title: Notch4_Ozone_24h_Rep_1

status: Public on Feb 24 2015

city: Research Triangle Park

first: Dr. Steven

last: Kleeberger

address: 111 T.W. Alexander Drive

institute: NIEHS

hyb_protocol: Arrays were hybridized sixteen hours at 45°C in a rotating hybridization oven using Affymetrix Eukaryotic Target Hybridization Controls and protocol, washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual and stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure

scan_protocol: Affymetrix Scanner 3000

data_processing: Expression intensity values were normalized with the Robust Multichip Average method using GeneSpring (GeneSpring GX 11.0 Expression Analysis Software, Agilent Technologies)

source_name: Notch 4 KO left lung_ozone_24 hr

label_protocol: Standard Affymetrix procedures

extract_protocol: Total whole lung RNA extracted using the Qiagen Mini RNA plus isolation kit and quality control performed using Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA), samples that passed QC were transcribed to cRNA

treatment_protocol: Lungs were snap-frozen prior to analysis.

value: Notch 4 knockout

tag: age

value: 7-13 weeks

tag: exposed to

value: 0.3 ppm ozone

tag: route

value: Continuous whole body inhalation

tag: time of exposure

value: 24 hour

tag: tissue

value: lung


title: Notch4_Air_Rep_1

type: RNA

state: NC

country: USA

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Notch 4 KO left lung_air

tag: genotype/variation

value: air (control)


title: Notch4_Ozone_48h_Rep_1

source_name: Notch 4 KO left lung_ozone_48 hr

value: 48 hour


title: Notch4_Air_Rep_2


title: B11 clone

status: Public on Feb 25 2015

type: genomic

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: mouse clone from strain

hyb_protocol: Hybridized to Agilent-027411 arrays.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

source_name: B11 clone

label_protocol: Probe labeling used Agilent Technologies Genomic DNA Enzymatic Labeling Kit. Labeling was performed following manufacturer's instructions.

extract_protocol: Chromosomal DNA were extracted using Qiagen DNA extraction Kit following manufacturer's instructions.

tag: strain/background

tag: cell line

tag: cell type

value: acute myeloid leukemia (AML) cell line

source_name: T leukocytes

value: T lymphocytes


title: Notch4_Ozone_6h_Rep_3

source_name: Notch 4 KO left lung_ozone_6 hr

value: 6 hour


title: LCMV memory P14 CD8 T cells_rep1

city: Atlanta

first: Shruti

last: Subramaniam

state: GA

address: Clifton Road

institute: Emory University

description:
The array used was GeneChip Mouse Genome 430 2.0 Array. There are three cell types : Naive, PR8-33 and LCMV.  There are two technical replicates for each of the cell types. The  replicates are numbered 1 to 2 for the cell types . The data was analyzed using GeneSpring software.
This sample is called LCMV-1

hyb_protocol: Standard Affymetrix hybridization protocols for eukaryotic total RNA were used for the samples.All samples were hybed at 45C,16 hours,60 RPM in 640 Affymetrix Hyb oven. Affymetrix fludics program EUKGEWS2v4_450 was used for washing

scan_protocol: Standard Affymetrix protocol

data_processing: GeneSpring

label: Generation of cDNA, amplification, biotinylation and fragmentation was performed using the NuGen Ovation biotin system.

source_name: Memory P14 T cells from spleen

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA was isolated from sorted cells using a QIAGEN RNeasy kit according to the manufacturer's instructions.

treatment_protocol: P14 cells from spleen were sorted by flow cytometry based on CD8a and CD90.1 expression.

tag: C57BL/6 mice, 90 days after LCMV infection.

tag: Mice infected with LCMV Armstrong by intraperitoneal route.


title: Notch4_Air_Rep_3


title: Notch4_Ozone_24h_Rep_3


title: Naive P14 CD8 T cells_rep1

description:
The array used was GeneChip Mouse Genome 430 2.0 Array. There are three cell types : Naive, PR8-33 and LCMV.  There are two technical replicates for each of the cell types. The  replicates are numbered 1 to 2 for the cell types . The data was analyzed using GeneSpring software.
This sample is called Naïve-1

source_name: Naïve P14 T cells from spleen

tag: 6 week old naïve transgenic P14 mice on a C57BL/6 background.


title: Notch4_Ozone_48h_Rep_3


title: Notch4_Ozone_48h_Rep_2


title: Notch4_Ozone_6h_Rep_2


title: Notch3_Ozone_48h_Rep_1

source_name: Notch 3 KO left lung_ozone_48 hr

value: Notch 3 knockout


title: Notch4_Ozone_24h_Rep_2


title: Notch3_Ozone_48h_Rep_2


title: Notch3_Ozone_48h_Rep_3


title: Notch4_Ozone_6h_Rep_1


title: C5 clone

description: mouse clone from strain

source_name: C5 clone


title: Notch3_Ozone_24h_Rep_1

source_name: Notch 3 KO left lung_ozone_24 hr


title: Notch3_Ozone_24h_Rep_2


title: Notch3_Ozone_24h_Rep_3


title: Notch3_Ozone_6h_Rep_1

source_name: Notch 3 KO left lung_ozone_6 hr


title: R-RNA-rep1

city: Urbana

first: Tong Geon

last: Lee

state: IL

address: 1101 W Peabody

institute: University of Illinois

description: This sample is of rye. It is the first of two biological replicates used in this experiment.

hyb_protocol: Hybridization was performed by GreenGene Biotech Inc (http://www.ggbio.com), Republic of Korea following their standard operating protocol.

scan_protocol: Scanning was performed by GreenGene Biotech Inc (http://www.ggbio.com), Republic of Korea following their standard operating protocol.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis).

organism: Secale cereale

source_name: The third leaf stage, RNA

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

growth_protocol: Seeds were planted in Sunshine Mix #1 (Sun Gro, Canada) and maintained in a plant growth chamber with an average day/night temperature of 23/20°C, 14 h of light (12,000 LUX), and a relative humidity of 60% for 10 days. When plants reached the third leaf stage, the whole seedling including leaf and roots were harvested for RNA isolation.

extract_protocol: Total RNA was isolated from seedlings using TRIzol reagent (Invitrogen, USA), according to the manufacturer’s protocol.

value: Diploid rye


title: R-RNA-rep2

description: This sample is of rye. It is the second of two biological replicates used in this experiment.


title: KO AMPK alpha 2 -/- Animal Replicate 4

city: CHATENAY-MALABRY

first: Claudine

last: DELOMENIE

address: 5, rue Jean-Baptiste Clément

department: Transcriptomique

institute: University Paris Sud 11

description: Biological replicate 4 of  6. KO mouse AMPK alpha2 -/-, cardiac ventricle tissue.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially using Gene Expression Wash Buffers (Agilent)

scan_protocol: Scanned on GenePix 4000B scanner with 5-µm resolution. Images were quantified using GenePix Pro Software (version 6.01.25).

data_processing: MAnGO Software (script version 1.0, package 1.0.0) was used for background subtraction and LOWESS normalization.

source_name: universal mouse reference RNA, Stratagene #740100

label_protocol: 1 µg of total RNA together with RNA Spike-In controls (Agilent), were converted to Cy3- or Cy5-labelled cRNA using Low RNA Input Linear Amp Kit (Agilent) using manufacturer's instructions. Dye-swap was performed upon distinct animals.

growth_protocol: Animals were housed under temperature-controlled conditions (21°C) and had free access to water and to a standard mouse chow. Mice were anaesthetized by intraperitoneal injection of pentobarbital (200 mg/kg) and the hearts were quickly removed.

extract_protocol: Total RNA was extracted using RNeasy Fibrous Tissue Mini Kit (Qiagen) following manufacturer's instructions

tag: reference

value: 11 mouse cell lines

tag: strain

value: 7 months

value: cardiac ventricle muscle


title: KO AMPK alpha 2 -/- Animal Replicate 3

description: Biological replicate 3 of  6. KO mouse AMPK alpha2 -/-, cardiac ventricle tissue.


title: D-RNA-rep2

description: This sample is of D genome progenitor of hexploaid wheat. It is the second of two biological replicates used in this experiment.

organism: Aegilops tauschii

value: Diploid progenitor of hexaploid wheat


title: KO AMPK alpha 2 -/- Animal Replicate 5

description: Biological replicate 5 of  6. KO mouse AMPK alpha2 -/-, cardiac ventricle tissue.


title: ABD-RNA-rep2

description: This sample is of hexploaid wheat. It is the second of two biological replicates used in this experiment.

organism: Triticum aestivum

value: Hexaploid wheat


title: 2BS2RL-RNA-rep1

description: This sample is of 2BS.2RL wheat-rye translocation. It is the first of two biological replicates used in this experiment.

value: Hexaploid wheat-rye translocation


title: 2BS2RL-RNA-rep2

description: This sample is of 2BS.2RL wheat-rye translocation. It is the second of two biological replicates used in this experiment.


title: KO AMPK alpha 2 -/- Animal Replicate 6

description: Biological replicate 6 of  6. KO mouse AMPK alpha2 -/-, cardiac ventricle tissue.


title: KO AMPK alpha 2 -/- Animal Replicate 2

description: Biological replicate 2 of  6. KO mouse AMPK alpha2 -/-, cardiac ventricle tissue.


title: Notch3_Air_Rep_3

source_name: Notch 3 KO left lung_air

value: 7-13 weeks


title: Notch3_Ozone_6h_Rep_3

value: 0.3 ppm ozone

value: Continuous whole body inhalation


title: ABD-RNA-rep1

description: This sample is of hexploaid wheat. It is the first of two biological replicates used in this experiment.


title: KO AMPK alpha 2 -/- Animal Replicate 1

description: Biological replicate 1 of  6. KO mouse AMPK alpha2 -/-, cardiac ventricle tissue.


title: WT control AMPK alpha 2 +/+ Animal Replicate 5

description: Biological replicate 5 of  6. Control WT mouse, cardiac ventricle tissue.


title: WT control AMPK alpha 2 +/+ Animal Replicate 6

description: Biological replicate 6 of  6. Control WT mouse, cardiac ventricle tissue.


title: Notch3_Ozone_6h_Rep_2

value: lung


title: WT control AMPK alpha 2 +/+ Animal Replicate 3

description: Biological replicate 3 of  6. Control WT mouse, cardiac ventricle tissue.


title: Notch3_Air_Rep_2

value: air (control)


title: PARKIN patient line #4 iPSC

city: novato

first: Ying

last: Pei

state: ca

address: 8001 redwood blvd

institute: Buck Institute

description:
Sample name: B119 iPSC
9405740107_B
PARKIN patient line #4 iPSC

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Data was generated from Imagedata using Illumina software, GenomeStudio. Normalized data was generated using “Cubic Spline” Model in software.

label: Biotin

organism: Homo sapiens

source_name: iPSC

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

growth_protocol: iPSC clones were growing on MEF in ES condition media with bFGF. Fibroblast clones were growing in PD media. Cells were split at 100% confluency.

extract_protocol: RNA was extracted and purified with QIAGEN RNeasy Plus Mini Kit. Quality control was performed by gel electrophoresis.

tag: individual

value: PARKIN patient #4

tag: gender

value: Female

value: Skin

value: iPSC


title: PARKIN patient line #3 iPSC

description:
Sample name: S110 iPSC
9405740107_G
PARKIN patient line #3 iPSC

scan_protocol: Standard Illumina hybridization protocol

value: PARKIN patient #3


title: WT control AMPK alpha 2 +/+ Animal Replicate 4

description: Biological replicate 4 of  6. Control WT mouse, cardiac ventricle tissue.


title: WT control AMPK alpha 2 +/+ Animal Replicate 2

description: Biological replicate 2 of  6. Control WT mouse, cardiac ventricle tissue.


title: PARKIN patient line #2 iPSC

description:
Sample name: P1 iPSC
9023874060_K
PARKIN patient line #2 iPSC

value: PARKIN patient #2

value: Male


title: plasma_XenoRA_07

city: Columbia

first: Rene

middle: Gabriel

last: Cortese

state: MO

address: 1 Hospital Dr. MA104E

department: Child health Research Institute

institute: University of Missouri

description:
plasma circulating DNA from xenografted mouse exposed to RA
RC6.CEL.pimg

hyb_protocol: According to Affymetrix standard protocols

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

data_processing:
GCOS 1.3 software (Affymetrix) was used to produce .cel files. Data were analyzed using the Partek Genomic Suite Software (PGS) (St. Louis, MO).
Signals were adjusted according to probe sequence and background corrected using the Robust Multiarray method (RMA). Model-based analysis of tiling-arrays (MAT) was used to identify regions of differential cirDNA modification by combining adjacent probes showing significant differences between the groups. A sliding windows of 500 bp was set, according to the average size of the fragments produced in the amplicon preparation step

source_name: plasma cirDNA from xenografted mice exposed to RA

growth_protocol: Mice were pre-exposed during 2 weeks to either RA or IH, and were then injected with 1 x 10^5 TC1 murine lung tumor cells in the left flank. Every 3 days, tumor volume was estimated. After 4 weeks from tumor injection, mice were sacrificed and tumors excised and weighed. All experimental procedures were approved by The Institutional Animal Care and Use Committee of the University of Chicago.

extract_protocol: Plasma cirDNA was isolated from 1 mL plasma using the QiAmp Circulating Nucleic Acids kit (Qiagen). 50 ng of cirDNA were blunted using T4 DNA polymerase (NEB, Ipswich MA) and universal adaptors were ligated by overnight incubation at 4°C with T4 ligase (NEB, Ipswich MA). Blunt universal adaptors were prepared by annealing two oligonucleotides (oligo 1: GCGGTGACCCGGGAGATCTGAATTC and oligo 2: GAATTCAGATC). Next, adaptor-ligated DNA was digested using a cocktail of DNA modification-sensitive restriction enzymes (HpaII, HinP1I and HpyCH4IV) (NEB, Ipswich MA), which do not cut when the corresponding restriction sites contain modified nucleotides, 5-mC or 5-hmC. Therefore, the subsequent PCR, with primers complementary to the adaptors, amplifies only the fragments bearing such modifications. The digestion product was amplified in 25 µL final volume under the following conditions: 1x PCR buffer (Sigma-Aldrich, St. Lous MO) 2.875 mM MgCl2 (Sigma-Aldrich, Sigma-Aldrich, St. Lous MO), 275 µM aminoallyl dNTP mix (Ambion, Austin, TX), 1.6 µM oligo 1 and 25 units Taq DNA polymerase (NEB, Ipswich MA). A "two-cycling" PCR strategy was used. The first PCR program started with an initial extension at 72°C for 5 min followed by 10 cycles of denaturation at 95°C for 1 minute, annealing at 94°C for 40 seconds and elongation at 72°C for 2.5 minutes, with a final extension step at 72°C for 5 minutes. Five mL of the first PCR product were used a template for the second PCR program. The second PCR program was identical to the forst program, but used 15 cycles of denaturation/annealing/extension. Amplification was checked by electrophoresis in agarose gels. PCR products were purified using the MinElute kit (Qiagen, Valencia CA) and quantified using a Nanodrop 2000.

treatment_protocol: Mice were subjected to IH with alternating cycles of 90 seconds (6% FIO2 followed by 21% FIO2, 20 cycles/hour) for 12 hours/day during daylight. The control group was exposed to continuous circulating room air (RA).

value: male

value: xenografted with TC1 murine lung tumor cells

value: room air (RA)


title: Notch3_Air_Rep_1

value: Notch 3 knockout


title: D-RNA-rep1

description: This sample is of D genome progenitor of hexploaid wheat. It is the first of two biological replicates used in this experiment.

value: Diploid progenitor of hexaploid wheat


title: Wildtype_Ozone_48h_Rep_3

source_name: Wildtype left lung_ozone_48 hr

value: Wildtype

value: 7-13 weeks

value: 48 hour


title: WT control AMPK alpha 2 +/+ Animal Replicate 1

description: Biological replicate 1 of  6. Control WT mouse, cardiac ventricle tissue.

value: 7 months

value: cardiac ventricle muscle

value: 11 mouse cell lines


title: Control iPSC

description:
Sample name: Y9 iPSC
8473515067_C
Control iPSC

value: control patient

value: Female


title: B-RNA-rep2

description: This sample is of B genome progenitor of hexploaid wheat. It is the second of two biological replicates used in this experiment.

organism: Aegilops speltoides


title: Wildtype_Ozone_24h_Rep_3

source_name: Wildtype left lung_ozone_24 hr

value: 0.3 ppm ozone

value: Continuous whole body inhalation

value: 24 hour

value: lung


title: PPP3R1 starved, biological replicate2

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Gene expression data from PPP3R1 cell line

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse 430A_2 Array

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 .

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

source_name: starved PPP3R1 cell line

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT labelling kit (Affymetrix).

growth_protocol: The PPP3R1 cells were starved for 6 hours, while the MEFs wt cells grown in Normal Medium were used as control

extract_protocol: Total RNAs from either starved and control PPP3R1 cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.


title: PARKIN patient line #1 fibroblast

description:
Sample name: I3 Fibroblast
9405740107_K
PARKIN patient line #1 fibroblast

source_name: fibroblast

value: PARKIN patient #1

value: Male

value: Skin

value: Fibroblast


title: PARKIN patient line #3 fibroblast

description:
Sample name: S110 Fibroblast
9405740107_F
PARKIN patient line #3 fibroblast

value: PARKIN patient #3


title: A-RNA-rep2

description: This sample is of A genome progenitor of hexploaid wheat. It is the second of two biological replicates used in this experiment.

organism: Triticum urartu

value: Diploid progenitor of hexaploid wheat


title: plasma_XenoRA_03

description:
plasma circulating DNA from xenografted mouse exposed to RA
RC4.CEL.pimg

label_protocol: According to Affymetrix standard protocols

value: male

value: xenografted with TC1 murine lung tumor cells

value: room air (RA)


title: plasma_XenoRA_04

description:
plasma circulating DNA from xenografted mouse exposed to RA
RC5.CEL.pimg


title: A-RNA-rep1

description: This sample is of A genome progenitor of hexploaid wheat. It is the first of two biological replicates used in this experiment.


title: plasma_XenoIH_08

description:
plasma circulating DNA from xenografted mouse exposed to IH
RC3.CEL.pimg

source_name: plasma cirDNA from xenografted mice exposed to IH

value: intermittent hypoxia (IH)


title: Wildtype_Ozone_48h_Rep_2

value: Wildtype

value: 7-13 weeks

value: 48 hour


title: Wildtype_Ozone_24h_Rep_2

value: 0.3 ppm ozone


title: PPP3R1 CTL, biological replicate 2

source_name: PPP3R1 cell line

treatment_protocol: The PPP3R1 cells were starved for 6 hours, while the MEFs wt cells grown in Normal Medium were used as control


title: PARKIN patient line #1 iPSC

description:
Sample name: I3 iPSC
8473515067_B
PARKIN patient line #1 iPSC

value: iPSC


title: PPP3R1 starved, biological replicate1


title: PARKIN patient line #4 fibroblast

description:
Sample name: B119 Fibroblast
9405740107_A
PARKIN patient line #4 fibroblast

value: PARKIN patient #4

value: Female


title: Wildtype_Ozone_48h_Rep_1

value: Continuous whole body inhalation

value: lung


title: B-RNA-rep1

description: This sample is of B genome progenitor of hexploaid wheat. It is the first of two biological replicates used in this experiment.


title: Wildtype_Ozone_24h_Rep_1

value: 24 hour


title: plasma_XenoIH_07

description:
plasma circulating DNA from xenografted mouse exposed to IH
RC2.CEL.pimg


title: Larger cell sized virus specific CD8+ T cells from day7 p.i.  Sample2

city: Sydney

first: Wolfgang

last: Weninger

state: NSW

address: Locked Bag 6, Newtown

country: Australia

institute: Centenary Institute

description: Activated CD44hi CD8+ T cells (large cell-size)

hyb_protocol: by Ramaciotti Centre for Gene Function Analysis (The University of New South Wales, Sydney, NSW) according to the Affymetrix protocol

data_processing: The CEL files were analyzed using Bioconductor of R project. The raw intensity data of all samples were first RMA normalized and the differential expression analysis was conducted with the lmfit and ebayes model.

source_name: mouse splenocytes

growth_protocol: Naïve CD44lo CD8+ T cells were isolated from uninfected C57BL/6 mice and Kb-OVA257-264-specific CD8+ T cells were sorted on day7 p.i. with PR8-OVA or sorted from in vitro culture on day7 after stimulation with SIINFEKL peptide.

extract_protocol: Total RNA was extracted and purified with miRNeasy Micro Kit from QIAGEN.

tag: cd8+ t cell subsets

value: Kb-OVA257-264-specific CD44hi CD8+ T cells (large cell-size)

tag: time points

value: Day7 p.i.

tag: infection/ in vitro stimulation

value: PR8-OVA influenza virus infection


title: PARKIN patient line #2 fibroblast

description:
Sample name: P1 Fibroblast
9405740107_L
PARKIN patient line #2 fibroblast

value: PARKIN patient #2

value: Male

tag: age

value: Skin

value: Fibroblast


title: plasma_XenoIH_04

description:
plasma circulating DNA from xenografted mouse exposed to IH
RC1.CEL.pimg

value: male

value: xenografted with TC1 murine lung tumor cells

tag: exposed to

value: intermittent hypoxia (IH)


title: PPP3R1 starved, biological replicate3


title: PPP3R1 CTL, biological replicate 3


title: Control fibroblast

description:
Sample name: Y9 Fibroblast
9372850048_K
Control fibroblast

value: control patient

tag: tissue


title: Wildtype_Ozone_6h_Rep_3

source_name: Wildtype left lung_ozone_6 hr

tag: genotype/variation

value: Wildtype

value: 7-13 weeks

value: 0.3 ppm ozone

tag: route

tag: time of exposure

value: 6 hour


title: Wildtype_Ozone_6h_Rep_2

value: Continuous whole body inhalation

value: lung


title: MEFs starved, biological replicate3

description: Gene expression data from starved MEFs wt cells

source_name: starved MEFs wt cells

growth_protocol: The MEFs wt cells were starved for 6 hours, while the MEFs wt cells grown in Normal Medium were used as control

extract_protocol: Total RNAs from either starved and control MEFs wt cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

tag: cell line

value: MEF


title: PPP3R1 CTL, biological replicate 1

description: Gene expression data from PPP3R1 cell line


title: Wildtype_Ozone_6h_Rep_1


title: MEFs starved, biological replicate2

treatment_protocol: The MEFs wt cells were starved for 6 hours, while the MEFs wt cells grown in Normal Medium were used as control


title: AD at the age of 6month 003

type: protein

city: Mainz

first: Hyobin

last: Jeong

state: Germany

address: Richard shirrmann Str 12.

country: Germany

institute: IMB

description:
6mo_AD_003
Cy3-labeled proteins from normal and AD mice model at the age of two month and 6month were hybridized to newly developed dendron-coated phosphokinase antibody array(DPA) in which four technical replicates of 22 phospho-site specific antibodies (overall 88 spots) are immobilized.

hyb_protocol: Before the hybridization, to reduce nonspecific binding, we added 200μl of a blocking buffer with 3% Block Ace (SCETI K.K., Japan, Cat. UK-B80) in PBST to each chamber of Agilent 2 chamber gasket slides (Cat. G2534-60002) and then incubated the slides for 4hrs with rotation. The slides were washed with PBST and incubated for 2 hrs with 25μg of Cy3-labeled proteins in a final volume of 200μl filled with PBST.

scan_protocol: After a series of thorough washing with PBST, PBS, and ddH2O, the slides were dried and the Cy3 fluorescence intensities were obtained by a confocal lase scanner (GenePix 4000B, Molecular Devices).

data_processing: Signal intensities obtained from the array experiment were converted into log2-intensities and normalized by scale normalization method as previously reported(Yang, Y.H. et al, Nucleic Acids Res, 2002). To identify differentially phosphorylated sites, we performed one-way ANOVA and median fold change test.

molecule: protein

source_name: cortical region of brain tissue

label_protocol: Cy3 dyes were labeled to extracted proteins using Amersham CyDye mono-Reactive NHS Ester (GE Healthcare Cat. PA13101).

extract_protocol: Male animals were killed at 2 or 6 months of age(n=3). The cortical regions were used, and the tissues were solubilized with RIPA buffer which contains protease inhibitor, phosphatase inhibitor, and phenylmethane-sulfonylfluoride(PMSF).

value: cortical region of brain tissue

value: 6 months

tag: disease model


title: Wildtype_Air_Rep_2

source_name: Wildtype left lung_air

value: air (control)


title: Native_Ctrl_3

city: Houston

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

description:
replicate 3
9250945087_K

hyb_protocol: Biotinylated cRNA samples were hybridized to MouseWG-6v2 arrays at 58°C for 18 h according to manufacturer's protocol.

scan_protocol: Standard Illumina protocol with the iScan reader.

data_processing: Raw data was obtained from GenomeStudio and subsequently background-subtracted and quantile-normalized using the lumi package in R.

label_protocol: cRNA synthesis and labeling were performed using Illumina® TotalPrep™-96 RNA Amplification Kit (Ambion). Biotin labeling in vitro transcription reaction was performed at 37°C for 14 h.

growth_protocol: Caco2 was maintained in MEM supplemented with 20% FBS, 1% nonessential amino acids, and antibiotics.  Cells were cultured at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol: Cells were harvested at 96 hours post induction using Trizol reagent (Life Technologies), and Total RNA harvested using PureLink RNA Mini Kit (Ambion) according to the manufacturer’s protocol

treatment_protocol: LRH-1 shRNA expression was induced by the addition of 5 μg/ml of doxycycline when the cells approached 75% confluence, and total RNA harvested 96 hours later.

tag: cell type

value: colorectal cancer (CRC) cells

value: non-silencing (vector) control


title: shRNA_Doxy_2

description:
replicate 2
9250945087_H

value: inducible shRNA-mediated LRH-1 knockdown

tag: induced with

value: 5 μg/ml of doxycycline


title: shRNA_Ctrl_3

description:
replicate 3
9250945087_J


title: MEFs CTL, biological replicate 1

description: Gene expression data from MEFs wt cells

source_name: MEFs wt cells


title: MEFs starved, biological replicate1


title: MEFs CTL, biological replicate 3

description: Gene expression data from MEFs wt cells


title: Wildtype_Air_Rep_3


title: shRNA_Ctrl_2

description:
replicate 2
9250945087_G


title: Native_Doxy_1

description:
replicate 1
9250945087_I


title: AD at the age of 6month 002

description:
6mo_AD_002
Cy3-labeled proteins from normal and AD mice model at the age of two month and 6month were hybridized to newly developed dendron-coated phosphokinase antibody array(DPA) in which four technical replicates of 22 phospho-site specific antibodies (overall 88 spots) are immobilized.

value: Male


title: MEFs CTL, biological replicate 2

description: Gene expression data from MEFs wt cells


title: shRNA_Doxy_3

description:
replicate 3
9250945087_F


title: Wildtype_Air_Rep_1


title: Primary ciliary dyskinesia patient 6

city: Poznań

first: Maciej

last: Geremek

address: Strzeszyńska

country: Poland

institute: IGCZ PAN

description: Primary ciliary dyskinesia patient 6

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with background subtraction in BeadStudio 3.1.3.0

source_name: bronchial biopsy

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

tag: pcd disease status

value: affected


title: Control individual 9

description: Control individual 9

value: unaffected


title: AD at the age of 6month 001

description:
6mo_AD_001
Cy3-labeled proteins from normal and AD mice model at the age of two month and 6month were hybridized to newly developed dendron-coated phosphokinase antibody array(DPA) in which four technical replicates of 22 phospho-site specific antibodies (overall 88 spots) are immobilized.


title: Native_Doxy_2

description:
replicate 2
9250945087_E


title: normal at the age of 6month 003

description:
6mo_normal_003
Cy3-labeled proteins from normal and AD mice model at the age of two month and 6month were hybridized to newly developed dendron-coated phosphokinase antibody array(DPA) in which four technical replicates of 22 phospho-site specific antibodies (overall 88 spots) are immobilized.

value: normal


title: Control individual 8

description: Control individual 8


title: brain_akt3_rep3a

city: La Jolla

first: Kristen

last: Turner

state: CA

address: 9500 Gilman Dr

department: Molecular Pathology

institute: Ludwig Institute for Cancer Research

description:
akt_2_4.txt
Biological replicate 3 of 3. PDGFB and AKT3 treated

hyb_protocol: Samples were hybridized in 55ul of 2x Agilent hybridization buffer for 17 hours at 65C.

scan_protocol: Slides were scanned immediately after washing on an Agilent dual-laser-based scanner (G2505C). Images were quantified using Agilent Feature Extraction software (v 10.7.3.1).

data_processing: Background correction and within- and between-array normalization were performed using R 2.15.2.

source_name: PDGFB and AKT3 co-infected brain tissue

label_protocol: Total RNA was labeled with Cy3- or Cy5-CTP

growth_protocol: Mouse glioblastomas were generated via injection of DF-1 cells carrying the RCAS virus

extract_protocol: 500 ng of total RNA was extracted from each sample using Trizol following manufacturer's instructions

treatment_protocol: Mice with glioblastoma were euthanized, brain removed, and tumor grossly dissected

tag: strain

tag: observed tumor grade

value: high-grade glioma


title: Native_Doxy_3

description:
replicate 3
9250945087_D


title: Control individual 6

description: Control individual 6


title: brain_akt3_rep3b


title: brain_akt3_rep2

description:
akt_2_3.txt
Biological replicate 2 of 3. PDGFB and AKT3 treated


title: normal at the age of 6month 002

description:
6mo_normal_002
Cy3-labeled proteins from normal and AD mice model at the age of two month and 6month were hybridized to newly developed dendron-coated phosphokinase antibody array(DPA) in which four technical replicates of 22 phospho-site specific antibodies (overall 88 spots) are immobilized.

tag: gender


title: AD at the age of 2month 003

description:
2mo_AD_003
Cy3-labeled proteins from normal and AD mice model at the age of two month and 6month were hybridized to newly developed dendron-coated phosphokinase antibody array(DPA) in which four technical replicates of 22 phospho-site specific antibodies (overall 88 spots) are immobilized.

value: 2 months


title: AD at the age of 2month 002

description:
2mo_AD_002
Cy3-labeled proteins from normal and AD mice model at the age of two month and 6month were hybridized to newly developed dendron-coated phosphokinase antibody array(DPA) in which four technical replicates of 22 phospho-site specific antibodies (overall 88 spots) are immobilized.


title: Control individual 5

description: Control individual 5


title: Native_Ctrl_2

description:
replicate 2
9250945087_A


title: brain_akt3_rep1

description:
akt_2_3.txt
Biological replicate 1 of 3. PDGFB and AKT3 treated


title: brain_akt2_rep2

description:
akt_2_2.txt
Biological replicate 2 of 3. PDGFB and AKT2 treated

source_name: PDGFB and AKT2 co-infected brain tissue


title: normal at the age of 6month 001

description:
6mo_normal_001
Cy3-labeled proteins from normal and AD mice model at the age of two month and 6month were hybridized to newly developed dendron-coated phosphokinase antibody array(DPA) in which four technical replicates of 22 phospho-site specific antibodies (overall 88 spots) are immobilized.


title: Control individual 4

description: Control individual 4


title: brain_akt2_rep3

description:
akt_2_2.txt
Biological replicate 3 of 3. PDGFB and AKT2 treated


title: AD at the age of 2month 001

description:
2mo_AD_001
Cy3-labeled proteins from normal and AD mice model at the age of two month and 6month were hybridized to newly developed dendron-coated phosphokinase antibody array(DPA) in which four technical replicates of 22 phospho-site specific antibodies (overall 88 spots) are immobilized.


title: brain_akt2_rep1

description:
akt_2_1.txt
Biological replicate 1 of 3. PDGFB and AKT2 treated


title: shRNA_Doxy_1

description:
replicate 1
9250945087_C


title: Panc1 rep-2

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

description:
replicate 2
5957936057_H

data_processing: The data were normalised using quantile normalisation and log2 transformed with 'beadarray' Bioconductor package in R

source_name: Panc1 cell line

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

value: dasatinib-resistant pancreatic cancer cell line


title: Primary ciliary dyskinesia patient 5

description: Primary ciliary dyskinesia patient 5


title: brain_akt1_rep3

description:
akt_2_1.txt
Biological replicate 3 of 3. PDGFB and AKT1 treated

source_name: PDGFB and AKT1 co-infected brain tissue

value: low-grade glioma


title: brain_akt1_rep2

description:
akt_1_4.txt
Biological replicate 2 of 3. PDGFB and AKT1 treated


title: Control individual 3

description: Control individual 3


title: Panc1 rep-3

description:
replicate 3
5957936057_I


title: normal at the age of 2month 003

description:
2mo_normal_003
Cy3-labeled proteins from normal and AD mice model at the age of two month and 6month were hybridized to newly developed dendron-coated phosphokinase antibody array(DPA) in which four technical replicates of 22 phospho-site specific antibodies (overall 88 spots) are immobilized.


title: Primary ciliary dyskinesia patient 4

description: Primary ciliary dyskinesia patient 4


title: normal at the age of 2month 002

description:
2mo_normal_002
Cy3-labeled proteins from normal and AD mice model at the age of two month and 6month were hybridized to newly developed dendron-coated phosphokinase antibody array(DPA) in which four technical replicates of 22 phospho-site specific antibodies (overall 88 spots) are immobilized.


title: shRNA_Ctrl_1

description:
replicate 1
9250945087_B


title: normal at the age of 2month 001

description:
2mo_normal_001
Cy3-labeled proteins from normal and AD mice model at the age of two month and 6month were hybridized to newly developed dendron-coated phosphokinase antibody array(DPA) in which four technical replicates of 22 phospho-site specific antibodies (overall 88 spots) are immobilized.


title: brain_akt1_rep1

description:
akt_1_4.txt
Biological replicate 1 of 3. PDGFB and AKT1 treated


title: MiaPaCa2 rep-3

description:
replicate 3
5957936057_C

source_name: MiaPaCa2 cell line


title: Primary ciliary dyskinesia patient 1

description: Primary ciliary dyskinesia patient 1


title: Panc1 rep-1

description:
replicate 1
5957936057_G


title: Control individual 1

description: Control individual 1


title: MiaPaCa2 rep-2

description:
replicate 2
5957936057_B


title: Primary ciliary dyskinesia patient 3

description: Primary ciliary dyskinesia patient 3


title: brain_pdgfb_rep2

description:
akt_1_3.txt
Biological replicate 2 of 3. PDGFB treated

source_name: PDGFB-infected brain tissue


title: Control individual 2

description: Control individual 2


title: SU8686 rep-3

description:
replicate 3
5957936056_I

source_name: SU8686 cell line


title: Primary ciliary dyskinesia patient 2

description: Primary ciliary dyskinesia patient 2


title: brain_pdgfb_rep3

description:
akt_1_3.txt
Biological replicate 3 of 3. PDGFB treated


title: Control individual 7

description: Control individual 7


title: brain_ref_rep2

description:
akt_1_1.txt
Pooled reference

source_name: pooled reference, GFP-infected brain tissue

value: Normal


title: brain_pdgfb_rep1

description:
akt_1_2.txt
Biological replicate 1 of 3. PDGFB treated


title: S16-I2-D13

city: Davis

first: Matt

middle: L

last: Settles

address: 451 Health Sciences Sr

department: Genome Center

institute: University of California, Davis

hyb_protocol: Samples were hybridized on two 12-plex chips in conjunction with another experiment and spread randomly across chips. An 18-hour hybridization was conducted at 42 degrees in a NimbleGen Hybridization System 4 chamber (NimbleGen, Madison, WI).

scan_protocol: The chips were washed and then scanned on a Roche MS200 scanner.

data_processing: The NimbleGen 12-plex Human microarrays used in this study were designed based on the HG18 genome build.  NimbleScan software (NimbleGen; Madison, WI) was used to align a chip-specific grid to control features and extract raw intensity data for each probe and each array. Chip images were then visually checked for each array and verified not to contain any significant spatial artifacts. Raw intensity data was then read into the R statistical computing environment and checked for quality. Further, chip intensity distributions, boxplots and hierarchical clusters were compared and checked for any unusual global patterns. Each array was then background corrected and normalized using the quantile normalization procedure and finally each probeset was summarized using the median polish procedure as described with the robust multichip average (RMA) procedure. The median Polish procedure is a robust method for summarizing all probes contained within each probeset to a single expression value for each gene taking into account individual probe effects. Probesets with low levels of expression variation across all samples (Interquartile range: IQR < 0.5) were removed from further analysis, reducing the overall number of statistical tests to be performed (30,854 total genes).

source_name: Subject 16 Timepiont 2 nonfat

label_protocol: Double-stranded cDNAs were synthesized using Invitrogen’s SuperScript cDNA Synthesis Kit with the standard protocol using random hexanucleotide primers (Invitrogen, Carlsbad, CA). cDNAs were fluorescently labeled with Cy3 using the standard NimbleGen Gene Expression Analysis protocol.

extract_protocol: RNA was extracted from the milk fat globule using the Qiagen Rneasy lipid midi kit and protocol

treatment_protocol: 10mL of milk were centrifuged for 10 minutes at 2800xg and the milk fat globule removed with a sterile spatula.

tag: subject id

value: Subject 16

value: female

tag: time point

tag: diet enriched in

value: non-fat dairy products

tag: sample type

value: milk fat globule


title: SU8686 rep-1

description:
replicate 1
5957936056_G


title: Panc1005 rep-2

description:
replicate 2
5957936056_B

source_name: Panc1005 cell line

value: dasatinib-sensitive pancreatic cancer cell line


title: SU8686 rep-2

description:
replicate 2
5957936056_H


title: Panc1005 rep-1

description:
replicate 1
5957936056_A


title: Panc1005 rep-3

description:
replicate 3
5957936056_C


title: S13-I2-D14

source_name: Subject 13 Timepiont 2 nonfat

value: Subject 13


title: MiaPaCa2 rep-1

description:
replicate 1
5957936057_A


title: S14-I1-D14

source_name: Subject 14 Timepoint 1 fullfat

value: Subject 14

value: full-fat dairy products


title: Panc0504 rep-2

description:
replicate 2
5957936041_H

source_name: Panc0504 cell line


title: brain_ref_rep3

description:
akt_1_2.txt
Pooled reference


title: S10-I1-D14

source_name: Subject 10 Timepoint 1 fullfat

value: Subject 10


title: S13-I1-D14

source_name: Subject 13 Timepoint 1 fullfat


title: brain_ref_rep1

description:
akt_1_1.txt
Pooled reference


title: S14-I2-D13

source_name: Subject 14 Timepiont 2 nonfat


title: Panc0504 rep-1

description:
replicate 1
5957936041_G


title: S10-I2-D14

source_name: Subject 10 Timepiont 2 nonfat


title: Panc0504 rep-3

description:
replicate 3
5957936041_I


title: Panc0403 rep-3

description:
replicate 3
5957936041_C

source_name: Panc0403 cell line


title: Panc0403 rep-1

description:
replicate 1
5957936041_A


title: S09-I1-D14

source_name: Subject 9 Timepoint 1 nonfat

value: Subject 9


title: S09-I2-D14

source_name: Subject 9 Timepiont 2 fullfat


title: 0942C

status: Public on Feb 23 2015

city: San Francisco

first: Seung-Tae

address: 1450 3rd Street

institute: UCSF

description:
Gene expression data of B-cell acute lymphoblastic leukemia cells
B-ALL, others

hyb_protocol: Following fragmentation, cRNA were hybridized onto GeneChip Human Gene 1.0 ST Array (Affymetrix) according to Affymetrix's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix genechip scanner

data_processing: Data was processed and normalized using the Expression Console software (Affymetrix) with the standard Robust Multi-array Average (RMA) algorithm

source_name: B-cell acute lymphoblastic leukemia with other cytogenetics

label_protocol: 1 μg of high-quality total RNA was amplified and labeled (NuGen Ovation)

extract_protocol: AllPrep DNA/RNA Mini Kit (Qiagen) according to manufacturer's instructions

treatment_protocol: Bone marrow was isolated from B-ALL patients

value: bone marrow / peripheral blood

tag: subjects

value: children with B-ALL (California Childhood Cancer Study)

tag: age

value: F

tag: cytogenetics

value: others


title: 1397C

description:
Gene expression data of B-cell acute lymphoblastic leukemia cells
B-ALL, TCF3/PBX1

source_name: B-cell acute lymphoblastic leukemia with TCF3/PBX1 translocation

tag: tissue


title: S05-I2-D13

source_name: Subject 5 Timepiont 2 fullfat

value: Subject 5


title: 1379C

value: M


title: S05-I1-D13

source_name: Subject 5 Timepoint 1 nonfat


title: 1264C


title: 1295C


title: 1007C


title: Panc0403 rep-2

description:
replicate 2
5957936041_B


title: 0945C


title: 1005C


title: 1420C


title: 0537C


title: 0831C


title: 0758C


title: 0879C


title: 0659C


title: 0366C


title: 0485C


title: 0859C


title: 0772C


title: 1603C


title: 0150C


title: 0194C


title: 1344C

description:
Gene expression data of B-cell acute lymphoblastic leukemia cells
B-ALL, ETV6/AML1

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML24 translocation


title: 0973C


title: 0952C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML22 translocation


title: 1412C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML25 translocation


title: 0995C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML23 translocation


title: 1372C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML20 translocation


title: 1348C


title: 0365C


title: 1539C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML18 translocation


title: 1094C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML16 translocation


title: 0705C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML21 translocation


title: 1120C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML19 translocation


title: 1041C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML14 translocation


title: 1046C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML9 translocation


title: 1579C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML12 translocation


title: 0809C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML13 translocation


title: 0648C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML11 translocation


title: 0727C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML10 translocation


title: 0941C

description:
Gene expression data of B-cell acute lymphoblastic leukemia cells
B-ALL, hyperdiploid

source_name: B-cell acute lymphoblastic leukemia with hyperdiploid chromosomes

value: hyperdiploid


title: 0587C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML8 translocation


title: 1595C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML7 translocation


title: 0532C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML6 translocation


title: 0990C


title: 1473C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML1 translocation


title: 0676C


title: 0370C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML3 translocation


title: 0423C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML4 translocation


title: 0403C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML5 translocation


title: 1285C


title: 0431C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML2 translocation


title: 0925C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML15 translocation


title: 1556C


title: 0794C


title: 0985C


title: 0741C


title: 0916C


title: 1270C


title: S16-I1-D14

source_name: Subject 16 Timepoint 1 fullfat

value: Subject 16


title: 1592C


title: 0240C


title: 1073C


title: 0770C


title: 1144C


title: 0802C


title: 0388C


title: 0490C


title: 0244C


title: U020C

description:
Methylation data of B-cell acute lymphoblastic leukemia cells
B-ALL, unknown

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Illumina GenomeStudio software
Non-normalized data file contains unmethylated and methylated signal intensities
Normalized data file contains Average Beta

label: Cy5 and Cy3

source_name: B-cell acute lymphoblastic leukemia with unknown cytogenetics

label_protocol: Standard Illumina Protocol

value: unknown


title: 0610C


title: U021C


title: 0957C


title: U018C


title: U019C


title: U015C


title: U016C


title: 0376C


title: 0556C


title: 0186C


title: 0166C


title: 0354C


title: NT siRNA Rep 3

city: Helsinki

first: Markku

last: Heikinheimo

address: Tukholmankatu 8

department: Children's Hospital

country: Finland

institute: University of Helsinki

description: 9402708010_F replicate 3

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Assay Guide, Rev. A

data_processing: quantile normalization was performed usingIllumina Genome Studio software

source_name: mLTC-1 cell line

label_protocol: llumina®  TotalPrep RNA Labeling Kit-protocol, revision E (Ambion)

growth_protocol: mLTC-1 cells were cultured in Waymouth’s medium supplemented with 5% FBS, 10% horse serum, and 100 mg/L gentamicin (all from Life Technologies).

extract_protocol: RNA was extracted with Nucleospin RNA/Protein kit (Machrey-Nagel, Dueren, Germany), followed by clean-up with NucleoSpin RNA Clean-up XS kit (Machrey-Nagel, Düren, Germany). RNA quality was assessed via Bioanalyzer (Agilent, Santa Clara, CA). Array hybridization was performed using an Illumina MouseWG-6 v2.0 oligonucleotide BeadChip.

treatment_protocol: mLTC-1 cells passage 14 were transiently transfected in the absence of antibiotics with a pool of 4 siRNAs targeting Gata4 (5’-AGAGAAUAGCUUCGAACCA-3’, 5’-GGAUAUGGGUGUUCCGGGU-3’, 5’-CUGAAUAAAUCUAAGACGC-3’, 5’-GGACAUAAUCACCGCGUAA-3’) or with non-targeting control siRNA (5’-UGGUUUACAUGUCGACUAA-3’; all from Dharmacon, Lafayette, CO) using Lipofectamine® RNAiMAX transfection reagent in Opti-MEM (Life Technologies) at a final concentration of 0.1 µM

tag: passage #

tag: transfection

value: NT siRNA


title: 0891C


title: 0371C


title: 0553C

source_name: B-cell acute lymphoblastic leukemia with other cytogenetics


title: U017C


title: 0427C


title: 0544C


title: NT siRNA Rep 1

description: 9402708010_D replicate 1

tag: cell line


title: Gata4 siRNA Rep 3

description: 9402708010_C replicate 3

value: Gata4 siRNA


title: NT siRNA Rep 2

description: 9402708010_E replicate 2


title: Gata4 siRNA Rep 1

description: 9402708010_A replicate 1


title: U013C


title: U010C


title: U011C


title: U009C


title: Gata4 siRNA Rep 2

description: 9402708010_B replicate 2


title: U008C


title: U004C


title: U007C


title: U006C


title: U003C


title: U002C


title: U001C


title: U005C


title: 0441C

description:
Methylation data of B-cell acute lymphoblastic leukemia cells
B-ALL, MLL

source_name: B-cell acute lymphoblastic leukemia with MLL translocation

value: MLL


title: U014C


title: 0711C

description:
Methylation data of B-cell acute lymphoblastic leukemia cells
B-ALL, TCF3/PBX1

source_name: B-cell acute lymphoblastic leukemia with TCF3/PBX1


title: 0878C


title: 1026C


title: 1397C


title: U012C


title: 0398C


title: 0416C


title: 0851C


title: 1393C

description:
Methylation data of B-cell acute lymphoblastic leukemia cells
B-ALL, other

source_name: B-cell acute lymphoblastic leukemia with other cytogenetic abnormalities


title: 0942C


title: 1015C


title: 0222C


title: 0715C


title: 0950C


title: 1348C


title: 1307C


title: 0978C


title: 1264C


title: 0964C


title: 0981C


title: 0665C


title: 0776C


title: 0902C


title: 1561C


title: 0961C


title: 1439C


title: 0970C


title: 1292C


title: 1517C

source_name: B-cell acute lymphoblastic leukemia with ETV6/AML17 translocation


title: 0665C


title: 0818C


title: 1007C


title: 0768C


title: 1446C


title: 1420C


title: 0973C


title: 1071C


title: 0758C


title: 1152C


title: 1428C


title: 0850C


title: 0772C


title: 0553C


title: HVE_DonorA_50uMTNF_D14

city: Seattle

first: Lamar

last: Ballweber Fleming

state: WA

address: 1100 Fairview Ave N

department: VIDD

institute: Fred Hutchinson Cancer Res Ctr

data_processing: NON NORMALIZED DATA FROM GENOME STUDIO WITH BACKGROUND SUBTRACTION/ROBUST SPLINE NORMALIZATION AND VST TRANSFORMATION USING LUMI PACKAGE IN R:BIOCUNDUCTOR

label: BIOTIN

source_name: Primary Human vaginal epithelial cells

label_protocol: Biotinylated cRNA were prepared with the Ambion ILLUMINA TOTAL PREP KIT  for Illumina arrays

extract_protocol: RNA was extracted and DNase I treatment with RNA-ZOL KIT in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: female

tag: cell type

value: primary vaginal epithelial cells

tag: um tenofovir

tag: timeindays

tag: donor

value: A


title: 0859C


title: HVE_DonorC_NoTXT_D4

value: C


title: HVE_DonorA_50uMTNF_D7


title: HVE_DonorA_NoTXT_D7


title: HVE_DonorB_NoTXT_D1

value: B


title: HVE_DonorA_500uMTNF_D7


title: HVE_DonorA_NoTXT_D4


title: 1465C

value: bone marrow / peripheral blood


title: 0659C

value: children with B-ALL (California Childhood Cancer Study)


title: HVE_DonorC_50uMTNF_D14


title: HVE_DonorC_NoTXT_D14


title: HVE_DonorA_NoTXT_D1


title: 1557C

value: F


title: 0831C

value: others


title: HVE_DonorC_50uMTNF_D1


title: HVE_DonorB_NoTXT_D7


title: HVE_DonorA_NoTXT_D14


title: HVE_DonorB_500uMTNF_D4


title: HVE_DonorB_500uMTNF_D7


title: 0738C


title: 0808C


title: HVE_DonorB_NoTXT_D4


title: HVE_DonorC_NoTXT_D7


title: 1617C


title: 0366C


title: 0617C


title: 0377C


title: 0501C


title: 0537C


title: 0651C


title: HVE_DonorA_50uMTNF_D1


title: 0524C


title: 0400C


title: 0194C


title: HVE_DonorB_50uMTNF_D4


title: 0609C


title: HVE_DonorB_50uMTNF_D7


title: HVE_DonorC_500uMTNF_D1


title: HVE_DonorA_500uMTNF_D14


title: HVE_DonorA_500uMTNF_D4


title: 0645C


title: HVE_DonorC_500uMTNF_D14


title: HVE_DonorB_NoTXT_D14


title: HVE_DonorB_50uMTNF_D14


title: HVE_DonorB_500uMTNF_D1


title: HVE_DonorC_500uMTNF_D4


title: 0529C


title: 0150C


title: 0497C


title: 0345C


title: 0567C


title: 0383C


title: 0362C


title: HVE_DonorC_50uMTNF_D7


title: 0479C


title: 1603C


title: 0369C


title: 0572C


title: 0418C


title: 0392C


title: HVE_DonorB_500uMTNF_D14


title: HVE_DonorA_500uMTNF_D1


title: Native_Ctrl_1

description:
replicate 1
9250945087_L

value: colorectal cancer (CRC) cells

tag: genotype/variation

value: non-silencing (vector) control


title: HVE_DonorB_50uMTNF_D1

tag: gender


title: 0394C


title: 317000017_TENOFOVIR_ARB_V2

data_processing: NON NORMALIZED DATA FROM GENOME STUDIO WITH BACKGROUND SUBTRACTION/Normalized Data was normalized using the ROBUST SPLINE NORMALIZATION AND VST TRANSFORMATION from the LUMI PACKAGE IN R:BIOCUNDUCTOR

source_name: 9 CM ANOSCOPY RECTAL BIOPSY

extract_protocol: RNA was extracted and DNase I treatment with QIAGEN RNeasy FIBROUS TISSUE mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: tissue type

value: ANOSCOPY RECTAL BIOPSY

tag: gel applications

tag: ptid

tag: vid

tag: treatment

value: TENOFOVIR

value: ARB


title: 0485C

tag: subjects

tag: age

value: M


title: 302400262_N9_FSR_V3

source_name: 15 CM FLEX SIGMOIDOSCOPY BIOPSY

value: FLEX SIGMOIDOSCOPY BIOPSY

tag: tissue

value: FSR


title: HVE_DonorA_50uMTNF_D4

value: female


title: HVE_DonorC_NoTXT_D1

value: primary vaginal epithelial cells


title: HVE_DonorC_500uMTNF_D7


title: 302400254_N9_ARB_V3


title: HVE_DonorC_50uMTNF_D4


title: 302400195_TENOFOVIR_ARB_V2


title: 0277C

tag: cytogenetics


title: 315200147_NOTXT_FSR_V6

value: NOTXT


title: 315200286_NOTXT_FSR_V6


title: 302400146_TENOFOVIR_ARB_V6


title: 302400113_TENOFOVIR_FSR_V2


title: 302400083_NOTXT_FSR_V6


title: 1650C


title: 0425C


title: 0365C


title: 1074C

description:
Methylation data of B-cell acute lymphoblastic leukemia cells
B-ALL, ETV6/RUNX1

source_name: B-cell acute lymphoblastic leukemia with ETV6/RUNX1 translocation


title: 1086C


title: 317000207_HEC_FSR_V3

value: HEC


title: 0946C


title: 1344C


title: 0995C


title: 317000075_HEC_FSR_V2


title: 0952C


title: 302400262_N9_ARB_V3


title: 315200123_N9_ARB_V2


title: 1372C


title: 1286C


title: 0445C


title: 302400083_NOTXT_ARB_V2


title: 302400210_N9_ARB_V3


title: 317000301_NOTXT_ARB_V6


title: 317000301_NOTXT_FSR_V3


title: 1120C


title: 1539C


title: 315200253_NOTXT_FSR_V2


title: 315200170_HEC_ARB_V2


title: 315200123_N9_ARB_V6


title: 315200147_NOTXT_FSR_V2


title: 317000254_TENOFOVIR_ARB_V6


title: 317000171_HEC_ARB_V3


title: 1517C


title: 315200057_TENOFOVIR_FSR_V2


title: 317000262_N9_ARB_V2


title: 317000301_NOTXT_FSR_V6


title: 317000249_NOTXT_ARB_V3


title: 1213C


title: 1294C


title: 1094C


title: 0708C


title: 317000249_NOTXT_FSR_V2


title: 1558C


title: 1544C


title: 302400083_NOTXT_ARB_V3


title: 1436C


title: 317000221_N9_FSR_V6


title: 1477C


title: 315200253_NOTXT_ARB_V6


title: 317000249_NOTXT_FSR_V6


title: 315200057_TENOFOVIR_ARB_V2


title: 315200151_N9_FSR_V2


title: 317000327_TENOFOVIR_FSR_V6


title: 317000327_TENOFOVIR_FSR_V2


title: 0690C


title: 0925C


title: 1041C


title: 0809C


title: 1579C


title: 317000249_NOTXT_FSR_V3


title: 1447C


title: 302400171_HEC_FSR_V2


title: 315200147_NOTXT_ARB_V2


title: 1489C


title: 0940C


title: 0727C


title: 1046C


title: 0824C


title: 315200170_HEC_FSR_V6


title: 315200272_HEC_FSR_V3


title: 317000075_HEC_ARB_V6


title: 0587C


title: 0163C


title: 315200272_HEC_FSR_V6


title: 0565C


title: 315200170_HEC_FSR_V3


title: 0718C


title: 302400262_N9_FSR_V6


title: 1595C


title: 315200253_NOTXT_FSR_V3


title: 302400210_N9_FSR_V3


title: 0532C


title: 1669C


title: 1636C


title: 302400146_TENOFOVIR_ARB_V2


title: 0423C


title: 0403C


title: 315200151_N9_ARB_V2


title: 317000262_N9_ARB_V3


title: 302400171_HEC_FSR_V6


title: 302400083_NOTXT_FSR_V3


title: 317000221_N9_FSR_V2


title: 317000207_HEC_FSR_V2


title: 0575C


title: 302400171_HEC_ARB_V6


title: 317000207_HEC_ARB_V6


title: 317000262_N9_FSR_V6


title: 317000207_HEC_ARB_V3


title: 1656C


title: 315200151_N9_FSR_V6


title: 0399C


title: 0444C


title: 0370C


title: 0372C


title: 0558C


title: 317000171_HEC_FSR_V6


title: 0431C


title: 302400109_NOTXT_FSR_V6


title: 0060C


title: 1029C

description:
Methylation data of B-cell acute lymphoblastic leukemia cells
B-ALL, hyperdiploid

source_name: B-cell acute lymphoblastic leukemia with hyperdiploid chromosomes

value: hyperdiploid


title: 0670C

value: bone marrow / peripheral blood


title: 0439C

value: children with B-ALL (California Childhood Cancer Study)


title: 0829C

value: F


title: 1473C


title: 1481C


title: 1272C


title: 317000017_TENOFOVIR_FSR_V3


title: 302400254_N9_ARB_V6


title: 317000327_TENOFOVIR_FSR_V3


title: 0873C


title: 0409C


title: 302400083_NOTXT_ARB_V6


title: 302400146_TENOFOVIR_FSR_V6


title: 0990C


title: 1285C


title: 315200170_HEC_ARB_V3


title: 0857C


title: 315200147_NOTXT_FSR_V3


title: 315200057_TENOFOVIR_ARB_V6


title: 302400138_HEC_FSR_V2


title: 302400113_TENOFOVIR_ARB_V2


title: 302400138_HEC_ARB_V2


title: 315200123_N9_FSR_V6


title: 315200272_HEC_ARB_V3


title: 302400262_N9_FSR_V2


title: 315200286_NOTXT_FSR_V3


title: 0993C


title: 0870C


title: 0620C


title: 317000034_TENOFOVIR_ARB_V3


title: 302400138_HEC_FSR_V6


title: 317000034_TENOFOVIR_FSR_V6


title: 302400210_N9_FSR_V6


title: 1370C


title: 0985C


title: 1115C


title: 0697C


title: 0953C


title: 0907C


title: 0862C


title: 0794C


title: 0774C


title: 0676C


title: 0916C


title: 317000171_HEC_ARB_V2


title: 0770C


title: 317000017_TENOFOVIR_FSR_V2


title: 0741C


title: 1099C


title: 317000254_TENOFOVIR_ARB_V3


title: 302400210_N9_FSR_V2


title: 317000301_NOTXT_FSR_V2


title: 317000083_N9_FSR_V6


title: 317000254_TENOFOVIR_FSR_V3


title: 315200286_NOTXT_FSR_V2


title: 0778C


title: 1556C


title: 317000171_HEC_FSR_V3


title: 1270C


title: 302400254_N9_FSR_V2


title: 0779C


title: 302400171_HEC_ARB_V2


title: 1592C


title: 317000249_NOTXT_ARB_V6


title: 1073C


title: 302400207_HEC_FSR_V6


title: 302400171_HEC_FSR_V3


title: 302400109_NOTXT_ARB_V2


title: 302400195_TENOFOVIR_FSR_V2


title: 315200057_TENOFOVIR_FSR_V3


title: 315200123_N9_ARB_V3


title: 302400113_TENOFOVIR_FSR_V3


title: 0802C


title: 0568C


title: 317000221_N9_ARB_V3


title: 1184C


title: 0798C


title: 317000083_N9_FSR_V3


title: 0580C


title: 0393C


title: 1261C


title: 0448C


title: 0543C


title: 317000262_N9_FSR_V3


title: 315200151_N9_FSR_V3


title: 0591C


title: 302400207_HEC_ARB_V2


title: 317000034_TENOFOVIR_FSR_V2


title: 0519C


title: 302400138_HEC_ARB_V6


title: 302400113_TENOFOVIR_ARB_V6


title: 317000017_TENOFOVIR_ARB_V3


title: 0240C


title: 317000017_TENOFOVIR_FSR_V6


title: 315200057_TENOFOVIR_ARB_V3


title: 1662C


title: 0354C


title: 0364C


title: 0490C


title: 0388C


title: 0488C


title: 0244C


title: 0401C


title: 0269C


title: 1663C


title: 302400207_HEC_FSR_V2


title: 317000042_NOTXT_ARB_V2


title: 315200272_HEC_ARB_V2


title: 315200170_HEC_FSR_V2


title: 317000017_TENOFOVIR_ARB_V6


title: 0427C


title: 302400195_TENOFOVIR_FSR_V6


title: 317000075_HEC_FSR_V3


title: 302400138_HEC_FSR_V3


title: 317000207_HEC_ARB_V2


title: 315200272_HEC_FSR_V2


title: 317000034_TENOFOVIR_ARB_V2


title: 302400210_N9_ARB_V6


title: 0891C


title: 0506C


title: 302400113_TENOFOVIR_ARB_V3


title: 0371C


title: colorectal cancer tissues from patient 77

city: Shanghai

first: Lisha

last: Wang

address: 270 DongAn Road

country: China

institute: Fudan University Shanghai Cancer Center

description: Gene expression data from patients with colorectal cancer

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Data reading was performed using QuantArray R software.

data_processing: Data analysis was performed using Cluster3.0 and SAM2.0 software. To reduce variation between individual microarrays, the intensity values for the samples in each microarray were rescaled by means of a quantile normalization method.

source_name: Patient 77, non-recurrent

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50-500 ng total RNA.

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

value: Male

tag: tumor stage

value: stage Ⅲ


title: colorectal cancer tissues from patient 80

source_name: Patient 80, non-recurrent

value: stage Ⅱ


title: colorectal cancer tissues from patient 76

source_name: Patient 76, recurrent


title: 317000207_HEC_FSR_V6


title: colorectal cancer tissues from patient 75

source_name: Patient 75, recurrent


title: colorectal cancer tissues from patient 79

source_name: Patient 79, non-recurrent

value: Female


title: 0186C


title: colorectal cancer tissues from patient 81

source_name: Patient 81, recurrent


title: 317000327_TENOFOVIR_ARB_V3

value: ANOSCOPY RECTAL BIOPSY

value: TENOFOVIR


title: 302400207_HEC_ARB_V3

value: ARB


title: colorectal cancer tissues from patient 78

source_name: Patient 78, non-recurrent


title: colorectal cancer tissues from patient 74

source_name: Patient 74, non-recurrent


title: 317000083_N9_ARB_V3


title: colorectal cancer tissues from patient 73

source_name: Patient 73, recurrent


title: colorectal cancer tissues from patient 70

source_name: Patient 70, non-recurrent


title: 302400146_TENOFOVIR_FSR_V3

value: FLEX SIGMOIDOSCOPY BIOPSY


title: 0684C

value: M


title: 0247C


title: colorectal cancer tissues from patient 72

source_name: Patient 72, non-recurrent


title: colorectal cancer tissues from patient 69

source_name: Patient 69, non-recurrent


title: colorectal cancer tissues from patient 71

source_name: Patient 71, non-recurrent


title: 0556C


title: colorectal cancer tissues from patient 68

source_name: Patient 68, lost to follow-up


title: 317000254_TENOFOVIR_ARB_V2

source_name: 9 CM ANOSCOPY RECTAL BIOPSY


title: colorectal cancer tissues from patient 67

source_name: Patient 67, recurrent


title: 317000221_N9_FSR_V3

source_name: 15 CM FLEX SIGMOIDOSCOPY BIOPSY

value: FSR


title: colorectal cancer tissues from patient 65

source_name: Patient 65, non-recurrent


title: 0363C

source_name: B-cell acute lymphoblastic leukemia with hyperdiploid chromosomes


title: colorectal cancer tissues from patient 61

source_name: Patient 61, non-recurrent


title: 0689C


title: colorectal cancer tissues from patient 63

source_name: Patient 63, non-recurrent


title: 0610C


title: colorectal cancer tissues from patient 62

source_name: Patient 62, non-recurrent


title: 315200147_NOTXT_ARB_V3


title: 0957C


title: 317000042_NOTXT_FSR_V2


title: colorectal cancer tissues from patient 66

source_name: Patient 66, recurrent


title: 317000075_HEC_ARB_V2


title: 315200123_N9_FSR_V3


title: colorectal cancer tissues from patient 59

source_name: Patient 59, non-recurrent


title: colorectal cancer tissues from patient 56

source_name: Patient 56, recurrent


title: colorectal cancer tissues from patient 60

source_name: Patient 60, non-recurrent


title: 0429C


title: 317000262_N9_ARB_V6


title: 0286C


title: 0376C


title: colorectal cancer tissues from patient 57

source_name: Patient 57, non-recurrent


title: 0166C


title: colorectal cancer tissues from patient 54

source_name: Patient 54, non-recurrent


title: colorectal cancer tissues from patient 55

source_name: Patient 55, recurrent


title: 0592C


title: 317000083_N9_ARB_V2


title: 0544C


title: 317000042_NOTXT_FSR_V6


title: colorectal cancer tissues from patient 52

source_name: Patient 52, non-recurrent


title: 302400109_NOTXT_FSR_V2


title: colorectal cancer tissues from patient 53

source_name: Patient 53, recurrent


title: colorectal cancer tissues from patient 51

source_name: Patient 51, recurrent


title: colorectal cancer tissues from patient 64

source_name: Patient 64, non-recurrent


title: colorectal cancer tissues from patient 58

source_name: Patient 58, lost to follow-up


title: 0419C


title: 0121C


title: 315200286_NOTXT_ARB_V3

source_name: 9 CM ANOSCOPY RECTAL BIOPSY


title: colorectal cancer tissues from patient 48

source_name: Patient 48, non-recurrent


title: colorectal cancer tissues from patient 47

source_name: Patient 47, non-recurrent


title: colorectal cancer tissues from patient 46

source_name: Patient 46, non-recurrent


title: 302400254_N9_FSR_V6

source_name: 15 CM FLEX SIGMOIDOSCOPY BIOPSY


title: colorectal cancer tissues from patient 49

source_name: Patient 49, recurrent


title: colorectal cancer tissues from patient 44

source_name: Patient 44, non-recurrent


title: Biological replicate 7 of 7: panaxydol treatment

city: Saint John

first: Haoxin

last: Li

state: New Brunswick

address: 100 Tucker Park Road

department: Biology

country: Canada

institute: University of New Brunswick

hyb_protocol: Agilent one color protocol; Microarrays were washed the following day according to the supplemental Agilent protocol “Preventing Ozone-Related Problems”.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, acetonitrile wash at room temperature for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm at both 10 and 100 PMT (Agilent G2505 B Microarray Scanner).  Agilent Feature Extraction Software (v9.5) formed a composite of the two scans and calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided here is Quantile Normalization.

organism: Mycolicibacterium smegmatis MC2 155

source_name: Panaxydol treatment

label_protocol: Agilent one color protocol for Cy3

growth_protocol: Mycobacterium smegmatis was grown in 96 well plates at 37 degree for 48 hours prior to treatments

extract_protocol: Trizol manufacture protocol

treatment_protocol: Each treatment was consist of 10 × MIC90 for six hours; negative control was consist of 2% DMSO in broth as vaicle control

tag: strain


title: 302400083_NOTXT_FSR_V2


title: 317000171_HEC_ARB_V6


title: 317000171_HEC_FSR_V2


title: colorectal cancer tissues from patient 50

source_name: Patient 50, lost to follow-up


title: colorectal cancer tissues from patient 43

source_name: Patient 43, lost to follow-up


title: Biological replicate 6 of 7: panaxydol treatment


title: colorectal cancer tissues from patient 42

source_name: Patient 42, recurrent


title: Biological replicate 5 of 7: panaxydol treatment


title: colorectal cancer tissues from patient 45

source_name: Patient 45, non-recurrent


title: 302400207_HEC_ARB_V6


title: 302400262_N9_ARB_V6


title: 302400138_HEC_ARB_V3


title: 302400207_HEC_FSR_V3


title: Biological replicate 6 of 6: negative control

source_name: Negative control


title: Biological replicate 6 of 6: isoniazid treatment

source_name: Isoniazid treatment


title: Biological replicate 7 of 7: ethambutol treatment

source_name: Ethambutol treatment


title: colorectal cancer tissues from patient 37

source_name: Patient 37, non-recurrent


title: colorectal cancer tissues from patient 41

source_name: Patient 41, non-recurrent


title: colorectal cancer tissues from patient 40

source_name: Patient 40, recurrent


title: 317000083_N9_ARB_V6

source_name: 9 CM ANOSCOPY RECTAL BIOPSY


title: colorectal cancer tissues from patient 39

source_name: Patient 39, non-recurrent


title: 315200253_NOTXT_FSR_V6


title: Biological replicate 6 of 7: ethambutol treatment


title: colorectal cancer tissues from patient 38

source_name: Patient 38, non-recurrent


title: 317000254_TENOFOVIR_FSR_V2

source_name: 15 CM FLEX SIGMOIDOSCOPY BIOPSY


title: Biological replicate 6 of 7: falcarinol treatment

source_name: Falcarinol treatment


title: G1E GATA-ER +E2 biological replicate 3

city: Philadelphia

first: Aaron

middle: James

last: Stonestrom

state: PA

address: 315 ARC 3615 Civic Center Blvd

department: Hematology

institute: Children's Hospital of Philadelphia

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal. Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters.

data_processing:
Initial data normalization was performed with RMA. Subsequently data was Loess normalized in R based on ERCC Spike-in control mix probeset ID #s.
MoGene-2_0-st-v2.11.1.refseq.mm9.csv

source_name: G1E GATA1-ER cells induced to express GATA1 with 100nM estradiol treatment for 24 hours

label_protocol: 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: G1E cells were grown in IMDM +20% FBS, glutamine, penicillin/streptomycin, MTG, and Epoetin alpha in a standard tissue culture incubator at 37 degree with 5% CO2.

extract_protocol: Cells were initially harvested in Trizol (Life Technologies) and nucleic acids subsequently precipitated with EtOH and purified by Qiagen Rneasy column.

treatment_protocol: 10mM JQ1 was added to a final concentration of 250nM. 10mM E2 was added to a final concentration 100nM.

tag: cells

value: GATA1 null erythroblasts (G1E cells)


title: G1E GATA-ER +E2 +JQ1 biological replicate 3

source_name: G1E GATA1-ER cells induced to express GATA1 (as above) and treated concurrently with 250nM JQ1


title: Biological replicate 6 of 6: kanamycin treatment

source_name: Kanamycin treatment


title: G1E+JQ1 biological replicate 3

source_name: G1E cells treated with 250nM JQ1 for 24 hours


title: colorectal cancer tissues from patient 34

source_name: Patient 34, non-recurrent


title: colorectal cancer tissues from patient 36

source_name: Patient 36, non-recurrent


title: G1E biological replicate 3

source_name: G1E cells


title: 315200286_NOTXT_ARB_V6

value: NOTXT


title: colorectal cancer tissues from patient 35

source_name: Patient 35, recurrent


title: Biological replicate 5 of 7: ethambutol treatment

source_name: Ethambutol treatment


title: 317000327_TENOFOVIR_ARB_V6


title: 302400210_N9_ARB_V2


title: colorectal cancer tissues from patient 32

source_name: Patient 32, non-recurrent


title: 317000221_N9_ARB_V2


title: colorectal cancer tissues from patient 33

source_name: Patient 33, recurrent


title: G1E GATA-ER +E2 biological replicate 2


title: colorectal cancer tissues from patient 31

source_name: Patient 31, recurrent


title: Biological replicate 5 of 6: kanamycin treatment


title: Biological replicate 4 of 7: panaxydol treatment

source_name: Panaxydol treatment


title: Biological replicate 5 of 6: isoniazid treatment

source_name: Isoniazid treatment


title: 315200253_NOTXT_ARB_V2

source_name: 9 CM ANOSCOPY RECTAL BIOPSY


title: G1E GATA-ER +E2 +JQ1 biological replicate 2


title: colorectal cancer tissues from patient 30

source_name: Patient 30, non-recurrent


title: colorectal cancer tissues from patient 29

source_name: Patient 29, non-recurrent


title: G1E+JQ1 biological replicate 2


title: G1E biological replicate 2


title: Biological replicate 5 of 6: negative control

source_name: Negative control


title: G1E GATA-ER +E2 +JQ1 biological replicate 1

source_name: G1E GATA1-ER cells induced to express GATA1 (as above) and treated concurrently with 250nM JQ1


title: 317000083_N9_FSR_V2

source_name: 15 CM FLEX SIGMOIDOSCOPY BIOPSY


title: 317000042_NOTXT_ARB_V3


title: Biological replicate 4 of 6: kanamycin treatment

source_name: Kanamycin treatment


title: 317000075_HEC_FSR_V6

value: HEC


title: colorectal cancer tissues from patient 27

source_name: Patient 27, non-recurrent


title: colorectal cancer tissues from patient 28

source_name: Patient 28, non-recurrent


title: G1E+JQ1 biological replicate 1

source_name: G1E cells treated with 250nM JQ1 for 24 hours


title: G1E GATA-ER +E2 biological replicate 1

source_name: G1E GATA1-ER cells induced to express GATA1 with 100nM estradiol treatment for 24 hours


title: 302400195_TENOFOVIR_ARB_V3


title: colorectal cancer tissues from patient 26

source_name: Patient 26, non-recurrent


title: 317000034_TENOFOVIR_FSR_V3


title: Biological replicate 3 of 7: panaxydol treatment


title: Biological replicate 5 of 7: falcarinol treatment

source_name: Falcarinol treatment


title: Biological replicate 4 of 7: falcarinol treatment


title: colorectal cancer tissues from patient 24

source_name: Patient 24, recurrent


title: Biological replicate 3 of 6: kanamycin treatment


title: 317000301_NOTXT_ARB_V2


title: Biological replicate 4 of 7: ethambutol treatment

source_name: Ethambutol treatment


title: 315200057_TENOFOVIR_FSR_V6


title: colorectal cancer tissues from patient 23

source_name: Patient 23, non-recurrent


title: Biological replicate 3 of 6: isoniazid treatment

source_name: Isoniazid treatment


title: colorectal cancer tissues from patient 21

source_name: Patient 21, lost to follow-up


title: WT.osteoclasts

city: Kyotanabe

first: Keizo

last: Nishikawa

state: Kyoto

address: 1-3, Tatara Miyakodani

department: Medical Life Systems

country: Japan

institute: Graduate School of Life and Medical Sciences

description: WT

hyb_protocol: Gene Expression Hybridization Kit (Agilent)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for SurePrint G3 Mouse GE 8x60K Microarray slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: WT BMMs

label_protocol: Low Input Quick Amp Labeling Protocol v 6.5 (Agilent)

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions. (QIAGEN RNeasy).

treatment_protocol: Nonadherent bone marrow cells derived from mice were seeded and cultured in alpha-MEM with 10%FBS containing M-CSF. After 2 days, adherent cells were used as bone marrow-derived monocyte/macrophage precursor cells (BMMs). The BMMs were further cultured in the presence of RANKL and M-CSF to generate osteoclasts.

tag: strain background

value: female

value: wild type

tag: cell type

value: Bone marrow-derived osteoclasts


title: G1E biological replicate 1

source_name: G1E cells


title: colorectal cancer tissues from patient 22

source_name: Patient 22, recurrent


title: 315200286_NOTXT_ARB_V2

source_name: 9 CM ANOSCOPY RECTAL BIOPSY


title: colorectal cancer tissues from patient 25

source_name: Patient 25, non-recurrent


title: 317000254_TENOFOVIR_FSR_V6

source_name: 15 CM FLEX SIGMOIDOSCOPY BIOPSY


title: colorectal cancer tissues from patient 20

source_name: Patient 20, recurrent


title: 315200151_N9_ARB_V6


title: 315200170_HEC_ARB_V6


title: Biological replicate 4 of 6: negative control

source_name: Negative control


title: 302400195_TENOFOVIR_ARB_V6


title: Biological replicate 4 of 6: isoniazid treatment


title: colorectal cancer tissues from patient 19

source_name: Patient 19, recurrent


title: Biological replicate 3 of 7: falcarinol treatment


title: Biological replicate 2 of 7: panaxydol treatment

source_name: Panaxydol treatment


title: Dnmt3a KO.osteoclasts

description: Dnmt3a KO

source_name: DNmt3a KO BMMs

value: Dnmt3a knockout


title: 317000249_NOTXT_ARB_V2


title: Biological replicate 3 of 7: ethambutol treatment


title: Biological replicate 2 of 7: falcarinol treatment

source_name: Falcarinol treatment


title: Biological replicate 2 of 6: isoniazid treatment


title: colorectal cancer tissues from patient 16

source_name: Patient 16, non-recurrent


title: Biological replicate 3 of 6: negative control


title: 302400109_NOTXT_FSR_V3


title: colorectal cancer tissues from patient 17

source_name: Patient 17, non-recurrent

value: Male


title: 315200151_N9_ARB_V3


title: colorectal cancer tissues from patient 18

source_name: Patient 18, non-recurrent

value: stage Ⅲ


title: 317000034_TENOFOVIR_ARB_V6


title: 302400109_NO_ARB_V6

value: NO


title: colorectal cancer tissues from patient 15

source_name: Patient 15, non-recurrent

value: Female

value: stage Ⅱ


title: 302400171_HEC_ARB_V3

value: ANOSCOPY RECTAL BIOPSY


title: Biological replicate 7 of 7: falcarinol treatment


title: colorectal cancer tissues from patient 12

source_name: Patient 12, non-recurrent


title: 302400254_N9_FSR_V3


title: Biological replicate 2 of 6: negative control


title: 317000327_TENOFOVIR_ARB_V2

value: TENOFOVIR

value: ARB


title: 317000042_NOTXT_FSR_V3

value: FLEX SIGMOIDOSCOPY BIOPSY


title: colorectal cancer tissues from patient 13

source_name: Patient 13, recurrent


title: colorectal cancer tissues from patient 14

source_name: Patient 14, recurrent


title: colorectal cancer tissues from patient 11

source_name: Patient 11, non-recurrent


title: Biological replicate 2 of 7: ethambutol treatment

source_name: Ethambutol treatment


title: Biological replicate 1 of 6: isoniazid treatment

source_name: Isoniazid treatment


title: 317000262_N9_FSR_V2

source_name: 15 CM FLEX SIGMOIDOSCOPY BIOPSY

value: FSR


title: 317000301_NOTXT_ARB_V3

source_name: 9 CM ANOSCOPY RECTAL BIOPSY


title: colorectal cancer tissues from patient 10

source_name: Patient 10, non-recurrent


title: Biological replicate 1 of 7: ethambutol treatment


title: colorectal cancer tissues from patient 8

source_name: Patient 8, recurrent


title: Biological replicate 1 of 7: falcarinol treatment


title: Biological replicate 1 of 7: panaxydol treatment

source_name: Panaxydol treatment


title: colorectal cancer tissues from patient 9

source_name: Patient 9, recurrent


title: Biological replicate 1 of 6: negative control

source_name: Negative control


title: Biological replicate 1 of 6: kanamycin treatment

source_name: Kanamycin treatment


title: 302400146_TENOFOVIR_FSR_V2


title: 315200123_N9_FSR_V2


title: 302400109_NOTXT_ARB_V3


title: DKC6575_leaves at T2 fully irrigated

city: Parma

first: Mariolina

last: Gulli

address: Parco Area delle Scienze 11a

department: Life Sciences

institute: University of Parma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Maize Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChip 3000 scanner device

data_processing: Partek Genomics Suite versione 6.5

organism: Zea mays

source_name: DKC6575 T2 control

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

growth_protocol: Seeds were sown at a density of 80,000 plants/ha and were treated following standard agricultural practices. Each plot was fully irrigated until plants reached the vegetative six-leaf (V6) stage; from V6 to harvest they were irrigated differently : plot 1 was irrigated at 100% field capacity (control);  plot 2 was not irrigated (0% field capacity, stress 2).

extract_protocol: Total RNA was extracted using the Spectrum® Plant Total RNA Kit (Sigma) according to the manufacturer's instruction

treatment_protocol: Leaves were collected from plants  at the vegetative eight-leaves (V8) (T1 stage) and at the silking (R1) (T2 stage), all at the same time of the day, immediately frozen in liquid nitrogen and stored at -80°C

tag: variety

tag: developmental stage

value: silking (R1) (T2 stage)

tag: growth condition

value: fully irrigated

value: leaves


title: Tietar_leaves at T2 not irrigated

description: STRESST

source_name: Tietar T2 stress

value: Tietar

value: irrigation deficit


title: DKC6575_leaves at T2 not irrigated

description: STRESSD

source_name: DKC6575 T2 stress


title: 315200147_NOTXT_ARB_V6

tag: tissue type

value: NOTXT


title: 317000221_N9_ARB_V6

tag: gel applications


title: colorectal cancer tissues from patient 3

source_name: Patient 3, non-recurrent

tag: gender


title: colorectal cancer tissues from patient 7

source_name: Patient 7, non-recurrent


title: DKC6575_leaves at T1 fully irrigated

source_name: DKC6575 T1 control

value: vegetative eight-leaves (V8) (T1 stage)


title: Tietar_leaves at T1 fully irrigated

source_name: Tietar T1 control


title: colorectal cancer tissues from patient 4

source_name: Patient 4, non-recurrent

value: Male


title: 302400113_TENOFOVIR_FSR_V6

tag: ptid

tag: vid


title: Tietar_leaves at T2 fully irrigated

source_name: Tietar T2 control


title: 317000042_NO_ARB_V6

tag: treatment


title: colorectal cancer tissues from patient 5

source_name: Patient 5, non-recurrent


title: 317000075_HEC_ARB_V3

source_name: 9 CM ANOSCOPY RECTAL BIOPSY

value: HEC


title: 302400262_N9_ARB_V2


title: 302400195_TENOFOVIR_FSR_V3

source_name: 15 CM FLEX SIGMOIDOSCOPY BIOPSY


title: 302400254_N9_ARB_V2


title: colorectal cancer tissues from patient 2

source_name: Patient 2, recurrent

value: stage Ⅲ


title: 302400146_TENOFOVIR_ARB_V3


title: colorectal cancer tissues from patient 6

source_name: Patient 6, lost to follow-up

value: Female


title: 315200272_HEC_ARB_V6


title: colorectal cancer tissues from patient 1

source_name: Patient 1, recurrent


title: LN-229 induced WIF1_48h (biological rep. 1)

city: lausanne

first: Irene

last: Vassallo

state: vaud

address: av bugnon 46

country: Switzerland

institute: CHUV

description: LN-229_induced WIF1_1

hyb_protocol: Following fragmentation, 17.5  ug of cRNA were hybridized for 16 hr at 45C.

scan_protocol: GeneChips were scanned using the 7G scanner.

data_processing: Raw CEL files were processed using the robust multichip average (RMA) algorithm available in the Affy package (affy_1.38.1).

source_name: LN-229 induced WIF1_48h

label_protocol: cRNA synthesis performed with Ambion’s MessageAmpTM II-Biotin Enhanced, according to the manufacturer's instructions.

growth_protocol: Cells were grown at 37 °C.

extract_protocol: Total RNA was extracted using the RNeasy total RNA extraction kit (Qiagen)

tag: cell line

value: glioblastoma cell line

tag: treated with

value: Doxocyclin (to express WIF1) for 48hr


title: LN-229 control (biological rep. 2)

source_name: LN-229 control

value: none (control)


title: Control (DMSO) treated Replication 2

status: Public on Feb 22 2015

city: Seoul

first: Hana

last: Cho

address: Anam 5ga, Sungbukku

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

description: replicate 2

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each human-12 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).

scan_protocol: Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions. Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4).

data_processing: Array data export processing and analysis was performed usingIllumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected gene signal value was transformed by logarithm and normalized by quantile method

source_name: HeLa cells

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: HeLa cells were grown in Dulbecco’s Modified Eagle’s Medium (Hyclone) containing 10% fetal bovine serum (Hyclone).

extract_protocol: Total RNA was extracted using Trizol (Ambion, Austin, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Cells were treated with dexamethasone or DMSO(Simga)

value: HeLa cells

value: Control (DMSO)


title: LN-229 control (biological rep. 1)


title: Dexamethasone treated Replication 2

description: replicate 2

value: Dexamethasone


title: LN-229 induced WIF1_48h (biological rep. 2)

description: LN-229_induced WIF1_2


title: Oxidative stress in E. coli O157 (Sakai) #3

city: BIRMINGHAM

first: Martin

middle: D.

last: Goldberg

address: Edgbaston

department: School of Chemical Engineering

country: United Kingdom

institute: University of Birmingham

hyb_protocol: Cy3-labeled cDNA were added to a final volume of 80 ul of hybridization

scan_protocol: Slide was scanned at 532 and 630 nm by using a Genepix 4000A scanner (Axon Instruments, Union City, CA).

data_processing: GenePix software (Axon Instruments, Union City, CA) version 5.1 was used to process the scanned data and generate the gpr files.

organism: Escherichia coli

source_name: Escherichia coli O157 (Sakai) treated with menadione_rep#3

label_protocol: 20 ug total RNA was converted to Cy5-labelled cDNA using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE Healthcare) according to manufacturer’s instructions. Amino-allyl labelled nucleotides were incorporated into the cDNA by reverse transcription of the total RNA, followed by a direct chemical coupling of Cy5 NHS-dye esters to the amino-allyl-labelled cDNAs.

extract_protocol: An RNeasy kit (Qiagen Ltd) was used to extract the total RNA according to manufacturers’ instructions. Contaminating DNA was removed by using on-column DNase I digestion (Qiagen Ltd). The quality and quantity of the RNA preparations were determined with an Agilent 2100 Bioanalyzer by using the RNA 6000 nano assay Labchip (Agilent, Stockport, United Kingdom).

treatment_protocol: A 5ml overnight culture of E. coli O157:H7 was grown in Neidhardt's EZ Rich Defined Medium for 18 h at 37C. The culture was diluted 1:100 into 50 ml of fresh, prewarmed Neidhardt's EZ Rich Defined Medium in a 125 ml Ehrlenmeyer flask and shaken at 37C, 150 rpm in a New Brunswick Shaking water bath until the culture density reached 0.4. Half of the culture was transferred to a second identical flask containing menadione bisulphite to a final concentration of 0.5 mg/ml (this sample). The flasks were shaken for a further 10 min before 2 volumes of RNAprotect (TM) (Qiagen Ltd) were added to stabilise the RNA. Three independent cultures were processed on different occasions to make the 3 replicates used in this study.

value: o157:H7 (Sakai) wild-type

tag: medium

value: Neidhardt's EZ Rich Defined Medium (Teknova, USA)

value: 0.5 mg/ml menadione

source_name: E. coli O157 (Sakai) untreated (reference sample)_rep #3

label_protocol: 20 ug total RNA was converted to Cy3-labelled cDNA using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE Healthcare) according to manufacturer’s instructions. Amino-allyl labelled nucleotides were incorporated into the cDNA by reverse transcription of the total RNA, followed by a direct chemical coupling of Cy3 NHS-dye esters to the amino-allyl-labelled cDNAs.

treatment_protocol: A 5ml overnight culture of E. coli O157:H7 (Sakai) was grown in Neidhardt's EZ Rich Defined Medium for 18 h at 37C. The culture was diluted 1:100 into 50 ml of fresh, prewarmed Neidhardt's EZ Rich Defined Medium in a 125 ml Ehrlenmeyer flask and shaken at 37C, 150 rpm in a New Brunswick Shaking water bath until the culture density reached 0.4. Half of the culture was transferred to a second identical flask containing menadione bisulphite to a final concentration of 0.5 mg/ml. The flasks were shaken for a further 10 min before 2 volumes of RNAprotect (TM) (Qiagen Ltd) were added to stabilise the RNA. This sample corresponds to the culture that was not treated with menadione. Three independent cultures were processed on different occasions to make the 3 replicates used in this study.


title: Oxidative stress in E. coli O157 (Sakai) #1

source_name: Escherichia coli O157 (Sakai) treated with menadione_rep#1

source_name: E. coli O157 (Sakai) untreated (reference sample)_rep #1


title: Oxidative stress in E. coli O157 (Sakai) #2

source_name: Escherichia coli O157 (Sakai) treated with menadione_rep#2

source_name: E. coli O157 (Sakai) untreated (reference sample)_rep #2


title: Dexamethasone treated Replication 1

description: replicate 1


title: Control (DMSO) treated Replication 1

description: replicate 1


title: Oxidative stress in E. coli K-12 #1

source_name: Escherichia coli K-12 treated with menadione_rep#1

treatment_protocol: A 5ml overnight culture of MG1655 was grown in Neidhardt's EZ Rich Defined Medium for 18 h at 37C. The culture was diluted 1:100 into 50 ml of fresh, prewarmed Neidhardt's EZ Rich Defined Medium in a 125 ml Ehrlenmeyer flask and shaken at 37C, 150 rpm in a New Brunswick Shaking water bath until the culture density reached 0.4. Half of the culture was transferred to a second identical flask containing menadione bisulphite to a final concentration of 0.5 mg/ml (this sample). The flasks were shaken for a further 10 min before 2 volumes of RNAprotect (TM) (Qiagen Ltd) were added to stabilise the RNA. Three independent cultures were processed on different occasions to make the 3 replicates used in this study.

value: k-12 MG1655 wild-type

source_name: E. coli K-12 untreated (reference sample)_rep #1

treatment_protocol: A 5ml overnight culture of MG1655 was grown in Neidhardt's EZ Rich Defined Medium for 18 h at 37C. The culture was diluted 1:100 into 50 ml of fresh, prewarmed Neidhardt's EZ Rich Defined Medium in a 125 ml Ehrlenmeyer flask and shaken at 37C, 150 rpm in a New Bruswick Shaking water bath until the culture density reached 0.4. Half of the culture was transferred to a second identical flask containing menadione bisulphite to a final concentration of 0.5 mg/ml. This sample corresponds to the culture that was not treated with menadione. The flasks were shaken for a further 10 min before 2 volumes of RNAprotect (TM) (Qiagen Ltd) were added to stabilise the RNA. Three independent cultures were processed on different occasions to make the 3 replicates used in this study.


title: Oxidative stress in E. coli K-12 #2

source_name: Escherichia coli K-12 treated with menadione_rep #2

source_name: E. coli K-12 untreated (reference sample)_rep #2

treatment_protocol: A 5ml overnight culture of MG1655 was grown in Neidhardt's EZ Rich Defined Medium for 18 h at 37C. The culture was diluted 1:100 into 50 ml of fresh, prewarmed Neidhardt's EZ Rich Defined Medium in a 125 ml Ehrlenmeyer flask and shaken at 37C, 150 rpm in a New Brunswick Shaking water bath until the culture density reached 0.4. Half of the culture was transferred to a second identical flask containing menadione bisulphite to a final concentration of 0.5 mg/ml. This sample corresponds to the culture that was not treated with menadione. The flasks were shaken for a further 10 min before 2 volumes of RNAprotect (TM) (Qiagen Ltd) were added to stabilise the RNA. Three independent cultures were processed on different occasions to make the 3 replicates used in this study.


title: 4199Y204

status: Public on Feb 21 2015

city: Guelph

first: Tamas

last: Revay

state: ON

address: 50 Stone Rd E

department: Biomedical Sci

institute: University of Guelph

hyb_protocol: The protocol followed the manufacturers recommendations by the service provider DNA Landmarks, Quebec, Canada

data_processing: This work analysed DNA copy number variations only. The starting points were the GenomeStudio project files (.bsc) provided by DNAL Landmarks. The LogR data was  exported from GenomeStudio using the GoldenHelix SVS exporter. Copy number analysis was done in SNP and Variation Suite ver. 7.7.8. (SVS, GoldenHelix Inc.)

organism: Sus scrofa

source_name: gDNA from ear notch

extract_protocol: Genomic DNA was extracted using a standard Proteinase K and phenol/chlorophorm method.

tag: tissue

value: ear notch

tag: breed

value: Yorkshire

tag: Sex

value: male

tag: fertility

value: high


title: 3978Y204

scan_protocol: The protocol followed the manufacturers recommendations by the service provider DNA Landmarks, Quebec, Canada

value: low


title: 4059Y204

label_protocol: The protocol followed the manufacturers recommendations by the service provider DNA Landmarks, Quebec, Canada


title: 3721Y204


title: 3801L204

value: Landrace


title: 3574Y204


title: 3828L204


title: 1907Y301


title: Oxidative stress in E. coli K-12 #3

source_name: Escherichia coli K-12 treated with menadione_rep #3

tag: strain

source_name: E. coli K-12 untreated (reference sample)_rep #3

treatment_protocol: A 5ml overnight culture of MG1655 was grown in Neidhardt's EZ Rich Defined Medium for 18 h at 37C. The culture was diluted 1:100 into 50 ml of fresh, prewarmed Neidhardt's EZ Rich Defined Medium in a 125 ml Ehrlenmeyer flask and shaken at 37C, 150 rpm in a New Brunswick Shaking water bath until the culture density reached 0.4. Half of the culture was transferred to a second identical flask containing menadione bisulphite to a final concentration of 0.5 mg/ml. The flasks were shaken for a further 10 min before 2 volumes of RNAprotect (TM) (Qiagen Ltd) were added to stabilise the RNA. This sample corresponds to the culture that was not treated with menadione. Three independent cultures were processed on different occasions to make the 3 replicates used in this study.


title: 1741L301


title: 3608L204


title: 795L185


title: 4216L204


title: 1648Y301


title: 2046D301

value: Duroc


title: 3457Y204


title: Biological replicate 2 of 6: kanamycin treatment

source_name: Kanamycin treatment


title: 4041L204


title: 3585L204


title: 703Y185


title: 672Y185


title: 1919Y301


title: 841Y185


title: 722Y185


title: 429Y185


title: 2112D301


title: 1928Y301


title: 236L185


title: 750Y185


title: 876Y185


title: 192L185


title: 200Y185


title: 66Y185


title: 95L185


title: esa1-L254P WT S MMS Treatment Replicate 2

city: Calgary

first: Jennifer

last: Cobb

state: Alberta

address: 2A18 HRIC 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

description: esa1 WT S MMS-rep2

hyb_protocol: Hybridization was performed according to the manufactruer's instruction (Agilent Technology). Microarray was washed in 6X SSPE/0.005% sodium N-lauroylsarcosine at room temperature for 5 min followed by a second wash in pre-heated 42°C 0.6X SSPE for 2 min.

scan_protocol: Microarrays were scanned on an GenePix 4200A instrument with GenePix 3.0 software

data_processing: The raw data was lowess normalized and the average log2 ratios with the corresponding t-test p values from the dye-swap experiments were obtained using the R version 3.1.1 Bioconductor Limma package version 3.0.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Wild Type S MMS

label_protocol: 2 ug of mRNA were converted into cDNA using 140 nmol of Oligo-dT(25) anchored primer (Sigma), 20 nmol of aminoallyl dUTP dNTP (Sigma) mixture, and 200 units of SuperScript II reverse transcriptase (Invitrogen). 1 ug of cDNA each from overexpression or deletion strain and empty vector control strain was labeled with Cy3 or Cy5 (GE Healthcare) and were combined for QIAquick purification (QIAGEN).

growth_protocol: Cells were synchronized in G1 with α-factor for two hours, washed in YPAD media, and released into media with or without 0.05% MMS for 1 hour.

extract_protocol: Total RNA was extracted using hot phenol-chloroform method, followed by mRNA isolation using gravity-flow Oligo-dT cellulose beads.

tag: strain background

tag: genotype/variation

value: wild type

tag: cell cycle phase

value: synchronized in G1 with α-factor for 2hrs and released into media

value: 0.05% MMS for 1 hr

source_name: esa1-L254P S MMS


title: esa1-L254P S MMS Treatment Replicate 1

description: esa1 S MMS-rep1

source_name: esa1-L254P S

value: none (untreated control)


title: esa1-L254P WT S MMS Treatment Replicate 1

description: esa1 WT S MMS-rep1

source_name: esa1_L254P S MMS