml of the substrate working solution (1:1 mixture of Luminol Enhancer and Peroxide Solution, both provided by the manufacturer).
Drain the substrate working solution from the membrane and place into a piece of plastic, cover the membrane with another piece of plastic.
Exposure: 20 seconds see strong signals, 40-60 seconds see most of the signals, signals last for over 30 minutes. Using Kodac BioMax XAR film (Kodak, 8532665).

hyb_protocol: Place the array membrane into a hybridisation bottle. Fill the bottle with deionised water. Decant carefully the water. Add 5 ml of pre-warmed (42ºC) Hybridisation Buffer (provided by the manufacturer). Place the bottle in the hybridisation oven at 42ºC for 2 hours. Add the labelled cDNA probe to the hybridisation bottle and hybridise at 42ºC overnight. Decant the hybridisation mixture from the bottle and wash twice (20 minutes each, 42ºC) with pre-warmed (42ºC) 2x SSC buffer (provided by the manufacturer) supplemented with 0.5 % of SDS (Sigma-Aldrich Co., Dorset, UK). Wash twice (20 minutes each, 42ºC) with pre-warmed (42ºC) 0.1x SSC buffer (provided by the manufacturer) supplemented with 0.5 % SDS.

scan_protocol: Standard, best quality.

data_processing:
The dots of the array were quantified through densitometric analysis using ImageJ (Rasband, W.S., ImageJ, U. S. National Institutes of Health, Bethesda,
Maryland, USA, http://rsb.info.nih.gov/ij). The 2 spots intensities acquired for each gene were averaged to obtain the VALUE.

label: Biotin

organism: Mus musculus

source_name: CCE 1.19 mouse embryonic stem cells grown in the absense of leukemia inhibitory factor

label_protocol:
Preheat a termal cycler to 70ºC.
Mix in a PCR tube 10 ul of total RNA (2 ug/ul) and 5 ul of the NFkB primer mix (provided by the manufacturer).
Heat samples at 70ºC for 2 minutes. Then reduce the temperature to 42 ºC and incubate for 2 minutes.
Prepare the cDNA synthesis mixture: 12 ul of labelling mix and 2 ul of Biotin-UDP (provided by the manufacturer), and 1ul of Reverse transcriptase (Roche Diagnostics Ltd., 1495062). Incubate the mixture at 42ºC for 2 minutes.
Transfer the cDNA synthesis mixture to the tube containing the RNA sample, mix and incubate at 42 for 2 hours.
After incubation, add 3 ul of 10x Denaturing Solution (provided by the manufacturer), mix and incubate at 68ºC for 20 minutes.
Add 33 ul of 2x Neutralization Buffer (provided by the manufacturer) and incubate at 72ºC for 10 minutes. The labelled cDNA probes can be stored at -20ºC.

extract_protocol: Total RNA was extracted using Tri-Reagent (Helena Biosciences Europe, TR118100).

tag: CCE1.19 mouse embryonic stem cells plated at 2000 cells per cm2 on gelatine-coated dishes and grown for 4 days in the absence of Leukemia Inhibitory factor.


title: H37Rv_hypoxia_1day_rep7


title: H37Rv_hypoxia_4day_rep6


title: H37Rv_hypoxia_1day_rep6


title: NFkB target gene expression in ES cells in the presence of LIF

source_name: CCE 1.19 mouse embryonic stem cells grown in the presence of leukemia inhibitory factor

extract_protocol: Total RNA was extracted using Tri-Reagent (Helena Biosciences Europe, TR118100)

tag: CCE1.19 embryonic stem cells plated on gelatine-coated dishes at 2000 cells/cm2 and grown for 4 days in the presence of Leukemia Inhibitory Factor (1000 units/ml).


title: H37Rv_hypoxia_1day_rep5


title: H37Rv_hypoxia_1day_rep3


title: H37Rv_hypoxia_12hr_rep2

source_name: Rv_12 RNA

value: 12 hour exposure to 0.2%O2


title: H37Rv_hypoxia_12hr_rep1


title: H37Rv_hypoxia_8hr_rep1


title: H37Rv_hypoxia_4hr_rep5

source_name: Rv_4h RNA


title: H37Rv_hypoxia_4hr_rep6


title: H37Rv_hypoxia_4hr_rep4


title: H37Rv_hypoxia_7day_rep2


title: H37Rv_hypoxia_1day_rep2


title: H37Rv_hypoxia_7day_rep3


title: H37Rv_hypoxia_4hr_rep1


title: H37Rv_hypoxia_4day_rep1


title: H37Rv_hypoxia_7day_rep4


title: H37Rv_hypoxia_4day_rep3


title: H37Rv_hypoxia_4hr_rep2


title: H37Rv_hypoxia_1day_rep10


title: H37Rv_hypoxia_1day_rep4


title: 2007012321b

type: genomic

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: X chromosome-specific Array-CGH of XLMR patient

hyb_protocol: For each hybridisation, 1 µg of the Cy5- and 2 µg of the Cy3- labeled probes, with a specific activity < 40 were mixed together with 50 µg Cot-1 DNA (Invitrogen, Carlsbad, CA). Probe preparation, pre-blocking and washing of the slides was performed as described previously (Van Buggenhout G, et al. 2004. J. Med. Genet. 41: 691-698).

scan_protocol: Arrays were scanned at 532 nm (Cy3) and 635 nm (Cy5) using the Genepix 4000B scanner (Axon Instruments, Aberdeen, UK) and the acquired images were analyzed using the Genepix Pro software (Axon Instruments).

data_processing: Spot intensities were corrected for local background and only those spots with Cy5 as well as Cy3 signal intensities at least 1.7-fold above the local background, were further analyzed. For each clone, a ratio of Cy5 to Cy3 fluorescent intensity was calculated. Normalization of the data was achieved by dividing the fluorescent intensity ratio of each spot by the mean of the ratios of all spots. Finally, the normalized ratio values of the duplicates were averaged and a log2 value was calculated.

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Genomic DNA was labeled with the Bioprime DNA Labeling System (Invitrogen, Carlsbad, CA) using Cy3- and Cy5-labelled dCTP's (Amersham Biosciences, Buckinghamshire, UK) as described by the manufacturer. The concentrations and labeling efficiencies were measured with the Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Rockland, DE).

extract_protocol: Genomic DNA from patients as well as from healthy controls was isolated from peripheral blood using the Wizard Genomic DNA purification Kit (Promega, Madison, WI) and using manufacture's protocol.

tag: XLMR patient 46,XY


title: H37Rv_hypoxia_12hr_rep3


title: H37Rv_dosR mutant_hypoxia_12hour_rep3

value: H37RvΔdosR Condition:aerobically grown

source_name: dosR_mutant_12h RNA

tag: Strain H37RvΔdosR Condition


title: H37Rv_dosR mutant_hypoxia_1day_rep7

source_name: dosR_mutant_1d RNA


title: 2005122235b


title: H37Rv_hypoxia_4hr_rep3


title: H37Rv_hypoxia_8hr_rep3


title: 2006073114b


title: H37Rv_dosR mutant_hypoxia_8hour_rep2

source_name: dosR_mutant_8h RNA


title: 2006073110a


title: 2006073114a


title: ecoli_aerobicanaerobic_55min_rep2

status: Public on Feb 19 2008

city: Los Angeles

first: Jason

last: Ernst

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

description:
First time point in aerobic-anaerobic shift response. Note: Aerobic standard was not
consistently labeled across all time series.

hyb_protocol: Unincorporated Cy-dyes were removed with a QiaQuick PCR Purification Kit (Qiagen, Valencia, CA) as follows: 35μl 100mM Na-acetate pH 5.2 and 50 μl water were added to each sample, along with 500μl Buffer PB. Thereafter, the standard QiaQuick protocol was followed, with the exception that 75% EtOH was used in place of Buffer PE. Samples were eluted in water in place of Buffer EB. 0.5-1μg of cDNA from each sample was mixed with ~125μl ArrayHyb microarray hybridization buffer (Sigma-Aldrich) and hybridized to full-genome microarray slides using a GeneTAC HybStation (Genomic Solutions, Ann Arbor, MI)

scan_protocol: images were scanned from the completed hybridization using a GenePix 4000B array scanner (Molecular Devices, Union City, CA).

data_processing:
Two color cDNA microarray data are never devoid of spurious technical contributions that
originate during array printing, as well as during the collection and processing of samples,
fluorescent labeling and hybridization and scanning of the microarray images (Balazsi et al.
2003, PNAS). To minimize the effect of such contributions, microarray data were
normalized as described before (Tong et al. 2004 BBRC). Briefly, spots were excluded from
further analysis if the foreground intensity of less than 50% of the pixels within the spot
were above 2 standard deviations of the background. We generated expression data tables
in Microsoft Excel, containing the following information for each of the 14,352 entries: block
(B), column (X), and row (Y) number, red foreground (f_r) and background (b_r), green
foreground (f_g) and background (b_g) intensity. The position of each probe within a block,
P is defined by the pair of integers (X,Y). Log ratios were defined as the base 10 logarithm
of (F_r-B_r)/(F_g-B_g), where F_r, B_r, F_g and B_g represent the median Cy5 (red)
foreground and background, and the median Cy3 (green) foreground and background
intensities, respectively. In some cases, when the intensity of the background was higher
than or equal to the intensity of the foreground, the resulting log ratios became complex or
infinity. These values were eliminated using the find, imag, and isfinite functions in Matlab.
Next, data were normalized, by averaging the log ratios resulting from all spots printed by a
print tip, and subtracting the resulting average from all the individual log ratios
corresponding to the same tip. Finally, all the log ratios of the same gene from each slide
were averaged and listed in a new file.

organism: Escherichia coli

source_name: E coli, 55 min

label_protocol:
The generated cDNAs from RNA were coupled with Cy5 by dissolving the pellets together
with a dried aliquot of dye in 9μl of 0.1M Na-Bicarbonate pH 8.5-9 and incubation in the
dark at room temperature for 1.5-3 hours. This reaction was quenched with 4.5μl 4M
hydroxylamine pH 8.5-9 and incubation in the dark for 15 minutes.

extract_protocol: Epicentre MasterPure RNA isolation Kit, Madison, WI

tag: 55 min after turning off oxygen

source_name: E coli, 0 min

label_protocol:
The generated cDNAs from RNA were coupled with Cy3 by dissolving the pellets together
with a dried aliquot of dye in 9μl of 0.1M Na-Bicarbonate pH 8.5-9 and incubation in the
dark at room temperature for 1.5-3 hours. This reaction was quenched with 4.5μl 4M
hydroxylamine pH 8.5-9 and incubation in the dark for 15 minutes.

tag: completely aerobic conditions


title: ecoli_aerobicanaerobic_55min_rep1


title: ecoli_aerobicanaerobic_5min_Rep1

description:
5 min time point in aerobic-anaerobic shift response.
Note: Aerobic standard was not consistently labeled across all time series.

hyb_protocol: Unincorporated Cy-dyes were removed with a QiaQuick PCR Purification Kit (Qiagen, Valencia, CA) as follows: 35μl 100mM Na-acetate pH 5.2 and 50 μl water were added to each sample, along with 500μl Buffer PB. Thereafter, the standard QiaQuick protocol was followed, with the exception that 75% EtOH was used in place of Buffer PE. Samples were eluted in water in place of Buffer EB. 0.5-1μg of cDNA from each sample was mixed with ~125μl ArrayHyb microarray hybridization buffer (Sigma-Aldrich) and hybridized to full-genome  microarray slides using a GeneTAC HybStation (Genomic Solutions, Ann Arbor, MI)

data_processing: Two color cDNA microarray data are never devoid of spurious technical contributions that originate during array printing, as well as during the collection and processing of samples, fluorescent labeling and hybridization and scanning of the microarray images (Balazsi et al. 2003, PNAS).  To minimize the effect of such contributions, microarray data were normalized as described before (Tong et al. 2004 BBRC). Briefly, spots were excluded from further analysis if the foreground intensity of less than 50% of the pixels within the spot were above 2 standard deviations of the background. We generated expression data tables in Microsoft Excel, containing the following information for each of the 14,352 entries: block (B), column (X), and row (Y) number, red foreground (f_r) and background (b_r), green foreground (f_g) and background (b_g) intensity. The position of each probe within a block, P is defined by the pair of integers (X,Y). Log ratios were defined as the base 10 logarithm of (F_r-B_r)/(F_g-B_g), where F_r, B_r, F_g and B_g represent the median Cy5 (red) foreground and background, and the median Cy3 (green) foreground and background intensities, respectively.  In some cases, when the intensity of the background was higher than or equal to the intensity of the foreground, the resulting log ratios became complex or infinity. These values were eliminated using the find, imag, and isfinite functions in Matlab. Next, data were normalized, by averaging the log ratios resulting from all spots printed by a print tip, and subtracting the resulting average from all the individual log ratios corresponding to the same tip. Finally, all the log ratios of the same gene from each slide were averaged and listed in a new file.

source_name: E coli, 5 min

label_protocol: The generated cDNAs from RNA were coupled with Cy5 by dissolving the pellets together with a dried aliquot of dye in 9μl of 0.1M Na-Bicarbonate pH 8.5-9 and incubation in the dark at room temperature for 1.5-3 hours. This reaction was quenched with 4.5μl 4M hydroxylamine pH 8.5-9 and incubation in the dark for 15 minutes.

source_name: E coli, 5 min after turning off oxygen first replicate

label_protocol: The generated cDNAs from RNA were coupled with Cy3 by dissolving the pellets together with a dried aliquot of dye in 9μl of 0.1M Na-Bicarbonate pH 8.5-9 and incubation in the dark at room temperature for 1.5-3 hours. This reaction was quenched with 4.5μl 4M hydroxylamine pH 8.5-9 and incubation in the dark for 15 minutes.


title: ecoli_aerobicanaerobic_0min

description:
First time point in aerobic-anaerobic shift response.
Note: Aerobic standard was not consistently labeled across all time series.

source_name: E coli, immediately after turning off oxygen

tag: Immediately after turning off oxygen


title: ecoli_aerobicanaerobic_5min_rep2

source_name: Ecoli, 5 min after turning off oxygen

tag: 5 min after turning off oxygen

source_name: Ecoli, completely aerobic conditions


title: ecoli_aerobicanaerobic_45min

source_name: E coli, 45 min

tag: E coli, 45 min after turning off oxygen


title: ecoli_aerobicanaerobic_35min

source_name: E coli, 35 min

tag: E coli, 35 min after turning off oxygen


title: ecoli_aerobicanaerobic_25min_rep1

source_name: E coli, 25 min

tag: E coli, 25 min after turning off oxygen


title: XIST-positive and XIST-negative HSF6 hESCs Gene Expression

first: Yin

last: Shen

address: 695 Charles E. Young Dr.

description: All cell cultures were maintained at 37 °C with 5% CO2. The culture of hESCs were maintained in DMEM supplemented with 20% KSR , glutamate and penicillin/streptomycin.

hyb_protocol: 1000ng of RNA for each channel was labelled using Agilent Low Input Linear Amplification protocol. Labelled cRNA mixed with Agilent 10x Control targets and Agilent 25x Fragmentation Buffer. This was incubated at 37C for 30 min and the reaction was stopped by the addition of 2x Agilent hybridization buffer. This mix was hybridized to arrays for 17 hours at 65C at 4rpms. Arrays were washed as per Agilent protocol and scanned immediately

scan_protocol: The arrays were scanned with Agilent DNA microarray scanner (G2565BA), and probe features were extracted using Feature Extraction Software (version 8.5)

data_processing: Arrays were processed using Agilent Feature Extraction (Version 8.5). Log 10 ratio were calculated from processed Cy5/ processed Cy3 signals

source_name: XIST-positive HSF6 hESCs

label_protocol: Cy3 Labelled with Agilent Low Input Linear Amplification Kit

extract_protocol: Trizol Extracted and cleaned with Qiagen RNeasy kit

tag: HSF6 hESCs with XIST expression

source_name: XIST-negative HSF6 hESCs

label_protocol: Cy5 Labelled with Agilent Low Input Linear Amplification Kit

tag: HSF6 hESCs without XIST expression


title: ecoli_aerobicanaerobic_25min_rep2

source_name: E coli, 25 min after turning off oxygen

tag: 25 min after turning off oxygen


title: ecoli_aerobicanaerobic_15min

source_name: E coli, 15 min

tag: 15 min after turning off oxygen


title: Mouse RelA

status: Public on Feb 14 2008

city: Piscataway

first: Celine

last: Gelinas

state: NJ

address: 679 Hoes Lane

department: UMDNJ-Robert Wood Medical School

institute: Center for Advanced Biotechnology and Medicine

description: Replicates G1vsDT40,  G2vsDT40,  G3vsDT40,  DT40vsG1,  DT40vsG2,  DT40vsG3

hyb_protocol: Hybridization buffer: 3X SSC, 0.23% SDS, 20 mg poly(dA)     Slide blocking: No prehybridization     Probe blocking: 20 mg poly(dA) during hybridization     Quantity of labeled target used: All labeled cDNA generated with 30 ug total RNA     Hybridization time, volume, temperature: 16 hrs, 26.6 microliters, 63 degrees C     Hybridization instrument: Manual, TelChem hybridization chambers in water bath     Wash procedure:      Wash 1: 1X SSC, 0.03% SDS  Wash 2: 1X SSC, dip slides 15 times  Wash 3: 0.2X SSC, shake slides 75 rpm for 20 minutes  Wash 4: 0.05X SSC, shake slides 75 rpm for 10 minutes  Spin-dry slides in centrifuge 50 g for 5 minutes

scan_protocol: Scanned using GenePix 4000A and 4000B scanners

data_processing: For each array result, spot intensity signals were assessed for signal quality and those identified as poor quality were removed from further analysis. Spot-level ratios were background corrected, ln-transformed, and loess normalized. Sample comparisons were performed using three biological independent experimental replicates that were each compared to a reference. For each comparison, a dye-swapped technical replicate was also performed and the paired results were averaged and used as a single observation. Accordingly, a total of six arrays contributed to three independent observations. Triplicate data sets were averaged to identify changes in gene expression in response to expression of each of these proteins.

label: Cy3, Cy5 (dye-swap)

organism: Gallus gallus

source_name: Mouse RelA

label_protocol: Reverse transcription was performed by mixing 30 ug total RNA with  oligo(dT)18, Superscript II-RT enzyme and buffer (Invitrogen), 25 mM of each  dATP, dCTP and dGTP, 12.5 mM dTTP and 12.5 mM amino-allyl-dUTP (Sigma).  Incubate at 42 degree C for 2 hours. Add 10 ul of NaOH and 10 ul of 0.5 M  EDTA. Incubate at 65 degree C for 15 minutes. Neutralize by adding 25 ul 1M  HEPES pH7.4. Filter on Microcon-30 concentrator. Dry on speed-vac, resuspend  in water. Cy3 and Cy5 Monoreactive dyes (Amersham) were resuspended in DMSO,  activated by Sodium Bicarbonate and incubated with purified cDNA for 1 hour.  Coupling reactions were quenched by addition of Hydroxylamine and incubation  for 15 minutes. Combine Cy3 and Cy5 labeled cDNA pairs and purify with  QIAquick PCR purification columns. Final elute was dried in speed-vac and  resuspended in 20 ul water. Add 4 ul 20X SSC and 2 ul of 10 mg/mL polyA  (Roche). Filter through Millipore 0.45 micron spin membranes. Mix with SDS  to final concentration before hybridization.

growth_protocol: DT40 cells were maintained at 37°C, 5% CO2 in RPMI 1640, 10% fetal  bovine serum (FBS), 1% chicken serum and 1% antibiotics. Stable cell lines were supplemented with 0.5mg/ml puromycin.

extract_protocol: Microarrays were performed with RNA extracted with RNAzolTM (Tel-Test) followed by purification using Rneasy MinEluteTM (Qiagen)

tag: v-Rel, c-Rel (chicken, mouse, human), RelA (mouse, human) or a human RelA/v-Rel chimera were stably expressed at equivalent levels in the chicken pre-B-cell line DT46

tag: chicken DT40 pre-B cell line


title: Chicken c-Rel

description: Replicates F1vsDT40,  F2vsDT40,  F3vsDT40,  DT40vsF1,  DT40vsF2,  DT40vsF3

source_name: Chicken c-Rel

tag: v-Rel, c-Rel (chicken, mouse, human), RelA (mouse, human) or a human RelA/v-Rel chimera were stably expressed at equivalent levels in the chicken pre-B-cell line DT45


title: Human c-Rel

description: Replicates A1vsDT40,  A2vsDT40,  A3vsDT40,  DT40vsA1,  DT40vsA2,  DT40vsA3

source_name: Human c-Rel

tag: v-Rel, c-Rel (chicken, mouse, human), RelA (mouse, human) or a human RelA/v-Rel chimera were stably expressed at equivalent levels in the chicken pre-B-cell line DT40


title: Mouse c-Rel

description: Replicates B1vsDT40,  B2vsDT40,  B3vsDT40,  DT40vsB1,  DT40vsB2,  DT40vsB3

source_name: Mouse c-Rel

tag: v-Rel, c-Rel (chicken, mouse, human), RelA (mouse, human) or a human RelA/v-Rel chimera were stably expressed at equivalent levels in the chicken pre-B-cell line DT41


title: v-Rel

description: Replicates E1vsDT40,  E2vsDT40,  E3vsDT40,  DT40vsE1,  DT40vsE2,  DT40vsE3

source_name: v-Rel (viral Rel)

tag: v-Rel, c-Rel (chicken, mouse, human), RelA (mouse, human) or a human RelA/v-Rel chimera were stably expressed at equivalent levels in the chicken pre-B-cell line DT44


title: Human RelA/v-Rel

description: Replicates D1vsDT40,  D2vsDT40,  D3vsDT40,  DT40vsD1,  DT40vsD2,  DT40vsD3

source_name: Human RelA/v-Rel

tag: v-Rel, c-Rel (chicken, mouse, human), RelA (mouse, human) or a human RelA/v-Rel chimera were stably expressed at equivalent levels in the chicken pre-B-cell line DT43


title: Explant_rep1

status: Public on Feb 15 2008

city: Paris

first: Luce

last: Dauphinot

address: 47 boulevard de l'hôpital

department: ICM

country: France

institute: INSERM U1127-CNRS UMR7225-UPMC

description: First replicate of CGE explant experiment performed with 5µg total RNA

hyb_protocol: RNG-MRC_MM25k_EVRY microarrays (Le brigand et al., NAR, 2006) were first incubated in a humid chamber for 2 hours to rehydrate the spots then placed for 1 hour in a dessicator and blocked for 1 hour at room temperature in 50mM Sodium Borate pH 9, 0.003% ethanolamine. Slides were then washed 5 minutes with water and dried by centrifugation. Hybridizations were performed in 50% formamide, 5X Denhardt’s, 4x SSC and 0.1% SDS solution at 42°C for 16 hours. Microarrays were then washed at room temperature 5 minutes in 2X SSC, 0.1% SDS, 5 minutes in 1X SSC, 5 minutes in 0.2X SSC and 5 minutes in 0.05X SSC. Slides were finally dried by centrifugation 4 minutes at 900rpm.

scan_protocol: Microarray images were obtained using a ScanArray Gx scanner (Perkin Elmer) with laser power = 90% and PMT gain = 80%. Median signal and median local background intensities were extracted from the images using Mapix v2.2.4 software (Innopsys).

data_processing:
Intensity/background ratios were calculated for each spot in each experiment.
Features which were not interpretable in all the replicates were excluded for further analysis. For comparing experiments, the sum of F/B values for each slide was then multiplied by a correcting factor so that the sum of the corrected ratios was equal in all experiments.

source_name: Embryonic CGE explant, replicate 1

label_protocol: 5µg of total RNA were reverse-transcribed in the presence of 7.5µM random hexamers (GE Healthcare), 75µM aa-dUTP (Sigma-Aldrich) and 100U Rtases Reverse-iT Blend (ABgene) overnight at 37°C. Aminoallyl cDNAs were then labelled with Cy5 mono-Reactive Dye (GE Healthcare) according to the manusfacturer’s instructions.

extract_protocol: Total RNA was extracted from wild-type embryonic (E14) mouse telencephalon and treated with DNAse using Nucleospin RNA L kit (Macherey-Nagel) according to the manusfacturer’s instructions.

tag: Strain

value: OF1, Age :E14, Tissue :CGE


title: ecoli_aerobicanaerobic_2min

description:
2 min time point in aerobic-anaerobic shift response.
Note: Aerobic standard was not consistently labeled across all time series.

source_name: Ecoli, 2 min

tag: completely aerobic conditions

source_name: E coli, 2 min after turning off oxygen

tag: 2 min after turning off oxygen


title: Human RelA

description: Replicates C1vsDT40,  C4vsDT40,  C6vsDT40,  DT40vsC1,  DT40vsC4,  DT40vsC6

source_name: Human RelA

tag: v-Rel, c-Rel (chicken, mouse, human), RelA (mouse, human) or a human RelA/v-Rel chimera were stably expressed at equivalent levels in the chicken pre-B-cell line DT42


title: Explant_rep3

description: Third replicate of CGE explant experiment performed with 5µg total RNA

source_name: Embryonic CGE explant, replicate 3


title: Petunia_control_vs_salt_0h_2

status: Public on Feb 13 2008

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

description: Seven different Solanaceae species, Potato (Solanum tubersosum), Tomato (Solanum lycopersicum), Eggplant (Solanum melongena), Pepper (Capsicum annuum), Tobacco (Nicotiana tabaccum), Petunia and Nicotiana benthiamana were subjected to salt stress. The stress applied was 150mM NaCl and control plants were watered without the additional salt. Samples were collected at 0, 6, 12, 24, 48 and 96 hours after the first application of the salt. RNA was isolated using Qiagen RNeasy.

hyb_protocol: Hybridization with indirectly labeled mRNA (SGED_SOP_6.1.1, SGED_SOP_6.2.1-4)

scan_protocol: Axon 4000B scanner. Both the 635nm (red, Cy5) and 532nm (green, Cy3) channels are scanned simultaneously at 100% laser power, the PMT set between 600 and 950. Slides are scanned at a resolution of 10micron

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.

organism: Petunia x hybrida

label_protocol: Amino allyl labeling and direct labeling (SGED_SOP_5.1.1 + SGED_SOP_6.1.1)

growth_protocol: 25C; 16 hr light, 8 hr dark

extract_protocol: Phenol method with carbohydrate-enriched tissue such as tubers and trizol for other tissues such as leaves (SGED_SOP_3.1.1 + SGED_SOP_3.3.1)

treatment_protocol: 150mM NaCl dissolved in plant nutrient solution; 0h

tag: Petunia hybrida, leaves, Abiotic stress

treatment_protocol: control, nutrient solution only; 0h


title: N_benthamiana_control_vs_salt_12h_2

organism: Nicotiana benthamiana

treatment_protocol: 150mM NaCl dissolved in plant nutrient solution; 12h

tag: Nicotiana benthamiana, leaves, Abiotic stress

treatment_protocol: control, nutrient solution only; 12h


title: N_tabacum_control_vs_salt_48h_2

organism: Nicotiana tabacum

treatment_protocol: 150mM NaCl dissolved in plant nutrient solution; 48h

tag: Nicotiana tabacum, leaves, Abiotic stress

treatment_protocol: control, nutrient solution only; 48h


title: N_benthamiana_control_vs_salt_24h_2

treatment_protocol: 150mM NaCl dissolved in plant nutrient solution; 24h

treatment_protocol: control, nutrient solution only; 24h


title: N_benthamiana_control_vs_salt_96h_2

treatment_protocol: 150mM NaCl dissolved in plant nutrient solution; 96h

treatment_protocol: control, nutrient solution only; 96h


title: CpG island methylation of hESCs without XIST expression

description: All cell cultures were maintained at 37 °C with 5% CO2. The culture of hESCs were maintained in DMEM supplemented with 20% KSR, glutamate and penicillin/streptomycin. After genomic DNA isolation, the DNA was RNase treated and 2ug was used for methylated DNA immunoprecipitation (Weber et al., 2005. Nat Genetics. 37, 853-62. Zhang et al., 2006. Cell. 126:1189-1201.) Immunoprecipitated DNA was checked with Q-PCR to ensure that it was enriched for methylated DNA. This DNA was then used for labelling.

hyb_protocol: 250ng of DNA for each channel was labelled using Agilent CGH labelling protocol. Labelled DNA mixed with mouse Cot-1 DNA, yeast tRNA and Agilent 10x Control targets. This mix was hybridized to arrays for 40 hours at 65C. Arrays were washed as per Agilent protocol and scanned immediately

source_name: Sonicated XIST-negative HSF6 genomic DNA

label_protocol: Cy3 Labelled with Agilent CGH protocol

extract_protocol: DNA lysis buffer plus proteinase K. Ethanol precipitated. RNase treated and phenol:choloroform cleaned

tag: XIST-negative HSF6

source_name: Pull down XIST-negative HSF6 genomic DNA

label_protocol: Cy5 Labelled with Agilent CGH protocol


title: N_benthamiana_control_vs_salt_0h_2


title: N_tabacum_control_vs_salt_96h_2


title: N_tabacum_control_vs_salt_0h_2


title: N_benthamiana_control_vs_salt_48h_2


title: N_benthamiana_control_vs_salt_6h_2

treatment_protocol: 150mM NaCl dissolved in plant nutrient solution; 6h

treatment_protocol: control, nutrient solution only; 6h


title: Explant_rep2

description: Second replicate of CGE explant experiment performed with 5µg total RNA

source_name: Embryonic CGE explant, replicate 2


title: N_tabacum_control_vs_salt_6h_2


title: CpG island methylation of hESCs with XIST expression

source_name: Sonicated XIST-positive HSF6 genomic DNA

tag: XIST-positive HSF6

source_name: Pull down XIST-positive HSF6 genomic DNA


title: C_annuum_control_vs_salt_24h_2

organism: Capsicum annuum

tag: Capsicum annuum, leaves, Abiotic stress


title: S_melongena_control_vs_salt_48h_2

organism: Solanum virginianum

tag: Solanum melongena, leaves, Abiotic stress


title: S_melongena_control_vs_salt_24h_2


title: C_annuum_control_vs_salt_48h_2


title: S_melongena_control_vs_salt_12h_2


title: L_esculentum_control_vs_salt_24h_2

organism: Solanum lycopersicum

tag: Lycopersicum esculentum, leaves, Abiotic stress


title: C_annuum_control_vs_salt_0h_2


title: C_annuum_control_vs_salt_12h_2


title: L_esculentum_control_vs_salt_96h_2


title: S_melongena_control_vs_salt_0h_2


title: L_esculentum_control_vs_salt_48h_2


title: L_esculentum_control_vs_salt_6h_2


title: L_esculentum_control_vs_salt_12h_2


title: L_esculentum_control_vs_salt_0h_2


title: S_tuberosum_control_vs_salt_96h_2

organism: Solanum tuberosum

tag: Solanum tuberosum, leaves, Abiotic stress


title: Petunia_control_vs_salt_96h_1

tag: Petunia hybrida, Leaves, Abiotic stress


title: Petunia_control_vs_salt_48h_1


title: H7 hESCs Sty genotyping

description: no additional description

hyb_protocol: Affymetrix 250K genotyping standard protocol

data_processing: standard normalization by Affymetirx Gtype software

label: biotin

source_name: H7 hESCs

label_protocol: Affymetrix 250K SNP genotype standard protocol

tag: cultured H7 hESCs


title: S_melongena_control_vs_salt_6h_2


title: Petunia_control_vs_salt_24h_1


title: H7 hESCs Nsp Genotyping

description: no additional description

scan_protocol: Affymetrix 250K genotyping standard protocol


title: Petunia_control_vs_salt_12h_1


title: Petunia_control_vs_salt_2h_1


title: C_annuum_control_vs_salt_6h_2


title: Petunia_control_vs_salt_0h_1


title: N_benthamiana_control_vs_salt_96h_1

tag: Nicotiana benthamiana, Leaves, Abiotic stress


title: S_tuberosum_control_vs_salt_0h_2


title: S_tuberosum_control_vs_salt_48h_2


title: C_annuum_control_vs_salt_96h_2


title: S_tuberosum_control_vs_salt_6h_2


title: H9 hESCs Sty genotyping

description: no additional description

hyb_protocol: Affymetrix 250K SNP genotype standard protocol

source_name: H9 hESCs

tag: cultured H9 hESCs


title: N_tabacum_control_vs_salt_2h_1

tag: Nicotiana tabacum, Leaves, Abiotic stress


title: N_benthamiana_control_vs_salt_24h_1


title: N_benthamiana_control_vs_salt_12h_1


title: N_tabacum_control_vs_salt_0h_1


title: N_benthamiana_control_vs_salt_0h_1


title: N_benthamiana_control_vs_salt_48h_1


title: HSF6 hESCs Nsp genotyping

description: no additional description

source_name: HSF6 hESCs

tag: cultured hESCs


title: N_tabacum_control_vs_salt_96h_1


title: C_annuum_control_vs_salt_2h_1

tag: Capsicum annuum, Leaves, Abiotic stress


title: C_annuum_control_vs_salt_0h_1


title: C_annuum_control_vs_salt_48h_1


title: C_annuum_control_vs_salt_24h_1


title: C_annuum_control_vs_salt_12h_1


title: N_benthamiana_control_vs_salt_2h_1


title: S_melongena_control_vs_salt_96h_1

tag: Solanum melongena, Leaves, Abiotic stress


title: S_melongena_control_vs_salt_12h_1


title: S_melongena_control_vs_salt_48h_1


title: H9 hESCs Nsp genotyping

description: no additional description


title: HSF6 hESCs Sty genotyping

description: no additional description

scan_protocol: Affymetrix 250K SNP genotype standard protocol

tag: cultured HSF6 hESCs


title: N_tabacum_control_vs_salt_12h_1


title: C_annuum_control_vs_salt_96h_1


title: S_melongena_control_vs_salt_2h_1


title: N_tabacum_control_vs_salt_48h_1


title: L_esculentum_control_vs_salt_96h_1

tag: Solanum lycopersicum, Leaves, Abiotic stress


title: L_esculentum_control_vs_salt_12h_1


title: L_esculentum_control_vs_salt_24h_1


title: S_tuberosum_control_vs_salt_12h_1

tag: Solanum tuberosum, Leaves, Abiotic stress


title: S_tuberosum_control_vs_salt_96h_1


title: L_esculentum_control_vs_salt_48h_1


title: S_tuberosum_control_vs_salt_2h_1


title: S_tuberosum_control_vs_salt_48h_1


title: L_esculentum_control_vs_salt_2h_1


title: S_tuberosum_control_vs_salt_24h_1


title: S_tuberosum_control_vs_salt_0h_1


title: S_melongena_control_vs_salt_24h_1


title: L_esculentum_control_vs_salt_0h_1


title: Aoryzae_Glucose_rep1

status: Public on Feb 10 2008

city: Kgs. Lyngby

first: Mikael

middle: R

last: Andersen

address: Søltofts plads, bygn 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

hyb_protocol: Hybridization was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Fluidics Station FS-400.

scan_protocol: Scanning was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Scanner 3000.

data_processing: Affymetrix CEL-data files were preprocessed using the statistical language and environment R~\cite{RLanguage} version 2.5. The probe intensities were normalised for background using the robust multiarray average (RMA) method (Irizarry, 2003) using only perfect match (PM) probes. Normalization was performed subsequently using the quantiles algorithm (Bolstad, 2003). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

organism: Aspergillus oryzae

source_name: A. oryzae mycelium grown in a glucose medium

label_protocol: Labeled was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

extract_protocol: Total RNA was isolated from ground frozen mycelium using the Qiagen RNeasy Mini Kit.

tag: Strain

value: A. oryzae A1560. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:1.


title: Klf5 ChIP Biol. rep. 3

status: Public on Feb 11 2008

city: Urbana

first: jun

last: cai

state: IL

address: Springfield Ave, DCL

institute: UIUC

description:
109748
Klf5 ChIP-chip in E14 cells using Klf5 antibody

hyb_protocol: After denaturation, hybridization was carried out in a MAUI® (MicroArray User Interface) Hybridization System ( BioMicro Systems, Salt Lake City, UT, USA) for 18 h at 42°C.

scan_protocol: The arrays were washed using wash buffer system (NimbleGen Systems), dried by centrifugation, and scanned at 5 μm resolution using the GenePix® 4000B scanner (Axon Instruments). Fluorescence intensity raw data were obtained from scanned images of arrays using NimbleScan™ 2.0 extraction software (NimbleGen Systems).

data_processing: The arrays were scanned at 5 μm resolution using the GenePix® 4000B scanner (Axon Instruments). Fluorescence intensity raw data were obtained from scanned images of arrays using NimbleScan™ 2.0 extraction software (NimbleGen Systems).

source_name: Klf5 ChIP in E14TG2a mouse embryonic stem cells

label_protocol: Each of test and reference DNA samples (1 μg) was denatured in the presence of 5′ Cy3-or Cy5-labeled random nonamers (TriLink Biotechnologies) and incubated with 100U (exo-) Klenow fragment (New England Biolabs) and dNTP mixture [6 mM each in TE buffer (10 mM Tris, 1 mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reactions were terminated by addition of 0.5 M EDTA, pH 8.0, precipitated with isopropanol, and resuspended in water. Then, 13 μg Cy5-labeled ChIP sample and 13 μg Cy3-labeled total sample were mixed, dried down, and resuspended in 40 μL hybridization buffer (NimbleGen Systems).

growth_protocol: Mouse embryonic stem Cells were cross-linked with 1% formaldehyde for 10 min at    room temperature and formaldehyde was then inactivated by the addition of 125 mM glycine.

extract_protocol: Cells were cross-linked with 1% formaldehyde for 10 min at room temperature and formaldehyde was then inactivated by the addition of 125 mM glycine. Chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using anti-Klf2 (amino-acids 90-255 of mouse Klf2 raised in rabbit), anti-Klf4 (amino-acids 1-320 of mouse Klf4 raised in rabbit), anti-Klf5 (amino-acids 1-320 of  mouse Klf5 raised in rabbit), anti-p53 (sc-100, Santa Cruz). Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.

tag: antibody for Klf5

source_name: E14TG2a mouse embryonic stem cells (ATCC, CRL-1821)

tag: reference


title: Aoryzae_Glucose_rep3

value: A. oryzae A1560. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:3.


title: Aoryzae_Glucose_rep2

value: A. oryzae A1560. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:2.


title: p53 ChIP Biol. rep. 3

description:
108187
p53 ChIP-chip in E14 cells using p53 antibody

source_name: p53 ChIP in E14TG2a mouse embryonic stem cells

tag: antibody for p53


title: S_melongena_control_vs_salt_96h_2

tag: Solanum melongena, leaves, Abiotic stress


title: Aniger_Xylose_rep3

data_processing: Affymetrix CEL-data files were preprocessed using the statistical language and environment R, version 2.5. The probe intensities were normalised for background using the robust multiarray average (RMA) method (Irizarry, 2003) using only perfect match (PM) probes. Normalization was performed subsequently using the quantiles algorithm (Bolstad, 2003). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

organism: Aspergillus niger

source_name: A. niger mycelium grown on a xylose medium

value: A. niger BO-1. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:3.


title: H1 (R3 replicate)

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: see the NimbleGen website

hyb_protocol: see the NimbleGen website

scan_protocol: see the NimbleGen website

data_processing: Genomic data analysis was performed using the statistical programming language R (R Development Core Team) (5).  All data processing scripts are available upon request.  The log2 ratio data from each of the arrays was subjected to lowess normalization.

source_name: input

label_protocol: see the NimbleGen website

extract_protocol: MCF-7 breast cancer cells were grown to ~80 to 90% confluence, cross-linked with 1% paraformaldehyde in PBS for 10 min. at 37°C, and quenched in 125 mM glycine in PBS for 5 min at 4°C.  The cells were collected by centrifugation and sonicated in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail) to generate chromatin fragments of ~500 bp in length.  The material was clarified by centrifugation, diluted 10-fold in dilution buffer (0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail), and pre-cleared with protein A-agarose beads.  The pre-cleared, chromatin-containing supernatant was extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol.  The DNA was then amplified by LM-PCR.

tag: MCF-7 cells ChIP input

source_name: H1 IP

extract_protocol: MCF-7 breast cancer cells were grown to ~80 to 90% confluence, cross-linked with 1% paraformaldehyde in PBS for 10 min. at 37°C, and quenched in 125 mM glycine in PBS for 5 min at 4°C.  The cells were collected by centrifugation and sonicated in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail) to generate chromatin fragments of ~500 bp in length.  The material was clarified by centrifugation, diluted 10-fold in dilution buffer (0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail), and pre-cleared with protein A-agarose beads.  The pre-cleared, chromatin-containing supernatant was used in immunoprecipitation reactions with antibodies against H1.  The immunoprecipitated genomic DNA was cleared of protein and residual RNA by digestion with proteinase K and  RNase H, respectively.  The DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol.

tag: MCF-7 cell H1 IP


title: S_tuberosum_control_vs_salt_24h_2

tag: Solanum tuberosum, leaves, Abiotic stress


title: Klf5 ChIP Biol. rep. 2

description:
108880
Klf5 ChIP-chip in E14 cells using Klf5 antibody


title: Nanog ChIP Biol. rep. 2

description:
110925
Nanog ChIP-chip in E14 cells using nanog antibody

source_name: Nanog ChIP in E14TG2a mouse embryonic stem cells

tag: antibody for Nanog

source_name: Input DNA E14TG2a mouse embryonic stem cells (ATCC, CRL-1821)


title: Aniger_Xylose_rep2

value: A. niger BO-1. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:2.


title: Aoryzae_Xylose_rep2

source_name: A. oryzae mycelium grown in a xylose medium

value: A. oryzae A1560. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:2.


title: p53 ChIP Biol. rep. 1

description:
107994
p53 ChIP-chip in E14 cells using p53 antibody


title: Klf4 ChIP Biol. rep. 1

description:
110571
Klf4 ChIP-chip in E14 cells using Klf4 antibody

source_name: Klf4 ChIP in E14TG2a mouse embryonic stem cells

tag: antibody for Klf4


title: H1 (M replicate)

description: see the NimbleGen website

tag: MCF-7 cell ChIP input


title: H3 (R3 replicate)

description: see the NimbleGen website

data_processing: Genomic data analysis was performed using the statistical programming language R (R Development Core Team) (5). All data processing scripts are available upon request. The log2 ratio data from each of the arrays was subjected to lowess normalization.

extract_protocol: MCF-7 breast cancer cells were grown to ~80 to 90% confluence, cross-linked with 1% paraformaldehyde in PBS for 10 min. at 37°C, and quenched in 125 mM glycine in PBS for 5 min at 4°C. The cells were collected by centrifugation and sonicated in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail) to generate chromatin fragments of ~500 bp in length. The material was clarified by centrifugation, diluted 10-fold in dilution buffer (0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail), and pre-cleared with protein A-agarose beads. The pre-cleared, chromatin-containing supernatant was extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol. The DNA was then amplified by LM-PCR.

source_name: H3 IP

extract_protocol: MCF-7 breast cancer cells were grown to ~80 to 90% confluence, cross-linked with 1% paraformaldehyde in PBS for 10 min. at 37°C, and quenched in 125 mM glycine in PBS for 5 min at 4°C. The cells were collected by centrifugation and sonicated in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail) to generate chromatin fragments of ~500 bp in length. The material was clarified by centrifugation, diluted 10-fold in dilution buffer (0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail), and pre-cleared with protein A-agarose beads. The pre-cleared, chromatin-containing supernatant was used in immunoprecipitation reactions with antibodies against H1. The immunoprecipitated genomic DNA was cleared of protein and residual RNA by digestion with proteinase K and RNase H, respectively. The DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol.

tag: MCF-7 cell H3 IP


title: Klf4 ChIP Biol. rep. 3

description:
108000
Klf4 ChIP-chip in E14 cells using Klf4 antibody


title: Aniger_Xylose_rep1

value: A. niger BO-1. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:1.


title: Klf4 ChIP Biol. rep. 2

description:
108001
Klf4 ChIP-chip in E14 cells using Klf4 antibody


title: Klf2 ChIP Biol. rep. 2

description:
108888
Klf2 ChIP-chip in E14 cells using Klf2 antibody

source_name: Klf2 ChIP in E14TG2a mouse embryonic stem cells

tag: antibody for Klf2


title: Nanog ChIP Biol. rep. 1

description:
102398
Nanog ChIP-chip in E14 cells using nanog antibody


title: Klf2 ChIP Biol. rep. 1

description:
109740
Klf2 ChIP-chip in E14 cells using Klf2 antibody


title: Klf5 ChIP Biol. rep. 1

description:
108190
Klf5 ChIP-chip in E14 cells using Klf5 antibody


title: S_tuberosum_control_vs_salt_12h_2


title: Aniger_Glucose_rep3

source_name: A. niger mycelium grown on a glucose medium

value: A. niger BO-1. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:3.


title: Aniger_Glucose_rep2

value: A. niger BO-1. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:2.


title: PARP (R3 replicate)

description: see the NimbleGen website

source_name: PARP IP

tag: MCF-7 cell PARP IP


title: Anidulans_Xylose_rep2

organism: Aspergillus nidulans

source_name: A. nidulans mycelium grown on a xylose medium

value: A. nidulans A4. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 5.5. Sampling time:mid-late exponential phase. Replicate no:2.


title: p53 ChIP Biol. rep. 2

description:
107998
p53 ChIP-chip in E14 cells using p53 antibody


title: Anidulans_Xylose_rep1

value: A. nidulans A4. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 5.5. Sampling time:mid-late exponential phase. Replicate no:1.


title: Anidulans_Glucose_rep2

source_name: A. nidulans mycelium grown on a glucose medium

value: A. nidulans A4. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 5.5. Sampling time:mid-late exponential phase. Replicate no:2.


title: Aniger_Glucose_rep1

value: A. niger BO-1. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:1.


title: Anidulans_Xylose_rep3

value: A. nidulans A4. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 5.5. Sampling time:mid-late exponential phase. Replicate no:3.


title: Klf2 ChIP Biol. rep. 3

description:
109727
Klf2 ChIP-chip in E14 cells using Klf2 antibody


title: Anidulans_Glucose_rep3

value: A. nidulans A4. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 5.5. Sampling time:mid-late exponential phase. Replicate no:3.


title: Aoryzae_Xylose_rep3

value: A. oryzae A1560. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:3.


title: Nanog ChIP Biol. rep. 3

description:
110926
Nanog ChIP-chip in E14 cells using nanog antibody


title: PARP (R replicate)

description: see the NimbleGen website


title: Aoryzae_Xylose_rep1

value: A. oryzae A1560. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:1.


title: Anidulans_Glucose_rep1

value: A. nidulans A4. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 5.5. Sampling time:mid-late exponential phase. Replicate no:1.


title: H3K9Ac ChIP HRG 2hr, chip 14 of 14

status: Public on Feb 08 2008

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

description: Input and ChIP DNA was amplified by LM-PCR method.

hyb_protocol: Biotinylated DNA was hybridized to the Affymetrix tiled, human whole genome arrays, washed, and stained according to manufacturer's instructions.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Cel files were generated using Affymetrix's GCOS software and Analyzed using the Affymetrix TAS analysis software.

source_name: H3K9Ac ChIP, HRG 2hr, MCF-7

label_protocol: Amplified ChIP (or matching input) DNA was fragmented with DNase I, and then biotin-labeled using terminal transferase (TdT).

growth_protocol: Prior to the growth factor (GF) treatment, cells were serum starved for 16-18 hours with serum-free DMEM medium and incubated at 37C/5% CO2. The medium was again changed 2 hr prior to the GF treatment.

extract_protocol: The MCF-7 cell were cross-linked with 1% formaldehyde for 10 min followed by addition of glycine in PBS at a final concentration of 125 mM. The cross-linked cells were collected by centrifugation and washed twice in cold 1 x PBS. The cells were sonicated for 6 min with a Branson 450 Sonicator to shear the chromatin. Acetylated histone H3 (Lys9)-DNA complexes were immunoprecipitated with an anti-acetyl histone H3 (Lys9) antibody(#07-352,Upstate) overnight at 4C on a rotater. Immunoprecipitation samples were incubated with magnetic beads/Protein G (Dynal) for 1 hour at 4C followed by one wash with each of: 1. Low salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris.HCl (pH8.1), 150mM NaCl) 2. High salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris.HCl (pH8.1), 500mM NaCl) 3. LiCl wash buffer (10mM Tris.HCl(pH8.1), 0.25M LiCl, 0.5% NP-40, 0.5% Sodium deoxycholate, 1mM EDTA, and two washes with TE buffer. The antibody- Acetylated histone H3 (Lys9) -DNA complexes were eluted from the magnetic beads by addition of 1% SDS and 100 mM NaHCO3, and vortexing for 60 min at RT. The supernatants were incubated for 3.5 hours at 65C to reverse the cross-linking, followed by incubation for further 30 minutes at 65$B!k(BC in the presence of 20mg/ml RNaseA. To purify the DNA, proteinase K solution was added to a final concentration of 100mg/ml, and the samples were incubated overnight at 45C followed by a phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation to recover the DNA.

treatment_protocol: Before treatments, medium were changed with serum-free medium again and incubated at 37C for 2 hours. Followed by incubation, added each ligand and incubated for each time.

tag: Cell line

value: MCF-7 (Obtained from ATCC (American Type Culture Collection))

tag: Organ

value: mammary gland; breast

tag: Cell type

value: epithelial

tag: Disease

value: adenocarcinoma

tag: Derived from metastatic site

value: pleural effusion

tag: Age

value: 69 years adult

tag: Gender

value: female

tag: Ethnicity

value: Caucasian

source_name: WCE control, HRG 2hr, MCF-7


title: H3K9Ac ChIP HRG 0hr, chip 14 of 14

source_name: H3K9Ac ChIP, HRG 0hr, MCF-7

source_name: WCE control, HRG 0hr, MCF-7


title: RNA HRG 2hr, chip 13 of 14

description: Tanscript mapping for total RNA.

source_name: RNA, HRG 2hr, MCF-7

label_protocol: Double-stranded cDNA was fragmented with DNase I, and then biotin-labeled using terminal transferase (TdT).

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) and then purified using QIAGEN Rneasy kit. 15ug total RNA were reverse transcribed by using SuperScript II reverse transcriptase (Invitrogen). The first strand cDNA was used for the second-strand cDNA synthesis in the presence of E. coli DNA Ligase, E. coli DNA polymerase I, and E. coli RNAse H. Upon treatment with RNAse H (Epicentre) and RNAse A/T1 (Ambion), double-stranded cDNA was extracted using QIAquick PCR purification kit (Qiagen).


title: RNA HRG 0hr, chip 12 of 14

description: Tanscript mapping for total RNA.

source_name: RNA, HRG 0hr, MCF-7


title: RNA HRG 0hr, chip 08 of 14

description: Tanscript mapping for total RNA.


title: RNA HRG 0hr, chip 13 of 14

description: Tanscript mapping for total RNA.


title: H3K9Ac ChIP HRG 0hr, chip 13 of 14


title: H3K9Ac ChIP HRG 0hr, chip 11 of 14


title: RNA HRG 2hr, chip 14 of 14

description: Tanscript mapping for total RNA.


title: H3K9Ac ChIP HRG 2hr, chip 02 of 14


title: H3K9Ac ChIP HRG 0hr, chip 08 of 14


title: H3K9Ac ChIP HRG 2hr, chip 12 of 14


title: RNA HRG 2hr, chip 06 of 14

description: Tanscript mapping for total RNA.


title: RNA HRG 0hr, chip 07 of 14

description: Tanscript mapping for total RNA.


title: H3K9Ac ChIP HRG 2hr, chip 08 of 14


title: H3K9Ac ChIP HRG 2hr, chip 11 of 14


title: RNA HRG 2hr, chip 02 of 14

description: Tanscript mapping for total RNA.


title: RNA HRG 0hr, chip 02 of 14

description: Tanscript mapping for total RNA.


title: RNA HRG 2hr, chip 12 of 14

description: Tanscript mapping for total RNA.


title: H3K9Ac ChIP HRG 0hr, chip 12 of 14


title: RNA HRG 2hr, chip 07 of 14

description: Tanscript mapping for total RNA.


title: H3K9Ac ChIP HRG 0hr, chip 07 of 14


title: RNA HRG 2hr, chip 11 of 14

description: Tanscript mapping for total RNA.


title: RNA HRG 0hr, chip 14 of 14

description: Tanscript mapping for total RNA.


title: H3K9Ac ChIP HRG 2hr, chip 07 of 14


title: Xoo_50pMol_LowPMT_Rep2

city: Davis

first: Malinee

last: Sriariyanun

address: 451 East Health Sciences Drive

department: Plant Pathology

institute: University of California, Davis

description: Technical replicate 2 of 2

hyb_protocol: Probes were resuspended in 28 ul of preheated 1X hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) at 42°C. To block non-specific hybridization, add 2 ul salmon sperm DNA (10 ug/ul) into the solution. Labeled probes were denatured by heating mixture at 95 °C for 3 mins and snap cool on ice for 30 seconds. Probed were applied into injector to hybridize with printed slides. Samples were hybridized for 16 hours (42°C in humidified water bath), sequentially washed with 42°C preheated low stringency wash buffer (2x SSC and 0.1% SDS) 5 minutes, then washed with high stringency wash buffer (0.1x SSC and 0.1% SDS) 5 minutes. Slides were transferred to 0.1x SSC buffer and agitated for 5 mins (2times) and dried under N2 (5 min, 30C). Slides were kept under N2 until scanning.

scan_protocol: Hybridized microarray slides were imaged using a GenePix 4000B dual laser microarray scanner (Axon Instruments, USA) at 5 µm resolution. Slides were imaged using 100% laser power for both lasers (532 and 635 nm) and scanned twice using a high and low power of the scanner photomultiplicator settings (PMT).

data_processing: All images were processed using GenePix software (Axon Instruments, USA) for element identification and quantitation. The metadata associated with the hybridizations, along with the “raw” intensities obtained from the GenePix quantitation.

organism: Xanthomonas oryzae pv. oryzae KACC 10331

source_name: Total RNA from Xoo phoP knockout mutant cultured in PSB labeled with Cyanine-5

label_protocol: Qualified RNA 20 ug was mixed with random hexamer and then was preheated at 70 °C 15 mins. Labeling mixture (final concentration containing 1X buffer, 6.7 mM DTT, 40 Unit of RNasin, 400 Unit of superscript III reverse transcriptase, 0.5 mM of dNTP-allyl-amino dUTP mixture [0.5mM each of dATP, cCTP, dGTP; 0.35mM aa-dUTP; 0.15mM dTTP]) was mixed and incubated at 25C  for 10min followed at 42C 2 hr. To eliminate residual RNA template, 30 ul mixture was mixed with3 μl of 2.5 N NaOH and incubated at 37C for 15 min and then neutralize solution by adding 15 μl of 2 M HEPES. Unincorporated primers and nucleotides were removed using the Zymo research kit according to the manufacturer’s protocol (Genetix, UK) and the purified amino allyl-modified cDNA was resuspended in 30 μl of 0.1 M Sodium Bicarbonate (pH 9.0). The amino allyl-modified cDNA was used to re-suspend lyophilized Cy3 or Cy5 fluorescent dye and incubated for 1 hr at room temperature in the dark. The reaction was quenched by adding 15 μl of 4M Hydroxylamine (15 min). The dye coupled cDNA was then purified by using the Zymo research Kit.

growth_protocol: Cells were grown at 28 0C with shaking at 200 rpm, in nutrient-rich PSB media containing 10 g of peptone, 10 g of sucrose, 1 g of L-glutamic acid (monosodium salt)(Shen et al 2002).

extract_protocol: A bacterial 1010-cells culture was harvested in a centrifuge tube and cell pellets were frozen in -80 0C immediately until RNA isolation. RNA was isolated using Trizol reagent (Invitrogen Corp.) and protocol is described in manufacturer manual. The RNA samples were treated with DNaseI (10 units, Promega Corp., Madison, WI, U.S.A.) for 30 mins at 37 0C, followed by column purification using RNeasy midi kit (Qiagen, Germantown, MD, U.S.A.). The quality of RNA was determined by gel electrophoresis on a 1% agarose gel and verified visually on a Nanodrop, or by Agilent 2100 Bioanalyzer (Agilent Technologies). The quantity of total RNA and mRNA were determined by measuring the absorbance at 260nm and 280nm. In addition, the level of protein contamination in the RNA was measured by using A260/A280 ratio.

treatment_protocol: Bacterial cells were cultured in PSB media until OD600 is 0.5. Cells were washed twice and harvested.

tag: cultured in PSB until OD =0.5

source_name: Total RNA from Xoo rpfC knockout mutant cultured in PSB labeled with Cyanine-3


title: Xoo_40pMol_LowPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_50pMol_LowPMT_Rep1

description: Technical replicate 1 of 2

source_name: Total RNA from Xoo rpfC knockout mutant cultured in PSB labeled with Cyanine-5

source_name: Total RNA from Xoo phoP knockout mutant cultured in PSB labeled with Cyanine-3


title: Xoo_10pMol_LowPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_20pMol_LowPMT_Rep2

description: Technical replicate 2 of 2


title: H3K9Ac ChIP HRG 2hr, chip 13 of 14


title: Xoo_20pMol_LowPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_40pMol_LowPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_30pMol_LowPMT_Rep2

description: Technical replicate 2 of 2


title: RNA HRG 2hr, chip 08 of 14

description: Tanscript mapping for total RNA.


title: RNA HRG 0hr, chip 06 of 14

description: Tanscript mapping for total RNA.


title: Xoo_10pMol_LowPMT_Rep1

description: Technical replicate 1 of 2


title: RNA HRG 0hr, chip 11 of 14

description: Tanscript mapping for total RNA.


title: H3K9Ac ChIP HRG 0hr, chip 02 of 14


title: Xoo_40pMol_HighPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_50pMol_HighPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_20pMol_HighPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_30pMol_HighPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_40pMol_HighPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_20pMol_HighPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_30pMol_HighPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_50pMol_HighPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_10pMol_HighPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_44C_LowPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_52C_LowPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_42C_LowPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_52C_LowPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_44C_LowPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_10pMol_HighPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_48C_LowPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_48C_LowPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_42C_LowPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_52C_HighPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_48C_HighPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_52C_HighPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_42C_HighPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_44C_HighPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_48C_HighPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_44C_HighPMT_Rep2

description: Technical replicate 2 of 2


title: Xoo_30pMol_LowPMT_Rep1

description: Technical replicate 1 of 2


title: Xoo_42C_HighPMT_Rep1

description: Technical replicate 1 of 2


title: Xanthomonas oryzae pv. oryzicola cultured in two different media, PSB and XOM2 replicate3, dye swap

description: Biologiacl replicate3 of 3

organism: Xanthomonas oryzae pv. oryzicola BLS256

source_name: Total RNA from Xoc cultured in PSB labeled with Cyanine-5

growth_protocol: Cells were grown at 28 0C with shaking at 200 rpm, in nutrient-rich PSB media containing 10 g of peptone, 10 g of sucrose, 1 g of L-glutamic acid (monosodium salt)(Shen et al 2002). Modified minimal XOM2, hrp-inducing, media (Tsuge et al 2002) consisted of 1% xylose sugar, 670 uM D,L-methionine, 10mM sodium L(+)-glutamate, 14.7 mM KH2PO4, 40 uM MnSO4, 240 uM Fe(III).EDTA and 5 mM MgCl2, pH 6.5.

treatment_protocol: Bacterial cells were cultured in PSB media until OD600 is 0.2, washed twice, and immediately transfer into XOM2 media for 16 hrs to test effect of XOM2 media. Cells were washed twice and harvested. Three separated cultures were used for each microarray studies

tag: cultured in PSB until OD =0.2 and keep incubated more 16 hrs

source_name: Total RNA from Xoc cultured in XOM2 labeled with Cyanine-3.

tag: cultured in PSB until OD =0.2 and incubated in XOM2 media more 16 hrs


title: MCF7_Nsp_EA

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

description: Genomic DNA was used for identifying variable copy number regions in the genome.

hyb_protocol: Standard Affymetrix Protocol was used.

scan_protocol: A GeneChip was scanned using the GeneChip Scanner 3000 7G with default parameter.

data_processing: Genotyes reported by dynamic modeling algorithm.

source_name: breast epithelial cell, adherent

label_protocol: Standard Affymetrix Protocol was used.

extract_protocol: DNA extraction was proceeded by the following reagent, Wizard genomic DNA purification kit, Promega, according to the instruction.

value: MCF-7 (Obtained from ATCC (American Type Culture Collection)), Organ:mammary gland; breast, Cell type:epithelial, Disease:adenocarcinoma, Derived from metastatic site:pleural effusion, Age:69 years adult, Gender:female, Ethnicity:Caucasian


title: H3K9Ac ChIP HRG 0hr, chip 06 of 14


title: Xanthomonas oryzae pv. oryzicola cultured in two different media, PSB and XOM2 replicate2, dye swap

description: Biologiacl replicate2 of 3


title: Xanthomonas oryzae pv. oryzicola cultured in two different media, PSB and XOM2 replicate3

description: Biologiacl replicate3 of 3

source_name: Total RNA from Xoc cultured in XOM2 labeled with Cyanine-5.

source_name: Total RNA from Xoc cultured in PSB labeled with Cyanine-3


title: Xanthomonas oryzae pv. oryzicola cultured in two different media, PSB and XOM2 replicate1

description: Biologiacl replicate1 of 3


title: H3K9Ac ChIP HRG 2hr, chip 06 of 14


title: H3K9Ac ChIP HRG 2hr, chip 05 of 14


title: Xanthomonas oryzae pv. oryzae cultured in two different media, PSB and XOM2 replicate3, dye swap

description: Biologiacl replicate3 of 3

source_name: Total RNA from Xoo cultured in PSB labeled with Cyanine-5

source_name: Total RNA from Xoo cultured in XOM2 labeled with Cyanine-3.


title: Xanthomonas oryzae pv. oryzae cultured in two different media, PSB and XOM2 replicate3

description: Biologiacl replicate3 of 3

source_name: Total RNA from Xoo cultured in XOM2 labeled with Cyanine-5.

source_name: Total RNA from Xoo cultured in PSB labeled with Cyanine-3


title: RNA HRG 0hr, chip 04 of 14

description: Tanscript mapping for total RNA.


title: Xanthomonas oryzae pv. oryzicola cultured in two different media, PSB and XOM2 replicate1, dye swap

description: Biologiacl replicate1 of 3


title: Xanthomonas oryzae pv. oryzae cultured in two different media, PSB and XOM2 replicate2, dye swap

description: Biologiacl replicate2 of 3


title: RNA HRG 2hr, chip 05 of 14

description: Tanscript mapping for total RNA.


title: RNA HRG 2hr, chip 04 of 14

description: Tanscript mapping for total RNA.


title: Xanthomonas oryzae pv. oryzicola cultured in two different media, PSB and XOM2 replicate2

description: Biologiacl replicate2 of 3


title: RNA HRG 0hr, chip 05 of 14

description: Tanscript mapping for total RNA.


title: H3K9Ac ChIP HRG 2hr, chip 04 of 14

source_name: H3K9Ac ChIP, HRG 2hr, MCF-7

source_name: WCE control, HRG 2hr, MCF-7


title: H3K9Ac ChIP HRG 0hr, chip 04 of 14

source_name: H3K9Ac ChIP, HRG 0hr, MCF-7

source_name: WCE control, HRG 0hr, MCF-7


title: Xanthomonas oryzae pv. oryzae cultured in two different media, PSB and XOM2 replicate2

description: Biologiacl replicate2 of 3


title: H3K9Ac ChIP HRG 0hr, chip 05 of 14


title: ler-DMEM-rep2

status: Public on Feb 01 2008

city: Suita

first: Toru

last: Tobe

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine

institute: Osaka University

description: Bacteria were grown in DMEM to logarithmic phase

hyb_protocol: The labeled cDNA probes were then dissolved in water, mixed with hybridization buffer (5x SSC, 0.5% SDS, 1 mg/ml yeast RNA), and heat-denatured. Hybridization was carried out at 50 °C for 16 h. Slides were washed with 2x SSC containing 0.2% SDS at 50 °C twice, then with 0.2x SSC containing 0.2% SDS at 20 °C twice.

scan_protocol: The slides were scanned for fluorescence intensity using a GMS 418 array scanner (Genetic Microsystems), and the information was converted to 16-bit image files.

data_processing: The signal density of each spot was quantified using IMAGENE software (BioDiscovery). We first corrected the intensity of each spot by subtracting the local background. The mean values of the negative control spots containing yeast oligo DNA and the spots containing spotting buffer alone were determined, with the standard deviation (SD).

organism: Escherichia coli O157:H7 str. Sakai

source_name: Total RNA from wild type EHEC harboring pGEM vector labeled with Cy5.

label_protocol: Fluorescent-labeled cDNA probes were synthesized in a reverse-transcriptase reaction with AMVXL (XL Life Science) and Cy3-dUTP or Cy5-dUTP (Amersham Pharmacia) and the mixture of specific primers made from the total EHEC RNA. The specific primer was a 16-mer oligo DNA that was anti-sense to the downstream sequence of the spotted oligo DNA for each gene. Labeled cDNA probes were purified by Centri-sep (Princeton Separations), phenol-chloroform extraction, and ethanol precipitation.

growth_protocol: Bacteria were grown in LB or DMEM at 37 °C to logarithmic phase.

extract_protocol: Total RNA was extracted from bacteria harvested from 10 ml culture by using TRI reagent (Sigma) according to the manufacturer’s instruction.

tag: Enterohaemorrhagic E. coli O157:H7 Sakai harboring pGEM plasmid

source_name: Total RNA from ler mutant of EHEC harboring pGEM vector labeled with Cy3.

tag: Enterohaemorrhagic E. coli O157:H7 Sakai ler mutant harboring pGEM plasmid


title: ler-DMEM-rep1

source_name: Total RNA from wild type EHEC harboring pGEM vector labeled with Cy3.

source_name: Total RNA from ler mutant of EHEC harboring pGEM vector labeled with Cy5.


title: Xanthomonas oryzae pv. oryzae cultured in two different media, PSB and XOM2 replicate1

description: Biologiacl replicate1 of 3


title: pchABC-DMEM-rep2

source_name: Total RNA from pchABC mutant of EHEC harboring pGEM vector labeled with Cy3.

tag: Enterohaemorrhagic E. coli O157:H7 Sakai pchABC mutant harboring pGEM plasmid


title: PchA-high-DMEM-rep2

source_name: Total RNA from wild type EHEC harboring pGEM-PchA labeled with Cy3.

tag: Enterohaemorrhagic E. coli O157:H7 Sakai harboring pGEM-Pch plasmid


title: pchABC-DMEM-rep1

source_name: Total RNA from pchABC mutant of EHEC harboring pGEM vector labeled with Cy5.


title: ler-PchA-high-DMEM-rep1

source_name: Total RNA from ler mutant of EHEC harboring pGEM-pchA labeled with Cy5.

tag: Enterohaemorrhagic E. coli O157:H7 Sakai ler mutant harboring pGEM-pchA plasmid


title: ler-PchA-high-DMEM-rep2

source_name: Total RNA from ler mutant of EHEC harboring pGEM-pchA labeled with Cy3.


title: pchABC-Ler-high-DMEM-rep2

source_name: Total RNA from pchABC mutant of EHEC harboring pGEM-ler labeled with Cy3.

tag: Enterohaemorrhagic E. coli O157:H7 Sakai pchABC mutant harboring pGEM-ler plasmid


title: PchA-high-DMEM-rep1

source_name: Total RNA from wild type EHEC harboring pGEM-PchA labeled with Cy5.


title: Ler-high-DMEM-rep2

source_name: Total RNA from wild type EHEC harboring pGEM-ler labeled with Cy3.

tag: Enterohaemorrhagic E. coli O157:H7 Sakai harboring pGEM-ler plasmid


title: pchABC-Ler-high-DMEM-rep1

source_name: Total RNA from pchABC mutant of EHEC harboring pGEM-ler labeled with Cy5.


title: H3K9Ac ChIP HRG 2hr, chip 10 of 14

source_name: H3K9Ac ChIP, HRG 2hr, MCF-7

tag: Cell line

tag: Organ


title: pchABC-Ler-high-LB-rep2

description: Bacteria were grown in LB to logarithmic phase


title: pchAB-Ler-high-LB-rep2

source_name: Total RNA from pchAB mutant of EHEC harboring pGEM vector labeled with Cy5.

tag: Enterohaemorrhagic E. coli O157:H7 Sakai pchAB mutant harboring pGEM plasmid

source_name: Total RNA from pchAB mutant of EHEC harboring pGEM-ler labeled with Cy3.

tag: Enterohaemorrhagic E. coli O157:H7 Sakai pchAB mutant harboring pGEM-ler plasmid


title: pchABC-Ler-high-LB-rep1


title: Ler-high-DMEM-rep1

source_name: Total RNA from wild type EHEC harboring pGEM-ler labeled with Cy5.


title: pchAB-Ler-high-LB-rep1

source_name: Total RNA from pchAB mutant of EHEC harboring pGEM vector labeled with Cy3.

source_name: Total RNA from pchAB mutant of EHEC harboring pGEM-ler labeled with Cy5.


title: ler-Pch-high-LB-rep1

source_name: Total RNA from ler mutant of EHEC harboring pGEM vector labeled with Cy3.


title: ler-Pch-high-LB-rep2

source_name: Total RNA from ler mutant of EHEC harboring pGEM vector labeled with Cy5.


title: RNA HRG 0hr, chip 10 of 14

description: Tanscript mapping for total RNA.

source_name: RNA, HRG 0hr, MCF-7

tag: Cell type

tag: Disease

tag: Derived from metastatic site

tag: Age


title: ler-LB-rep2

source_name: Total RNA from wild type EHEC harboring pGEM vector labeled with Cy5.


title: Pch-high-LB-rep2

source_name: Total RNA from wild type EHEC harboring pGEM-PchA labeled with Cy3.


title: pchABC-LB-rep2

source_name: Total RNA from pchABC mutant of EHEC harboring pGEM vector labeled with Cy3.


title: H3K9Ac ChIP HRG 0hr, chip 10 of 14

source_name: H3K9Ac ChIP, HRG 0hr, MCF-7

tag: Gender

tag: Ethnicity

source_name: WCE control, HRG 0hr, MCF-7


title: pchABC-LB-rep1

source_name: Total RNA from wild type EHEC harboring pGEM vector labeled with Cy3.

tag: Enterohaemorrhagic E. coli O157:H7 Sakai harboring pGEM plasmid

source_name: Total RNA from pchABC mutant of EHEC harboring pGEM vector labeled with Cy5.


title: Pch-high-LB-rep1

source_name: Total RNA from wild type EHEC harboring pGEM-PchA labeled with Cy5.


title: RNA HRG 2hr, chip 10 of 14

description: Tanscript mapping for total RNA.

source_name: RNA, HRG 2hr, MCF-7


title: RNA HRG 0hr, chip 01 of 14

description: Tanscript mapping for total RNA.


title: Ler-high-LB-rep2

source_name: Total RNA from wild type EHEC harboring pGEM-ler labeled with Cy3.


title: Ler-high-LB-rep1


title: RNA HRG 2hr, chip 03 of 14

description: Tanscript mapping for total RNA.


title: Brain_ProtocolG_rep2

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

description: Samples labeling and hybridization day 1, replicate 2

hyb_protocol: Affymetrix GeneChip®  Human Gene 1.0 ST arrays were hybridized to 11 mg of labeled, amplified cDNA, washed, stained and scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

source_name: Ambion Human Brain Reference RNA (Catalog #6050)

label_protocol: 100ng of total RNA were amplified and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

extract_protocol: total RNA extracted


title: Universal_ProtocolG_rep3

description: Samples labeling and hybridization day 2, replicate 1

source_name: Stratagene Universal Human Reference RNA (Catalog #740000)


title: Universal_ProtocolG_rep4

description: Samples labeling and hybridization day 2, replicate 2


title: Brain_ProtocolG_rep1

description: Samples labeling and hybridization day 1, replicate 1


title: Universal_ProtocolG_rep1


title: Brain_ProtocolG_rep4


title: Brain_ProtocolG_rep3


title: Universal_ProtocolG_rep2


title: Pre inoculation__09.13.04 39 HG Focus

first: Michael

last: Hornsby

address: County Road 98 and Hutchison Drive

description: Stomach Biopsy pre inoculation control

hyb_protocol: Hybridization to Affymetrix HumanFL (HuFL) chips were done according to the recommendations of the manufacturer (Affymetrix, Santa Clara, Calif.).

scan_protocol: Arrays were scanned with an Agilent GeneArray scanner according to manufacturer recommentations.

data_processing: Data were collated and scaled in Microarray Suite 5.0 (MAS 5.0, Affymetrix, Santa Clara, CA). Of 8,793 probe sets, approximately 5,000 passed filtering and were analyzed with BRB ArrayTools (version 3.3). Triple comparisons were performed (Control, WT, KO) for the data at weeks 1 and 13 using an F statistic, with p<0.01.

organism: Macaca mulatta

source_name: Stomach Biopsy pre inoculation control

label_protocol: Labeling to Affymetrix HumanFL (HuFL) chips were done according to the recommendations of the manufacturer (Affymetrix, Santa Clara, Calif.). Briefly, biotin-labeled RNA was prepared by first reverse transcribing the RNA into double-stranded cDNA (Superscript II; Invitrogen Life Technologies, Carlsbad, Calif.) with an oligo(dT)24 primer containing a T7 RNA polymerase promoter. Then an in vitro transcription reaction was carried out (Enzo High Yield RNA Transcript Labeling kit; Enzo Biochem, Farmingdale, N.Y.) during which biotin-labeled ribonucleotides were incorporated into the cRNA followed by fragmentation of cRNA by heating to 94°C for 35 min.

extract_protocol: Ten gastric biopsy specimens were pooled, ground with a glass pestle in Trizol reagent (Sigma), and RNA was isolated according to protocols provided by the manufacturer. All RNA samples were treated with DNase I (Roche Applied Science, Mannheim, Germany), purified with an RNeasy kit (Qiagen, Valencia, Calif.) according to the RNA cleanup protocol, and resuspended in molecular-biology-grade water (BioWhittaker, Rockland, Maine).

tag: SPF Macaque stomach antrum and corpus pooled biopsy


title: Pre inoculation__09.13.04 38 HG Focus

description: Stomach Biopsy pre inoculation control


title: Pre inoculation__09.13.04 37 HG Focus

description: Stomach Biopsy pre inoculation control


title: H3K9Ac ChIP HRG 0hr, chip 09 of 14

organism: Homo sapiens


title: RNA HRG 2hr, chip 09 of 14

description: Tanscript mapping for total RNA.


title: H3K9Ac ChIP HRG 0hr, chip 03 of 14


title: H3K9Ac ChIP HRG 2hr, chip 01 of 14

source_name: H3K9Ac ChIP, HRG 2hr, MCF-7

source_name: WCE control, HRG 2hr, MCF-7


title: H3K9Ac ChIP HRG 2hr, chip 03 of 14


title: H3K9Ac ChIP HRG 0hr, chip 01 of 14


title: RNA HRG 0hr, chip 03 of 14

description: Tanscript mapping for total RNA.


title: Pre inoculation__09.13.04 40 HG Focus

description: Stomach Biopsy pre inoculation control


title: Pre inoculation__09.13.04 12 HG Focus

description: Stomach Biopsy pre inoculation control


title: Xanthomonas oryzae pv. oryzae cultured in two different media, PSB and XOM2 replicate1, dye swap

description: Biologiacl replicate1 of 3

source_name: Total RNA from Xoo cultured in PSB labeled with Cyanine-5

tag: cultured in PSB until OD =0.2 and keep incubated more 16 hrs

source_name: Total RNA from Xoo cultured in XOM2 labeled with Cyanine-3.

tag: cultured in PSB until OD =0.2 and incubated in XOM2 media more 16 hrs


title: Pre inoculation__09.13.04 09 HG Focus

description: Stomach Biopsy pre inoculation control


title: Pre inoculation__09.13.04 11 HG Focus

description: Stomach Biopsy pre inoculation control


title: 13 weeks PI_KO_09.13.04 55 HG Focus

description: Stomach Biopsy 13 wks PI with cag PAI KO


title: 13 weeks PI_WT_09.13.04 25 HG Focus

description: Stomach Biopsy 13 wks PI with WT

source_name: Stomach Biopsy 13 wks PI with WT


title: Control__09.14.04 61 HG Focus

description: Stomach Biopsy uninfected control

source_name: Stomach Biopsy uninfected control


title: RNA HRG 2hr, chip 01 of 14

description: Tanscript mapping for total RNA.


title: 13 weeks PI_WT_09.13.04 28 HG Focus

description: Stomach Biopsy 13 wks PI with WT


title: 1 week PI_WT_10.26.04 13 HG Focus

description: Stomach Biopsy 1wk PI with WT

source_name: Stomach Biopsy 1wk PI with WT


title: Control__09.14.04 63 HG Focus

description: Stomach Biopsy uninfected control


title: ler-LB-rep1

source_name: Total RNA from ler mutant of EHEC harboring pGEM vector labeled with Cy5.

tag: Enterohaemorrhagic E. coli O157:H7 Sakai ler mutant harboring pGEM plasmid


title: 13 weeks PI_WT_09.13.04 27 HG Focus

description: Stomach Biopsy 13 wks PI with WT


title: 13 weeks PI_KO_09.13.04 56 HG Focus

source_name: Stomach Biopsy 13 wks PI with cag PAI KO


title: Control__09.14.04 73 HG Focus

description: Stomach Biopsy uninfected control


title: 13 weeks PI_WT_09.13.04 26 HG Focus

description: Stomach Biopsy 13 wks PI with WT


title: Pre inoculation__09.13.04 10 HG Focus

description: Stomach Biopsy pre inoculation control


title: Control__09.14.04 60 HG Focus

description: Stomach Biopsy uninfected control


title: 13 weeks PI_KO_09.13.04 54 HG Focus


title: 1 week PI_WT_10.26.04 14 HG Focus

description: Stomach Biopsy 1wk PI with WT


title: RNA HRG 0hr, chip 09 of 14

description: Tanscript mapping for total RNA.

source_name: RNA, HRG 0hr, MCF-7


title: Control__09.14.04 58 HG Focus

description: Stomach Biopsy uninfected control


title: 1 week PI_WT_10.26.04 15 HG Focus

description: Stomach Biopsy 1wk PI with WT


title: 1 week PI_KO_10.26.04 41 HG Focus

description: Stomach Biopsy 1wk PI with cag PAI KO

source_name: Stomach Biopsy 1wk PI with cag PAI KO


title: 1 week PI_KO_10.26.04 42 HG Focus

description: Stomach Biopsy 1wk PI with cag PAI KO


title: 13 weeks PI_KO_09.13.04 53 HG Focus


title: 1 week PI_WT_10.26.04 16 HG Focus

description: Stomach Biopsy 1wk PI with WT


title: 1 week PI_KO_10.26.04 43 HG Focus

description: Stomach Biopsy 1wk PI with cag PAI KO


title: Control__09.14.04 70 HG Focus

description: Stomach Biopsy uninfected control


title: Brain_ProtocolI_rep4

hyb_protocol: Illumina HumanRef-8 BeadChips were hybridized, washed, stained and scanned according to Illumina’s protocol using the updated wash procedure

scan_protocol: Processed arrays were read using Illumina BeadReader according to the manufacturer's instructions.

data_processing: Data were extracted with Illumina BeadStudio software using background subtraction and cubic spline normalization. Data were then adjusted by shifting the absolute minimum value for each array to be equal to 1; and then log2 transformed.

label_protocol: Targets were prepared from 200 ng total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion, catalog #AMIL1791)


title: Universal_ProtocolI_rep4


title: Brain_ProtocolI_rep3


title: Universal_ProtocolI_rep3


title: Universal_ProtocolI_rep1


title: 1 week PI_KO_10.26.04 44 HG Focus

description: Stomach Biopsy 1wk PI with cag PAI KO


title: Universal_ProtocolI_rep2


title: Brain_ProtocolI_rep1


title: H3K9Ac ChIP HRG 2hr, chip 09 of 14


title: oxyR disruption strains vs. wildtype strains (Cy5/Cy3) rep1

city: Hangzhou

first: Yuejin

last: Hua

state: Zhejiang

address: 268 KaiXuan Road

department: Institute of Nuclear-Agricultural Sciences

country: China

institute: Zhejiang University

description: Biological replicate 1 of 4.

hyb_protocol: Samples were applied to microarrays enclosed in  hybridization chambers. After hybridization, slides were washed sequential. Dye-swap is carried out.

scan_protocol: Scanned on an Genepix 4000B scanner. Images were quantified using Genepix (version 5.0).

data_processing: Prior to channel normalization, microarray outputs were fitered to remove spots of poor signal quality by excluding those data points with a signal mean intensity less than two standard deviations above background in both channels.  LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Limma software was used. Furthemore, the replicate spots on each array were merged to one value using lmFit function within Limma (the merged data is included in a Series supplementary file).

organism: Deinococcus radiodurans

source_name: Total RNA from oxyR disruption strains labeled with Cyanine-5 (red).

label_protocol: 10 µg of total RNA were primed with 9 µg of Hexadeoxyribonucleotide mixture at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

growth_protocol: Cells were grown in an normal condition.

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

tag: oxyR disruption strains are sensitive to hydrogen peroxide

source_name: Total RNA from wildtype strains labeled with Cyanine-3 (green).

tag: Wildtype strains are resistant to hydrogens peroxide


title: oxyR disruption strains vs. wildtype strains (Cy5/Cy3) rep3

description: Biological replicate 3 of 4.


title: wildtype strains vs. oxyR disruption strains(Cy5/Cy3) rep4

description: Biological replicate 4 of 4 with dye-swap.

source_name: Total RNA from wildtype strains labeled with Cyanine-5 (red).

source_name: Total RNA from oxyR disruption strains labeled with Cyanine-3 (green).


title: Brain_ProtocolI_rep2

source_name: Ambion Human Brain Reference RNA (Catalog #6050)


title: wildtype strains vs. oxyR disruption strains(Cy5/Cy3) rep2

description: Biological replicate 2 of 4 with dye-swap.


title: CDC96

city: Ithaca

first: Tavan

last: Janvilisri

state: NY

address: Veterinary Research Tower, College of Veterinary Medicine, Cornell University

institute: Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC96 (human isolate)

hyb_protocol: Genomic DNA from C. difficile 630 was used as a reference DNA for all hybridizations. Dye swaps were performed to test dye-incorporation bias. The microarray slides were prehybridized using a solution containing 25% formamide, 5x SSC (1x SSC consists of 0.15M NaCl with 0.015M sodium citrate), 0.2% (w/v) sarcosyl, and 10 mg/ml bovine serum albumin at 42 °C for 1 h. The slides were then washed in MilliQ water and blow dried using compressed nitrogen gas. Equivalent amounts of labeled probes from reference and tested strains were pooled, lyophilized, and resuspended in 70 µl of hybridization buffer (25% formamide, 5x SSC, 0.2% sodium dodecyl sulfate (SDS), 1 mg/ml salmon sperm DNA, and 1 mg/ml yeast tRNA). The probes were then denatured at 99 °C for 5 min, centrifuged briefly at 13,800 x g and applied to the microarray under a 22 x 60mm LifterSlip (Erie Scientific Co.). Hybridizations were performed at 42 °C for 16 h in a sealed humidified hybridization chamber (Corning). Following the hybridization, excess hybridization solution and unbound probes were washed away during four washing steps including 5 min in 2x SSC, 1% SDS at 42 °C and 5 min in 0.1% SSC at room temperature for three times. The slides were then dried and scanned immediately.

scan_protocol: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments).

data_processing: The Cy3 and Cy5 signals and the local background intensities were quantified using GenePix Pro 6.1 software. The local background value was subtracted from the intensity of each spot. Spots were examined manually, and poor spots were flagged for elimination from the analysis. All subsequent data analyses were performed by using Microsoft Excel and a genomotyping analysis software GACK to determine present/divergent genes.

organism: Clostridioides difficile

source_name: Genomic DNA from Clostridium difficile strain CDC96 (human isolate)

label_protocol: Three micrograms of genomic DNA from each strain was fragmented by DraI digestion at 37°C for 3 h and cleaned up with QIAquick PCR purification kit (Qiagen). Fragmented DNA was then labeled with 10 µg of exo-resistant random primers (Fermentas), 25 U of Klenow fragment (New England Biolabs), dNTP mix (0.12 mM each dATP, dCTP, and dGTP and 0.03 mM dTTP), and 0.1 mM of either Cy3- or Cy5-dUTP (Amersham Biosciences). Probes were purified from unincorporated dyes using the QIAquick PCR purification kit (Qiagen). Labeled DNA sample yields and dye incorporation efficiencies were determined using spectrometry.

extract_protocol: Genomic DNA was isolated from C. difficile by using DNeasy Blood and Tissue Mini Kit (Qiagen) as described in the manufacturer’s protocol for gram-positive bacteria.

tag: Human isolate

source_name: Genomic DNA from Clostridium difficile reference strain 630

tag: Sequenced strain 630 (Human isolate)


title: Wild type vs glnPA slide187759

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description: glnPA-mutant of Streptococcus pneumoniae D39 versus Wild type D39

hyb_protocol: Hybridization (16 h at 45 °C) of labeled cDNA was performed in Ambion Slidehyb #1 hybridization buffer (Ambion Europe) on superamine glass slides (Array-It; SMMBC), containing technical replicates.

scan_protocol: Slides were scanned using the Genepix 4200AL DNA micro array slide scanner. Quantification of the signal of the spots on slides was done with ArrayPro 4.5

data_processing: Slide data were processed and normalized using MicroPreP, and CyberT implementation of the Student's t test (PMID: 15130795).

organism: Streptococcus pneumoniae

source_name: wt OD 0.3

label_protocol: Synthesis of cDNA and indirect Cy-3/Cy-5-dCTPs labeling of 15–20 µg of total RNA was performed with the CyScribe Post labeling kit (Amersham Biosciences) according to the supplier's instructions.

extract_protocol: 50 ml of GM17-broth with 0.5 mg/ml glutamine was inoculated in 4 replicates with 10-20 colonies from agar plates, and these cultures were statically grown at 37°C. Samples for RNA isolation were taken when the cultures reached an optical density (OD600) of 0.3 (mid-log growth). RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (PMID: 17085554). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures. Synthesis, subsequent labeling of cDNA, and microarray hybridization was performed as described (PMID: 17085554 and 15907200).

source_name: glnPA OD 0.3


title: Wild type vs glnPA slide187757


title: CDC97

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC97 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC97 (human isolate)


title: QCD32g58

description: Comparative Genomic Hybridization of Clostridium difficile strain QCD32g58 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain QCD32g58 (human isolate)


title: Wild type vs glnPA slide187760


title: MDA-MB-231 GL2 siRNA Replicate 2

city: Phoenix

first: Heather

middle: E

last: Cunliffe

state: AZ

address: 445 N 5th Street

department: Cancer and Cell Biology

institute: Translational Genomics Research Institute

description: MDA-MB-231 biological replicate 2 of 2. GL2 siRNA treated vs control, harvest following 16hrs transfection.

hyb_protocol: Probes were hybridized to Agilent 22k Human 1A (V2) Oligo Microarrays according to the manufacturer’s protocols and washed in an ozone-controlled environment (<0.1 ppb).

scan_protocol: Slides were scanned using the Agilent Microarray Scanner (model G2505B).

data_processing: Data was extracted, processed and normalized using Agilent’s Feature Extraction software (v8.1.1.1). Data was filtered using the p-value of the ratio as calculated by Agilent’s Feature Extraction software (v8.1.1.1). Genes selected were significantly up or down regulated (p<0.001) in all four Fn14 siRNA-treatment arrays and non-significant in the GL2 siRNA-control arrays.

source_name: Total RNA from untreated human breast cancer cell line MDA-MB-231.

label_protocol: 1 ug of total RNA was labeled for each probe using the Agilent Low RNA Imput Linear Amplification kit following the manufacturers recommendations.

growth_protocol: Both cell lines were grown at 37ºC with constant humidity and 5% CO2 using RPMI-1640 media supplimented with 10% fetal bovine serum (Invitrogen).

extract_protocol: Total RNA was collected in Trizol and exctrated using the Qiagen Rneasy mini kit.

treatment_protocol: Both Fn14 and GL2 siRNA were transfected at a concentration of 60 nmol/L using Lipofectamine 2000 (Invitrogen). Cells were then incubated for 16hrs prior to lysate collection.

tag: MDA-MB-231 cell line

source_name: Total RNA from GL2 siRNA treated human breast cancer cell line MDA-MB-231.


title: MDA-MB-436 Fn14 siRNA Replicate 1

description: MDA-MB-436 biological replicate 1 of 2. Fn14 siRNA treated vs control, harvest following 16hrs transfection.

source_name: Total RNA from untreated human breast cancer cell line MDA-MB-436.

tag: MDA-MB-436 cell line

source_name: Total RNA from Fn14 siRNA treated human breast cancer cell line MDA-MB-436.


title: CDC89

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC89 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC89 (human isolate)


title: CDC90

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC90 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC90 (human isolate)


title: MDA-MB-436 GL2 siRNA Replicate 2

description: MDA-MB-436 biological replicate 2 of 2. GL2 siRNA treated vs control, harvest following 16hrs transfection.

source_name: Total RNA from GL2 siRNA treated human breast cancer cell line MDA-MB-436.


title: MDA-MB-436 GL2 siRNA Replicate 1

description: MDA-MB-436 biological replicate 1 of 2. GL2 siRNA treated vs control, harvest following 16hrs transfection.


title: CDC94

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC94 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC94 (human isolate)


title: CDC88

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC88 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC88 (human isolate)


title: CDC83

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC83 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC83 (human isolate)


title: MDA-MB-231 GL1 siRNA Replicate 1

description: MDA-MB-231 biological replicate 1 of 2. GL2 siRNA treated vs control, harvest following 16hrs transfection.


title: CDC86

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC86 (food isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC86 (food isolate)

tag: Food isolate


title: Wild type vs glnPA slide187758

source_name: wild-type OD 0.3

extract_protocol: 50 ml of GM17-broth with 0.5 mg/ml glutamine was inoculated in 4 replicates with 10-20 colonies from agar plates, and these cultures were statically grown at 37°C. Samples for RNA isolation were taken when the cultures reached an optical density (OD600) of 0.2 (mid-log growth). RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (PMID: 17085554). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures. Synthesis, subsequent labeling of cDNA, and microarray hybridization was performed as described (PMID: 17085554 and 15907200).


title: CDC84

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC84 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC84 (human isolate)

source_name: Genomic DNA from Clostridium difficile reference strain 630


title: MDA-MB-436 Fn14 siRNA Replicate 2

description: MDA-MB-436 biological replicate 2 of 2. Fn14 siRNA treated vs control, harvest following 16hrs transfection.


title: CDC81

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC81 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC81 (human isolate)


title: MDA-MB-231 Fn14 siRNA Replicate 2

description: MDA-MB-231 biological replicate 2 of 2. Fn14 siRNA treated vs control, harvest following 16hrs transfection.

source_name: Total RNA from Fn14 siRNA treated human breast cancer cell line MDA-MB-231.


title: MDA-MB-231 Fn14 siRNA Replicate 1

description: MDA-MB-231 biological replicate 1 of 2. Fn14 siRNA treated vs control, harvest following 16hrs transfection.


title: CDC79

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC79 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC79 (human isolate)