title: Arsenic-treated rat L2 Cells D1_D3 replication3

source_name: Total RNA from L2 cells treated with arsenite for 1 day labeled with Alexa546 (green).


title: Arsenic-treated rat L2 Cells D3_D5 replication2

status: Public on Dec 23 2011

type: RNA

city: Stillwater

first: Tingting

last: Weng

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

country: USA

institute: Oklahoma State University

description: Sample replication 1 of 6. L2 cells were exposed with 0.75 uM of arsenite for 0, 1, 3, 5, and 7 days (C, D1, D3, D5 and D7). The samples were arranged for hybridization using a loop design. For each paired sample, dye flip and three biological replications were performed for each sample.

hyb_protocol: The cDNAs were column-purified and mixed with 2x formamide hybridization buffer (50% formamide, 6 x SSC, 0.2% SDS) in equal volume.  The paired cDNAs were then combined in 1:1 ratio (v/v) and denatured at 80oC for 10 min.  The slide was blocked with 0.1% SDS, 1% BSA and 3 x SSC at 42oC for 40 min and hybridized with labeled cDNAs at 45oC for 48 h.  The slide was then washed and incubated with Cy-3 or Alexa 647-labeled dendrimers at 45oC for 3 h.

scan_protocol: ScanArray Express laser scanner (PerkinElmer, Boston, MA). The signal intensity for each spot was obtained from the scanned slides using GenePix 5.0

data_processing: The raw data were LOWESS normalized, the bad and weak spots were removed,  followed by one-class statistical SAM test using a false discovery rate (q value) of <0.05 to identify significantly changed genes.

molecule: total RNA

organism: Rattus norvegicus

source_name: Total RNA from L2 cells treated with arsenite for 3 days labeled with Alexa546 (green).

label_protocol: Total RNA (3 ug each) were reverse-transcribed into cDNA with Alexa 546 (green)- or Alexa 647 (red)-specific primer of the 3DNA 350 expression kit (Genishere Inc., Hatfield, PA, USA), purified with Microcom YM-30 columns, and mixed with an equal amount of 2x formamide hybridization buffer (50% formamide, 6x SSC, 0.2% SDS, and 10x Denhardt solution).

growth_protocol: L2 cells (passages 30-40) were cultured in 30 or 100 mm cell culture dishes in F12 K medium supplemented with 10% of heat-inactivated FBS and antibiotics (1 x penicillin/streptomycin). When grown to 80 to 90% confluence, the cells were treated with arsenite (0-5 uM) for various times (0 to 7 days).  At the end of incubation, the cells were used for the viability assay, DNA microarray analysis and real-time PCR analysis.

extract_protocol: TRI reagents (Molecular Research Center, Cincinnati, OH, USA).

tag: Lung epithelial cell line (L2)

source_name: Total RNA from L2 cells treated with arsenite for 5 days labeled with Alexa647 (red).


title: Arsenic-treated rat L2 Cells D1_C replication6

source_name: Total RNA from L2 cells treated with arsenite for 0 day labeled with Alexa647 (red).


title: Arsenic-treated rat L2 Cells D3_D1 replication4

growth_protocol: L2 cells (passages 30-40) were cultured in 30 or 100 mm cell culture dishes in F12 K medium supplemented with 10% of heat-inactivated FBS and antibiotics (1 x penicillin/streptomycin). When grown to 80 to 90% confluence, the cells were treated with arsenite (0-5 µM) for various times (0 to 7 days).  At the end of incubation, the cells were used for the viability assay, DNA microarray analysis and real-time PCR analysis.

source_name: Total RNA from L2 cells treated with arsenite for 1 day labeled with Alexa647 (red).


title: Arsenic-treated rat L2 Cells D7_C replication5

source_name: Total RNA from L2 cells treated with arsenite for 7 days labeled with Alexa546 (green).


title: UPN94 t(8;21)-AML_Peripheral Blood_No dilution_Good Quality Controls_Diagnosis

status: Public on Dec 24 2011

city: Angers

first: Philippe

last: Guardiola

state: Maine et Loire

address: 4 rue Larrey

country: France

institute: Angers University Hospital

hyb_protocol: Hybridization on Illumina HumanHT-12 v3 Expression BeadChips and staining were performed according to Illumina’s protocol.

scan_protocol: Detection of cRNAs on microarrays using an I-Scan system were performed according to Illumina’s protocol.

data_processing: GenomeStudio 2010.3 software (Illumina Inc., San Diego, USA) and its Gene Expression Analysis Module (version 1.8.0) were used for signal extraction. No normalization was applied to the primary probe data.

label: biotin

organism: Homo sapiens

source_name: Human acute myeloid leukemic cells

label_protocol: The Illumina Total Prep RNA Amplification Kit (Applied Biosystems / Ambion, Austin, USA) was used to generate biotinylated, amplified cRNA according to the manufacturer recommendations.

extract_protocol: Total RNAs were extracted from 10e7 thawed cells using RNEasy® Mini Kits (Qiagen Incorporation, Valencia, USA). Total RNA quantification was performed using the Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Incorporation, Waltham, USA) according to manufacturer recommendations. Integrity of the extracted RNAs was assessed with the Bioanalyzer 2100 and the RNA6000 Nano kit (Agilent Technologies Incorporation, Santa Clara, USA).

treatment_protocol: Blasts and mononuclear cells were purified by Ficoll-Hypaque density gradient centrifugation from bone marrow or peripheral blood samples (Nygaard, Oslo, Norway). Isolated cell samples were then immediately cryopreserved.

tag: duplicates

value: no

tag: aml subtype

tag: cell source

value: Peripheral Blood

tag: time point

value: Diagnosis

tag: dilution

value: No dilution

tag: quality control

value: Good Quality Controls


title: Arsenic-treated rat L2 Cells D1_C replication5


title: Arsenic-treated rat L2 Cells D7_D5 replication6


title: Liver control tech rep 2

city: Paris

first: Daniel

last: Vaiman

address: 24 rue du Faubourg St Jacques

department: Genetics and Development

institute: INSERM

description: Mix of placentas from 6 animals from three females obtained by cesarean delivery at 19 days of gestation

hyb_protocol: Hybridization was performed by Nimblegen facility (Reikjavijk, Iceland)  following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc.,(Reikjavijk, Iceland) following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: Liver control

label_protocol: Labeling was performed by NimbleGen Systems Inc., (Reikjavijk, Iceland)following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Animals were grown in standard animal facilities with a 12h day period.

extract_protocol: Total RNA was extracted using  Trizol, treated with RNAse free DNASe. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Nimblegen facility (Reikjavijk, Iceland)

treatment_protocol: Females were fed from the first day of gestation either with a normal chow (controls) or with a isocaloric chow depleted to 1/3 in protein (casein) content. Details in Buffat et al (Journal of Pathology 2007a and Endocrinology, 2007b)

tag: tissue

value: Liver

tag: disease state


title: Arsenic-treated rat L2 Cells C_D1 replication3

source_name: Total RNA from L2 cells treated with arsenite for 0 day labeled with Alexa546 (green).


title: Lung control tech rep 2

description: Mix of lungs from 6 animals from three females obtained by cesarean delivery at 19 days of gestation

source_name: Lung control

value: Lung


title: Arsenic-treated rat L2 Cells D1_C replication4


title: Arsenic-treated rat L2 Cells C_D1 replication2


title: Lung protein restriction tech rep 1

description: Mix of lungs from 6 animals from three females submitted to a hypoproteic diet during gestation obtained by cesarean delivery at 19 days of gestation

source_name: Lung protein restriction

value: IUGR


title: Liver protein restriction tech rep 2

description: Mix of livers from 6 animals from three females submitted to a hypoproteic diet during gestation obtained by cesarean delivery at 19 days of gestation

source_name: Liver protein restriction


title: Liver control tech rep 1


title: Arsenic-treated rat L2 Cells C_D1 replication1


title: Heart control tech rep 2

description: Mix of hearts from 6 animals from three females obtained by cesarean delivery at 19 days of gestation

source_name: Heart control

value: Heart


title: Liver protein restriction tech rep 1


title: Arsenic-treated rat L2 Cells D3_D5 replication1


title: Lung protein restriction tech rep 2


title: Heart protein restriction tech rep 1

description: Mix of hearts from 6 animals from three females submitted to a hypoproteic diet during gestation obtained by cesarean delivery at 19 days of gestation

source_name: Heart protein restriction


title: Heart control tech rep 1


title: Heart protein restriction tech rep 2


title: Lung control tech rep 1


title: w1_x_Har_21Day_Rep3

city: Worcester

first: Jie

last: Wang

state: MA

address: 364 Plantation St.

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

description: The first column is the transposon ids from flybase or transcript ids from RefSeq. The second column is the the summarized/normalized expression value.

hyb_protocol: Recommended Affymetrix protocol

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G according to manufacturer's instructions.

data_processing: Since transposons account for more than 10% of the probes on the tiling array, a special normalization workflow has been taken to avoid over-normalization of signals. Coordinates and raw signal values for Drosophila tiling 2.0R array probes were extracted from Affymetrix Tiling Array Software. Then probes mapped to transposon regions were identified. The remaining non-transposon probes were quantile-normalized across wild type and mutant replicates based on the assumption that the overall signal distribution of these probes should remain the same across the different strains. Then the signals for transposon probes were calculated by looking up the normalized values of non-transposon probes at same raw signal level. To summarize the signal for each transposon element, probes mapped to any copy of the element were grouped together and Hodges-Lehmann estimator (ref1) was used to calculate the pseudomedian of their normalized signals. We used pseudomedian as it is less sensitive to the large number of outlier probes (probes with value of 1) in the tiling array experiments. Differentially expressed transposon elements were identified by contrasting their pseudomedian values in three mutant replicates against three wild type replicates. To correct for multiple testing, False Discovery Rates (FDRs) were calculated from t-test P-values. FDR<0.05 were used to call significantly changed transposons. Expression values of mRNAs were summarized by calculating the pseudomedian of probes mapped to each of the RefSeq mRNA transcripts. Differentially expressed transcripts were identified using FDR<0.05 cutoff.

organism: Drosophila melanogaster

source_name: w1_x_Har, 21Day

label_protocol: GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix)

growth_protocol: The flies were raised at 25 deg C, on standard cornmeal media, and the adults were fed wet yeast paste.

extract_protocol: The RNA was purified using Qiagen RNAeasy® kit following the manufacturer's protocol (Qiagen)

treatment_protocol: The ovaries were dissected in 1X Robb's medium, follwed by RNA extraction.

tag: genotype/variation

tag: age

value: 21 day

value: ovaries


title: w1_x_Har_21Day_Rep2


title: Placenta protein restriction tech rep 2

description: Mix of placentas from 6 animals from three females submitted to a hypoproteic diet during gestation obtained by cesarean delivery at 19 days of gestation

source_name: Placenta protein restriction

value: Placenta


title: Kidney control tech rep 2

description: Mix of kidneys from 6 animals from three females obtained by cesarean delivery at 19 days of gestation

source_name: Kidney control

value: Kidney


title: Kidney protein restriction tech rep 1

description: Mix of kidneys from 6 animals from three females submitted to a hypoproteic diet during gestation obtained by cesarean delivery at 19 days of gestation

source_name: Kidney protein restriction


title: w1_x_Har_2-4Day_Rep2

source_name: w1_x_Har, 2-4Day

value: 2-4 day


title: w1_x_Har_21Day_Rep1


title: w1_x_Har_2-4Day_Rep1


title: w1_x_Har_2-4Day_Rep3


title: Placenta control tech rep 1

source_name: Placenta control


title: Har_2-4Day_Rep3

source_name: Har, 2-4Day

value: Har


title: Placenta protein restriction tech rep 1


title: Placenta control tech rep 2


title: HCC1937/BRCA1, replicate2

city: Madrid

first: Beatriz

last: Martinez

address: Calle Melchor Fernandez Almagro 3

department: Human Cancer Genetics

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: BRCA1 gene is expressed.

hyb_protocol: Exiqon miRNA microarray slides containing denaturated labeled RNA in 1x hybridization buffer were hybridized at 56ºC for 16h.

scan_protocol: Slides were scanned using an Agilent array scanner set to 10μm wit 100PMT sensitivity in an ozone-free-environment. Fluorescence intensities on scanned images were quantified using Feature Extraction software (Agilent) using the modified Exiqon protocol.

data_processing: Background correction was carried out using normexp, and data was normalized using quantiles between-arrays normalization. Data processing was carried out using Bioconductor´s limma package.

label_protocol: 300ng of total RNA were treated with Calf Intestine Phosphatase and than labeled with Hy3 fluorescent dye.

growth_protocol: Cell lines were grown in 10% FBS DMEM media with 2% penicillin/streptomycin at 37ºC, 5% CO2 atmosphere and 80% humidity.

extract_protocol: Total RNA was extracted from cell pellets using Trizol following the manufacturer's recommendations.

tag: cell line

tag: cell type

value: breast cancer cells

tag: brca1 expression

value: yes


title: Har_2-4Day_Rep2


title: Har_2-4Day_Rep1

description: Results files: the first column is the transposon ids from flybase or transcript ids from RefSeq. The second column is the the summarized/normalized expression value.


title: Kidney control tech rep 1


title: Ax LN met R3b

type: genomic

city: Amsterdam

first: Chris

last: Doornebal

address: Plesmanlaan 121

department: Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: aCGH data axillary LN metastasis recipient 3b

hyb_protocol: Samples were hybridized and washed according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

scan_protocol: Arrays were scanned with the MS 200 Microarray Scanner and the MS 200 Data Collection Software according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

data_processing:
Background correction and normalization was performed in the NimbleScan program according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).
Probe annotation and corrected log2 ratios were imported into the R programming language from the NimbleScan output [*segMNT_GEO.txt].

molecule: genomic DNA

organism: Mus musculus

source_name: Axillary LN metastasis DNA from WT recipient

label_protocol: Tumor, metastasis and spleen samples were labeled with Nimblegen dual-color DNA labeling kit according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

extract_protocol: Genomic DNA of tumor, metastasis and spleen samples was extracted by proteinase K lysis and organic extraction with phenol-chloroform.

tag: donor/recipient

value: Recipient

value: Metastasis

tag: site

value: LN, axillary

tag: related to donor

tag: mouse id

source_name: Splenic DNA donor 3

value: spleen

tag: derived from donor (id)


title: Renal LN met R3c

description: aCGH data renal LN metastasis recipient 3c

source_name: Renal LN metastasis DNA from WT recipient

value: LN, renal


title: Lung met R3b

description: aCGH data lung metastasis recipient 3b

source_name: Lung metastasis DNA from WT recipient


title: Lung met R3c

description: aCGH data lung metastasis recipient 3c


title: Ax LN met R3c

description: aCGH data axillary LN metastasis recipient 3c


title: Caud LN met R3b

description: aCGH data caudal LN metastasis recipient 3b

source_name: Caudal LN metastasis DNA from WT recipient

value: LN, caudal


title: Caud LN met R3a

description: aCGH data caudal LN metastasis recipient 3a


title: Tumor R3c

description: aCGH data mammary tumor recipient 3c

source_name: Mouse mammary tumor DNA from WT recipient

value: Primary tumor

value: Mamma


title: Tumor R3b

description: aCGH data mammary tumor recipient 3b


title: WT vs d_cps4

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

description: Raw data file: slide4-3_1.txt

hyb_protocol: Agilent hybridization protocol for Two-color microarray-based Gene expression analysis. Version 5.5

scan_protocol: Scanned on an ScanArray Express 4000 scanner (Perkin Elmer, Wellesley, MA). Images were quantified using ImaGene Version 7.5 software (BioDiscovery Inc., Marina Del Rey, CA, USA).

data_processing: scanned slides were Lowess normalised using Prep (van Hijum, Applied Bioinformatics 2003 2(4):241-244).

organism: Lactiplantibacillus plantarum

source_name: cps cluster, wildtype

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: non-pH controlled Batch cultivation in CDM (chemical defined medium).

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

treatment_protocol: sampled at D600= 1 (or corresponding dry weight for delta cps1-3 and delta cps 1-4)

source_name: cps cluster, knockout


title: Kidney protein restriction tech rep 2

value: IUGR


title: d_cps1-4 vs d_cps1

description: Raw data file: slide4-2_2.txt


title: d_cps1 vs WT

description: Raw data file: slide4-3_2.txt


title: d_cps3 vs WT

description: Raw data file: slide4-2_1.txt


title: WT vs cps1-3

description: Raw data file: slide1-1_2.txt


title: Arsenic-treated rat L2 Cells D5_D3 replication4

description: Sample replication 1 of 6. L2 cells were exposed with 0.75 uM of arsenite for 0, 1, 3, 5, and 7 days (C, D1, D3, D5 and D7). The samples were arranged for hybridization using a loop design. For each paired sample, dye flip and three biological replications were performed for each sample.

source_name: Total RNA from L2 cells treated with arsenite for 5 days labeled with Alexa546 (green).

tag: Lung epithelial cell line (L2)

source_name: Total RNA from L2 cells treated with arsenite for 3 days labeled with Alexa647 (red).


title: d_cps4 vs d_cps1-4

description: Raw data file: slide4-4_1.txt


title: Lung met R3a

description: aCGH data lung metastasis recipient 3a

value: Lung


title: WT vs d_cps2

description: Raw data file: slide4-4_2.txt


title: Ax LN met R3a

description: aCGH data axillary LN metastasis recipient 3a


title: cps1-3 vs WT

description: Raw data file: slide1-1_1.txt


title: Lung met R2c

description: aCGH data lung metastasis recipient 2c

source_name: Splenic DNA donor 2


title: Tumor D3

description: aCGH data K14cre;Cdhf/f;Trp53f/f derived donor tumor 3

source_name: Mouse mammary tumor DNA from K14cre;Cdhf/f;Trp53f/f donor

value: Donor


title: Tumor R3a

description: aCGH data mammary tumor recipient 3a


title: Caud LN met R2b

description: aCGH data caudal LN metastasis recipient 2b


title: d_cps2 vs d_cps3

description: Raw data file: slide4-1_1.txt


title: WT vs d_cps1-4

description: Raw data file: slide4-1_2.txt


title: Tumor R2c

description: aCGH data mammary tumor recipient 2c


title: Arsenic-treated rat L2 Cells D1_D3 replication2

source_name: Total RNA from L2 cells treated with arsenite for 1 day labeled with Alexa546 (green).


title: Ax LN met R2b

description: aCGH data axillary LN metastasis recipient 2b


title: TSB_R4 transcriptome profile SVR

city: Cambridge

first: Tsute

last: Chen

address: 245 First Street

department: Microbiology

institute: The Forsyth Institute

hyb_protocol: RNA-DNA hybridization was performed on microarray slides covered with a HybriWell chamber (Grace Bio-Labs, Bend, OR, USA). Prehybridization was carried out for 90 min at 42°C in a 400 μl solution containing 343 μl Long Oligo hybridization buffer [94 mM Tris/HCl pH 7.0, 9.4 mM EDTA, 29.15% formamide, 5.83X SSC, 0.12% SDS], 0.5 mg/ml BSA, and 0.1 mg/ml salmon sperm DNA (Applied Biosystems/Ambion) . The HybriWell chamber was then removed and the slide washed with nuclease-free water. The slide was spin-dried at low-speed for 2 min, and a new HybriWell chamber was sealed onto the slide. For each microarray 3 μg of labeled RNA was denatured at 65°C for 5 min in a final volume of 300 μl hybridization solution containing 257 μl Long Oligo hybridization buffer, 3 μl Alignment Oligo (NimbleGen), and 0.7 mg/ml salmon sperm DNA. Denatured RNA was then loaded in the chamber and hybridization was carried out at 42°C for 16 hours with 10 rpm rotation in an oven (Labnet, Edison, NJ, USA). The slide was washed according to NimbleGen’s protocol (NimbleGen Arrays User’s Guide Gene Expression Analysis).

scan_protocol: After washing and drying, the microarray slides were immediately scanned in a GenePix 4000B Scanner (Axon Instruments, Union City, CA, USA) using the provided GenePix Pro 6.1 software. NimbleScan v2.5 software was then used for spot features extraction from the scanned images.

data_processing:
Two types of normalizations were performed – normalization by DNA reference array and between-array normalization. For DNA reference array normalization, intensities of RNA signals were normalized with signals from DNA reference arrays (raw array data provided additionally) that were hybridized with fragmented genomic DNA chemically labeled with The Label IT Cy3 Reagent (Mirus Bio, Madison, WI, USA) . Both normalizations were done using the Bioconductor R package “tilingArray”.
After normalization, the signal intensities for each probe were further adjusted and smoothed by the HM-SVM algorithm (Yu et al, Bioinformatics. 2010 26:1423-30).

organism: Porphyromonas gingivalis

source_name: Laboratory culture in TSB medium

label_protocol: The Label IT Cy3 Reagent (Mirus Bio, Madison, WI, USA) was used to directly label total RNA. To optimize the RNA labeling efficiency, 1 μg RNA was mixed with 4 μl Label IT Reagent and incubated in a 100-μl final volume for 4 hours at 37°C. To improve hybridization efficiency, the labeled RNA was fragmented to an average size of 80-100 nucleotides with 0.25 volume of 5X Fragmentation Buffer (Mirus Bio) and incubated at 94°C for 15 min. The fragmented and fluorescently labeled RNA was purified with the mirVana miRNA Isolation Kit before hybridization.

growth_protocol: P. gingivalis strain W83 was routinely maintained on the blood agar plates BAPHK containing defibrinated sheep blood (5% v/v), hemin (1µg/ml), and vitK/menadione (0.5µg/ml), at 37°C in an anaerobic chamber containing 95% nitrogen and 5% carbon dioxide. Cells were cultured under the same conditions in three different media: i) BAPHK; ii) TSB: trypticase soy broth supplemented with hemin (1µg/ml) and vitK/menadione (0.5µg/ml); and iii) MIN: a chemically defined minimal liquid medium providing alpha-ketogluterate and bovine serum albumin (BSA) as the only protein sources. For BAPHK cultures, colonies grown on the plates for 48 hours were used. For liquid cultures, pre-warmed and pre-reduced medium was inoculated with an aliquot of overnight TSB culture so that the dilution rates were 1:100 and 2:100 for TSB and MIN, respectively. Liquid cultures were allowed to reach mid-log phase (OD550 0.4-0.5) prior to harvest.

extract_protocol: Lysis of bacterial cells was performed according to the protocol provided with the MasterPure RNA Purification Kit (Epicentre, Madison, WI, USA). The lysate was treated with Proteinase K at 65°C for 15 min and then placed on ice. To increase the recovery rate of small RNA 0.1 volume of 5 M NaCl was added to the lysate. Acid-phenol: chloroform (5:1) (v:v) extraction was then done using Phase-Lock Gel Heavy tubes (Eppendorf, Hauppauge, NY, USA). Total RNA in the upper aqueous phase was purified with a solid-phase extraction filter supplied in the mirVana miRNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the recommended protocol. The filter-trapped RNA was then washed and eluted with the provided wash solutions and elution buffer. To completely remove genomic DNA, the RNA extract was treated twice with Turbo DNase (Applied Biosystems/Ambion) at 37°C for 30 min, and purified again with the mirVana miRNA Isolation Kit.

tag: strain

tag: media

value: TSB

tag: labeled molecule

value: RNA

tag: harvest time

value: mid-log phase


title: Tumor R2b

description: aCGH data mammary tumor recipient 2b

tag: tissue


title: Ax LN met R2a

description: aCGH data axillary LN metastasis recipient 2a


title: Tumor R2a

description: aCGH data mammary tumor recipient 2a


title: Lung met R2a

description: aCGH data lung metastasis recipient 2a


title: Ax LN met R1d

description: aCGH data axillary LN metastasis recipient 1d

source_name: Splenic DNA donor 1


title: Tumor D2

description: aCGH data K14cre;Cdhf/f;Trp53f/f derived donor tumor 2


title: Lung met R2b

description: aCGH data lung metastasis recipient 2b


title: Lung met R1d

description: aCGH data lung metastasis recipient 1d


title: Tumor R1d

description: aCGH data mammary tumor recipient 1d


title: Tumor R1c

description: aCGH data mammary tumor recipient 1c


title: Lung met R1c

description: aCGH data lung metastasis recipient 1c


title: Ax LN met R1b

description: aCGH data axillary LN metastasis recipient 1b


title: Lung met R1b

description: aCGH data lung metastasis recipient 1b


title: MIN_R3 transcriptome profile SVR

source_name: Laboratory culture in MIN medium

value: MIN


title: BAPHK_R15 transcriptome profile SVR

source_name: Laboratory culture on BAPHK blood plate

growth_protocol: P. gingivalis strain W83 was cultured anaerobically on trypticase soy agar (TSA) containing sheep blood, hemin and vitamin K (BAPHK) for 48 hours at 37°C. Upon harvest, a solution containing 2:1 (v:v) ratio of RNAprotect Bacteria Reagent (Qiagen, Valencia, CA, USA) and 1X PBS was poured onto the plates with colonies and incubated anaerobically for 5 min. The cells were mixed and suspended in this solution, centrifuged down in a microcentrifuge tube at 5,000×g, 4°C for 10 min, and then subjected to either RNA or DNA extraction.

value: BAPHK

value: two days on plate


title: Liver ISR12

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Institute for Genome Research

country: Japan

institute: The University of Tokushima

description: Total RNA from untreated TTR::Fv2E-PERK mouse liver. The data are part of 8 chip experiment comparing genes induced during activation of the Integrated Stress Response (ISR) by AP20187 induced dimerization of a Fv2E-PERK chimera in liver of TTR::Fv2E-PERK (high expression) mouse.

hyb_protocol: Microarrays were hybridized with fragmented biotinylated cRNA. Streptavidin-conjugated phycoerythrin was used for staining, followed by amplification using a biotinylated anti-streptavidin antibody.

scan_protocol: Scanned using a GeneChip Scanner (Affymetrix).

data_processing:
Primary image analysis of the arrays was performed using the Genechip 3.2 software (Affymetrix). The raw data from the hybridization experiments were analyzed by GeneSpring GX (Agilent Technologies). The raw signal from each gene was normalized to the mean strength of all genes from the same chip to obtain the normalized signal strength. Then, to allow visualization of all data on the same scale for subsequent analysis, the normalized signal strength of each gene was divided by the median signal strength for that gene among all samples to obtain the normalized expression level.
--------------------

source_name: untreated TTR::Fv2E-PERK

label_protocol: Biotinylated cRNA was produced in vitro using the GeneChip labeling kit (Affymetrix).

extract_protocol: Total RNA was extracted using STAT60 (Tel-test) and RNeasy (Qiagen) following the manufacturer's protocol.

tag: "Strain

value: FvB/n"

tag: "Gender

value: Male"


title: TSB_R5 transcriptome profile SVR


title: Liver ISR7

description: Total RNA from High Fat Diet (HFD) fed Alb:GC mouse liver. The data are part of 8 chip experiment comparing genes induced during activation of the Integrated Stress Response (ISR) by nutrient in liver of wildtype or Alb:GC mice.

source_name: HFD Alb::GC mouse liver


title: Liver ISR14

description: Total RNA from AP20187-treated TTR::Fv2E-PERK mouse liver. The data are part of 8 chip experiment comparing genes induced during activation of the Integrated Stress Response (ISR) by AP20187 induced dimerization of a Fv2E-PERK chimera in liver of TTR::Fv2E-PERK (high expression) mouse.

source_name: AP20187-treated TTR::Fv2E PERK mouse liver


title: Liver ISR13


title: Liver ISR10


title: Liver ISR16

source_name: a


title: Liver ISR8


title: Liver ISR5

description: Total RNA from High Fat Diet (HFD) fed wildtype mouse liver. The data are part of 8 chip experiment comparing genes induced during activation of the Integrated Stress Response (ISR) by nutrient in liver of wildtype or Alb:GC mice.

source_name: HFD wildtype mouse liver


title: MIN_R2 transcriptome profile SVR


title: Liver ISR15


title: Liver ISR9


title: TSB_R2 transcriptome profile SVR


title: Liver ISR11


title: Liver ISR4

description: Total RNA from Low Fat Diet (LFD) fed Alb::GC mouse liver. The data are part of 8 chip experiment comparing genes induced during activation of the Integrated Stress Response (ISR) by nutrient in liver of wildtype or Alb:GC mice.

source_name: LFD Alb::GC mouse liver


title: Liver ISR3


title: Tumor R1b

description: aCGH data mammary tumor recipient 1b

source_name: Mouse mammary tumor DNA from WT recipient

value: Recipient


title: Renal LN met R1a

description: aCGH data renal LN metastasis recipient 1a

source_name: Renal LN metastasis DNA from WT recipient

value: Metastasis

value: spleen


title: BAPHK_R16 transcriptome profile SVR


title: MIN_R1 transcriptome profile SVR


title: Lung met R1a

description: aCGH data lung metastasis recipient 1a

source_name: Lung metastasis DNA from WT recipient


title: Tumor D1

description: aCGH data K14cre;Cdhf/f;Trp53f/f derived donor tumor 1


title: Tumor R1a

description: aCGH data mammary tumor recipient 1a


title: Liver ISR6


title: Liver ISR24

description: Total RNA from AP20187-treated ATF4-/- TTR::Fv2E-PERK mouse liver. The data are part of 8 chip experiment comparing genes induced during activation of the Integrated Stress Response (ISR) by AP20187 induced dimerization of a Fv2E-PERK chimera in liver of ATF4+/+ or ATF4-/- mice

data_processing: Primary image analysis of the arrays was performed using the Genechip 3.2 software (Affymetrix). The raw data from the hybridization experiments were analyzed by GeneSpring GX (Agilent Technologies). The raw signal from each gene was normalized to the mean strength of all genes from the same chip to obtain the normalized signal strength. Then, to allow visualization of all data on the same scajavascript:ValidateSubmitForm()le for subsequent analysis, the normalized signal strength of each gene was divided by the median signal strength for that gene among all samples to obtain the normalized expression level.

value: FvB/n; Swiss Webster background"


title: Aorta from mouse on chow diet rep3

city: New York

first: Nino

last: Mzhavia

state: NY

address: 630 West 168 Street PH 8-405

department: Medicine Cardiology

institute: Columbia University Medical Centre

description: Aortic Gene expression

hyb_protocol: Following fragmentation, 10 microgram of cRNA were hybridized to GeneChip Mouse Genome Array according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G and Affymetrix GeneChip Operatin Software v1.3

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150

label: Biotin

source_name: Aorta from mouse on chow diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microgram RNA

growth_protocol: Mice were fed chow diet.

extract_protocol: Qiagen RNeasy Kit

tag: Jackson Lab. Strain:C57BL/6J. Gender male. Stock Number


title: Liver ISR2

description: Total RNA from Low Fat Diet (LFD) fed wildtype mouse liver. The data are part of 8 chip experiment comparing genes induced during activation of the Integrated Stress Response (ISR) by nutrient in liver of wildtype or Alb:GC mice.

data_processing: Primary image analysis of the arrays was performed using the Genechip 3.2 software (Affymetrix). The raw data from the hybridization experiments were analyzed by GeneSpring GX (Agilent Technologies). The raw signal from each gene was normalized to the mean strength of all genes from the same chip to obtain the normalized signal strength. Then, to allow visualization of all data on the same scale for subsequent analysis, the normalized signal strength of each gene was divided by the median signal strength for that gene among all samples to obtain the normalized expression level.

source_name: wildtype Alb::GC mouse liver


title: Aorta from mouse on chow diet rep1

description: Aortic Gene expression

tag: 26-28 weeks old


title: Liver ISR1

source_name: LFD wildtype mouse liver


title: Aorta from mouse on chow diet rep2

description: Aortic Gene expression


title: Liver ISR21

description: Total RNA from AP20187-treated  ATF4+/+ TTR::Fv2E-PERK mouse liver. The data are part of 8 chip experiment comparing genes induced during activation of the Integrated Stress Response (ISR) by AP20187 induced dimerization of a Fv2E-PERK chimera in liver of ATF4+/+ or ATF4-/- mice


title: Liver ISR20

description: Total RNA from untreated ATF4-/- TTR::Fv2E-PERK mouse liver. The data are part of 8 chip experiment comparing genes induced during activation of the Integrated Stress Response (ISR) by AP20187 induced dimerization of a Fv2E-PERK chimera in liver of ATF4+/+ or ATF4-/- mice


title: Aorta of mouse on high fat diet rep2

description: Aortic Gene expression

source_name: Aorta of mouse on high fat die

growth_protocol: Starting at 10 weeks mice were fed high fat diet for 16-18 weeks

tag: Jackson Lab. Strain:C57BL/6J. Gender

value: male. Stock Number:000664

tag: 26-28 weeks old mice


title: Aortas from Lepr^db/db mice rep3

description: Aortic Gene expression

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized to GeneChip Mouse Genome Array according to the standard Affymetrix protocol.

source_name: Aortas from Lepr^db/db mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microg RNA

growth_protocol: 16-20 weeks old mice on regular chow diet

tag: Homozygote from the colony of Jakson Lab. Strain

value: BKS.Cg-m +/+ Lepr^db/J. Gender:male Stock Number:000642


title: Liver ISR23

source_name: AP20187-treated ATF4-/- TTR::Fv2E-PERK mouse liver


title: Liver ISR18

description: Total RNA from untreated ATF4+/+ TTR::Fv2E-PERK mouse liver. The data are part of 8 chip experiment comparing genes induced during activation of the Integrated Stress Response (ISR) by AP20187 induced dimerization of a Fv2E-PERK chimera in liver of ATF4+/+ or ATF4-/- mice.


title: Aorta of mouse on high fat diet rep1

description: Aortic Gene expression

source_name: Aorta of mouse on high fat die for 16-18 weeks

growth_protocol: 16-20 weeks old mice

tag: Jackson Lab. Strain:C57BL/6J. Stock Number


title: Aorta of mouse on high fat diet rep3

description: Aortic Gene expression


title: Liver ISR22

source_name: AP20187-treated ATF4+/+ TTR::Fv2E-PERK mouse liver


title: Aortas from  Lepr^db/db rep1

description: Aortic Gene expression

growth_protocol: 16-20 weeks old mice on regular chow diet.

tag: Homozygot from the colony of Jakson Lab. Strain

value: BKS.Cg-m +/+ Lepr^db/J. Gender:male. Stock Number:000642


title: Aortas from  Lepr^db/+ mice rep2

description: Aortic Gene expression

source_name: Aortas from Lepr^db/+ mice

tag: Heterozygote from the colony of Jakson Lab. Strain


title: Aortas from  Lepr^db/db mice rep2

description: Aortic Gene expression


title: Liver ISR19

source_name: untreated ATF4-/- TTR::Fv2E-PERK mouse liver


title: Aortas from Lepr^db/+ mice rep3

description: Aortic Gene expression

value: BKS.Cg-m +/+ Lepr^db/J. Gender:male. Stock Number:000642.


title: Liver ISR17

source_name: ATF4+/+ TTR::Fv2E-PERK mouse liver


title: T4_vs_N4

city: Hangzhou

first: Meng

last: Xia

address: 866 Yuhangtang Road

country: China

institute: Institute of Immunology, Zhejiang University School of Medicine

description: Surgically removed tissue samples from hepatocellular carcinoma patient.

hyb_protocol: Each slide was hybridized with 825ng Cy3-labeled cRNA and 825ng Cy5-labeled cRNA using the Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in a Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with the Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US) following the manufacturer’s instructions.

scan_protocol: Slides were scanned by an Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US) with default settings.

source_name: nontumor sample 4

label_protocol: Total RNA were amplified and labeled by the Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX, US), Cy3 NHS ester (Cat#PA13105, GE healthcare Biosciences, Pittsburgh, PA, US), Cy5 NHS ester (Cat#PA15100, GE healthcare Biosciences, Pittsburgh, PA, US) following the manufacturer’s instructions. Labeled cRNA were purified by the RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Hepatocellular carcinoma tissues and nontumor liver tissues were obtained from hepatocellular carcinoma patients during surgery.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by the RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Human tissues were surgically removed from hepatocellular carcinoma patients and snap-frozen in liquid nitrogen until further analysis.

tag: gender

value: male

tag: disease state

value: hepatocellular carcinoma

value: nontumor liver tissue

source_name: tumor sample 4

value: hepatocellular carcinoma tissue


title: Maize tissue from phenotype B73, biological replicate 3

city: Norwich

first: Andreas

last: Magusin

address: Norwich Research Park

department: Crop Genetics

country: United Kingdom

institute: John Innes Centre

description: Expression data from Maize leaf tissue

hyb_protocol: Hybridisation overnight at 45 degrees Celsius and 60RPM (Hybridisation Oven 640), washing and staining (GeneChip® Fluidics Station 450, using the EukGEws2_450 Antibody amplification protocol)

scan_protocol: Scanning (GeneArray® 2500) was carried out according to the Affymetrix Manual II.

data_processing: Microarray suite 5.0 (Affymetrix) was used for image analysis and to determine probe signal intensities. The average intensity of each microarray was scaled to 100. Further calculations were performed in GeneSpring® software (version 5.1). Within-chip normalisation was carried out across all processed arrays, to the 50th percentile of the signal values of each microarray. Similarly, each probe set was then normalised to the 50th percentile across all the microarrays. A cut-off value of 10 was imposed on the raw signal value.

organism: Zea mays

source_name: Plants were grown from seeds for 2 weeks.  All plants were harvested as close as practicable to the middle of the photoperiod.

label_protocol: cRNA production was performed according to the Affymetrix Manual II with the following modifications:  11microlitres of cDNA was used as a template to produce biotinylated cRNA using half the recommended volumes of the ENZO BioArray High Yield RNA Transcript Labelling Kit. Labelled cRNAs were purified following the “Cleanup and Quantification of Biotin-Labelled cRNA” protocol (Affymetrix Manual II). cRNA quality was assessed by on Agilent RNA6000nano LabChips® (Agilent Technology 2100 Bioanalyzer Version A.01.20 SI211). 20µg of cRNA was fragmented according to the Affymetrix Manual II.

growth_protocol: Plants used for transcriptome analysis were grown from seeds for 2 weeks. Maize seeds were first imbibed in distilled water for 2 days in glasshouse conditions to break dormancy, before transfer to peat and sand P7 pots. They were grown in long day glass house conditions (16 hours photoperiod) at 22 degrees Celsius.  Aerial parts above the coleoptiles were excised, weighed and frozen in liquid nitrogen.  All plants were harvested as close as practicable to the middle of the photoperiod.  Plants for yield trials were grown in the field at Clayton, NC, U.S.A. in 2005.  Forty plants of each hybrid were grown in duplicate 0.0007 hectare plots.

extract_protocol: Approximately 200mg of plant tissue was ground to a fine powder using liquid nitrogen in a baked pre-cooled mortar, and using a chilled spatula, transferred to labelled chilled 1.5ml tube. To these tubes 1ml of TRI Reagent (Sigma-Aldrich, Saint Louis USA) was added, then shaken to suspend the tissue. After a 5 minute incubation at room temperature 0.2ml of chloroform was added, and thoroughly mixed with the TRI Reagent by inverting the tubes for around 15 seconds, followed by 2-3 minutes incubation at room temperature. The tubes were centrifuged at 12000rpm for 15 minutes and the upper aqueous phase transferred to a clean, labelled tube.  0.5ml of isopropanol was then added to the tubes, which were inverted repeatedly for 30 seconds to precipitate the RNA, followed by a10 minute incubation at room temperature. The tubes were then were centrifuged at 12000rpm for 10 minutes at 4 degrees Celsius, revealing a white pellet on the side of the tube. The supernatant was poured off of the pellet, and the lip of the tube gently blotted with tissue paper. 1ml 75% ethanol was added and the tubes shaken to detach the pellet from the side of the tube, followed by centrifugation at 7500rpm for 5 minutes. Again the supernatant was poured off of the pellet, which was quickly spun down again and any remaining liquid removed using a pipette. The pellet was then dried in a laminar flow hood, before 50 microliters of DEPC treated water (Severn Biotech Ltd. Kidderminster, UK) was added to dissolve the pellet.  Sample concentrations were determined using an Eppendorf BioPhotometer (Eppendorf UK Limited. Cambridge. UK), and RNA quality was determined by running out 1microlitre on a 1% agarose gel for 1 hour.  RNA from replicated plants were then pooled according concentration in order to ensure an equal contribution of each replicate.  The pooled samples were then cleaned using Qiagen Rneasy columns (Qiagen Sciences. Maryland. USA) following the protocol on page 79 of the Rneasy Mini Handbook (06/2001), before again determining the concentrations using an Eppendorf BioPhotometer, and analysis of 1l on a 1% agarose gel for confirmation of quality.

tag: tag

value: Adult leaf


title: Maize tissue from phenotype B73, biological replicate 2

description: Expression data from Maize leaf tissue


title: Maize tissue from phenotype B97, biological replicate 3

description: Expression data from Maize leaf tissue


title: Arabidopsis tissue from phenotype Br, biological replicate 3

description: Expression data from Arabidopsis leaf tissue

organism: Arabidopsis thaliana

growth_protocol: Plants used for transcriptome analysis were grown from seeds for 2 weeks.  All plants were harvested as close as practicable to the middle of the photoperiod.


title: Maize tissue from phenotype B97, biological replicate 1

description: Expression data from Maize leaf tissue


title: Arabidopsis tissue from phenotype Ag, biological replicate 2


title: Arabidopsis tissue from phenotype Br, biological replicate 1


title: Maize tissue from phenotype B73, biological replicate 1

description: Expression data from Maize leaf tissue


title: Arabidopsis tissue from phenotype Ag, biological replicate 3


title: Arabidopsis tissue from phenotype Br, biological replicate 2


title: T2_vs_N2

source_name: nontumor sample 2

source_name: tumor sample 2


title: T1_vs_N1

source_name: nontumor sample 1

source_name: tumor sample 1


title: T3_vs_N3

source_name: nontumor sample 3

source_name: tumor sample 3


title: Arabidopsis tissue from phenotype Ag, biological replicate 1


title: BEAS-2B cells 10-9M N-OH-PhIP rep3

status: Public on Dec 22 2011

city: piscataway

first: Qi

state: NJ

address: 170 Frelinghuysen Road

department: EOHSI

institute: Rutgers University

description: NuGEN Ovation amplification

hyb_protocol: Hybridization, staining and washing of all arrays were prerormed in the Affymetrix hybridization oven and Fluidics module as per the manufacturer's protocols

scan_protocol: GeneChips were scanned using a Affymetrix GeneArray Scanner 3000

data_processing: The detection and quantitation of target hybridization was performed with a Affymetrix GeneArray Scanner 3000 (Affymetrix). All arrays referred to in this study were assessed for array performance prior to data analysisusing Affymetrix GeneChip Operating Software (GCOS) and Quality Reporter.

source_name: bronchioepithelial cells, 24 hour exposure

label_protocol: Forty nanograms of total RNA from each sample were used to generate a high fidelity cDNA for array hybridization.  The cDNA were amplified, fragmented and labeled with biotin using NuGEN Ovation Amplification version 2 and Biotin Labeling kits (NuGEN, San Diago, CA).  Amplified cDNA product and fragmented cDNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.  An aliquot containing 3.75ug of amplified, biotin labeled cDNA was then added to the hybridization cocktail for GeneChip analysis.  Detailed protocols for sample preparation using the NuGEN Ovation amplification and labeling kits can be found at http://www.nugeninc.com

growth_protocol: BEAS-2B cells were culured on 150 cm tissue culture plates pre-incubated for 12-24 h with Plate Coat solution prepared by adding 5 mg bovine fibronectin (Sigma), 5 mL of collagen solution, and 50 mL of BSA stock solution (Biofluids, Rockville, MD) to LHC Basal medium (Biofluids). Cells were  with LHC-9 medium prepared by adding 1 mL of 3.3 mM retinoic acid and 1 mL of epinephrine to LHC-8 medium (all from Biofluids). Cell cultures were maintained at 37ºC in a 5% CO2, water saturated atmosphere. Cells were passaged 24 hours prior to exposures to achieve ~ 70% confluence.

extract_protocol: Cells were then washed with ice cold PBS and harvested for simultaneous isolation of total RNA and DNA using All-Prep Kits™ (Qiagen, Valencia, CA) according to the manufacturer’s protocol, and stored at -80ºC until used for analysis.

treatment_protocol: Cells were passaged 24 hours prior to exposures to achieve ~ 70% confluence. N-OH-PhIP was serially diluted in anhydrous DMSO and added to culture medium. The final concentration of DMSO in all samples including controls was 1%. Triplicate cell cultures were  exposed to either DMS (control) or nine different doses of N-OH-PhIP at concentrations ranging from 1 x 10-6 to 5 x 10-10 M.

tag: cell line

tag: treatment

value: 10-9M N-OH-PhIP


title: BEAS-2B cells 5x10-9M N-OH-PhIP rep2

description: NuGEN Ovation amplification

value: 5x10-9M N-OH-PhIP


title: BEAS-2B cells 10-10M N-OH-PhIP rep3

description: NuGEN Ovation amplification

value: 10-10M N-OH-PhIP


title: BEAS-2B cells 5x10-9M N-OH-PhIP rep1

description: NuGEN Ovation amplification


title: BEAS-2B cells 10-10M N-OH-PhIP rep1

description: NuGEN Ovation amplification


title: BEAS-2B cells 10-8 M N-OH-PhIP rep1

description: NuGEN Ovation amplification

value: 10-8 M N-OH-PhIP


title: Maize tissue from phenotype B97, biological replicate 2

description: Expression data from Maize leaf tissue


title: BEAS-2B cells 5x10-9M N-OH-PhIP rep3

description: NuGEN Ovation amplification


title: BEAS-2B cells 5x10-10M N-OH-PhIP rep3

description: NuGEN Ovation amplification

value: 5x10-10M N-OH-PhIP


title: BEAS-2B cells 10-9M N-OH-PhIP rep2

description: NuGEN Ovation amplification


title: BEAS-2B cells  5x10-8 M N-OH-PhIP rep2

description: NuGEN Ovation amplification

value: 5x10-8 M N-OH-PhIP


title: BEAS-2B cells 10-9M N-OH-PhIP rep1

description: NuGEN Ovation amplification


title: BEAS-2B cells 5x10-10M N-OH-PhIP rep1

description: NuGEN Ovation amplification


title: BEAS-2B cells 10-8 M N-OH-PhIP rep3

description: NuGEN Ovation amplification


title: BEAS-2B cells 10-8 M N-OH-PhIP rep2

description: NuGEN Ovation amplification


title: BEAS-2B cells  5x10-8 M N-OH-PhIP rep3

description: NuGEN Ovation amplification


title: BEAS-2B cells  5x10-8 M N-OH-PhIP rep1

description: NuGEN Ovation amplification


title: BEAS-2B cells  10-7 M N-OH-PhIP rep3

description: NuGEN Ovation amplification

value: 10-7 M N-OH-PhIP


title: BEAS-2B cells  10-7 M N-OH-PhIP rep2

description: NuGEN Ovation amplification


title: slowly proliferating single cell derived mesenchymal cell from bone marrow 2

city: Tokyo

first: Yo

last: Mabuchi

address: 35 Shinanomachi, Shinjuku-ku

department: Physiology

institute: Keio University School of Medicine

hyb_protocol: Experimental and reference targets for each hybridization were purified using a Microcon YM-30 column (Millipore) and validated using a NanoDrop ND-1000 to ensure the yield and specific incorporation of the labeled gDNA.  Labeled test and reference DNAs were combined, denatured, pre-annealed with Cot-1 DNA (Invitrogen, Carlsbad, CA) and blocking reagent (Agilent), and then hybridized to Agilent Human 4x180K CGH arrays (Design ID = 022060) for 24 hours in a rotating oven (Agilent Technologies) at 65°C and 20 rpm.

scan_protocol: After the hybridization, the array slides were washed and then scanned at 3 μm resolution with an Agilent G2565CA Scanner.  Data were extracted from the microarray images using Agilent Feature Extraction Software v10.5.1.1 with the Feature Extraction protocol CGH-105_Dec09.  These ratio data, along with the associated error values and flagged features, were imported into the DNA Analytics Software v5.0.14 (Agilent).

data_processing: To make aberration calls, an aberration detection algorithm, ADM-2, was used with a threshold of 5.5 and an aberration filter set at 2 for the minimum number of probe regions and 0.25 for the minimum absolute average log2 ratio for regions in the DNA Analytics to reduce false positives.

source_name: Human Control gDNA

label_protocol: 1.0 μg aliquots of sample DNA from RPCs, MPCs or SPCs, as well as reference DNA (Promega, female, p/n G1521), were digested with AluI and RsaI restriction enzymes and fluorescently labeled with Cy5 (test) or Cy3 (reference) using an Agilent Genomic DNA Enzymatic Labeling Kit (p/n 5190-0449).

extract_protocol: A maximum of 5x10^6 cells (RPCs, MPCs and SPCs at six weeks) were centrifuged for 5 minutes at 300 g.  The pellet was resuspended in 200 μl PBS, and 20 μl proteinase K (Qiagen DNeasy Blood & Tissue Kit) and 4 μl RNase A (100 mg/ml) were added, mixed on a vortex mixer, and incubated for 2 min at room temperature.  Then the suspension was spun in a microcentrifuge for 30 seconds at 6,000 g to drive the contents off the walls and lid.  Genomic DNA (gDNA) was isolated using a Qiagen DNeasy Blood & Tissue Kit and Agilent’s recommended procedure (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90040 CGH Bravo Protocol 1.1.pdf).  The final elution volume was 400 μl in Buffer AE.  The yield and purity of the gDNA were measured using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific).  To assess the quality and average molecular weight of the collected gDNA, aliquots from each sample were subjected to agarose gel electrophoresis.  For experimentation, high-quality gDNA samples with a 260/280 ratio of 1.8 to 2.0 (the 260/230 ratio for pure DNA is >1.8) were used.

tag: sample type

value: Promega gDNA female, G152A Lot. 25707301

source_name: Human Mesenchymal Stem Cells

value: female

tag: age

tag: cell type


title: BEAS-2B cells  5x10-7 M N-OH-PhIP rep1

description: NuGEN Ovation amplification

value: 5x10-7 M N-OH-PhIP


title: BEAS-2B cells  10-7 M N-OH-PhIP rep1

description: NuGEN Ovation amplification


title: slowly proliferating single cell derived mesenchymal cell from bone marrow 3


title: BEAS-2B cells  10-6 M N-OH-PhIP rep1

description: NuGEN Ovation amplification

value: 10-6 M N-OH-PhIP


title: BEAS-2B cells  DMSO control rep2

description: NuGEN Ovation amplification

value: DMSO control


title: BEAS-2B cells  5x10-7 M N-OH-PhIP rep3

description: NuGEN Ovation amplification


title: moderately proliferating single cell derived mesenchymal cell from bone marrow 1


title: rapidly proliferating single cell derived mesenchymal cell from bone marrow 3


title: BEAS-2B cells  10-6 M N-OH-PhIP rep3

description: NuGEN Ovation amplification


title: BEAS-2B cells  10-6 M N-OH-PhIP rep2

description: NuGEN Ovation amplification


title: BEAS-2B cells  5x10-7 M N-OH-PhIP rep2

description: NuGEN Ovation amplification


title: BEAS-2B cells  DMSO control rep3

description: NuGEN Ovation amplification


title: BEAS-2B cells  DMSO control rep1

description: NuGEN Ovation amplification


title: rapidly proliferating single cell derived mesenchymal cell from bone marrow 1


title: rapidly proliferating single cell derived mesenchymal cell from bone marrow 2


title: slowly proliferating single cell derived mesenchymal cell from bone marrow 1


title: SP-49 Mock2

city: Toronto

first: Robert

last: Kridel

state: ON

address: 101 College Street, Rm 12-311

country: Canada

institute: Princess Margaret Cancer Centre

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned.

data_processing: normalization by RMA , fold-changes by limma in R

source_name: SP-49 cell line, 24h Mock treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug of RNA.

growth_protocol: cells were grown in RPMI 15%FBS (Mino) or RPMI 10%FBS (Rec-1 and SP-49) for 24 hours at 37C in a humidified incubator (5% CO2)

extract_protocol: Qiagen Allprep

treatment_protocol: cells were treated either with 1 micromolar of compound E (GSI group) or 0.1% DMSO (Mock group)

value: Mantle Cell Lymphoma (MCL)


title: SP-49 GSI1

source_name: SP-49 cell line, 24h GSi treatment


title: moderately proliferating single cell derived mesenchymal cell from bone marrow 2


title: Rec-1 GSI2

source_name: Rec-1 cell line, 24h GSI treatment


title: Rec-1 Mock1

source_name: Rec-1 cell line, 24h Mock treatment


title: Mino GSI1

source_name: Mino cell line, 24h GSi treatment

value: Mino


title: Mino GSI2

source_name: Mino cell line, 24h GSI treatment


title: Rec-1 GSI1

source_name: Rec-1 cell line, 24h GSi treatment


title: Rec-1 Mock2


title: SP-49 GSI2

source_name: SP-49 cell line, 24h GSI treatment


title: patient 28G

city: Durham

first: Christina

last: Augustine

state: NC

address: VAMC RmE4001 508 Fulton St.

department: Surgery

institute: Duke University Medical Center

hyb_protocol: labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols

scan_protocol: Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000

data_processing: Expression values across 54675 probe sets were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS).  A present/absent call (based on a statistical p-value) is included.

source_name: melanoma

label_protocol: one-cycle cDNA synthesis of total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA

extract_protocol: Tissue was homogenized and RNA isolated using Qiagen Rneasy kit.  A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue.  Each RNA isolation included treatment with DNase to minimize genomic DNA.

treatment_protocol: 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board.  Biopsies were snap frozen and stored at -130.

value: in-transit melanoma

value: isolated limb infusion w/ melphalan

tag: response

value: progressive disease PD

tag: tissue

value: melanoma biopsy


title: patient 23G

value: non-evaluable n.e.


title: patient 25G


title: patient 21G

value: isolated limb perfusion w/ melphalan


title: Mino Mock1

source_name: Mino cell line, 24h Mock treatment


title: patient 27G

value: complete response CR

tag: genotype

value: Braf-WT Nras-mutant


title: SP-49 Mock1


title: patient 29G


title: patient 24G


title: Mino Mock2


title: patient 22G-B


title: patient 20G

value: Braf-mutant Nras-WT


title: moderately proliferating single cell derived mesenchymal cell from bone marrow 3


title: patient 26G

value: partial response PR


title: patient 18G-B


title: patient 15G


title: patient 30G

value: stable disease SD


title: patient 9G


title: patient 19G


title: patient 16G


title: patient 8G


title: patient 22G-A


title: patient 7G


title: Tumor-IHC2_FISH+ -13

city: Barcelona

first: Francisco

middle: Javier

last: Lopez

address: Rossello, 153

department: Centre Esther Koplowitz

institute: Center for International Health Research at Barcelona (CRESIB)

hyb_protocol: Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The quality of the outcome was assessed by different plots produced by the R software package ArrayQualityMetrics

source_name: Tumor tissue with HER2 IHC2+ score and proved amplification

label_protocol: Affymetrix protocol using Two Cycle Labeling Kit (Affymetrix, Santa Clara, CA).

extract_protocol: RNAs were extracted from macrodissected frozen samples according to standard procedures using Trizol reagent (Invitrogen,Carlsbad, CA). Quantity and integrity of RNAs were checked by spectrophotometry and the Agilent 2100 Bioanalyzer, respectively.

value: Tumor tissue with HER2 IHC2+ score

tag: her2 ihc

tag: her2 fish


title: BEAS-2B cells 10-10M N-OH-PhIP rep2

description: NuGEN Ovation amplification

value: 10-10M N-OH-PhIP


title: patient 18G-A


title: Tumor-IHC2_FISH- -14

source_name: Tumor tissue with HER2 IHC2+ score and proved no-amplification


title: Tumor-IHC3_FISH+ -12

source_name: Tumor tissue with HER2 IHC3+ score and proved amplification

value: Tumor tissue with HER2 IHC3+ score


title: Tumor-IHC2_FISH+ -11


title: patient 13G


title: Tumor-IHC01_FISH- -9

source_name: Tumor tissue with HER2 IHC0/1 score and proved no-amplification

value: Tumor tissue with HER2 IHC0/1 score

tag: Stage

value: grade III

tag: re

tag: rp

value: no

tag: metastasis


title: Tumor-IHC01_FISH- -8

value: yes


title: Tumor-IHC2_FISH+ -12


title: Tumor-IHC01_FISH- -10

value: grade I


title: Tumor-IHC01-2

source_name: Tumor tissue with HER2 IHC0/1 score


title: Tumor-IHC01-3


title: Tumor-IHC01_FISH- -6


title: Tumor-IHC01_FISH- -3


title: Tumor-IHC01_FISH- -7


title: Tumor-IHC01_FISH- -5


title: Tumor-IHC01-1

value: grade II


title: Tumor-IHC2_FISH- -12


title: Tumor-IHC01_FISH- -4


title: Tumor-IHC01_FISH- -2


title: Tumor-IHC2_FISH- -11


title: Tumor-IHC2_FISH- -8


title: Tumor-IHC2_FISH- -5


title: Tumor-IHC01_FISH- -1


title: Tumor-IHC2_FISH- -10


title: Tumor-IHC2_FISH- -7


title: Tumor-IHC2_FISH+-10


title: Tumor-IHC2_FISH- -4


title: Tumor-IHC2_FISH- -3


title: Tumor-IHC2_FISH- -2


title: Tumor-IHC2_FISH+-5


title: Tumor-IHC2_FISH+-7


title: Tumor-IHC2_FISH+-9


title: Tumor-IHC2_FISH- -9


title: Tumor-IHC2_FISH+-4


title: Tumor-IHC2_FISH- -6


title: Tumor-IHC2_FISH+-8


title: Tumor-IHC2_FISH+-2


title: Tumor-IHC3_FISH+-9


title: Tumor-IHC2_FISH+-6


title: Tumor-IHC3_FISH+ -11


title: Tumor-IHC2_FISH- -1


title: Tumor-IHC3_FISH+-6


title: Rc30_F33_HD

city: Espoo

first: Mikko

middle: Ilari

last: Arvas

address: Tietotie 2

department: Cell Factory

country: Finland

institute: VTT Technical Research Centre of Finland

description: Trichoderma reesei RutC-30 in lactose fed chemostat with growth rate 0.03 with high cell density. It is the third of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Trichoderma reesei

source_name: T. reesei on lactose fed chemostat with growth rate 0.03 and high cell density

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: The cultivations have been described in 'Detecting novel genes with sparse arrays' Arvas & al 2010 Gene. 2010 Nov 1;467(1-2):41-51. PUBMED id 20691772. The medium contained: KH2PO4 15 g l-1, (NH4)2SO4 5 g l- 1, CaCl2x2H2O, 0.6 g l-1, MgSO4x6H2O 0.6 g l-1, CuSO4x5H2O 30 mg l-1, FeSO4x5H2O 5 mg l-1, MnSO4xH2O 1.6 mg l-1, ZnSO4x7H2O 1.4 mg l-1, CoCl2x6H2O 3.7 mg l-1 and lactose 20 or 80 g L-1. Salt concentrations in cultivations containing 80 g lactose l-1 were increased to: KH2PO4 15 g l-1, (NH4)2SO4 12.5 g l-1, CaCl2x2H2O 1.5 g l-1, MgSO4x6H2O 1.5 g l-1, CuSO4x5H2O 30 mg l-1, FeSO4x5H2O 12.5 mg l-1, MnSO4xH2O 4.0 mg l-1, ZnSO4x7H2O 5.6 mg l-1, CoCl2x6H2O 14.8 mg l-1.

extract_protocol: RNA was extracted from the homogenate with Total RNA kit (A&A Biotechnologies, Gnydia, Poland). Quality and quantity of RNA was monitored by absorbance measurement at A260 (DNA Quant, Pharmacia, Uppsala, Sweden) and Agilent Bioanalyser and RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA, USA).

tag: strain

tag: growth rate

tag: cell density

value: High

tag: accession


title: Tumor-IHC3_FISH+-4

tag: disease state


title: Rc30_F26_D06

description: Trichoderma reesei RutC-30 in lactose fed chemostat with growth rate 0.06. It is the first of three biological replicates used in this experiment, each from separate cultures.

source_name: T. reesei on lactose fed chemostat with growth rate 0.06

value: Normal


title: Tumor-IHC3_FISH+-7


title: Tumor-IHC2_FISH+-3


title: Tumor-IHC3_FISH+-1


title: Tumor-IHC3_FISH+-3


title: Tumor-IHC2_FISH+-1


title: Rc30_F25_D03

description: Trichoderma reesei RutC-30 in lactose fed chemostat with growth rate 0.03. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: T. reesei on lactose fed chemostat with growth rate 0.03


title: Tumor-IHC3_FISH+-10


title: Tumor-IHC3_FISH+-8


title: Tumor-IHC3_FISH+-5


title: Rc30_F27_D06

description: Trichoderma reesei RutC-30 in lactose fed chemostat with growth rate 0.06. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Tumor-IHC3_FISH+-2


title: Rc30_F30_HD

description: Trichoderma reesei RutC-30 in lactose fed chemostat with growth rate 0.03 with high cell density. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Rc30_F23_D06


title: Tumor-IHC3-3

source_name: Tumor tissue with HER2 IHC3+ score


title: Normal-12

source_name: Breast normal tissue from a breast cancer patient


title: Tumor-IHC3-1


title: Normal-10


title: Rc30_F21_D03

description: Trichoderma reesei RutC-30 in lactose fed chemostat with growth rate 0.03. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Normal-11


title: Normal-9


title: Normal-6


title: Normal-7


title: Normal-8


title: Rc30_F20_D03

description: Trichoderma reesei RutC-30 in lactose fed chemostat with growth rate 0.03. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Normal-4


title: Normal-5


title: Normal-2


title: Drosophila-Cbx-replicate2 (Test vs Mock) [Agilent-014817]

city: Pune

first: Pavan

last: Agrawal

state: Maharashtra

address: First floor, Central Tower, Sai Trinity Building, Pashan

department: Biology

country: India

institute: Indian Institute of Science Education and Research (IISER)

description:
Rep2_Agilent-014817
Biological replicate 2 of 3 slide 2, Cbx discs, Ubx ChIP
Agilent Feature Extraction File: US45103024_251481710122_S01.txt

hyb_protocol: Using Agilent’s In situ Hybridzation kit 5184-3568. As per Manufacturer's instructions.

scan_protocol: Post-hybridization, the slides were washed as per Agilent protocol and scanned at 5 micron resolution using Agilent Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.2) was used for background subtraction and LOWESS normalization. The maximun distance(bp) for two probes to be considered as  neighbors was taken as 500 bp in chip analytics software. The updated Agilent design file was used to extract the data Build April 2006. (dm3).

source_name: [MockIP_WCE] CbxHM/+ wing discs

label_protocol: The LMPCR samples (1.5 micrograms each) were labeled in replicates using Agilent Genomic DNA Labeling Kit PLUS and Cy3 or Cy5 dUTP from Agilent. DNA yield and incorporation of label (specific activity) was measured using NanoDrop spectrophotometer. For all hybridizations, 5 micrograms each of Cy3-labeled Mock IP (labelled as WCE in raw data) was mixed with 5 micrograms of Cy5-labeled Test-IP DNA

growth_protocol:
Wildtype (CS) flies were crossed to flies of CbxHm/TM6B genotype and reared at 25oC. From resultant progeny CbxHm/+ wing discs were manually dissected in chilled PBS and fixed in 1% formaldehyde solution at room temperature. Chromatin was sheared to obtain average 500 bp fragments and pulled down using polyclonal antibodies generated against N-terminal region of Ubx
1:500 dilution of Ubx antibody was used to carry out pull down in 300 µl volume. Upstate Ez ChIP kit (Catalog # 17-371) was used for binding and washing the immune complex as per manufacturer's instructions.

extract_protocol: DNA was eluted and processed as per Agilent ChIP-on-chip protocol available at www.agilent.com

tag: genotype/variation

value: CbxHm/+

tag: developmental stage

value: Third Instar larvae

value: wing discs

source_name: [ChIP fraction] CbxHM/+ wing discs

tag: chip antibody

value: anti-Ubx (against N-terminal region of Ubx protein)

tag: chip antibody supplier

value: generated in-house


title: Tumor-IHC3-2

tag: age


title: Normal-1


title: Normal-3


title: ExCol-0_0hr_0.1 mM AgNO3_rep3

city: Sakai

first: Hirohisa

last: Saga

state: Osaka

address: Gakuen-cho 1-1

institute: Osaka Prefecture University

description: Gene expression after 0h in AgNO3 treated plants

hyb_protocol: Samples were hybridized on Arabidopsis 3 microarray 4x44K (Agilent). For detailed instructions see the One-Color Microarray-Based Gene Expression Analysis Protocol (Qick Amp Labeling) Version 5.7 (Agilent) including the Gene Expression Hybridization Kit (Agilent).

scan_protocol: The slide was scanned on an Agilent DNA Microarray Scanner (G2505BA) using one color scan setting for 1x44k array slides (Scan Area 61 x 21.6 mm, Scan resolution 5 mm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images was processed with Agilent Feature Extraction v9.5.3.1 using the GE1-v5_95_Feb07 protocol.

source_name: Col-0_0 h_0.1mM AgNO3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the Quick Amp Labeling Kit version 5.7 (Agilent technologies) according to the manufacturer's instructions.

growth_protocol: Arabidopsis thaliana ecotype Columbia (Col-0) seedlings were grown at 22°C under continuous light (100 mE/m2/s). Arabidopsis seedlings were germinated under sterile conditions on 0.8% (w/v) agar plates containing GM (Germination Medium) supplemented with 1x Murashige and Skoog salts and 1% (w/v) sucrose. Seedlings (one-week after germination) were then transferred to GM liquid culture and shaken at 100 rpm at 22°C for two weeks under continuous light.

extract_protocol: Total RNA was prepared using the RNeasy Plant Mini Kit (QIAGEN).

treatment_protocol: AgNO3 (final 0.1 mM) was added to the culture medium, and the seedlings were washed with distilled water and sampled 0 h, 48 h, and 72 h after AgNO3 addition.

tag: ecotype

tag: tissue

value: whole plants (seedlings)


title: Whole_Forebrain_2 [ChIP-chip 244K array, 1 of 2]

city: Brest

first: Gaelle

last: Friocourt

address: 46 rue Félix Le Dantec, CS51819

department: Molecular Genetics

institute: Inserm U613

hyb_protocol: 5 µg of labelled DNA was hybridized to mouse promoter 244K ChIP-Chip microarrays set (Agilent Technologies) for 40 hours, at 65°C, at 20 rpm.

scan_protocol: Hybridization images were obtained using an Agilent DNA microarray scanner (G2505B). Scan Region : Agilent HD (61 x 21,6 mm) / Resolution : 5 µm / TIFF : 16 bit / Red PMT : 100% / Green PMT : 100%. Intensity data were extracted using Feature Extraction software (FE v9,5,1) (Agilent Technologies).

data_processing: Intensity data on each array were normalized with the Lowess method. To identify regions of significant Arx association, the enrichment of each probe on the array was calculated as the ratio of the intensities of Arx-immunoprcipitated DNA (y-axis) to control Input chromatin (x-axis). One first important assumption is that points corresponding to non positive probes are distributed symmetrically around the axis x=y. A threshold spline curve was then defined by considering only the probes below this axis. Reporting this curve above the axis allowed discrimination between positive and negative probes. For each probe, a P-Value was obtained using a normalised distance between it and the axis x=y.

label: Alexa Fluor 647

source_name: Embryonic brains [IP DNA]

label_protocol: Immunoprecipitated chromatin and total Input DNA were amplified using GenomePlex Complete Whole Genome Amplification kit (Sigma).Then, two micrograms of IP and Input DNA were labelled with Alexa Fluor 647 or Alexa Fluor 555 respectively, by use of the BioPrime Plus Array CGH Indirect Genomic Labbeling System (Invitrogen).

growth_protocol: CELLS : N2a cells were grown in Dulbecco's Modified Eagle Medium (DMEM) high glucose (PAA) which was supplemented with 10% fetal bovine serum gold (PAA), 2 mM L-glutamine (Lonza), 0,1 mM non essential amino-acids (Gibco) and 2 mM penicillin/streptomycin (PAA). Cells were grown at 37°C with 5% CO2. BRAINS :  Swiss outbred (RJOrl:SWISS) mice (Janvier, France) were used in all the studies. Mouse brains were extracted from day 15,5 embryos in cold PBS. Following brain isolation, the whole forebrain (ventral telecenphalon, thalamus, cerebral cortex and olfactory bulbs) were frozen in liquid nitrogen.

extract_protocol: DNA of cells and embryonic brains was fragmented by sonication. Immunoprecipitation was perfomed using anti-Arx antibody (ARX C-14; Santa-Cruz; Catalog sc-48843; Lot A2108). Immune complexes were captured by addition of dynabeads protein G. Following washes with gradient stringent buffers, protein-DNA complexes were eluted. Reverse cross-link was performed then, immunoprecipitated DNA and Input DNA were isolated via phenol-chloroform extraction followed by ethanol precipitation.

treatment_protocol: CELLS : Cells were transfected with an expression vector expressing Arx using Lipofectamine 2000 according to the guideline of the manufacturer (Invitrogen). Two days after transfection, cells were fixed in 1% formaldéhyde, followed by the addition of glycine. BRAINS : Embryonic brains disaggregation and homogenization were performed in liquid nitrogen using a pestle and a mortar. Samples were fixed in a solution containing PBS, formaldehyde and protease inhibitor cocktail. Reaction was stopped by the addition of glycine.

value: Swiss outbred (RJOrl:SWISS)

value: brain

value: anti-Arx antibody (ARX C-14)

tag: chip antibody vendor

value: Santa-Cruz

tag: chip antibody lot#

tag: chip antibody catalog#

label: Alexa Fluor 555

source_name: Embryonic brains [Input DNA]


title: Cells_Transfected_by_ARX_3 [ChIP-chip 244K array, 1 of 2]

source_name: Neuroblastoma cells [IP DNA]

tag: cell line

value: N2a neuroblastoma cells

source_name: Neuroblastoma cells [Input DNA]


title: Drosophila-Cbx-replicate3 (Test vs Mock) [Agilent-014816]

description:
Rep3_Agilent-014816
Biological replicate 3 of 3 slide 1, Cbx discs, Ubx ChIP
Agilent Feature Extraction File: US45103024_251481610143_S01.txt


title: ExCol-0_72hr_0.1 mM AgNO3_rep3

description: Gene expression after 72h in AgNO3 treated plants

source_name: Col-0_72 h_0.1mM AgNO3


title: Rc30_F31_HD

description: Trichoderma reesei RutC-30 in lactose fed chemostat with growth rate 0.03 with high cell density. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Drosophila-Cbx-replicate3 (Test vs Mock) [Agilent-014817]

description:
Rep3_Agilent-014817
Biological replicate 3 of 3 slide 2, Cbx discs, Ubx ChIP
Agilent Feature Extraction File: US45103024_251481710150_S01.txt


title: Cells_Transfected_by_ARX_2 [ChIP-chip 244K array, 1 of 2]


title: ExCol-0_48hr_0.1 mM AgNO3_rep3

description: Gene expression after 48h in AgNO3 treated plants

source_name: Col-0_48 h_0.1mM AgNO3


title: Drosophila-Cbx-replicate1 (Test vs Mock) [Agilent-014816]

description:
Rep1_Agilent-014816
Biological replicate 1 of 3 slide 1, Cbx discs, Ubx ChIP
Agilent Feature Extraction File: US45103024_251481610106_S01.txt


title: Drosophila-Cbx-replicate1 (Test vs Mock) [Agilent-014817]

description:
Rep1_Agilent-014817
Biological replicate 1 of 3 slide 2, Cbx discs, Ubx ChIP
Agilent Feature Extraction File: US45103024_251481710121_S01.txt


title: Cells_Transfected_by_ARX_1 [ChIP-chip 244K array, 1 of 2]


title: Whole_Forebrain_3 [ChIP-chip 244K array, 1 of 2]


title: Whole_Forebrain_1 [ChIP-chip 244K array, 1 of 2]


title: ExCol-0_48hr_0.1 mM AgNO3_rep2


title: ExCol-0_0hr_0.1 mM AgNO3_rep2


title: ExCol-0_0hr_0.1 mM AgNO3_rep1


title: dim4_control_rep3

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression after 6 H treatment with vehicle (H2O)

hyb_protocol: Hybridizations were performed for 17 h in a rotating hybridization oven at 65°C at 4 rpm. Slides were washed with a solution containing 6X SSPE (1XSSPE is 0.18 M NaCl, 10mM NaH2PO4, and 1 mM EDTA [pH 7.7]) plus 0.005% N-lauroyl sarcosine for 1 min and then washed in a solution containing 0.06X SSPE plus 0.005% N-lauroyl sarcosine for 1 min at 37 C

scan_protocol: The slides were scanned with an Agilent G2565 scanner (10 mm and with extended dynamic range).

data_processing: Data was obtained using Agilent Feature Extraction software (v9.5).

source_name: U2OS hGRdim4 cells, vehicle treated, 6 H

label_protocol: Total RNA was amplified using the Agilent Low RNA Input fluorescent linear amplification lit protocol.  Cy3-labeled cRNA was produced according to the manufacturer’s protocol. For each sample, 1.5 mg of Cy3-labeled cRNA was fragmented using the Agilent In Situ Hybridization kit protocol.

growth_protocol: The U-2 OS hGRdim4 cell line was maintained in DMEM/F-12 supplemented with 10% FCS:CS, 2mM glutamine and 100 IU of penicillin and 100mg/ml of streptomycin with the addition of 200 mg/ml geneticin and 200 mg/ml hygromycin and were maintained in a humidified, 5% CO2 atmosphere.

extract_protocol: RNA wasprepared using the Qiagen RNeasy midi kit (Qiagen Sciences, Germantown, MD) following the manufacturers instructions.  This included DNase treatment of all samples.

treatment_protocol: U-2 OS cells stably expressing hGRdim4 were cultured for twenty-four hours in media containing charcoal-stripped serum and subsequently treated for six hours with 100nM dexamethasone or vehicle (H2O).

value: U-2 OS hGRdim4


title: dim4_control_rep1


title: ExCol-0_72hr_0.1 mM AgNO3_rep2


title: Cy3-VC_Cy5-TTF1

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

hyb_protocol: standard Agilent protocol

scan_protocol: Whole Human Genome oligo DNA microarray with 41000 distinct probes was scanned using an Agilent DNA microarray scanner (G2505B, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version A.7.5.1).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using Agilent Feature Extraction Software (version A.7.5.1).

source_name: vector control in HPL1D

label_protocol: Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a Whole Human Genome oligo DNA microarray kit (Agilent Technologies) with 41000 distinct probes.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 500 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

tag: transfection

value: vector control

source_name: transiently transfected with TTF-1 in HPL1D


title: Drosophila-Cbx-replicate2 (Test vs Mock) [Agilent-014816]

description:
Rep2_Agilent-014816
Biological replicate 2 of 3 slide 1, Cbx discs, Ubx ChIP
Agilent Feature Extraction File: US45103024_251481610107_S01.txt


title: ExCol-0_48hr_0.1 mM AgNO3_rep1


title: Cy3-TTF1_Cy5-VC


title: dim4_control_rep2


title: dim4_dex_rep1

description: Gene expression after 6 H treatment with 100nM dexamethasone

source_name: U2OS hGRdim4 cells, 100nM dexamethasone treated, 6 H


title: dim4_dex_rep2


title: ExCol-0_72hr_0.1 mM AgNO3_rep1


title: dim4_dex_rep3


title: Whisker pad mutant biological rep2

first: Katherine

last: Fantauzzo

address: 1150 St. Nicholas Avenue Room 307

institute: Columbia University

description: Gene expression data during vibrissae placode formation

hyb_protocol: 15 ug of cRNA were hybridized to Affymetrix GeneChip® MOE430A microarrays.

scan_protocol: Affymetrix protocol

data_processing:
The data output was analyzed using GeneSpring GX 10.0 commercial software (Agilent Technologies Inc., Palo Alto, CA, USA).  p-values were calculated using an unpaired t-test.  Expression values with a p-value ≤0.05 and a fold difference of ≥1.5-fold relative to wild-type baseline expression levels were considered significant.
Affymetrix Gene Expression, MOE 430A chips   Filter by expression    Raw data    Filter by percentile    Upper cutoff = 100.0    Lower cutoff = 20.0    At least 1 out of 6 samples have values within range   T-test unpaired   p-value computation: Asymptotic   Multiple testing correction: No correction   p-value cutoff = 0.05   Fold change cutoff = 1.5   Clustering: Hierarchical    Interpretation: A. All Samples                 B. Genotype    Cluster on: Entities and Conditions

source_name: E12.5 Whisker pad Trps1 mutant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol:
Whole whisker pads were dissected from E12.5 embryos.
Total RNA was isolated using the RNeasy® Mini Kit (Qiagen).

value: whole whisker pad

tag: genotype

value: homozygous Trps1 mutant


title: Whisker pad WT biological rep3

source_name: E12.5 Whisker pad wild-type

value: wild-type


title: Whisker pad WT biological rep1


title: Whisker pad mutant biological rep1


title: Whisker pad WT biological rep2


title: Whisker pad mutant biological rep3


title: siLuciferase 4

city: Dayton

first: Michael

last: Markey

state: OH

address: 3640 Colonel Glenn Hwy.

department: Biochemistry and Molecular Biology

institute: Wright State Unviersity

description: Expression Results from AltAnalyze using constitutive exons

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the Wright State University Center for Genomics Research.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw .cel files were analyzed with AltAnalyze.  RMA was used for normalization within AltAnalyze.

source_name: HeLa

label_protocol: Whole Transcript (WT) Expression Array kit (Ambion) was used to generate biotinylated sense strand DNA targets from the isolated RNA as described in the kit protocol. DNA quality and quantity was analyzed by nanodrop spectrophotometry (Thermo Scientific) and subjected to fragmentation and labeling using the Affymetrix GeneChip WT terminal labeling kit (Affymetrix) according to kit protocols.

growth_protocol: HeLa cells were maintained in DMEM supplemented with penicillin/streptomycin and 10% fetal bovine serum.

extract_protocol: RNA was isolated from 560 µL of saliva supernatant with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.  All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA.

treatment_protocol: HeLa cells were transfected with a control siRNA (siLuciferase) or siRNA against SON for 48 hours.  Knockdown of SON was confirmed prior to microarray sample processing.

value: HeLa

tag: sirna

value: Luciferase


title: RasV12

city: Meguro-ku

first: Atsushi

last: Kaneda

state: Tokyo

address: 4-6-1 Komaba

department: RCAST

institute: The University of Tokyo

description: Infected with activated RasV12-expressing retrovirus. Senescent.

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GCOS (MAS5) was used with target intensity=100.

source_name: Mouse embryonic fibroblast

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

tag: cell type

value: Mouse embryonic fibroblast

tag: treatment

value: infected with activated RasV12-expressing retrovirus


title: siLuciferase 3


title: siLuciferase 2


title: NA_CON__CB_5

city: NEDLANDS

first: David

last: Martino

state: Western Australia

address: Perth Childrens Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute

description: neonatal CD4+

hyb_protocol: Infinium Methylation Assay according to manufacturers protocol (Illumina)

scan_protocol: iScan system

data_processing: Genome studio v2010.3 with Methylation Module v1.8.5 under default settings

label: Cy5 and Cy3

source_name: gDNA from CD4+ cells

label_protocol: Cy5 and Cy3

growth_protocol: cells cultured for 24 hours in AIM-V media + 2Mercapto ethanol (serum free)

extract_protocol: DNA and RNA co purified from source according to Qiagen all prep kit protocol

treatment_protocol: Anti-CD3 (0.5ug/mL) + rhIL2 (20Units) or UNTREATED

value: neonatal CD4+

tag: gender

value: female

tag: disease state

value: NORM

value: CON

tag: pool id

value: K


title: NA_CON_1Y_4

description: 12m CD4+

value: mixed

value: J


title: FA_CON_1Y_5

description: 12m CD4+

value: male

value: FOOD ALLERGY

value: H


title: RasG12

description: Infected with wild type RasG12-expressing retrovirus

value: infected with wild type RasG12-expressing retrovirus


title: NA_CON_1Y_6

description: 12m CD4+

value: L


title: Mock

description: Infected with mock pMXs retrovirus

value: infected with mock pMXs virus


title: NA_CON_1Y_5

description: 12m CD4+


title: siLuciferase 1

value: HeLa


title: siSON 4

value: SON


title: FA_CON__CB_6

description: neonatal CD4+

value: I


title: NA_CON__CB_6

description: neonatal CD4+


title: FA_CON_1Y_6

description: 12m CD4+


title: MEFp2

description: No infection

value: Mouse embryonic fibroblast

tag: passage


title: FA_CON_1Y_4

description: 12m CD4+

value: G


title: Mycelium 96h replicate 4 mat- fmr1-

city: Orsay

first: Frederique

last: Bidard

address: Bâtiment 400

department: SIGNAL TRANSDUCTION, REPRODUCTION & DEGENERATIVE PROCESSES

institute: Institut de Génétique et Microbiologie UMR 8621

description: Biological replicate 4 of 4. Mycelium mat-fmr1- after 96h of growth

hyb_protocol: Hybridization experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). 825 ng of each of the Cy3- and Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven at 10 rpm for a 4x44K array format, using an Agilent in situ hybridization kit. The slides were washed in Agilent’s Gene Expression Wash Buffers following manufacturer’s instructions, then, any traces of solution were removed by centrifugation at 800 rpm for 1 min.

scan_protocol: Microarrays were scanned using the Agilent DNA microarray Scanner model G2567AA at 5 microns resolution using the extended dynamic range (XDR) feature.

data_processing: Spot and background intensities were extracted with the Feature Extraction (FE, v9.5.3) software (Agilent) using the GE2-v4_95_Feb07 default protocol. Preliminary array quality was assessed through the use of Agilent control features as well as spike-in controls (Agilent 2-Color Spike-in Kit for RNA experiment). Subsequent flagging was done according to the GenePix Pro software (Molecular Devices Syunnyvale, CA, USA) nomenclature, including four levels of flags (good (100), bad (-100), not found (-50), moderate (0)). FE software raw data from arrays issued of GPL10115 platform were processed with the MAnGO software with no background subtraction and the Printtip loess normalization method (Smyth G.K. and Speed T., 2003, Methods). FE software normalized data (Local background was subtracted and LOWESS normalization) from arrays issued of GPL10116 platform were processed with the MAnGO. Moderate t-test with adjustment of p-values was computed to measure the significance with each expression difference.

organism: Podospora anserina

source_name: mycelium, fmr1-

label_protocol: Labelling experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). One microgram aliquots of total RNA were amplified and Cy-labelled with the Agilent’s Low RNA input fluorescent linear amplification (LRILAK) PLUS kit (Agilent) along with Agilent's Two-Color RNA Spike-in Kit. The labelling efficiency and the product integrity were checked by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent)

growth_protocol: P. anserina strains used in this study are derived from the S strain of either mat+ or mat- mating type. Growth was carried out on a minimal synthetic medium at 27°C (Esser K.,1974; pp. 531-51 in Handbook of Genetics)

extract_protocol: Strains were grown on cellophane sheet (cat#1650193, BioRad, Marne la Coquette, France) or cheesecloth (Sefar Nitex 03-48/31, Dominique Dutscher, Brumath, France) placed on Petri-dishes. In order to collect sufficient amounts of biological materials (20 to 100 mg), 1 to 5 Petri-dishes were simultaneously inoculated. Biological material was scraped from cellophane sheets or cheesecloth and flash frozen with buffer RLT (Qiagen, Courtaboeuf, France) in liquid nitrogen. The biological material was grinded with a Mikro-Dismembrator (Sartorius, Aubagne, France) in nitrogen freezed vessels. After removing cell debris by centrifugation, nucleic acids were passed through a Qiashreddrer (Qiagen) for sharing DNA and total RNA was purified on RNeasy Plant Mini Kit columns (Qiagen), with an additional DNase treatment. The quality and quantity of the total RNA was determined by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent).

value: mycelium

value: mat-  fmr1-

tag: growth condition

value: harvested after 96 hours of growth in constant light, on M2 media covered with a sheet of cellophane

tag: mating type

value: mat-

source_name: Common reference

tag: biosource 1

value: mat- fmr1-S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 1

tag: biosource 2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 2

tag: biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name biosource 3

tag: biosource 4

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.

tag: name biosource 4

tag: sample type

value: common reference


title: NA_CON_1Y_1

description: 12m CD4+

tag: cell type

value: female

tag: age

value: NORM

value: CON

value: D


title: FA_CON__CB_4

description: neonatal CD4+

value: neonatal CD4+

tag: gender

value: mixed

value: FOOD ALLERGY

tag: treatment


title: NA_CON_1Y_3

description: 12m CD4+

tag: disease state

tag: pool id

value: F


title: siSON 5

tag: cell line

value: HeLa

tag: sirna

value: SON


title: siSON 2


title: NA_CON_1Y_2

description: 12m CD4+

value: E


title: Mycelium 96h replicate 3 mat- fmr1-

description: Biological replicate 3 of 4. Mycelium mat-fmr1- after 96h of growth

tag: tissue

value: mycelium

tag: genotype

value: mat-  fmr1-

tag: growth condition

value: harvested after 96 hours of growth in constant light, on M2 media covered with a sheet of cellophane

tag: mating type

value: mat-

tag: biosource 1


title: siSON 1


title: Mycelium 96h replicate 2 mat- fmr1-

description: Biological replicate 2 of 4. Mycelium mat-fmr1- after 96h of growth

value: mat- fmr1-S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 1

tag: biosource 2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 2

tag: biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: NA_CON__CB_2

description: neonatal CD4+

tag: cell type

tag: age

value: NORM

value: CON


title: siLuciferase 5

value: Luciferase


title: Mycelium 96h replicate 1 mat- fmr1-

description: Biological replicate 1 of 4. Mycelium mat-fmr1- after 96h of growth

value: harvested after 96 hours of growth in light, on M2 media covered with a sheet of cellophane

tag: biosource 4

tag: name biosource 4

tag: sample type

value: common reference


title: NA_CON__CB_3

description: neonatal CD4+

value: neonatal CD4+

tag: gender

value: mixed

tag: disease state

tag: treatment

tag: pool id

value: F


title: siSON 3

tag: cell line

value: HeLa

tag: sirna

value: SON


title: FA_CON__CB_5

description: neonatal CD4+

value: male

value: FOOD ALLERGY

value: H


title: NA_CON__CB_4

description: neonatal CD4+

value: J


title: FA_CON_1Y_3

description: 12m CD4+

value: C


title: FA_CON_1Y_1

description: 12m CD4+

value: A


title: NA_CD3_1Y_5

description: 12m CD4+

value: female

value: K


title: Mycelium 96h replicate 10 mat+ fpr1-

description: Biological replicate 2 of 4. Mycelium mat+ fpr1-after 96h of growth

source_name: mycelium, fpr1-

tag: tissue

value: mycelium

tag: genotype

value: mat+  fpr1-

tag: growth condition

value: harvested after 96 hours of growth in constant light, on M2 media covered with a sheet of cellophane

tag: mating type

value: mat+

tag: biosource 1

value: mat+fpr1-S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: Mycelium 96h replicate 11 mat+ fpr1-

description: Biological replicate 3 of 4. Mycelium mat+ fpr1-after 96h of growth

tag: name biosource 1

tag: biosource 2

tag: name biosource 2

tag: biosource 3

tag: name biosource 3

value: common reference


title: FA_CON_CB_1

description: neonatal CD4+

tag: cell type

value: neonatal CD4+

value: mixed

tag: age

value: CON


title: NA_CD3_1Y_4

description: 12m CD4+

tag: gender

tag: disease state

value: NORM

value: J


title: FA_CON_CB_2

description: neonatal CD4+

value: male

value: FOOD ALLERGY

tag: treatment

tag: pool id

value: B


title: Mycelium 96h replicate 53 mat-

description: Biological replicate 3 of 4. Mycelium mat- wt after 96h of growth

source_name: mycelium, mat-

value: mycelium

value: mat-

value: mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: biosource 4

tag: name biosource 4

tag: sample type


title: NA_CD3__CB_5

description: neonatal CD4+

value: female

value: K


title: Whole_Forebrain_3 [ChIP-chip 244K array, 2 of 2]

source_name: Embryonic brains [IP DNA]

tag: strain

value: Swiss outbred (RJOrl:SWISS)

tag: tissue

value: brain

tag: developmental stage

tag: chip antibody

value: anti-Arx antibody (ARX C-14)

tag: chip antibody vendor

value: Santa-Cruz

tag: chip antibody lot#

tag: chip antibody catalog#

source_name: Embryonic brains [Input DNA]


title: NA_CD3_1Y_6

description: 12m CD4+

value: L