title: M.catarrhalis_Chinchilla_Rep4

first: Todd

middle: C.

last: Hoopman

address: 5323 Harry Hines Blvd.

department: Microbiology

institute: University of Texas Southwestern Medical Center

hyb_protocol: Equivalent amounts of the Cy3- and Cy5-labeled cDNA samples were mixed, lyophilized, and then dissolved in 21 microliters of H2O.  After denaturation for 3 minutes at 94 degrees Celsius these samples were kept on ice until they were used for DNA hybridization.  The hybridization mixture containing 15 microliters of 4X hybridization buffer (GE Healthcare), 24 microliters of formamide (40% volume/volume), and 21 microliters of the Cy3- and Cy5-labeled cDNA.  The mixture was added to a DNA microarray slide and incubated at 50 degrees Celsius overnight (~ 16 hours).  After hybridization the slides were washed twice in 6X SSPE containing 0.01% Tween 20 at 50 degrees Celsius for 5 min, twice in 0.8X SSPE containing 0.001% Tween 20 at 50 degrees Celsius for 5 min, and twice in 0.8X SSPE at room temperature.

scan_protocol: The slides were dried by centrifugation at 900 x g in loosely capped 50-ml conical tubes for 3 minutes.  Microarray slides were scanned with a GenePix 4100A microarray reader (Molecular Devices, Sunnyvale, CA) and analyzed with GenePix 4.0 software (Molecular Devices).

data_processing: The Acuity 4.0 software package (Molecular Devices) was utilized to analyze the microarray data.  Raw data were first normalized using a ratio-based normalization method to equalize the means and medians of the features to 1 and exclude ratios that were less than 0.1 or greater than 10.  Features that were flagged by the software as bad, absent, or not found were also excluded from further analysis.  Secondly, a Lowess-based normalization was applied to the microarray data prior to final analysis.  The RNA isolated from the in vitro broth-grown O35E.rpsl was utilized as the baseline gene expression template.  To identify those genes that exhibited an altered expression profile in the chinchilla nasopharynx relative to the in vitro broth-grown cells, a threshold of twofold-increased or decreased expression over the baseline was utilized.

organism: Moraxella catarrhalis

source_name: Moraxella catarrhalis strain O35E.rpsl, broth grown, Klett 200

label_protocol: Twenty micrograms of total RNA from the O35E.rpsl cells grown in BHI broth were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac.  Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes.  The mixture was then cooled to room temperature for 10 minutes.  cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions.  RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes.  15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit.  After purification, Cy3 dye (GE Heathcare) was added and labelling occured via the manufacturer's instructions.  The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns.  A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

growth_protocol: M. catarrhalis strain O35E.rpsl was grown in BHI broth to a Klett density of 200 units.

extract_protocol: Broth-derived M. catarrhalis O35E.rpsl cells were grown to 200 Klett units in 10 mL of BHI broth.  Once the desired bacterial density was achieved, 5 mL of 50 mM NaAzide NaNO3 was added.  Finally, 15 mL of 2% (wt/vol) saponin in TE buffer was added and the suspension was vortexed vigorously for 20 seconds (5 cycles).  This suspension was placed at 37 degrees Celsius for 10 minutes and then underwent centrifugation at 3,100 x g for 5 minutes.  The resulting cell pellet was processed for total RNA with the Qiagen RNease Midi kit per the manufacturer's instructions.  DNase I treatment with a Message Clean kit (GenHunter Corp) was performed per manufacturer's instructions.

treatment_protocol: M. catarrhalis strain O35e.rpsl was grown in BHI broth to a Klett density of 200 units.

tag: Moraxella catarrhalis strain O35E with resistance to streptomycin that was grown in BHI broth to a Klett density of 200 units.

source_name: Moraxella catarrhalis strain O35E.rpsl, chinchilla nasopharynx, 24 hours

label_protocol:
Twenty micrograms of total RNA from the O35E.rpsl cells isolated from the chinchilla nasopharynx were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac.  Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes.  The mixture was then cooled to room temperature for 10 minutes.  cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions.  RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes.  15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit.  After purification, Cy5 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions.  The CyDye-labeled cDNA sample w
as purified by using Microcon YM30 columns.  A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

growth_protocol: Twenty four hours after inoculation viable M. catarrhalis strain O35e.rpsl organisms were isolated from the chinchilla nasopharynx via the tissue homogenization method.

extract_protocol: The nasal and ethmoid turbinates from each inoculated chinchilla with their overlying mucosa were removed via standard dissection techniques and placed immediately in 10 mL of 50 mM NaAzide and kept on ice.  10 mL of 2% (wt/vol) saponin in TE buffer was added and the samples were vigorously vortexed for 20 seconds (5 cycles) and placed at 37 degrees Celsius for 10 minutes to lyse the superficial epithelial cell layer and release adherent bacteria.  After incubation, the tissue suspension was centrifuged at 200 x g for 1 minute to remove the large tissue fragments.  The supernatant was transferred to a clean, RNase-free 50 mL conical tube and centrifuged at 3,100 x g for 5 minutes.  The resulting pellet was processed for total RNA with the QIAGEN RNeasy Midi kit per the manufacturer's instructions.  DNase I treatment was performed with the Message Clean kit per manufacturer's instructions.

treatment_protocol: M. catarrhalis O35E.rpsl was grown in BHI broth to a Klett density of 200 units.  Cells were pelleted and resuspended in PBS-gelatin (0.15% wt/vol).  150 microliters of this suspension was utilized to inoculate the nasopharynx of the sedated chinchilla.

tag: Moraxella catarrhalis strain O35E with resistance to streptomycin that were recovered from the nasopharynx of the chinchilla after a 24 hour inoculation.


title: 3

status: Public on Apr 04 2012

type: RNA

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

country: Netherlands

institute: MicroLife Solutions

description:
4C
Used in analysis: yes
WK_1_1_2.txt

hyb_protocol: 300 ng of Cy3-labeled or Cy5-labeled cRNA (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with a 8x15k format for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), washed in acetonitril for 10 seconds, and hen dried immediately by air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red&Green and PMT is set to 100%, XDR Hi 100%, XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE2-v5_95 and Grid: 016342_D_F_20070323) to obtain mean Red or Green intensities and median Red or Green background intensities. In limma, the edwards method for background correction was used (min. offset = 30), and global loess normalizion (MAANOVA) was done.

molecule: total RNA

organism: Folsomia candida

source_name: 30 animals, field soil, 4C

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 500 ng total RNA using the Quick Amp Labeling Kit, two-color (Agilent Technologies) according to the manufacturer's guidelines with a slight modification where the transcription (labeling) reactions were done in half the volume, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures were first age synchronized before exposure to soil. 20 adult animals were incubated per container, which contained a plaster of Paris base mixed with charcoal, to lay eggs for 2 days. The incubation conditions were 20°C, 75% RH and 12:12 hour dark:light cycle.

extract_protocol: Total RNA was extracted from all animals (~30) per jar using the SV Total RNA isolation System (Promega).

treatment_protocol: Approximately 30 animals, 23 days old, were exposed for two days in glass jars containing ~30 g of soil at 50% of the soil WHC. Exposure was done at the same conditions as incubation. After exposure, the animals were extracted from soil with tap water via floatation, put in 1.5 mL tubes and frozen in liquid N2.

tag: age

value: 23 days

tag: tissue

value: whole body

tag: treatment

value: field soil

tag: copper level

tag: ph

value: C


title: 31

description:
2C
Used in analysis: no
WK_1_1_3.txt

source_name: 30 animals, field soil, 2C


title: M.catarrhalis_Chinchilla_Rep2

city: Dallas

state: TX

country: USA

label_protocol: Twenty micrograms of total RNA from the O35E.rpsl cells isolated from the chinchilla nasopharynx were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac.  Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes.  The mixture was then cooled to room temperature for 10 minutes.  cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions.  RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes.  15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit.  After purification, Cy5 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions.  The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns.  A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

treatment_protocol: M. catarrhalis strain O35E.rpsl was grown in BHI broth to a Klett density of 200 units.


title: M.catarrhalis_Chinchilla_Rep3


title: 23

description:
3A
Used in analysis: yes
WK_1_1_2.txt

source_name: 30 animals, field soil, 3A

value: A


title: AML-19

city: chicago

first: chunjiang

last: he

state: il

address: 900 east 57th st

institute: university of chicago

hyb_protocol: The amplified cRNA samples were hybridized overnight and then washed based on the protocol of the Agilent Oligo Microarray (One-Color Microarray-Based Gene Expression Analysis V5.7, GE 8x15K, Gene Expression Hybridization Kit).

scan_protocol: Array slides were scanned on a GenePix 4000B scanner at 570 PMT and 100% Power standard setting according to the manufacturer’s instruction (Molecular Devices Corporation, Sunnyvale, CA, USA).

data_processing: Array slide images were then analyzed using Agilent Feature Extraction software (9.5.1.1) to obtain gene expression signals and array QC reports. Partek Genomics Suite (Partek Inc., St. Louis, MO, USA) were used for the data normalization. Briefly, background-adjustment, quantile normalization, and log2-transformation were used to normalize and treat gene expression intensities, and then median-centering genes for each array and median-centering each gene across all arrays were conducted.

organism: Homo sapiens

label_protocol: 0.5ug total RNA per sample was reverse transcribed, amplified and labeled with Cy3 using the Agilent one-color amplification protocol (Agilent Quick-Amp Labeling Kit, One-color; One-Color Microarray-Based Gene Expression Analysis).

extract_protocol: Blasts and mononuclear cells were purified by use of NycoPrep 1.077A (Axis-Shield, Oslo, Norway) according to the manufacturer’s manual. Total RNA was isolated from each sample using the miRNeasy Mini Kit (Qiagen), Trizol reagent (Invitrogen), or guanidinium thiocyanate followed by cesium chloride-gradient purification.

tag: gender

value: female

tag: age (yrs)

value: bone marrow (BM)

tag: disease state

value: acute myeloid leukemia (AML)

tag: subtype

tag: abnormality

value: NK


title: AML-18

source_name: AML

value: male


title: AML-17

value: peripheral blood (PB)


title: 120

description:
2B
Used in analysis: no
WK_1_1_3.txt

source_name: 30 animals, field soil, 2B

value: B


title: M.catarrhalis_Chinchilla_Rep5


title: 114

description:
2D
Used in analysis: yes
WK_1_1_1.txt

source_name: 30 animals, field soil, 2D

value: D


title: AML-16


title: 48 hour CsA rep 1

city: Dublin

first: Sein

last: O'Connell

address: Belfield

country: Ireland

institute: University College Dublin

description: Cells treated for 48 hours with 4.2µM CsA

hyb_protocol: The following steps were carried out in the UCD Conway Institute Affymetrix GeneChip Core Technology, by core technology staff.  Fragmented cRNA was hybridised to Affymetrix GeneChip Test3 and HG-U133A arrays for 16 hours, according to Affymetrix protocols.  The arrays were then washed and stained using the Fluidics station.

scan_protocol: The stained arrays were scanned using a GeneArray® scanner.

data_processing:
Affymetrix® Microarray Suite (MAS) 5.0 was used to process the scanned image and generate files containing probe intensity information and present/absent/marginal calls for each probe. GeneSpring 7.1 was used to analyse the information generated by MAS 5.0 for each array.  Data was imported into GeneSpring and ‘per chip’ and ‘per gene’ normalisation was conducted.  A number of filters were applied to eliminate unchanging genes and genes with unreliable measurements from further analysis.  Lists were generated of genes that were greater than two fold differentially expressed in 12 hour or 48 hour treated cells versus control HMCs.  Lists of genes with expression levels that were statistically significantly (p<0.05) different in either treatment group versus control cells were also generated.  Merging of the statistical gene lists with the lists of genes with a greater than two fold change generated lists of genes worthy of further investigation.
annotation of gene lists: Gene lists generated using GeneSpring 7.1 were annotated using information obtained from Entrez Gene (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene). Gene lists generated from Genespring of differentially expressed genes following CsA treatment were uploaded onto the publicly available PANTHER website (www.pantherdb.org) or the commercially available Ingenuity Pathway Analysis (IPA) (Ingenuity Systems, Red Wood City, CA) program. Gene lists were categorised into pathways and biological processes. Following software analysis significantly enriched pathways and processes were identified.

label: biotin

source_name: HMCs treated for 48 hours with CsA (control) biological replicate 1

label_protocol: cDNA was in vitro transcribed into biotin labelled cRNA using the Enzo BioArrayTM HighYieldTM RNA transcript labelling kit.  Briefly, 10 µl of double stranded cDNA was placed into an RNase free microfuge tube and the following components were added: 12 µl of dH2O, 4 µl of 10X HY reaction buffer, 4 µl of 10X biotin-labelled ribonucleotides, 4 µl of 10X DTT, 4 µl of 10X RNase inhibitor mix and 4 µl T7 RNA polymerase.  Contents were mixed and were then incubated for 5 hr at 37°C in a thermal cycler, with gentle mixing every 45 min.  Labelled RNA was stored at -20°C.  An aliquot was retained for analysis by agarose gel electrophoresis.

growth_protocol: HMCs were cultured in suplemented DMEM medium + 1 % serum.

extract_protocol: RNA was extracted using the Trizol method according to the manufacturers protocol (Invitrogen). Total RNA was purifed using Qiagen columns according to the manufacturers protocol.

treatment_protocol: Cells were seeded onto 35 mm dishes and allowed to reach confluency.  HMCs were treated with 4.2 μM CsA, prepared from 4.2 mM stock, for 0, 12 and 48 hours.

tag: cell type

value: confluent human mesangial cells

value: treated for 48 hours with 4.2µM CsA


title: 48 hour CsA rep 2

source_name: HMCs treated for 48 hours with CsA (control) biological replicate 2


title: M.catarrhalis_Chinchilla_Rep1

label_protocol: Twenty micrograms of total RNA from the O35E.rpsl cells isolated from the chinchilla nasopharynx were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac.  Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes.  The mixture was then cooled to room temperature for 10 minutes.  cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions  RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes.  15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit.  After purification, Cy5 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions.  The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns.  A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

extract_protocol: The nasal and ethmoid turbinates from each inoculated chinchilla with their overlying mucosa were removed via standard dissection techniques and placed immediately in 10 mL of 50 mM NaAzide and kept on ice.  10 mL of 2% (wt/vol) saponin in TE buffer was added and the samples were vigorously vortexed for 20 seconds (5 cycles) and placed at 37 degrees Celsius for 10 minutes to lyse the superficial epithelial cell layer and release adherent bacteria.  After incubation, the tissue suspension was centrifuged at 200 x g for 1 minute to remove the large tissue fragments.  The supernatant was transferred to a clean, RNase-free 50 mL conical tube and centrifuged at 3,100 x g for 5 minutes.  The resulting pellet was processed for total RNA with the QIAGEN RNeasy Midi kit per the manufacturer's instructions  DNase I treatment was performed with the Message Clean kit per manufacturer's instructions.s

label_protocol: Twenty micrograms of total RNA from the O35E.rpsl cells grown in BHI broth were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac.  Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes.  The mixture was then cooled to room temperature for 10 minutes.  cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions  RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes.  15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit.  After purification, Cy3 dye (GE Heathcare) was added and labelling occured via the manufacturer's instructions.  The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns.  A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

extract_protocol: Broth-derived M. catarrhalis O35E.rpsl cells were grown to 200 Klett units in 10 mL of BHI broth.  Once the desired bacterial density was achieved, 5 mL of 50 mM NaAzide NaNO3 was added.  Finally, 15 mL of 2% (wt/vol) saponin in TE buffer was added and the suspension was vortexed vigorously for 20 seconds (5 cycles).  This suspension was placed at 37 degrees Celsius for 10 minutes and then underwent centrifugation at 3,100 x g for 5 minutes.  The resulting cell pellet was processed for total RNA with the Qiagen RNease Midi kit per the manufacturer's instructions  DNase I treatment with a Message Clean kit (GenHunter Corp) was performed per manufacturer's instructions


title: 4 wk Female mouse liver/8wk Female mouse liver - replicate#2

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: The RNA expression profile for a 4 wk old female liver pool (n=6) and an 8 wk old female liver pool (n=6) is given as a normalized ratio.  The purpose of this comparison is to highlight age related differences in female mouse liver gene expression.

hyb_protocol: Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 m scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software (version 9.5.3, protocol GE2-v5_91_0806).

data_processing: Linear and LOWESS normalization and analysis using Rosetta Resolver pipeline (version 5.1)

label: Alexa 647 (red)

organism: Mus musculus

source_name: 8 week female mouse liver

label_protocol: RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI).  Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature.  Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA).  Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.

extract_protocol: Trizol extraction of RNA

tag: strain

tag: Sex

value: Female

value: 8 wk

value: liver

label: Alexa 555 (green)

source_name: 4 week female mouse liver

value: 4 wk


title: 12 hour CsA rep 1

description: Cells treated for 12 hours with 4.2µM CsA

source_name: HMCs treated for 12 hours with CsA (control) biological replicate 1

value: treated for 12 hours with 4.2µM CsA


title: 12 hour CsA rep 2

source_name: HMCs treated for 12 hours with CsA (control) biological replicate 2


title: 0 hour control rep 2

description: control cells untreated

source_name: HMCs treated for 0 hours with CsA (control) biological replicate 2


title: 4 wk Female mouse liver/8wk Female mouse liver - replicate#1


title: AML-15


title: 14

description:
1A
Used in analysis: no
WK_1_1_1.txt

source_name: 30 animals, field soil, 1A

value: 23 days

value: whole body

value: field soil


title: AML-14

value: bone marrow (BM)


title: 0 hour control rep 1

description: control cells untreated

source_name: HMCs treated for 0 hours with CsA (control) biological replicate 1


title: Honey EMRSA-15 T240 biological rep 2

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

country: United Kingdom

institute: Cardiff University

description: gene expression data from honey treated cells

hyb_protocol: Following fragmentation, 3.5 µg of cDNA were hybridized for 16 hr at 45C on GeneChip S. aureus Genome Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Workstation 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 7G Autoloader

data_processing: The data were analyzed with Affymetrix Expression Console using the RMA algorithm

organism: Staphylococcus aureus

source_name: EMRSA-15 grown for 4 hours in MHB with 10% manuka honey

label_protocol: 10µg total RNA was reverse transcribed, cDNA fragmented, 3’ biotinylated, mixed with exogenous labeled “spike-in” transcripts and hybridized to S. aureus GeneChips following the manufacturer’s recommendations for antisense prokaryotic arrays (Affymetrix, Santa Clara, CA).

growth_protocol: Cells harvested after 4 hours growth in MHB at 37°C

extract_protocol: Extraction of RNA was done following manufacturers instructions using SV Total RNA extraction Sytem, Promega

treatment_protocol: Test cells were treated with 10% (w/v) manuka honey for th 4 hour incubation period


title: AML-13

value: female

value: acute myeloid leukemia (AML)


title: Honey EMRSA-15 T240 biological rep 3


title: 3 wk Female mouse liver/8wk Female mouse liver - replicate#2

description: The RNA expression profile for a 3 wk old female liver pool (n=5) and an 8 wk old female liver pool (n=6) is given as a normalized ratio.  The purpose of this comparison is to highlight age related differences in female mouse liver gene expression.

source_name: 3 week female mouse liver

value: 3 wk


title: AML-12

value: male


title: 4 wk Male mouse liver/8wk Male mouse liver - replicate#2

description: The RNA expression profile for a 4 wk old male liver pool (n=6) and an 8 wk old male liver pool (n=6) is given as a normalized ratio.  The purpose of this comparison is to highlight age related differences in male mouse liver gene expression.

source_name: 8 week male mouse liver

value: Male

source_name: 4 week male mouse liver


title: 3 wk Male mouse liver/8wk Male mouse liver - replicate#2

description: The RNA expression profile for a 3 wk old male liver pool (n=5) and an 8 wk old male liver pool (n=6) is given as a normalized ratio.  The purpose of this comparison is to highlight age related differences in male mouse liver gene expression.

source_name: 3 week male mouse liver


title: 4 wk Male mouse liver/8wk Male mouse liver - replicate#1


title: 3 wk Female mouse liver/8wk Female mouse liver - replicate#1


title: Honey EMRSA-15 T240 biological rep 1


title: 8 wk Male mouse liver/8wk Female mouse liver - replicate#2

description: The RNA expression profile for a 8 wk old male liver pool (n=6) and an 8 wk old female liver pool (n=6) is given as a normalized ratio.  The purpose of this comparison is to highlight sex-specific differences in 8 wk old mouse liver gene expression.


title: AML-11

source_name: AML

value: NK


title: 8 wk Male mouse liver/8wk Female mouse liver - replicate#1


title: MOI=0 Rep 3

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Buffy coat monocytes

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: multiplicity of infection

tag: duration of infection

value: monocyte

tag: infection


title: 3 wk Male mouse liver/8wk Male mouse liver - replicate#1


title: MOI=10 Rep 2

description: replicate 2

value: 6 hours

value: influenza A


title: Control EMRSA-15 T240 biological rep 3

description: gene expression data from untreated cells

source_name: EMRSA-15 grown for 4 hours in MHB


title: AML-10


title: 4 wk Male mouse liver/4wk Female mouse liver - replicate#2

description: The RNA expression profile for a 4 wk old male liver pool (n=6) and a 4 wk old female liver pool (n=6) is given as a normalized ratio.  The purpose of this comparison is to highlight sex-specific differences in 4 wk old mouse liver gene expression.

value: Female


title: MOI=10 Rep 3

description: replicate 3


title: Control EMRSA-15 T240 biological rep 2


title: AML-1


title: 3 wk Male mouse liver/3wk Female mouse liver - replicate#2

description: The RNA expression profile for a 3 wk old male liver pool (n=5) and a 3 wk old female liver pool (n=5) is given as a normalized ratio.  The purpose of this comparison is to highlight sex-specific differences in 3 wk old mouse liver gene expression.

value: liver


title: 4 wk Male mouse liver/4wk Female mouse liver - replicate#1

value: 4 wk


title: MOI=10 Rep 1

description: replicate 1


title: 3 wk Male mouse liver/3wk Female mouse liver - replicate#1


title: Control EMRSA-15 T240 biological rep 1


title: MOI=0 Rep 2

description: replicate 2


title: Frozen tissue_IVT_62A rep1

status: Public on Apr 03 2012

city: La Jolla

first: Maggie

last: Chow

state: CA

address: 8110 La Jolla Shores Dr. Ste 201

department: Neuroscience

institute: NIH-UC San Diego Autism Center of Excellence

description: Postmortem brain tissue

hyb_protocol: Illumina hybridization protocol

scan_protocol: Illumina scanning protocol

data_processing: Data not normalized

label: Biotin

source_name: Postmortem Brain

label_protocol: DASL- and IVT-based protocols

extract_protocol: Ambion MELT kit for frozen brain samples and Roche High Pure FFPE RNA Micro Kit for formalin fixed samples

value: postmortem brain

tag: tissue preservation

value: Frozen

tag: diagnosis

value: Autism

tag: assay

value: IVT


title: Reference_IVT_B75P25

description: Reference RNA

source_name: Ambion FirstChoice Human Brain Reference and Stratagene Universal Reference pooled RNA

tag: tissue

value: 75% Brain 25% Pooled


title: Reference_IVT_B0

description: Reference RNA

source_name: Ambion FirstChoice Human Brain Reference RNA

value: brain

tag: heat treatment

value: Heating at 95C for 0 min


title: Reference_IVT_P10

description: Reference RNA

source_name: Stratagene Universal Reference pooled RNA

value: Heating at 95C for 10 min


title: Frozen tissue_IVT_58C

description: Postmortem brain tissue


title: Reference_IVT_B10

description: Reference RNA


title: Reference_IVT_B25P75

description: Reference RNA

value: 25% Brain 75% Pooled


title: Reference_IVT_P60

description: Reference RNA

value: Stratagene Universal Reference pooled RNA

value: Heating at 95C for 60 min


title: Reference_IVT_B30

description: Reference RNA

value: Heating at 95C for 30 min


title: Reference_IVT_P0

description: Reference RNA


title: Reference_IVT_P30

description: Reference RNA


title: Frozen tissue_IVT_62A rep2

description: Postmortem brain tissue


title: MOI=0 Rep 1

description: replicate 1

value: monocyte


title: Frozen tissue_IVT_55C rep1

description: Postmortem brain tissue

value: Control


title: Frozen tissue_IVT_42A

description: Postmortem brain tissue


title: Frozen tissue_IVT_53B

description: Postmortem brain tissue


title: Frozen tissue_IVT_29A rep2

description: Postmortem brain tissue


title: Frozen tissue_IVT_39B

description: Postmortem brain tissue


title: Fixed tissue_IVT_M806 rep1

description: Postmortem brain tissue

value: Fixed


title: Frozen tissue_IVT_55C rep2

description: Postmortem brain tissue


title: Frozen tissue_IVT_30A rep2

description: Postmortem brain tissue


title: Fixed tissue_IVT_M1106

description: Postmortem brain tissue


title: Frozen tissue_IVT_28C

description: Postmortem brain tissue


title: Fixed tissue_IVT_EC6

description: Postmortem brain tissue


title: Frozen tissue_IVT_30A rep1

description: Postmortem brain tissue


title: Fixed tissue_IVT_M806 rep2

description: Postmortem brain tissue


title: Fixed tissue_IVT_EC5rep1

description: Postmortem brain tissue


title: Fixed tissue_IVT_EC5rep2

description: Postmortem brain tissue


title: Frozen tissue_IVT_29A rep1

description: Postmortem brain tissue


title: Fixed tissue_DASL_M806-G1 rep2

description: Postmortem brain tissue

value: DASL


title: Fixed tissue_DASL_M806-W2 rep2

description: Postmortem brain tissue


title: Fixed tissue_DASL_M806-W1 rep2

description: Postmortem brain tissue


title: Fixed tissue_DASL_M806-G2 rep2

description: Postmortem brain tissue


title: BW25113 wild-type stationary phase OD 3.0

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from stationary phase cells of E. coli BW25113 wild-type exposed to ampicillin 5 ug/mL for 30 mins

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (169 mini Format) with total 80 ul volume including 1X hybridization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labeled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Genome 2.0 Array, the hybridization was performed at 45°C, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: Channel 1

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: One-day old single colony was inoculated in 25 mL of LB for 16 h at 37C at 250 rpm. Overnight culture was diluted to be OD 0.05 at 600nm in 25 mL in LB and incubated at 37C at 250 rpm until OD 3.0 at 600nm (harvested at this OD). Ampicillin 5 µg/mL was then added directly to 22 mL of culture and incubated for an additional 30 mins. Cell pellet was collected by centrifuging at 8500 rpm at 4C for 2 min. Supernatant was discarded and the cell pellet was resuspended with 1 mL RNAlater. Then the sample was centrifuged and the supernatant was discarded, the final cell pellet was immediately frozen in dry ice and stored at -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

value: E. coli BW25113 wild-type

tag: growth phase

value: stationary phase OD 3.0

tag: time

tag: sample type

value: starting culture

tag: medium

value: LB

value: Planktonic cells inoculated at OD 0.05 at 600nm, grown to OD 3.0 at 600nm, exposed to 5 ug/mL ampicillin for 30 min.

tag: temp


title: Fixed tissue_DASL_M806-W2 rep1

description: Postmortem brain tissue

value: postmortem brain


title: BW25113 delta rpoS persisters T5 hrs ampicillin

description: RNA extracted from persister cells of E. coli BW25113 delta rpoS after 5 hours growth in LB ampicillin 20 ug/mL

extract_protocol: One-day old single colony was inoculated in 25 mL of LB Kan50 for 16 h at 37C at 250 rpm. Overnight culture was diluted to be OD 0.05 at 600 nm in 25 mL in LB and incubated at 37C at 250 rpm until OD 1.0 at 600 nm (harvested at this OD). 150 mL of cells were washed with 0.85% NaCl and then exposed to 20 µg/mL ampicillin for 5 h. After 5 h, cell pellet was collected by centrifuging at 8500 rpm at 4C setting for 2 min. Supernatant was discarded and the cell pellet was resuspended with 6 mL RNAlater. Then the sample was centrifuged and the supernatant was discarded, the final cell pellet was immediately frozen in dry ice and stored at -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

value: E. coli BW25113 delta rpoS

value: 5 h

tag: treatment

value: ampicillin 20 ug/mL

value: Planktonic cells inoculated at OD 0.05 at 600 nm, grown to OD 1.0 at 600 nm, then exposed to 20 ug/mL ampicillin for 5 h.


title: Fixed tissue_DASL_M806-W1 rep1

description: Postmortem brain tissue


title: Fixed tissue_DASL_M806-G1 rep1

description: Postmortem brain tissue


title: BW25113 mqsR/pBS(Kan)-mqsR 2-1 in LB with ampicillin

organism: Escherichia coli K-12

extract_protocol: The overnight culture (0.25 ml) was used to inoculate 25 ml of fresh LB medium. Planktonic cells were grown to a turbidity of 0.5 at 600 nm in LB medium with 1 mM IPTG at 37 °C, adjusted the turbidity to 1, and exposed to 20 μg/mL ampicillin with 1 mM IPTG for 1 h.  Cells were isolated by centrifuging at 0°C, and RNALater buffer (Ambion, Cat# AM7021) was added to stabilize RNA during the RNA preparation steps.  After breaking the cells with a bead beater, the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)

tag: strains

tag: genotype/variation

value: mqsR/pBS(Kan)-mqsR 2-1

value: 1 h with 20 μg/mL ampicillin

tag: cell type

value: Planktonic cells harvested at a turbidity of 0.5 at 600 nm, adjusted to the turbidity at 1, and then exposed to 20 μg/mL ampicillin for 1 h.


title: BW25113 wild-type H202 pre-treatment 5 h ampicillin persisters

description: RNA extracted from persister cells of E. coli BW25113 wild-type (pre-treated with 20 mM H202 10 mins) after 5 hours growth in LB ampicillin 20 ug/mL

extract_protocol: One-day old single colony was inoculated in 25 mL of LB Kan50 for 16 h at 37C at 250 rpm. Overnight culture was diluted to be OD 0.05 at 600nm in 25 mL in LB and incubated at 37C at 250 rpm until OD 1.0 at 600nm (harvested at this OD). 150 mL of cells were washed with 0.85% NaCl, resuspended in LB with 20 mM H2O2, and incubated at 37C at 250 rpm for 10 min. After H2O2 treatment, cells were washed with 0.85% NaCl and then exposed to 20 ug/mL ampicillin for 5 h. After 5 h, cell pellet was collected by centrifuging at 8500 rpm at 4C setting for 2 min. Supernatant was discarded and the cell pellet was resuspended with 6 mL RNAlater. Then the sample was centrifuged and the supernatant was discarded, the final cell pellet was immediately frozen in dry ice and stored at -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

tag: strain

value: Planktonic cells inoculated at OD 0.05 at 600 nm, grown to OD 1.0 at 600 nm, exposed to 20 mM H202 for 10 mins, then exposed to 20 ug/mL ampicillin for 5 h.


title: BW25113 mqsR/pBS(Kan)-mqsR in LB with ampicillin

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (169 mini Format) with total 80 μl volume including 1X hybridization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labeled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Genome 2.0 Array, the hybridization was performed at 45°C, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (Cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: The overnight culture (0.25 mL) was used to inoculate 25 mL of fresh LB medium. Planktonic cells were grown to a turbidity of 0.5 at 600 nm in LB medium with 1 mM IPTG at 37 °C, adjusted the turbidity to 1, and exposed to 20 μg/mL ampicillin with 1 mM IPTG for 1 h.  Cells were isolated by centrifuging at 0°C, and RNALater buffer (Ambion, Cat# AM7021) was added to stabilize RNA during the RNA preparation steps.  After breaking the cells with a bead beater, the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

value: mqsR/pBS(Kan)-mqsR


title: Reference_IVT_B60

description: Reference RNA

value: brain

value: IVT

value: Heating at 95C for 60 min


title: Fixed tissue_DASL_M1106-W1

description: Postmortem brain tissue

value: Fixed

value: Autism

value: DASL


title: Fixed tissue_DASL_M1106-W2

description: Postmortem brain tissue


title: Fixed tissue_DASL_M806-G2 rep1

description: Postmortem brain tissue

value: Control


title: Fixed tissue_DASL_M1106-G2

description: Postmortem brain tissue

value: postmortem brain


title: Fixed tissue_DASL_M1106-G1

description: Postmortem brain tissue


title: Fixed tissue_DASL_EC6-G2

description: Postmortem brain tissue


title: Fixed tissue_DASL_EC6-W1

description: Postmortem brain tissue


title: Fixed tissue_DASL_EC5-W1

description: Postmortem brain tissue


title: Fixed tissue_DASL_EC5-G2

description: Postmortem brain tissue


title: Frozen Tissue_DASL_1A

description: Postmortem brain tissue

data_processing: The data from frozen-tissue extracted DASL-processed RNA samples passing exclusion criteria were log2 transformed and normalized using quantile normalisation with lumi in R.  Quantile-normalized data available on Series record. Raw data included in Sample tables.

value: Frozen


title: Frozen Tissue_DASL_2B

description: Postmortem brain tissue


title: Fixed tissue_DASL_EC5-W2

description: Postmortem brain tissue


title: Frozen Tissue_DASL_74C

description: Postmortem brain tissue


title: Frozen Tissue_DASL_70B

description: Postmortem brain tissue


title: Fixed tissue_DASL_EC6-W2

description: Postmortem brain tissue


title: Fixed tissue_DASL_EC6-G1

description: Postmortem brain tissue


title: Frozen Tissue_DASL_1B

description: Postmortem brain tissue


title: Frozen Tissue_DASL_6B

description: Postmortem brain tissue


title: Frozen Tissue_DASL_6A

description: Postmortem brain tissue


title: Fixed tissue_DASL_EC5-G1

description: Postmortem brain tissue


title: Frozen Tissue_DASL_2A

description: Postmortem brain tissue


title: Frozen Tissue_DASL_5B

description: Postmortem brain tissue


title: Frozen Tissue_DASL_5A

description: Postmortem brain tissue


title: Frozen Tissue_DASL_4B

description: Postmortem brain tissue


title: Frozen Tissue_DASL_4A

description: Postmortem brain tissue


title: Frozen Tissue_DASL_3A

description: Postmortem brain tissue


title: Wholeflies_ED1231_Male_R3

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

hyb_protocol: Microarray glass slides were fitted with 12X mixers according to standard Nimblegen protocols, warmed to 42°C on a MAUI hybridization station (BioMicro Systems, Salt Lake City, Utah), and 7 μl of hybridization cocktail was loaded onto each microarray through the fill port. Vent and fill ports were sealed and arrays were loaded onto the MAUI station. Mix mode B on the MAUI hybridization station was started and samples were hybridized for 16 hours at 42°C in an ozone free chamber. The ozone free chamber consisted of a homemade Lexon box (182 cm x 67 cm x 67 cm). Two NoZone® Ozone Scrubbers (SciGene Corporation, Sunnyvale, CA) were used to pump ozone free air into the box. Ozone levels were measured using a Aeroqual Series 500 ozone monitor (Aeroqual Limited, Auckland, New Zealand) and found to be lower compared to levels of ozone external to the box. Hybridization, washing, and scanning were all performed in the ozone free chamber.  Microarray glass slides were washed using the following modified Nimblegen protocol. A glass slide with mixer was submerged for 10 seconds in warm (42°C) Buffer I (1 L H2O, 10 ml 20X SSC, 20 ml 10 % SDS, 100 μl 1 M DTT) and the mixer was removed. Slides were placed in a fresh beaker of 42°C Buffer I and agitated for 2 minutes, submerged for 1 minute in room temperature Buffer II (1000 L H2O, 10 ml 20X SSC, 100 μl 1 M DTT), followed by submerging for 15 sec in Buffer III (1 L H2O, 2.5 ml 20X SSC, 100 μl 1 M DTT). Microarray slides were placed in a ChipMate Mini Slide Centrifuge (Tomy Tech USA Inc., Menlo Park, California) and spun for 1 minute to dry. Dried microarray slides were covered with aluminum foil until scanning.

scan_protocol: Slides were scanned on a Axon GenePix® 4200 AL (Molecular Devices, Sunnyvale, California) scanner controlled by GenePix® 6.0 software. Laser PMT settings were calibrated using a dilution series of Cy3 and Cy5 dyes. For microarray data collection, Cy3 and Cy5 channels were balanced by visual inspection of histograms for Cy3 and Cy5 channels and if necessary by manually changing PMT settings for each laser. Each scan was conducted at 5 μm resolution with no line averaging and saved as a TIFF file.

data_processing:
TIFF flies were imported into Nimblescan v. 2.4.27 (Roche Nimblegen Inc., Madison, Wisconsin) for processing. We used the burst multiplex image function to separate each channel of the 2-color 12-plex image into 24 array single color images. Probe intensities for each subarray were extracted for probes mapping to Flybase Drosophila melanogaster r. 5.5 FBgn numbers using the autogrid function and then feature intensities were exported as individual pair files in Nimblescan. We updated the annotation to reflect Flybase D. melanogaster r. 5.29 but broad conclusions derived from our analysis were not dependent on differences in annotation.  Cy3 channel images were then analyzed for array to array contamination using sample tracking analysis in Nimblescan. Sample tracking provides a report of the sample tracking controls that were included with each array hybridization. All sample tracking analyses were co-linear with sample tracking controls indicating no contamination occurred across microarrays within a glass slide. Raw intensities in pair files for each probe were log2 transformed. Pearson’s r and Spearman’s rho correlation coefficients were calculated for all pairwise comparisons within replicates in order to identify outlier hybridizations. Replicates that had Spearman’s rho greater than 0.80 were retained for subsequent normalization and analysis. This eliminated 6 channels of data giving 134 channels for subsequent analysis.
Normalization was performed by loading the remaining single array pair files into Nimblescan v. 2.4.27 (Roche Nimblegen Inc., Madison, Wisconsin) and then normalizing all data together using Robust Multichip Averaging (RMA; Irizarry et al. 2003) both with and without background correction.  Results with background correction are depoisted here.

organism: Drosophila melanogaster

source_name: Wholeflies, 5 day mated adults

label_protocol: Microarrays were used in a two-color format with mRNA labeled with Cy3 or Cy5. Three or four biological replicates for each sex were labeled and hybridized as follows. For each sample of mRNA, 200 ng was simultaneously reverse-transcribed and labeled with dye along with three Arabidopsis in vitro transcribed spike-in controls (AY11387 at 1:1 ratio between Cy3 and Cy5 at 1 ng/ul; AF33972 at 1:2 ratio between Cy3 and Cy5 at 1:10 dilution (0.1ng/ul); and AY093727 at 1:1 ratio between Cy3 and Cy5 and 1:50 dilution (0.02ng/ul)). Reverse-transcription/labeling reactions consisted of 5 μl 5X First Strand Buffer (Invitrogen, Carlsbad, California), 1 μl 0.1 mM DTT (Invitrogen, Carlsbad, California), 3 μl of dye-mix containing Cy3 or Cy5 labeled nanomer primer (Trilink Biotechnologies, San Diego, CA), 1 μl RNase inhibitor (Ambion, Austin, Texas), 5 μl H2O plus Arabidopsis spike-in controls, and 1 μl Super-script II reverse transcriptase (Invitrogen, Carlsbad, California). Labeling reactions were incubated at 37°C for 2 hours then stopped by heat termination at 85°C for 5 min. Labeling reactions were purified using Clonetech columns (TE-10), Clonetech, Mountain View, California) following manufacture instructions. Samples to be co-hybridized onto one microarray were pooled and precipitated with 90 μl DEPC treated H2O, 1 μl glycogen (1 mg/ml), 60 μl 5M ammonium acetate, and 300 μl cold 100% EtOH and by cold centrifugation at max speed for 20 min. Different sexes were never co-hybridized and we tried to have all replicates for a particular Df/+ line be hybridized on the same glass slide. Probe pellets were re- suspended in 6.6 μl Sample Tracking Controls (Roche Nimblegen Inc., Madison, Wisconsin), 4.8 μl H2O, 12 μl warm 2X Hyb Buffer (250 μl formamide, 250 μl 20X SSC, 20 μl 10% SDS, 5 μl tRNA (2mg/ml)), 0.3 μl Nimblegen feducial Cy3 CPK6 and 0.3 μl Cy5 CPK6. Hybridization cocktails were heated to 95°C for 5 minutes then placed at 42°C until loaded onto arrays for hybridization.

growth_protocol: Flies were grown under constant light, temperature, and humidity (25°C; 60% relative humidity) on San Diego Stock Center cornmeal media (DSSC, 2008)

extract_protocol: Flies were immersed in 250 μl of TRIzol® (Invitrogen, Carlsbad, California) and thoroughly homogenized using a 1.5 ml RNAase free pestle (Kimble-Chase, Vineland, New Jersey) fitted to a Pellet Pestle Motor (Sigma-Aldrich, St. Louis, Missouri). After initial homogenization, 550 μl of TRIzol® was added and the solution was homogenized by hand until completely homogeneous. Chloroform (160 μl) was added to the homogenate and then the sample was centrifuged at 12,000 g for 15 minutes at 4°C. The aqueous layer was removed, precipitated with isopropyl alcohol and glycogen (8 μg), then centrifuged for 10 minutes at 4°C to pellet the RNA. The supernatant was removed and the RNA pellet was washed with fresh 75% ethanol. The pellet was dried briefly and then dissolved in 50-100 μl DEPC treated H2O. mRNA was enriched from total RNA by poly A+ selection using a QIAGEN Oligotex mRNA kit (Valencia, California) following manufacture instructions. mRNA was eluted from small spin columns twice with hot 30 μl buffer OEB. mRNA quality and quantity was determined by Bioanalyzer (Agilent, Santa Clara, California) and 260/280 ratio from Nanodrop ND-1000 UV spectrophotometer.

treatment_protocol: We collected replicates for experiments by outcrossing the balancer chromosome with the original wild-type stock (w1118) as follows; 18-24 vials were setup with 15 less than 8 day old virgin w1118 females paired with 5 less than 8 day old males of a particular deficiency line per vial. Df/+ female and males were placed together in vials at less than 60 per vial and then aged for five days. On day five, flies were anesthetized with CO2, sorted into males and females, then placed into 1.5 ml Eppendorf tubes and flash frozen on dry ice. All flies aged together for 5 days constituted a replicate. Flash frozen flies were stored in -80°C before RNA extraction.

tag: gender

value: male

value: whole flies

tag: developmental stage

value: 5 day old mated adults


title: Frozen Tissue_DASL_3B

description: Postmortem brain tissue

tag: tissue preservation


title: Frozen Tissue_DASL_7B rep2

description: Postmortem brain tissue

tag: diagnosis


title: Wholeflies_w1118_Male_R4


title: Wholeflies_ED793_Male_R3


title: Frozen Tissue_DASL_7B rep1

description: Postmortem brain tissue

tag: assay


title: Frozen Tissue_DASL_7A rep2

description: Postmortem brain tissue

tag: tissue


title: Frozen Tissue_DASL_8A

description: Postmortem brain tissue


title: Wholeflies_ED1231_Male_R2


title: Wholeflies_w1118_Male_R6


title: Frozen Tissue_DASL_8B

description: Postmortem brain tissue


title: Wholeflies_w1118_Male_R5


title: Frozen Tissue_DASL_13B rep2

description: Postmortem brain tissue


title: Wholeflies_ED793_Male_R2


title: Frozen Tissue_DASL_7A rep1

description: Postmortem brain tissue


title: Wholeflies_ED385_Male_R1


title: Frozen Tissue_DASL_17A

description: Postmortem brain tissue


title: Wholeflies_ED1231_Male_R1


title: Frozen Tissue_DASL_18B

description: Postmortem brain tissue


title: Frozen Tissue_DASL_15B

description: Postmortem brain tissue


title: Wholeflies_ED1231_Female_R3

value: female


title: Wholeflies_ED385_Male_R2


title: Wholeflies_ED1305_Male_R3


title: Wholeflies_ED793_Male_R1


title: Wholeflies_ED1305_Male_R2


title: Wholeflies_ED1231_Female_R2


title: Frozen Tissue_DASL_14A

description: Postmortem brain tissue


title: Wholeflies_ED1231_Female_R1


title: Frozen Tissue_DASL_12B

description: Postmortem brain tissue


title: Wholeflies_ED793_Female_R3


title: Frozen Tissue_DASL_11A

description: Postmortem brain tissue


title: Wholeflies_ED1305_Male_R1


title: Frozen Tissue_DASL_13B rep1

description: Postmortem brain tissue


title: Frozen Tissue_DASL_16A rep2

description: Postmortem brain tissue


title: Frozen Tissue_DASL_26B

description: Postmortem brain tissue


title: Frozen Tissue_DASL_22A

description: Postmortem brain tissue


title: Frozen Tissue_DASL_23A

description: Postmortem brain tissue


title: Wholeflies_ED793_Female_R1


title: Frozen Tissue_DASL_16A rep1

description: Postmortem brain tissue


title: Frozen Tissue_DASL_24A

description: Postmortem brain tissue


title: Wholeflies_ED793_Female_R2


title: Wholeflies_ED385_Female_R3


title: Wholeflies_ED1305_Female_R1


title: Wholeflies_ED385_Female_R2


title: Wholeflies_ED777_Male_R3


title: Wholeflies_ED385_Female_R1


title: Frozen Tissue_DASL_21C rep2

description: Postmortem brain tissue


title: Frozen Tissue_DASL_20A

description: Postmortem brain tissue


title: Frozen Tissue_DASL_35A

description: Postmortem brain tissue


title: Wholeflies_ED1305_Female_R2


title: Wholeflies_ED777_Male_R2


title: Frozen Tissue_DASL_34A

description: Postmortem brain tissue


title: Wholeflies_ED87_Male_R3


title: Frozen Tissue_DASL_19A

description: Postmortem brain tissue


title: Wholeflies_ED777_Male_R1


title: Frozen Tissue_DASL_32C

description: Postmortem brain tissue


title: Wholeflies_ED87_Male_R2


title: Wholeflies_ED292_Male_R3


title: Frozen Tissue_DASL_31A

description: Postmortem brain tissue


title: Wholeflies_ED87_Male_R1


title: Frozen Tissue_DASL_29B

description: Postmortem brain tissue


title: Frozen Tissue_DASL_33B

description: Postmortem brain tissue


title: Wholeflies_ED292_Male_R1


title: Wholeflies_ED292_Male_R2


title: Frozen Tissue_DASL_21C rep1

description: Postmortem brain tissue


title: Frozen Tissue_DASL_25A rep2

description: Postmortem brain tissue


title: Wholeflies_ED623_Male_R3


title: Wholeflies_ED623_Male_R2


title: Wholeflies_ED623_Male_R1


title: Frozen Tissue_DASL_41B

description: Postmortem brain tissue


title: Frozen Tissue_DASL_44A

description: Postmortem brain tissue


title: Wholeflies_ED2809_Female_R2


title: Wholeflies_ED2809_Female_R3


title: Wholeflies_ED87_Female_R3


title: Frozen Tissue_DASL_37B

description: Postmortem brain tissue


title: Frozen Tissue_DASL_25A rep1

description: Postmortem brain tissue


title: Frozen Tissue_DASL_27A rep2

description: Postmortem brain tissue


title: Wholeflies_ED777_Female_R2


title: Wholeflies_ED2809_Female_R1


title: Wholeflies_ED777_Female_R1


title: Wholeflies_ED777_Female_R3


title: Frozen Tissue_DASL_40B

description: Postmortem brain tissue


title: Frozen Tissue_DASL_50A

description: Postmortem brain tissue


title: Frozen Tissue_DASL_36A

description: Postmortem brain tissue


title: Frozen Tissue_DASL_51B

description: Postmortem brain tissue


title: Wholeflies_ED87_Female_R2


title: Frozen Tissue_DASL_49A

description: Postmortem brain tissue


title: Wholeflies_ED292_Female_R1


title: Wholeflies_ED87_Female_R1


title: Frozen Tissue_DASL_38B

description: Postmortem brain tissue


title: Frozen Tissue_DASL_47A

description: Postmortem brain tissue


title: Wholeflies_ED292_Female_R3


title: Wholeflies_ED2809_Male_R3


title: Frozen Tissue_DASL_46A

description: Postmortem brain tissue


title: Frozen Tissue_DASL_45B

description: Postmortem brain tissue


title: Frozen Tissue_DASL_48B rep2

description: Postmortem brain tissue


title: Frozen Tissue_DASL_27A rep1

description: Postmortem brain tissue


title: Wholeflies_ED292_Female_R2


title: Wholeflies_EDHsp60cED478_Female_R1


title: Wholeflies_ED2809_Male_R2


title: Frozen Tissue_DASL_60A

description: Postmortem brain tissue


title: Wholeflies_ED695_Female_R3


title: Frozen Tissue_DASL_52A

description: Postmortem brain tissue


title: Wholeflies_EDHsp60cED478_Female_R3


title: Frozen Tissue_DASL_55B

description: Postmortem brain tissue


title: Frozen Tissue_DASL_57B rep2

description: Postmortem brain tissue


title: Frozen Tissue_DASL_56A

description: Postmortem brain tissue


title: Frozen Tissue_DASL_54B

description: Postmortem brain tissue


title: Frozen Tissue_DASL_48B rep1

description: Postmortem brain tissue


title: Frozen Tissue_DASL_59A

description: Postmortem brain tissue


title: Wholeflies_ED695_Female_R1


title: Wholeflies_ED62_Male_R2


title: Wholeflies_EDHsp60cED478_Female_R2


title: Wholeflies_ED695_Female_R2


title: Frozen Tissue_DASL_69A

description: Postmortem brain tissue


title: Wholeflies_ED62_Male_R3


title: Wholeflies_ED2809_Male_R1


title: Frozen Tissue_DASL_57B rep1

description: Postmortem brain tissue


title: Frozen Tissue_DASL_61B

description: Postmortem brain tissue


title: Wholeflies_ED62_Female_R3


title: Wholeflies_ED62_Male_R1


title: Wholeflies_ED623_Female_R3


title: Frozen Tissue_DASL_64B

description: Postmortem brain tissue


title: Wholeflies_ED62_Female_R1


title: Wholeflies_ED62_Female_R2


title: Wholeflies_ED623_Female_R1


title: Wholeflies_ED695_Male_R2


title: Wholeflies_ED695_Male_R3


title: Wholeflies_ED623_Female_R2


title: TOLEDO

type: genomic

city: Cold Spring Harbor

first: Claudio

last: Scuoppo

address: 1 Bungtown Rd

institute: Cold Spring Harbor

hyb_protocol: Genomic DNA preparation, labeling and hybridization were performed according to Affymetrix's recommended protocols (Affymetrix, Santa Clara, CA, USA).Label used was biotin.

scan_protocol: Arrays were scanned with GeneChip GSC3000 7G Whole-Genome Association System (Affymetrix).

data_processing:
Data were analyzed using Biodiscovery Nexus 6.0 software; The Value field is the log2 of the ratio of probe intensity (Pi) of the sample over the Reference intensity (Ri).  Value = Log2(Pi/Ri). The Reference intensity has been calculated form hapmap sample arrays.
10 B-NHL cell lines. Affymetrix SNP 6.0 Arrays were used.

molecule: genomic DNA

source_name: B-NHL cell line

growth_protocol: Cells were grown according to the conditions indicated by  ATCC or DMSZ for each cell line.

extract_protocol: DNA from frozen cell pellets was isolated using the QUIAGEN Gentra Purigene Cell Kit, according to the manufacturer instructions.

treatment_protocol: No special treatment was applied to the cells.

tag: disease state

value: B-cell Non Hodgkin Lymphoma

tag: cell line

value: TOLEDO


title: FARAGE

label_protocol: Genomic DNA preparation, labeling and hybridization were performed according to Affymetrix's recommended protocols (Affymetrix, Santa Clara, CA, USA).

value: FARAGE


title: JVM-2


title: NAMALWA

value: NAMALWA


title: MINO

value: MINO


title: RI

value: RI


title: Wholeflies_ED695_Male_R1


title: Wholeflies_EDHsp60cED478_Male_R1


title: Wholeflies_EDHsp60cED478_Male_R3


title: Wholeflies_ED80_Male_R2


title: Wholeflies_ED80_Male_R1


title: Wholeflies_ED80_Female_R2


title: Wholeflies_ED775_Female_R2


title: Wholeflies_ED80_Female_R3


title: KARPAS-422


title: Wholeflies_ED775_Female_R1


title: Wholeflies_ED80_Female_R1


title: Wholeflies_ED775_Male_R1


title: Wholeflies_ED775_Male_R2


title: JEKO-1


title: Wholeflies_ED775_Male_R3


title: GRANTA-519


title: Wholeflies_ED280_Male_R3


title: Wholeflies_ED80_Male_R3


title: Wholeflies_ED775_Female_R3


title: SC-1


title: LPS-StimB_+fl_rep3

city: Freiburg

first: Soeren

last: Boller

address: Stuebeweg 51

department: Cellular & Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
Gene expression after conditional deletion of Ebf1 following LPS-stimulation
Sample name: p2059LPS

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Quick Amp Labeling Kit (One-Colo)r and RNA Spike-In Kit, One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared from sorted mouse splenic B cells using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Ebf1 fl/fl-RERT-Cre mice and heterozygote control animals were treated with 3mg Tamoxifen-Citrate on four consecutive days and were  sacrificed for analysis on the tenth day after the start of the experiment. B220+AA4.1- and B220+AA4.1-CD21lo splenic B cells were sorted from Tamoxifen-treated Ebf1+/flRERTCre and Ebf1fl/flRERTCre mice in triplicates, and total RNA was extracted.

value: spleen

value: B cell

value: Ebf1+/flRERTCre (heterozygote control)

tag: tamoxifen-citrate treatment

value: yes

tag: lps stimulation


title: Wholeflies_ED475_Male_R2


title: Wholeflies_ED475_Male_R3


title: Frozen Tissue_DASL_66B

description: Postmortem brain tissue

value: Control

value: DASL


title: LPS-StimB_+fl_rep2

description:
Gene expression after conditional deletion of Ebf1 following LPS-stimulation
Sample name: p2051LPS


title: LPS-StimB_+fl_rep1

description:
Gene expression after conditional deletion of Ebf1 following LPS-stimulation
Sample name: p2044LPS


title: Wholeflies_ED280_Male_R1


title: LPS-StimB_flfl_rep2

description:
Gene expression after conditional deletion of Ebf1 following LPS-stimulation
Sample name: p2057LPS


title: Wholeflies_ED280_Female_R2


title: RestingB_flfl_rep2

description:
Gene expression after conditional deletion of Ebf1
Sample name: p1785dd

value: no (resting)


title: RestingB_+fl_rep1

description:
Gene expression after conditional deletion of Ebf1
Sample name: p1989md


title: LPS-StimB_flfl_rep1

description:
Gene expression after conditional deletion of Ebf1 following LPS-stimulation
Sample name: p2052LPS


title: RestingB_+fl_rep3

description:
Gene expression after conditional deletion of Ebf1
Sample name: p2044md


title: Wholeflies_ED280_Female_R1


title: Wholeflies_ED475_Male_R1

value: male


title: RestingB_+fl_rep2

description:
Gene expression after conditional deletion of Ebf1
Sample name: p1990md


title: Wholeflies_EDHsp60cED478_Male_R2

value: whole flies


title: LPS-StimB_flfl_rep3

description:
Gene expression after conditional deletion of Ebf1 following LPS-stimulation
Sample name: p2106LPS


title: RestingB_flfl_rep1

description:
Gene expression after conditional deletion of Ebf1
Sample name: p1777dd


title: Wholeflies_ED800_Female_R1

value: 5 day old mated adults


title: Wholeflies_ED280_Female_R3

value: female


title: Wholeflies_ED280_Male_R2


title: Wholeflies_ED776_Male_R3


title: Wholeflies_ED800_Female_R2


title: Wholeflies_ED776_Male_R2


title: Wholeflies_ED800_Male_R2


title: Wholeflies_ED800_Male_R3


title: Wholeflies_ED800_Female_R3


title: Wholeflies_ED776_Male_R1


title: RestingB_flfl_rep3

description:
Gene expression after conditional deletion of Ebf1
Sample name: p1786dd


title: Wholeflies_ED475_Female_R4


title: Wholeflies_ED475_Female_R2


title: Wholeflies_ED475_Female_R3


title: Wholeflies_ED475_Female_R1


title: leaves of wellwater plant #16

city: Yokohama

first: Dung

middle: Tien

last: Le

state: Kanagawa

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

department: Plant Science Center

country: Japan

institute: RIKEN Yokohama Institute

description: Soybean plants were grown on pots. When the plants reached V6 stage (containing 8 trifoliates), drought treatment was imposed by withholding water. The soil moisture content was monitored during the process until the 6th day of water withholding, where soil moisture content reached 5%, the 4th, 6th and 8th trifoliate was collected for total RNA extraction while the 3rd, 5th, and 7th trifoliates were collected for leaves water content determination to identify the severity of the stress. Total RNA from 4th trifoliates were used for expression profiling using soybean gene 1.0 ST array. Four biological repeats per treatment was performed, three biological repeats were chosen for expression profiling

hyb_protocol: Each sample was then hybridized to an Affymetrix soybean gene 1.0 ST array by standard procedures.

scan_protocol: Affymetrix protocol

data_processing: Raw data from. CEL files were initially analyzed by Affymetrix Expression Console with library files supplied by Affymetrix. Analysis were done using RMA method for gene levels without normalization. The log2 transformed data were exported individually for use in analysis in GeneSpring software. The data in text format were imported to GeneSping software and normalized using a 75 percentage threshhold. T-test were used to analyze for statistical significance of the same gene in different condition. To further increase the liability, multivarate test, FDR, was to used to calculate for the corrected p-values. All these tests were performed with Gene Spring GX11 software. Fold change data on the Series record represents drought/well-water.

organism: Glycine max

source_name: soybean 4th trifoliate, V6 vegetative stage

label_protocol: Samples were then fragmented and end-labeled using Affymetrix GeneChip WT Terminal Labeling Kit according to the manufacturer's instructions.

growth_protocol: Soybean plants (cv. Williams 82) were grown on the pots (3 plants per 6-litter pot) containing supermix (Supermix A, Sakata, Japan), water were given to the pots once a day until plants reach V6 stage (35 days) under greenhouse conditions (continuous 30°C temperature, photoperiod of 12 h/12 h, 80 µmol m−2 s−1 photon flux density and 50% relative humidity)

extract_protocol: Soybean leaves were collected and quickly frozen in liquid nitrogen, and stored at -80oC. Total RNA was extracted using triazol reagent, DNAse I treatment was perform prior to quality accessment by Agilent 2100 Bioanalyzer. All samples were prepared using the Ambion WT expression kit for cDNA synthesis, cRNA amplification, and conversion to sense strand cDNA according to the manufacturer's instructions

treatment_protocol: Soybean plants at V6 stage ( 28 days after sowing, contained 7 trifoliates) was withheld from watering in the drought treated pot, in the control (well water) the water was given as usual

value: 4th trifoliate

tag: vegetative stage

value: well water


title: leaves of drought plant #2

value: water withholding


title: AML with normal karyotype (NK) AML69_nk

city: Cantanhede

first: Jacek

middle: Dariusz

last: Marzec

address: Biocant Park

country: Portugal

institute: CoLAB AccelBio

description: AML with normal karyotype (NK)

hyb_protocol: Fifteen ug mRNA was hybridized to the ABI Human Genome Survey Microarray v1

scan_protocol: DIG-labeled targets hybridize to the probes on the arrays and anti-digoxigenin-alkaline phosphatase is added to bind digoxigenin in cDNA targets. The ABI 1700 Expression Array System (ABI, U.S) was used to scan the arrays for chemiluminescence

data_processing: Signal intensity, S/N ratio (signal to noise ratio), and flags values were extracted for each array. The S/N ratio value of 3.0 and flags value of 5000 were used to exclude false positives and/or missing data. For those probes that passed the filtering criterion, the signal values were log2 transformed and normalized across arrays with quantile normalization method after control probes were removed.

label: digoxigenin (DIG)

source_name: peripheral blood

label_protocol: Labeling was done with the Applied Biosystems Chemiluminescent RT-IVT Labeling Kit  (P/N 4340472) using 2 ug high quality total RNA

growth_protocol: Patients’ samples (peripheral blood or bone marrow) were stored in the tissue bank of the St Bartholomew’s Hospital after informed written consent was obtained.

extract_protocol: Total RNA of AML patient samples was extracted from a total of 10 - 20 x 106 thawed cells using Trizol (Gibco-BRL) purification method. RNA quality  was evaluated on the 2100 Bioanalyzer (Agilent Technologies) and the concentration was measured using a NanoDrop spectrophotometer (NanoDrop Technologies).

tag: genotype

value: Normal Karyotype (NK)

value: peripheral blood

value: Acute Myeloid Leukaemia


title: AML with normal karyotype (NK) AML99_nk

description: AML with normal karyotype (NK)


title: leaves of wellwater plant #15

tag: treatment


title: Wholeflies_ED800_Male_R1


title: AML with t(15;17) AML4_1517

description: AML with t(15;17)


title: leaves of wellwater plant #14


title: AML with t(15;17) AML85_1517

description: AML with t(15;17)


title: leaves of drought plant #4


title: leaves of drought plant #1


title: AML with t(8;21) AML84_821

description: AML with t(8;21)


title: AML with t(8;21) AML39_821

description: AML with t(8;21)


title: Wholeflies_ED776_Female_R1


title: Wholeflies_ED489_Male_R2


title: Wholeflies_ED489_Male_R3


title: Wholeflies_ED776_Female_R2


title: Wholeflies_ED499_Male_R3


title: Wholeflies_ED776_Female_R3


title: Wholeflies_ED499_Female_R1


title: Wholeflies_ED499_Female_R3


title: Wholeflies_ED499_Male_R1


title: Wholeflies_ED489_Male_R1


title: antisense mRNA from contaminated site B, campaign 5, well P1 (SBC5P1)

city: AUBIERE

first: Peyret

last: Pierre

address: 24, avenue des landais

country: France

institute: CNRS - Blaise Pascal University

description:
Complex environment.
Enriched antisense mRNA.
Total RNA extracted from groundwater from a site (site B) contaminated with chlorinated solvents (TCE), after a biostimulation treatment, in well P1.

hyb_protocol: For each hybridization experiment, labeled antisenses RNA (Cy3) were vacuum dried and resuspended in the NimbleGen Hybridization Buffer. The arrays were hybridized on a 4-bay NimbleGen Hybridization System (Roche NimbleGen) at 42°C for 72 hr. Arrays were washed with NimbleGen wash buffers I, II and III according to vendor protocols.

scan_protocol: Arrays were scanned using a Scanner Innoscan 900AL (Innopsys, Carbonne, France) at 2 μm resolution. Individual array images were acquired independently, adjusting the PMT gain for each image as recommended using the software Mapix® (Innopsys). Then, for each array image, raw expression data was extracted using the NimbleScan software v2.5 (Roche NimbleGen) and feature intensities were exported as .pair files.

data_processing: The background noise was determined using random probes present on the microarrays (5,707 probes in our experiment). This background noise is defined by two components: the background median intensity (Bposition) and its dispersion (Bdispersion). Finally, a modified signal-to-noise ratio called SNR’ and based on the formula of Verdik (Verdick, D., Handran, S. and Pickett, S. (2002) In LLC, D. P. (ed.), In G. Kamberova (ed.), DNA array image analysis: nuts and bolts. Salem, MA., pp. p. 83-98) is calculated as follow in order to reduce-centralize our data: SNR’ = (probe signal intensity - Bposition)/ Bdispersion. However, spatial effect across array surface is a predominant within-slide experimental artifact that needs to be eliminated before any other normalization procedure (Wang, X., He, H., Li, L., Chen, R., Deng, X.W. and Li, S. (2006) NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinformatics, 22, 2955-2957). Thus, for all array images obtained in this work, surface was segmented to 16 sub-squares according to probe position (X, Y) indicated in pair report. A Perl script was developed to calculate local background noise in all sub-squares and the median SNR’ retrieved from the eight replicates of each probe. Finally, another Perl script was implemented to summarize each replicate probe treated and determine the median value between the eight replicates. Positive hybridization was considered significant for probes having an SNR’ > 1.5 (value to avoid all false positives).

organism: groundwater metagenome

source_name: Chlorinated solvent contaminated site B, campaign 5, well P1

label_protocol: Antisense mRNA obtained from groundwater samples were labelled with Cy3 fluorescent dye (CyDyeTM Post-Labeling Reactive Dye Packs, GE Healthcare) following the manufacturer's instructions.

growth_protocol: Groundwater samples were collected by SITA Remediation Company (Lyon, France) from a contaminated site (site B) by direct pumping from three monitoring wells (P1, P2 and P3) drilled in the deep aquifer. P1: well located upstream to the contamination source. P2: well in the contamination source. P3 : well located downstream to the contamination source.

extract_protocol:
Groundwater samples were transferred to the laboratory, filtered under vacuum and collected onto a 47 mm 0.2 µm pore size GTTP filter (Millipore). Filters were then cut in pieces and placed into 900 µL of nucleic extraction buffer (50 mM glucose, 10 mM EDTA, 25 mM Tris-HCl pH 8.0) as described by Vetriani (Vetriani, C., Tran, H.V. and Kerkhof, L.J. (2003) Fingerprinting Microbial Assemblages from the Oxic/Anoxic Chemocline of the Black Sea. Appl. Environ. Microbiol., 69, 6481-6488). In this protocol, freeze-thaw cycles were d by beat betting 1 min at 30 Hz with 1 g of glass beads of ≤106 μm in diameter (Sigma-Aldrich). Total RNA were extracted using a standard phenol-chloroform-isoamyl alcohol (25:24:1) method followed by a second extraction with an equal volume of chloroform. Nucleic acids were then precipitated, washed in 70% ethanol and resuspended in nuclease-free water. Co-extracted DNA was removed by digestion with 4U of (RNAse-free) DNase I (DNA-free, Ambion) at 37°C for 35 min.

4 µg of total RNA mixture were subjected to an mRNA enrichment protocol using the MicrobExpress kit (Ambion Applied Biosystems), which employs capture hybridization by magnetic separation to remove 16S and 23S rRNA. In a second step, antisense amino-allyl dUTP marked RNA (aRNA) was obtained by amplification with both the MessageAmp II-Bacteria and the Amino-Allyl MessageAmp II kits (Ambion).

tag: origin

value: monitoring well from TCE contaminated site

tag: site

value: B

tag: sampling campaign

tag: well

value: after ERD (enhanced reductive dechlorination)

tag: sample type

value: environmental sample


title: antisense mRNA from contaminated site B, campaign 5, well P3 (SBC5P3)

description:
Complex environment.
Enriched antisense mRNA.
Total RNA extracted from groundwater from a site (site B) contaminated with chlorinated solvents (TCE), after a biostimulation treatment, in well P3.

source_name: Chlorinated solvent contaminated site B, campaign 5, well P3


title: Wholeflies_ED499_Female_R2

tag: gender

tag: strain

tag: developmental stage


title: Wholeflies_ED499_Male_R2


title: gDNA from contaminated site H, well P3 (SHP3)

description:
Complex environment.
gDNA extracted from contaminated site H, after ERD (enhanced reductive dechlorination) treatment in the well P3.

hyb_protocol: For each hybridization experiment, labeled gDNA were vacuum dried and resuspended in the NimbleGen Hybridization Buffer. The arrays were hybridized on a 4-bay NimbleGen Hybridization System (Roche NimbleGen) at 42°C for 72 hr. Arrays were washed with NimbleGen wash buffers I, II and III according to vendor protocols.

scan_protocol: Arrays were scanned using a Scanner Innoscan 900AL (Innopsys, Carbonne, France) at 2 μm resolution. Individual array images were acquired independently, adjusting the PMT gain for each image as recommended using the software Mapix® (Innopsys). Then, for each array image, raw expression data was extracted using the NimbleScan software v2.5. (Roche NimbleGen) and feature intensities were exported as .pair files.

data_processing: The background noise was determined using random probes present on the microarrays (5,707 probes in our experiment). This background noise is defined by two components: the background median intensity (Bposition) and its dispersion (Bdispersion). Finally, a modified signal-to-noise ratio called SNR’ and based on the formula of Verdik (Verdick, D., Handran, S. and Pickett, S. (2002) In LLC, D. P. (ed.), In G. Kamberova (ed.), DNA array image analysis: nuts and bolts. Salem, MA., pp. p. 83-98) is calculated as follows in order to reduce-centralize our data: SNR’ = (probe signal intensity - Bposition)/ Bdispersion. However, spatial effect across array surface is a predominant within-slide experimental artifact that needs to be eliminated before any other normalization procedure (Wang, X., He, H., Li, L., Chen, R., Deng, X.W. and Li, S. (2006) NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinformatics, 22, 2955-2957). Thus, for all array images obtained in this work, surface was segmented to 16 sub-squares according to probe position (X, Y) indicated in pair report. A Perl script was developed to calculate local background noise in all sub-squares and the median SNR’ retrieved from the eight replicates of each probe. Finally, another Perl script was implemented to summarize each replicate probe treated and determine the median value between the eight replicates. Positive hybridization was considered significant for probes having an SNR’ > 1.5 (value to avoid all false positives).

source_name: Chlorinated solvent contaminated site H, well P3

label_protocol: The BioPrime Total Genomic Labelling System (Invitrogen, Carlsbad, California, USA) was used to label the gDNA with Alexa Fluor 3 or 5 fluorescent dyes. The reactions were performed from 1 µg of gDNA template following the manufacturer's instructions and allowed an increase of at least 6-fold the amount of starting gDNA material.

growth_protocol: Groundwater samples were collected by SITA Remediation Company (Lyon, France) from four contaminated sites (B, F, G and H) by direct pumping in four monitoring wells per site (P1, P2, P3 and P4) drilled in the deep aquifer. P1: well located upstream to the contamination source. P2: well in the contamination source. P3 and P4: wells located downstream to the contamination source. For site B, the monitoring of ERD demonstration was performed through a total of 5 sampling campaigns: C1 (T=0), C2 (T=104 days), C3 (T=231 days), C4 (T=291 days) and C5 (T=378 days). For the three other sites (F, G and H), only one sampling campaign was performed after the treatment.

extract_protocol: Groundwater samples were transferred to the laboratory, filtered under vacuum and collected onto a 47 mm 0.2 µm pore size GTTP filter (Millipore). Filters were then cut in pieces and placed into 900 µL of nucleic extraction buffer (50 mM glucose, 10 mM EDTA, 25 mM Tris-HCl pH 8.0) as described by Vetriani (Vetriani, C., Tran, H.V. and Kerkhof, L.J. (2003) Fingerprinting Microbial Assemblages from the Oxic/Anoxic Chemocline of the Black Sea. Appl. Environ. Microbiol., 69, 6481-6488). In this protocol, freeze-thaw cycles were replaced by beat betting 1 min at 30 Hz with 1 g of glass beads of ≤106 μm in diameter (Sigma-Aldrich). gDNA were extracted using a standard phenol-chloroform-isoamyl alcohol (25:24:1) method, followed by a second extraction with an equal volume of chloroform. Nucleic acids were then precipitated, washed in 70% ethanol and resuspended in nuclease-free water.

value: H


title: gDNA from contaminated site G, well P4 (SGP4)

description:
Complex environment.
gDNA extracted from contaminated site G, after ERD (enhanced reductive dechlorination) treatment in the well P4.

source_name: Chlorinated solvent contaminated site G, well P4

value: G


title: gDNA from contaminated site H, well P2 (SHP2)

description:
Complex environment.
gDNA extracted from contaminated site H, after ERD (enhanced reductive dechlorination) treatment in the well P2.

source_name: Chlorinated solvent contaminated site H, well P2


title: gDNA from contaminated site G, well P3 (SGP3)

description:
Complex environment.
gDNA extracted from contaminated site G, after ERD (enhanced reductive dechlorination) treatment in the well P3.

source_name: Chlorinated solvent contaminated site G, well P3


title: gDNA from contaminated site H, well P1 (SHP1)

description:
Complex environment.
gDNA extracted from contaminated site H, after ERD (enhanced reductive dechlorination) treatment in the well P1.

source_name: Chlorinated solvent contaminated site H, well P1


title: gDNA from contaminated site H, well P4 (SHP4)

description:
Complex environment.
gDNA extracted from contaminated site H, after ERD (enhanced reductive dechlorination) treatment in the well P4.

source_name: Chlorinated solvent contaminated site H, well P4


title: gDNA from contaminated site G, well P1 (SGP1)

description:
Complex environment.
gDNA extracted from contaminated site G, after ERD (enhanced reductive dechlorination) treatment in the well P1.

source_name: Chlorinated solvent contaminated site G, well P1


title: antisense mRNA from contaminated site B, campaign 5, well P2 (SBC5P2)

description:
Complex environment.
Enriched antisense mRNA.
Total RNA extracted from groundwater from a site (site B) contaminated with chlorinated solvents (TCE), after a biostimulation treatment, in well P2.

source_name: Chlorinated solvent contaminated site B, campaign 5, well P2


title: CD19+CD10+ cells4, miRNA

city: Madrid

first: Lorena

last: Di Lisio

address: C/ Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

description: 251643611655_S01_miRNA-v1_95_May07_2_4_CD10+CD19+CELLS

hyb_protocol: Hybridization settings: 20 hours, at 55ºC, at 20rpm. Blocking agent, hybridization and washing buffers was performed according to Agilent's recommendations.

scan_protocol: Scan resolution 5um on an Agilent scanner.

data_processing: Limma package was used to import the data. After between-array median normalization by the R program, significant analysis of microarray (SAM) Excel macro was used.

source_name: Non-tumoral control

label_protocol: 100ng of total RNA were dephosphorylated, denaturalizated, treated with ligase T4 and labelled with Cy3 for 2 hours at 16ºC.

extract_protocol: Total RNA was extracted by Trizol reagent (Invitrogen, Carlsbad, CA, USA).

value: CD19+CD10+ cells


title: Wholeflies_ED489_Female_R2


title: CD19+CD10+ cells3, miRNA

description: 251643611655_S01_miRNA-v1_95_May07_1_2_CD10+CD19+CELLS


title: CD19+CD10+ cells2, miRNA

description: US22502553_251643612245_S01_miRNA-v1_10_Apr08_1_2_CD19+CD10+CELLS


title: gDNA from contaminated site F, well P4 (SFP4)

description:
Complex environment.
gDNA extracted from contaminated site F, after ERD (enhanced reductive dechlorination) treatment in the well P4.

source_name: Chlorinated solvent contaminated site F, well P4

value: F


title: CD19+CD10+ cells1, miRNA

description: US22502553_251643612245_S01_miRNA-v1_10_Apr08_1_1_CD19+CD10+CELLS


title: Lymph Node6, miRNA

description: US22502553_251643611977_S01_miRNA-v1_95_May07_2_2_LYMPH-NODE

value: lymph node


title: gDNA from contaminated site F, well P1 (SFP1)

description:
Complex environment.
gDNA extracted from contaminated site F, after ERD (enhanced reductive dechlorination) treatment in the well P1.

source_name: Chlorinated solvent contaminated site F, well P1


title: gDNA from contaminated site F, well P2 (SFP2)

description:
Complex environment.
gDNA extracted from contaminated site F, after ERD (enhanced reductive dechlorination) treatment in the well P2.

source_name: Chlorinated solvent contaminated site F, well P2


title: gDNA from contaminated site F, well P3 (SFP3)

description:
Complex environment.
gDNA extracted from contaminated site F, after ERD (enhanced reductive dechlorination) treatment in the well P3.

source_name: Chlorinated solvent contaminated site F, well P3


title: Wholeflies_ED7007_Male_R3

source_name: Wholeflies, 5 day mated adults

value: male

value: whole flies

value: 5 day old mated adults


title: Lymph Node5, miRNA

description: US22502553_251643611977_S01_miRNA-v1_95_May07_2_1_LYMPH-NODE


title: Wholeflies_ED7007_Female_R2

value: female


title: Wholeflies_ED489_Female_R3


title: Wholeflies_ED7007_Male_R2


title: Lymph Node4, miRNA

description: US22502553_251643611977_S01_miRNA-v1_95_May07_1_4_LYMPH-NODE


title: Wholeflies_ED7007_Female_R1


title: Lymph Node3, miRNA

description: US22502553_251643611977_S01_miRNA-v1_95_May07_1_3_LYMPH-NODE


title: Wholeflies_w1118_Male_R3


title: Lymph Node7, mRNA

description: US22502553_251485029246_S01_GE2-v5_95_Feb07_1_3_LYMPH-NODE

hyb_protocol: Hybridization settings: 17 hours, at 65ºC, at 10rpm. Blocking agent, hybridization and washing buffers was performed according according to Agilent's recommendations.

data_processing: Normalization type: lowess, quantiles, normexp (R program). Analysis: t-test (limma).

source_name: Nom-tumoral control

label_protocol: 500ng RNA were used for cDNA and fluorescent cRNA synthesis. cRNA was purified and hybridized. All reagents and protocols were performed according to Agilent's recommendations.

extract_protocol: Total RNA was extracted by Trizol reagent, purified by QIAGEN RNeasy columns and treated with DNase enzyme.

source_name: Reference pool

value: reference


title: Wholeflies_ED7007_Female_R3


title: CD19+CD10+ cells1, mRNA

description: US22502553_251485042601_S01_GE2-v5_95_Feb07_1_1_CD10+CD19+CELLS

value: CD10+CD19+ cells


title: gDNA from contaminated site B, campaign 5, well P4 (SBC5P4)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C5 in the well P4.

source_name: Chlorinated solvent contaminated site B, campaign 5, well P4


title: gDNA from contaminated site B, campaign 5, well P3 (SBC5P3)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C5 in the well P3.

source_name: Chlorinated solvent contaminated site B, campaign 5, well P3


title: Wholeflies_w1118_Female_R1


title: Wholeflies_w1118_Female_R3


title: Wholeflies_w1118_Male_R2


title: Lymph Node2, miRNA

description: US22502553_251643611592_S01_miRNA-v1_95_May07_2_3_LYMPH-NODE


title: Wholeflies_w1118_Female_R2


title: CD19+CD10+ cells2, mRNA

description: US22502553_251485042601_S01_GE2-v5_95_Feb07_1_2_CD10+CD19+CELLS


title: Wholeflies_w1118_Male_R1


title: Wholeflies_ED7007_Male_R1


title: Lymph Node5, mRNA

description: US22502553_251485029246_S01_GE2-v5_95_Feb07_1_1_LYMPH-NODE


title: gDNA from contaminated site B, campaign 5, well P2 (SBC5P2)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C5 in the well P2.


title: Wholeflies_ED489_Female_R1


title: gDNA from contaminated site B, campaign 5, well P1 (SBC5P1)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C5 in the well P1.

source_name: Chlorinated solvent contaminated site B, campaign 5, well P1


title: Lymph Node6, mRNA

description: US22502553_251485029246_S01_GE2-v5_95_Feb07_1_2_LYMPH-NODE


title: Lymph Node1, miRNA

description: US22502553_251643611592_S01_miRNA-v1_95_May07_2_2_LYMPH-NODE


title: gDNA from contaminated site B, campaign 4, well P4 (SBC4P4)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C4 in the well P4.

source_name: Chlorinated solvent contaminated site B, campaign 4, well P4


title: Tonsil2, miRNA

description: US22502553_251643611460_S01_miRNA-v1_95_May07_1_2_TONSIL

value: tonsil


title: Tonsil4, miRNA

description: US22502553_251643611460_S01_miRNA-v1_95_May07_1_4_TONSIL


title: Tonsil3, miRNA

description: US22502553_251643611460_S01_miRNA-v1_95_May07_1_3_TONSIL


title: gDNA from contaminated site B, campaign 4, well P3 (SBC4P3)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C4 in the well P3.

source_name: Chlorinated solvent contaminated site B, campaign 4, well P3


title: Tonsil1, miRNA

description: US22502553_251643611460_S01_miRNA-v1_95_May07_1_1_TONSIL


title: gDNA from contaminated site B, campaign 4, well P2 (SBC4P2)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C4 in the well P2.

source_name: Chlorinated solvent contaminated site B, campaign 4, well P2


title: B Cells, mRNA

description: US22502553_251485019374_S01_GE2-v5_95_Feb07_1_3_Bcell_TONSIL

value: B cells


title: Lymph Node1, mRNA

description: US22502553_251485029245_S01_GE2-v5_95_Feb07_1_1_LYMPH-NODE


title: Lymph Node4, mRNA

description: US22502553_251485029245_S01_GE2-v5_95_Feb07_1_4_LYMPH-NODE


title: Burkitt Lymphoma12, miRNA

description:
251643612182_S01_miRNA-v1_95_May07_2_3_BL
Corresponds to GSM568278

source_name: Tumoral sample

value: B-cell lymphoma

tag: tumor type

value: Burkitt lymphoma


title: gDNA from contaminated site B, campaign 3, well P4 (SBC3P4)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C3 in the well P4.

source_name: Chlorinated solvent contaminated site B, campaign 3, well P4

value: monitoring well from TCE contaminated site

value: B

value: after ERD (enhanced reductive dechlorination)


title: Fresh tonsil, mRNA

description: US22502553_251485019374_S01_GE2-v5_95_Feb07_1_2_FRESH_TONSIL

tag: tissue

value: fresh tonsil


title: gDNA from contaminated site B, campaign 3, well P3 (SBC3P3)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C3 in the well P3.

source_name: Chlorinated solvent contaminated site B, campaign 3, well P3

value: environmental sample


title: Burkitt Lymphoma11, miRNA

description:
251643612182_S01_miRNA-v1_95_May07_2_2_BL
Corresponds to GSM568277


title: gDNA from contaminated site B, campaign 3, well P2 (SBC3P2)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C3 in the well P2.

source_name: Chlorinated solvent contaminated site B, campaign 3, well P2


title: gDNA from contaminated site B, campaign 3, well P1 (SBC3P1)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C3 in the well P1.

source_name: Chlorinated solvent contaminated site B, campaign 3, well P1


title: Burkitt Lymphoma10, miRNA

description:
251643611655_S01_miRNA-v1_95_May07_1_1_BL
Corresponds to GSM568276


title: gDNA from contaminated site B, campaign 2, well P4 (SBC2P4)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C2 in the well P4.

source_name: Chlorinated solvent contaminated site B, campaign 2, well P4


title: Burkitt Lymphoma9, miRNA

description:
251643611654_S01_miRNA-v1_95_May07_2_4_BL
Corresponds to GSM568275


title: gDNA from contaminated site B, campaign 4, well P1 (SBC4P1)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C4 in the well P1.

source_name: Chlorinated solvent contaminated site B, campaign 4, well P1


title: gDNA from contaminated site B, campaign 2, well P2 (SBC2P2)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C2 in the well P2.

source_name: Chlorinated solvent contaminated site B, campaign 2, well P2


title: Burkitt Lymphoma8, miRNA

description:
251643611654_S01_miRNA-v1_95_May07_2_3_BL
Corresponds to GSM568274


title: Tonsil4, mRNA

description: US22502553_251485019373_S01_GE2-v5_95_Feb07_1_4_TONSIL


title: Tonsil3, mRNA

description: US22502553_251485019373_S01_GE2-v5_95_Feb07_1_3_TONSIL


title: Tonsil5, mRNA

description: US22502553_251485019374_S01_GE2-v5_95_Feb07_1_1_TONSIL


title: Tonsil2, mRNA

description: US22502553_251485019373_S01_GE2-v5_95_Feb07_1_2_TONSIL


title: Tonsil1, mRNA

description: US22502553_251485019373_S01_GE2-v5_95_Feb07_1_1_TONSIL


title: gDNA from contaminated site B, campaign 2, well P3 (SBC2P3)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C2 in the well P3.

source_name: Chlorinated solvent contaminated site B, campaign 2, well P3


title: Burkitt Lymphoma6, mRNA

description: US22502553_251485032089_S01_GE2-v5_95_Feb07_1_4-BL

tag: tissue type


title: 155 P12 vs wt P12

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: Features were extracted with an image analysis tool version A.10.5.1.1 using the GE2-V4_95_Feb07 protocol (Agilent Technologies).

hyb_protocol: Labeled samples was mixed and hybridized to the microarray according to the supplier`s protocol (Agilent Technologies). Washing of the hybridized arrays was done with the SSC protocol according supplier`s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies) and recommended settings.

data_processing: The extracted MAGE-ML files was analyzed with the Rosetta Resolver Biosoftware, Build 7.2.2 SP 1.3.1 (Rosetta Biosoftware, Seattle, USA). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

label_protocol: RNA labeling was performed with the dual color Quick Amp Labeling Kit (Agilent Technologies) according the suppliers recommendation. In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and resulting cRNA was labeled either with Cyanine 3-CTP.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier. Briefly, 5x10e6 cells were resuspended in 1 ml TRIzol, shock frozen and stored at –80°C. Cells in Trizol were thawed and further processed for total RNA isolation as described by the manufacturer. The amount of RNA was determined by OD260/280 nm measurement using a NanoDrop 1000 spectrophotometer (Kisker, Steinfurt, Germany). The RNA size, integrity and the amount of total RNA were measured with a Bioanalyzer 2100 (Agilent Technologies, Waldbronn, Germany) on a RNA Nano 6000 microfluidics kit.

treatment_protocol: BMM were generated as described (Collins et al., J Cell Sci. 1997 Jan;110 ( Pt 2):191-200). In brief, monocytes were isolated from the femur and tibia of C57Bl/6 mice. These were plated in 10-cm dishes in RPMI medium containing 10% hi FCS and 30% L929 supernatant as source of M-CSF. After 7d in culture these cells were washed twice with PBS and replated ON in RPMI medium containing 10% hi FCS and 10% L929 supernatant.

tag: infection

value: H.pylori P12

tag: cell type

value: bone marrow derived macrophages (BMM)

tag: genotype/variation

value: miR-155 KO

label_protocol: RNA labeling was performed with the dual color Quick Amp Labeling Kit (Agilent Technologies) according the suppliers recommendation. In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and resulting cRNA was labeled either with Cyanine 5-CTP.

treatment_protocol: BMM were generated as described (Collins et al., J Cell Sci. 1997 Jan;110 ( Pt 2):191-200). In brief, monocytes were isolated from the femur and tibia of miR-155 KO mice on C57Bl/6 background (B6.Cg-Mir155tm1.1Rsky). These were plated in 10-cm dishes in RPMI medium containing 10% hi FCS and 30% L929 supernatant as source of M-CSF. After 7d in culture these cells were washed twice with PBS and replated ON in RPMI medium containing 10% hi FCS and 10% L929 supernatant.

value: wild type


title: Burkitt Lymphoma3, miRNA

description:
251643611653_S01_miRNA-v1_95_May07_2_4_BL
Corresponds to GSM568269


title: Burkitt Lymphoma4, miRNA

description:
251643611654_S01_miRNA-v1_95_May07_1_2_BL
Corresponds to GSM568270


title: wt P12 vs 155 P12

source_name: wt P12


title: Lymph Node2, mRNA

description: US22502553_251485029245_S01_GE2-v5_95_Feb07_1_2_LYMPH-NODE

source_name: Nom-tumoral control

value: lymph node

source_name: Reference pool


title: Burkitt Lymphoma7, miRNA

description:
251643611654_S01_miRNA-v1_95_May07_2_1_BL
Corresponds to GSM568273


title: Burkitt Lymphoma6, miRNA

description:
251643611654_S01_miRNA-v1_95_May07_1_4_BL
Corresponds to GSM568272


title: gDNA from contaminated site B, campaign 2, well P1 (SBC2P1)

description:
Complex environment.
gDNA extracted from contaminated site B, campaign C2 in the well P1.

source_name: Chlorinated solvent contaminated site B, campaign 2, well P1


title: Burkitt Lymphoma2, miRNA

description:
251643611653_S01_miRNA-v1_95_May07_2_3_BL
Corresponds to GSM568268