title: 30µM_amorfrutin4_1_expE

description: replicate 1, experiment E


title: 30µM_amorfrutin4_3_expE

status: Public on May 02 2012

type: RNA

city: Berlin

first: Christopher

last: Weidner

address: Ihnestraße 63

department: Otto Warburg Laboratory

country: Germany

institute: Max Planck-Institute for Molecular Genetics

description: replicate 3, experiment E

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using cubic spline normalization implemented in Illumina BeadStudio 3.3.

label: Biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: According Zen-Bio's Human Subcutaneous Adipocyte/Preadipocyte Care Manual

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to their manual. Genomic DNA was digested on column using the DNase-Set (QIAGEN). Quality control was performed with Agilent Bioanalyser

treatment_protocol: Compounds diluted in DMSO (0.1% final DMSO concentration), 24 hours at 37°C, 5% CO2

tag: agent

tag: gender

value: female

tag: developmental stage

value: differentiated

tag: tissue

value: Subcutaneous adipose tissue


title: p53 ChIP [2of2]

status: Public on May 03 2012

type: genomic

city: Jackson

first: Luis

middle: A

last: Martinez

state: MS

address: 1500 North State St

department: Biochemistry

country: USA

institute: University of Mississippi Medical Center

hyb_protocol: Performed by Nimblegen using standard protocol  http://www.nimblegen.com/products/chip/index.html

data_processing: Performed by Nimblegen using standard protocol  http://www.nimblegen.com/products/chip/dataguide/index.html

molecule: genomic DNA

source_name: MDAH087 fibroblast cell line, ChIP

growth_protocol: Cells were maintained in DMEM + GlutaMax (Invitrogen)

extract_protocol: ChIP DNA was extracted, purified, amplified according to Farnham lab protocol.  The amplicons were sent to Nimblegen where they performed the entire process including the analysis

treatment_protocol: No treatment, harvested at 80% confluency

tag: cell type

value: Fibroblast cells from Li Fraumeni patient

tag: antibody

source_name: MDAH087 fibroblast cell line, 1.0% Input


title: 30µM_amorfrutin4_4_expE

description: replicate 4, experiment E


title: 0.1%_DMSO_4_expD

description: replicate 4, experiment D

source_name: DMSO

value: DMSO


title: 30µM_amorfrutin4_2_expE

description: replicate 2, experiment E


title: 0.1%_DMSO_2_expC

description: replicate 2, experiment C


title: 0.1%_DMSO_1_expD

description: replicate 1, experiment D


title: 0.1%_DMSO_3_expC

description: replicate 3, experiment C


title: 30µM_amorfrutin3_1_expD

description: replicate 1, experiment D


title: 10µM_nTZDpa_1_expC

description: replicate 1, experiment C

source_name: nTZDpa

value: nTZDpa


title: 0.1%_DMSO_3_expB

description: replicate 3, experiment B


title: 10µM_nTZDpa_2_expC

description: replicate 2, experiment C


title: corticalNeurons_ICRF193_2

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

hyb_protocol: hybridization was performed according to standard Affymetrix procedure

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214

data_processing: probesets were summarized and probeset-level values normalized with rma(target=core) function from R/Bioconductor package oligo (version 1.14.0)

label: biotin

organism: Mus musculus

source_name: cortical glutamatergic neurons isolated from E16.5

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix

growth_protocol: For Stem Cell differentiation transcritome analysis, wild type and Top2β knockout cells were differentiated as previously described (Bibel et al. 2004; Plachta et al. 2004; Bibel et al. 2007)

extract_protocol: RNA was extracted using Rneasy kit (Qiagen)

treatment_protocol: Cells were treated with either DMSO or 50 μM ICRF-193 of the drug every 24 hours with fresh from TN day 2 to TN day 5.

tag: strain

tag: treatment


title: 10µM_nTZDpa_4_expC

description: replicate 4, experiment C


title: 0.1%_DMSO_1_expC

description: replicate 1, experiment C


title: corticalNeurons_ICRF193_3

value: cortical glutamatergic neurons isolated from E16.5


title: 30µM_telmisartan_2_expC

description: replicate 2, experiment C

source_name: Telmisartan

value: Telmisartan


title: 0.1%_DMSO_1_expB

description: replicate 1, experiment B


title: 30µM_telmisartan_4_expC

description: replicate 4, experiment C


title: 0.1%_DMSO_2_expD

description: replicate 2, experiment D


title: 30µM_amorfrutin3_3_expD

description: replicate 3, experiment D


title: 10µM_nTZDpa_3_expC

description: replicate 3, experiment C


title: corticalNeurons_ICRF193_1


title: 30µM_telmisartan_3_expC

description: replicate 3, experiment C


title: 0.1%_DMSO_2_expB

description: replicate 2, experiment B


title: 30µM_telmisartan_1_expC

description: replicate 1, experiment C


title: corticalNeurons_DMSO_2


title: corticalNeurons_DMSO_3


title: 10µM_pioglitazone_3_expB

description: replicate 3, experiment B

source_name: Pioglitazone

value: Pioglitazone


title: 10µM_pioglitazone_2_expB

description: replicate 2, experiment B


title: 10µM_pioglitazone_4_expB

description: replicate 4, experiment B


title: ICRF193_2

source_name: TN day 5 of neurons

value: TN day 5 of neurons


title: corticalNeurons_DMSO_1


title: 10µM_pioglitazone_1_expB

description: replicate 1, experiment B


title: 30µM_amorfrutin1_3_expB

description: replicate 3, experiment B


title: ICRF193_1


title: 0.1%_DMSO_4_expC

description: replicate 4, experiment C


title: TNd6_ko2

source_name: TN day 6 of neurons

value: TN day 6 of neurons

tag: genotype/variation

value: Top2β knockout


title: DMSO_1


title: TNd6_ko3


title: TNd6_wt3

value: wild type


title: TNd6_wt2


title: 30µM_amorfrutin3_2_expD

description: replicate 2, experiment D


title: TNd2_wt2

source_name: TN day 2 of neurons

value: TN day 2 of neurons


title: 30µM_amorfrutin1_1_expB

description: replicate 1, experiment B


title: 30µM_amorfrutin1_2_expB

description: replicate 2, experiment B


title: DMSO_2


title: TNd2_ko1


title: TNd6_wt1


title: HepG2 Oleate+TNF100 sample2

city: East Lansing

first: Xuewei

last: Wang

address: 2527 Engineering building, Michigan State University

institute: Michigan State University

description: Services/protocols provided at Van Andel Research Institute in Michigan

hyb_protocol: GO TO STEP 10 FOR MICROARRAY PREHYBRIDIZATION, THEN COMPLETE STEPS 8 AND 9. 8. Clean up cDNA. a) Get rid of RNA i) Add 50 µL water ii) 10 µL 10X RNAse One buffer iii) 2 µL RNAse One iv) Incubate at 37°C for 30 minutes. v) This should give a total of 99 µL b) Remove unincorporated label and small cDNA fragments using the QIAquick PCR Purification Kit. i) Add 500 µL Qiagen Buffer PB to probe and mix. ii) Apply the sample to QIAquick spin column and centrifuge at Room Temperature 45 seconds, 10 000 g. iii) Discard flow through, add 750 µL Buffer PE (wash buffer) to spin column and centrifuge for 45 seconds, 10 000 g. iv) Discard flow through and spin again for an additional minute to remove residual Buffer PE. v) Elute probe by adding 50 µL Buffer EB (elution buffer) to the center of the QIAquick membrane, let sit one minute and then centrifuge for one minute. vi) Place probe eluted from QIAquick column on a MICRON YM 50 column and centrifuge at Room Temperature for 1.5 minutes, 12400g. This should concentrate the probe to less than 15 µL. vii) To collect purified probe, invert column into new tube. Set centrifuge to 3000 RPM and spin for 15 seconds. viii) Check the volume and bring up to 15 µL. 9. Probe pre-hybridization. a) To purified probe, add 28.8 µL probe hybridization and 2.3_µL 20X Blocking solution to probe. This gives a total of 46 µL (extra is due to evaporation during prehybridizaiton ). b) Place in 94°C heating block for 2 minutes. c) To remove any particulate matter, centrifuge at 14K g for 5 minutes and transfer to a clean tube with a rubber o-ring cap to prevent excessive evaporation. d) Place probe at 50°C for one hour (minimum 45 minutes ) to pre-hybridize. Do not exceed 1.5 hours due to evaporation. e) Once probe has pre-hybridized, centrifuge 5 minutes at14K g and use 32-36 µL per microarray for hybridization in step 11. 10. Prehybridize microarrays. a) Add 34 µL of microarray prehybridization buffer solution (frozen aliquots at -20°) over microarray. This is accomplished by slowly ejecting the solution to form a drop on the pipettor tip and gently touching the drop (NOT the tip) to the middle of the microarray. b) Place coverslip over the prehybe. Use Plastic Coverslips or youâ€™ll have a difficult time removing it later! Coverslips are sandwiched between two plastic films. Break one film by bending coverslip to one side and remove coverslip with forceps. This gives a coverslip with the plastic film on one side. Using 90° forceps, lay so that tips are on line defining arrray. Coverslips will use this as a fulcrum to prevent sliding. While holding the corner of the coverslip, place the edge of the coverslip at the border of the micro array at ~45° angle, against the forcep. A line of prehybridization solution will form at the contact. Gently lower the slide until its almost down and then let go with the forceps. Do not drop the slide from too high a height or it will move. Once the coverslip is positioned, do NOT move it. c) Place the microarray with coverslip into hybridization chamber. Add 10 µL of 50% formamide/50% water to each dimple at the end of the CMT hybridization chamber. d) Place cover on chamber and place in 50°C water bath. Allow prehybridization of microarray to proceed for at least two hours. 11. Remove prehybridization and add hybridization solution. a) Rinse hybridization chamber and dry the outside of the chamber well. Make sure to keep chamber level at all times. Remove microarray from chamber and place on paper towel. b) Remove coverslip and microarray prehybridization solution. Using the left hand, tilt the slide so that its long edge remains in contact with paper towel and an acute angle forms between the coverslip side of the slide and the paper towel. Grasp the top corner of the coverslip with forceps and while holding coverslip in place, gently tilt the slide away. The prehybe solution will be seen to separate from the coverslip just like a acrlyamide gel pulling away from a glass plate. Make sure the slide and coverslip maintain contact at the bottom edge where all the solution will gather. Once the coverslip touches the paper towel, the prehybe will blot all over. c) Add 32-36 µL hybridization solution to each microarray and hybridize overnight. Add 10 µL of 50% formamide/50% water to each dimple at the end of the CMT hybridization chamber. The next day, wash and scan the microarrays and scan them. 12. Prepare 500 mL of the following wash solutions: a) 1X SSC/0.1% SDS (25 mL 20X SSC/2.5 mL 20% SDS) b) 0.2X SSC/0.1% SDS (5 mL 20X SSC/2.5 mL 20% SDS) c) 0.2X SSC (5 mL 20X SSC) d) 0.1X SSC (2.5 mL 20X SSC)

scan_protocol: Services provided at Van Andel Research Institute in Michigan (using GenePix Pro)

data_processing: log2 ratio of cy3 by cy5 [pre-processed by GenePix Pro 5.0 (Microarray Acquisition and Analysis Software from Molecular Devices, LLC)]

source_name: hepG2 cells treated with oleate+TNF100 for 48 hours

label_protocol:
This protocol requires 50 µg of each type of RNA to be compared for each microarray. The word probe will be used to describe the labeled cDNA that binds to the DNA on the microarray.
Materials
The following is a list of supplies required to perform cDNA microarray hybridizations. Most items are available in the Invitrogen Freezer Program.
Company Cat. Number Description Amersham Pharmacia Biotech 27-7836-01 poly d(A) sodium salt or use Sigma poly d(A) Perkin Elmer NEL576 Cy3-dCTP NEL577 Cy5-dCTP Ambion 9915G DepC treated water 9480 7.5 M LiCl solution Brinkmann/Eppendorf 0032 005.330 Phase Lock Gel-Heavy, 50 mL tubes Qiagen 28104 QIAquick PCR purification Kit (50 columns) Roche 799-017 Rnasin (2000 U) 1467140 ss Salmon Sperm DNA PGC Scientifics 62-6504-04 22 X 40 mm hybrislip, pack of 100 Fisher 42416 Microcon-50 microconcentrators (Amicon no. 42416) 2551 CMT Hybridization Chamber (Corning no. 2551), 5 chambers 08-812 Histology staining dish (horizontal) 08-953-E Jewelers Microforceps, 10.8 cm (straight) 13-812-14 Kelly Forceps, curved, 140 mm 12-548-5J 24 X 40 mm glass coverslips, 1 oz pack 05-669-39 1.5 mL microfuge tubes with screw cap O-ring seal, 500 tubes Gibco/BRL Invitrogen 15279-011 Human Cot-1 DNA, 500 ug 18064-014 SuperScript II RT. 18440-016 Mouse Cot-1 DNA (if required) 10297-018 100 mM dNTP Set 15596-026 TRIzol Reagent, 100 mL (200 mL bottle is also available) 15634-017 Herring Sperm DNA, 5 X 1 mL or below 15632-011 Salmon Sperm DNA, 5 X 1 mL or above Promega PRM-4261 Rnase One Sigma D-2532 Denhardt's Solution 50X concentrate, 5 mL S-2015 20X SSPE, 1 L S-6639 20X SSC, 1 L F-9037 Formamide, 100 mL P-9403 Poly d(A) or use Pharmacia Amersham. R-7876 2500 U tRNA (type V wheat germ) Ambion 9906 10 X 50mL DepC treated water 9480 100 mL 7.5 M LiCl solution for RNA purification, 100 mL
Reverse transcription of probes.
1. Start with 50 µg RNA of each type in 9 µL water.
2. Have the following temperatures available:
a) 37°C, 50°C water baths
b) 42°C, 68°C and 95°C heating blocks
c) Thaw 5X 1st strand buffer, 0.1M DTT, oligo d(T)20VN, Cy3-dCTP,
Cy5-dCTP, 10X Low dC/dNTP, microarray pre-hybridization and
hybridization solution.
3. Anneal oligo dT primers to RNA.
a) Add 1 µL dTVN primer (0.5 µg/µL) and incubate 5 minutes at 68°C
b) Give a quick spin to collect condensation. Keep at room temperature or
solution will get too viscous.
4. Prepare 2 separate tubes of each fluorescent mix.
(X4.5) (X 5.5 reactions)
a) 4 µL 5X 1st strand buffer 18 (22 µL)
b) 2 µL 0.1 M DTT 9 (11 µL)
c) 2 µL 10X low dC dNTP 9 (11 µL)
d) 2 µL Cy3 or Cy5 dCTP 9 (11 µL)
e) 0.5 µL RNAsin 2.2 (2.7 µL)
f) This should give a total of 10.5 µL.
5. Mix annealed RNA with appropriate fluorescent mix.
6. Add 1 µL SuperScript II RT per RNA reaction and incubate at 42°C for 45 minutes.
Using another pipettor at ~15 µL, pipette up and down to mix. This mixing step is VERY important. Since Cy5 and Cy3 are light sensitive, cover tops of tubes with foil during reaction. Do not let the temperature exceed 44°C.
7. Add another 1 mL SuperScript II RT per RNA reaction, mix with 15 mL pipette, and
incubate at 42°C for another 45 minutes. Subsequently place at 94°C for 2 minutes,
quench on ice and then combine reactions in one tube.

extract_protocol: Trizol

value: HepG2 cells

source_name: HepG2 cells treated with HepG2 medium 48 hours

value: HepG2 medium


title: HepG2 Oleate + TNF20 sample2

source_name: hepG2 cells treated with oleate + TNF20 for 48 hours

value: oleate + TNF20


title: TNd6_ko1


title: 0.1%_DMSO_1_expA

description: replicate 1, experiment A

value: female


title: HepG2 Oleate + TNF20


title: 0.1%_DMSO_3_expA

description: replicate 3, experiment A

value: differentiated


title: TNd2_ko2


title: HepG2 Oleate+TNF100


title: NPko_1

source_name: Neuronal Progenitor cells

value: Neuronal Progenitor cells


title: NPko_2


title: ESko_2

source_name: ES cells

value: ES cells


title: ESko_1


title: TNd2_wt1


title: 10µM_rosiglitazone_2_expA

description: replicate 2, experiment A

source_name: Rosiglitazone

value: Rosiglitazone

value: Subcutaneous adipose tissue


title: HepG2 Oleate

source_name: hepG2 cells treated with oleate for 48 hours

value: oleate


title: 0.1%_DMSO_2_expA

description: replicate 2, experiment A

value: DMSO


title: 30µM_amorfrutin2_3_expA

description: replicate 3, experiment A


title: HepG2 Oleate sample2


title: 10µM_rosiglitazone_1_expA

description: replicate 1, experiment A


title: 10µM_rosiglitazone_3_expA

description: replicate 3, experiment A


title: HepG2 palmitate + TNF20 sample2

source_name: hepG2 cells treated with palmitate + TNF20 for 48 hours

value: palmitate + TNF20


title: HepG2 palmitate+TNF100 sample2

source_name: hepG2 cells treated with palmitate + TNF100 for 48 hours

value: palmitate + TNF100


title: ESwt_1


title: HepG2 palmitate + TNF20


title: NPwt_1


title: Wt rep3

city: Seattle

first: Brian

middle: M

last: Iritani

state: WA

address: 1959 NE Pacific Street

department: Comparative Medicine

institute: University of Washington

description: Sample 3

hyb_protocol: Illumina Expressoin BeadChip was hybridized with the biotin-labled cRNA samples overnight

scan_protocol: Scanned with an Illumina BeadArray Reader

data_processing: Signal intensties were background subtracted and quantile normalized using the Bioconductor package, “lumi,”  with background subtraction performed using the ‘bg.adjust’ function from the “affy” package, then transformed to log2 scale

source_name: sorted bm cells

label_protocol: Following hybridization BeadChips were washed, stained with a streptavidin-Cy3 conjugate

extract_protocol: RNA 4pcr kit Ambion

tag: genotype

value: Wt

value: B220+CD43+ pre-B cell


title: 30µM_amorfrutin2_1_expA

description: replicate 1, experiment A


title: Fnip 1 -/- rep2

description: Sample 2

value: Fnip 1 -/-


title: Fnip 1 -/- rep3

description: Sample 3


title: NPwt_2

value: wild type


title: Liver_amorfrutin1_rep2

description: replicate 2

source_name: Liver, amorfrutin 1

extract_protocol: Liver tissue was first lysed and homogenized in RLT buffer (QIAGEN) with 5 mm steel beads at 20 Hz for 4 min (TissueLyser, QIAGEN). Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to their manual. Genomic DNA was digested on column using the DNase-Set (QIAGEN). Quality control was performed with Agilent Bioanalyser

value: amorfrutin 1

value: C57BL/6 DIO

value: male

tag: age

value: 18 weeks

value: liver


title: ESwt_2


title: 30µM_amorfrutin2_2_expA

description: replicate 2, experiment A

value: female

value: differentiated


title: HepG2 Linoleate + TNF100

source_name: hepG2 cells treated with Linoleate + TNF100 for 48 hours

value: HepG2 cells

value: Linoleate + TNF100

value: HepG2 medium


title: Liver_amorfrutin1_rep3

description: replicate 3


title: Wt rep2

description: Sample 2


title: HepG2 palmitate sample2

source_name: hepG2 cells treated with palmitate for 48 hours

value: palmitate


title: HepG2 palmitate


title: Fnip 1 -/- rep1

description: Sample 1


title: Liver_amorfrutin1_rep4

description: replicate 4


title: Liver_amorfrutin1_rep1

description: replicate 1


title: Liver_rosiglitazone_rep3

description: replicate 3

source_name: Liver, rosiglitazone

value: rosiglitazone


title: Wt rep1

description: Sample 1


title: Liver_rosiglitazone_rep2

description: replicate 2


title: Liver_rosiglitazone_rep4

description: replicate 4


title: Liver_rosiglitazone_rep1

description: replicate 1


title: HepG2 Linoleate + TNF20 sample2

source_name: hepG2 cells treated with Linoleate + TNF20 for 48 hours

value: Linoleate + TNF20


title: HepG2 Linoleate + TNF20


title: HepG2 Linoleate sample2

source_name: hepG2 cells treated with Linoleate for 48 hours

value: Linoleate


title: HepG2 palmitate + TNF100

value: palmitate + TNF100


title: Liver_vehicle_rep2

description: replicate 2

source_name: Liver, vehicle

value: vehicle


title: HepG2 Linoleate + TNF100 sample2


title: Liver_vehicle_rep4

description: replicate 4


title: Liver_vehicle_rep3

description: replicate 3


title: normal keratinocytes_untreated_biological rep 1

city: Turku

first: Veli-Matti

last: Kähäri

address: Tykistökatu 6A, 4. floor

country: Finland

institute: University of Turku, Turku University Hospital

hyb_protocol: Each sample was hybridized to Human Gene 1.0 ST Array at +45°C overnight (18 h) according to GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual.

scan_protocol: GeneChip® Scanner 3000 with AutoLoader was used to scan the arrays. CEL-files were extracted with GCOS Manager 1.4 and DTT file was created with GeneChip® Data Transfer Tool 1.4.

data_processing: The summarized probe set data were generted using Affymetrix Expression Console v1.1 and RMA-algorithm (RMA-sketch). The genes with intensity signal (RMA, log2) above the median of all intensity signals in at least one sample were concidered as present and taken account for subsequent analysis for gene expression levels.

source_name: normal epidermal keratinocytes, untreated

label_protocol: Biotinylated sense target DNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2007, Affymetrix Inc.)

extract_protocol: Qiagen RNeasy Mini Kit was used to extract total cellular RNA according to the manufacturer's instructions

tag: sample type

value: primary cells

tag: tissue source

value: normal foreskin

tag: metastatic status

value: normal tissue


title: Liver_vehicle_rep1

description: replicate 1

value: C57BL/6 DIO

value: male


title: HepG2 Linoleate

source_name: HepG2 cells treated with HepG2 medium 48 hours


title: SCC_KGF_biological rep 3

source_name: skin SCC cells, rKGF (10 ng/ml, 24h)

value: cell line

value: skin SCC

value: primary SCC


title: SCC_ctrl_biological rep 3

source_name: skin SCC cells, untreated


title: normal keratinocytes_untreated_biological rep 2

value: normal skin


title: SCC_ctrl_biological rep 2


title: HepG2 BSA + TNF20 sample2

source_name: hepG2 cells treated with BSA + TNF20 for 48 hours

value: HepG2 cells

value: BSA + TNF20


title: SCC_KGF_biological rep 2


title: HepG2 BSA sample2

source_name: hepG2 cells treated with BSA for 48 hours

value: BSA

value: HepG2 medium


title: HepG2 BSA + TNF20


title: HepG2 BSA + TNF100

source_name: hepG2 cells treated with BSA + TNF100 for 48 hours

value: BSA + TNF100


title: SCC_KGF_biological rep 1

value: metastatic SCC


title: HepG2 BSA


title: HepG2 BSA + TNF100 sample2


title: Melanoma Tumor V13, biological rep1

city: Nashville

first: Pengcheng

last: Lu

state: TN

address: 2200 Pierce Avenue

institute: Vanderbilt University

hyb_protocol: After purification, 2.3µg of fragmented, end-labeled CDNA target is hybridized to the Affymetrix Gene Chip Human Gene ST 1.0 Array at a final concentration of 25ng/µl in hybridization cocktail for 16 hours at 45°C, with rotation of 60 rpm in the Affymetrix Model 645 hybridization oven.  The chips were automatically washed and stained per standard Affymetrix Protocols with streptavidine-phycoerythrin using Affymetrix Hybridization Wash and Stain kit reagents.

scan_protocol: Gene Chip Scanner 7G plus

data_processing: Raw gene expression data (.cel files, Affymetrix human gene ST 1.0 platform) were pre-processed and normalized using the robust multi-array average (RMA) expression measure.  The pre-processing was performed using the justRMA function of the bioconductor package affy (http://www.bioconductor.org/packages/release/bioc/html/affy.html). The expression values were in log2 format after RMA. The R package limma of R2.10.0 statistics software was used to analyze the differential expressions between drug-response and non-response tumors. Since there were multiple arrays (technical replicates) for a single sample, we estimated the correlation between technical replicates from a series of arrays, and applied the correlation information for linear modeling, and moderated paired t-statistics were computed by empirical Bayes shrinkage of the standard errors towards a common value. Winner probes were selected based on the following cutoffs: (1) fold change >2; (2) false discovery rate based on the moderated t test followed by Benjamini and Hochberg's multiple-test adjustment <0.1; and (3) log odds ratio of differential expression (B statistic) >1. Pearson correlation coefficient was used to perform two way unsupervised gene expression hierarchical cluster analysis on both samples.

source_name: Melanoma tumor V13-863AR0021

label_protocol: Affymetrix Whole-Transcript Sense Target Labeling Protocol

extract_protocol: At the time of tumor resection, 20-30 mg aliquots of melanoma tissue was immediately placed into cryovials, each containing 1 ml of RNAlater solution (Ambion, USA). The sample cryovials were placed at room temperature for 24 h then stored at -70º C until RNA extraction. The total RNA from all the tissue samples was isolated by RNeasy Fibrous Tissue Mini Kit (Qiagen, Maryland, USA) with DNase I digestion, following the manufacturer’s protocol.

value: V600E BRAF mutation

value: Male

tag: responded to raf265 in mouse model

value: no

value: human metastatic melanoma tumor


title: Melanoma Tumor V15, biological rep2

source_name: Melanoma tumor V15-863AR0033


title: HepG2 medium+TNF100 sample2

source_name: hepG2 cells treated with medium+TNF100 for 48 hours

value: HepG2 medium+TNF100


title: Melanoma Tumor V13, biological rep2

source_name: Melanoma tumor V13-863AR0029


title: Melanoma Tumor V29, biological rep3

source_name: Melanoma tumor V29-863AR0079


title: Melanoma Tumor V29, biological rep2

source_name: Melanoma tumor V29-863AR0063


title: SCC_ctrl_biological rep 1


title: Melanoma Tumor V18, biological rep2

source_name: Melanoma tumor V18-863AR0035


title: Melanoma Tumor V18, biological rep1

source_name: Melanoma tumor V18-863AR0005


title: Melanoma Tumor V29, biological rep1

source_name: Melanoma tumor V29-863AR0047


title: HepG2 medium+TNF100


title: HepG2 medium+TNF20

data_processing: log2 ration of cy3 by cy5

source_name: hepG2 cells treated with medium+TNF20 for 48 hours

value: HepG2 medium+TNF20


title: Melanoma Tumor V23, biological rep2

source_name: Melanoma tumor V23-863AR0039


title: HepG2 medium+TNF20 sample2

data_processing:
log2 ratio of cy3 by cy5 [pre-processed by GenePix Pro 5.0 (Microarray Acquisition and Analysis Software from Molecular Devices, LLC)]
log2 ratio of cy3 by cy5 [pre-processed by GenePix Pro 5.0 (Microarray Acquisition and Analysis Software from Molecular Devices, LLC)]

source_name: HepG2 cells treated with HepG2 medium 48 hours


title: Melanoma Tumor V30, biological rep2

source_name: Melanoma tumor V30-863AR0064

value: Female


title: Melanoma Tumor V15, biological rep1

source_name: Melanoma tumor V15-863AR0003


title: Melanoma Tumor V12, biological rep1

source_name: Melanoma tumor V12-863AR0019


title: Melanoma Tumor V30, biological rep3

source_name: Melanoma tumor V30-863AR0080


title: Melanoma Tumor V05, biological rep1

source_name: Melanoma tumor V05-863AR0023

value: yes


title: Melanoma Tumor V23, biological rep1

source_name: Melanoma tumor V23-863AR0009


title: Melanoma Tumor V30, biological rep1

source_name: Melanoma tumor V30-863AR0048


title: Melanoma Tumor V12, biological rep2

source_name: Melanoma tumor V12-863AR0027


title: Melanoma Tumor V05, biological rep2

source_name: Melanoma tumor V05-863AR0015


title: Melanoma Tumor V27, biological rep3

source_name: Melanoma tumor V27-863AR0077


title: Wtpool

city: Heidelberg

first: Valentina

last: Kovaleva

address: INF 280

department: B060, Molecular Genetics

institute: DKFZ

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: data analysis has been carried out using GenomeStudio 2010.3

source_name: Peripheral Blood

label_protocol: labelling was performed according to the manufacturers instructions

extract_protocol: RNA was extracted using miRNeasy kit (Qiagen, Hilden, Germany) according to the manufacture's protocol

tag: FISH results

value: norm

tag: disease state

value: healthy


title: Top2β replicate 2

hyb_protocol: Hybridization was performed according to standard Nimblegen procedure

scan_protocol: Scanning was performed with NimbleScan.

data_processing: Nimblegen array intensity files were read and log2 enrichments (log2 bound/input ratios) for each individual probe were calculated using the R package Ringo (version 1.14.0, R version 2.12.1). To remove dye artifacts , both arrays were loess-normalized using the normalizeWithinArrays function from the limma package (version 3.6.9)

source_name: Top2β ChIP DNA from neuronal cells

label_protocol: According to Nimblegen guidelines

growth_protocol: neurons were derived as dercribed previously (Bibel 2007)

extract_protocol:
ChIP experiments were performed as described before (F. Mohn et al., Mol Cell 30, 755 (Jun 20, 2008)), starting with 70 µg of chromatin and 5 µg of the  Top2β antibody and the material was amplified using whole genome amplification kit (Sigma) before labeling for hybridization.
Antibodies are self-made and details will be provided in publication.

value: wildtype

value: neuronal cells

tag: chip antibody

source_name: Input DNA neuronal cells

value: wild type

value: none, input DNA


title: Melanoma Tumor V27, biological rep2

source_name: Melanoma tumor V27-863AR0061

tag: gender


title: Melanoma Tumor V27, biological rep1

source_name: Melanoma tumor V27-863AR0045


title: CLL26

value: chronic lymphocytic leukemia


title: CLL22


title: Melanoma Tumor V24, biological rep2

source_name: Melanoma tumor V24-863AR0041

value: BRAF WT


title: Melanoma Tumor V24, biological rep1

source_name: Melanoma tumor V24-863AR0011


title: CLL18


title: CLL19


title: CLL17

value: normal


title: Sleep recovery_volunteer9

city: Sao Paulo

first: Renata

last: Pellegrino

address: Rua NApoleao de Barros 925

country: Brazil

institute: UNIFESP

description: Human Genome Plus

hyb_protocol: IVT kit (affymetrix)

scan_protocol: GCOS

data_processing: Gene expression values were obtained using the three-step Robust Multi-array Average (RMA) pre-processing method (Irizarry et al., 2003), implemented in the Affymetrix Inc. package from R/Bioconductor. We applied the ComBat method prior to analysis for adjusting data for undesirable experimental variation (or batch effect) caused by different days in which the microarrays were processed. ComBat implements an empirical Bayes approach, that is commonly used in microarray analyses due to its ability to robustly handle high-dimensional data when sample sizes are small (Johnson et al, 2007).

source_name: Sleep recovery_volunteer9

label_protocol: IVT labeling kit

growth_protocol: RNA total from blood

extract_protocol: PAXgene kit

treatment_protocol: globin and DNAse treatment

value: blood


title: Sleep recovery_volunteer8

description: Human Genome Plus

source_name: Sleep recovery_volunteer8


title: Melanoma Tumor V25, biological rep1

source_name: Melanoma tumor V25-863AR0001

value: Male


title: Sleep recovery_volunteer7

description: Human Genome Plus

source_name: Sleep recovery_volunteer7


title: Melanoma Tumor V34, biological rep2

source_name: Melanoma tumor V34-863AR0067


title: Melanoma Tumor V25, biological rep2

source_name: Melanoma tumor V25-863AR0031

value: no


title: Cll12


title: Sleep recovery_volunteer5

description: Human Genome Plus

source_name: Sleep recovery_volunteer5


title: Melanoma Tumor V32, biological rep2

source_name: Melanoma tumor V32-863AR0081

value: human metastatic melanoma tumor


title: Melanoma Tumor V32, biological rep1

source_name: Melanoma tumor V32-863AR0065


title: Melanoma Tumor V32, biological rep3

source_name: Melanoma tumor V32-863AR0049


title: Melanoma Tumor V34, biological rep3

source_name: Melanoma tumor V34-863AR0051


title: Top2β replicate 1

source_name: Top2β ChIP DNA from neuronal cells


title: Melanoma Tumor V34, biological rep1

source_name: Melanoma tumor V34-863AR0083


title: Sleep recovery_volunteer4

description: Human Genome Plus

source_name: Sleep recovery_volunteer4


title: Melanoma Tumor V33, biological rep3

source_name: Melanoma tumor V33-863AR0050


title: Sleep recovery_volunteer6

description: Human Genome Plus

source_name: Sleep recovery_volunteer6


title: CLL31

source_name: Peripheral Blood


title: CLL34


title: CLL3n


title: CLL2n


title: Sleep recovery_volunteer3

description: Human Genome Plus

source_name: Sleep recovery_volunteer3


title: Melanoma Tumor V19, biological rep1

source_name: Melanoma tumor V19-863AR0037


title: Melanoma Tumor V19, biological rep2

source_name: Melanoma tumor V19-863AR0007


title: Melanoma Tumor V33, biological rep2

source_name: Melanoma tumor V33-863AR0082


title: Melanoma Tumor V33, biological rep1

source_name: Melanoma tumor V33-863AR0066


title: Sleep recovery_volunteer2

description: Human Genome Plus

source_name: Sleep recovery_volunteer2


title: Prolonged_wakefulness_volunteer8

description: Human Genome Plus


title: Sleep recovery_volunteer1

description: Human Genome Plus

source_name: Sleep recovery_volunteer1


title: Melanoma Tumor V35, biological rep3

source_name: Melanoma tumor V35-863AR0052


title: CLL17n


title: CLL1n


title: Melanoma Tumor V35, biological rep2

source_name: Melanoma tumor V35-863AR0068


title: CLL27


title: Prolonged_wakefulness_volunteer6

description: Human Genome Plus


title: Cll29


title: CLL28


title: Prolonged_wakefulness_volunteer9

description: Human Genome Plus


title: Melanoma Tumor V35, biological rep1

source_name: Melanoma tumor V35-863AR0084


title: Prolonged_wakefulness_volunteer7

description: Human Genome Plus


title: CLL15n


title: Melanoma Tumor V28, biological rep3

source_name: Melanoma tumor V28-863AR0107


title: Prolonged_wakefulness_volunteer1

description: Human Genome Plus


title: Prolonged_wakefulness_volunteer2

description: Human Genome Plus


title: Prolonged_wakefulness_volunteer5

description: Human Genome Plus


title: CLL16n


title: baseline_volunteer9

description: Human Genome Plus


title: Prolonged_wakefulness_volunteer3

description: Human Genome Plus


title: Melanoma Tumor V28, biological rep1

source_name: Melanoma tumor V28-863AR0105


title: AcB54, biological replicate 2

city: Montreal

first: Rob

last: Sladek

state: QC

address: 740 ave Dr. Penfield

country: Canada

institute: McGill University

description: Gene expression data from mouse whole lung tissue

hyb_protocol: The hybridization mixture was prepared by mixing 15 µg of biotinylated probe with Control Oligonucleotide B2 (final concentration 50 pM) (Affymetrix), Herring Sperm DNA (final concentration 0.1 mg/ml) (Research Genetics), Acetylated BSA (final concentration 0.5 mg/ml) (Invitrogen Canada Inc.) in a final volume of 300 µL of 1x MES Hybridization Buffer (100 mM MES, 1M NaCl, 20mM EDTA, 0.01% Tween-20) (all reagents from Sigma). The hybridization mix was denatured for 10 minutes at 99ºC, incubated for 5 minutes at 45ºC and spun for 5 minutes in a benchtop microcentrifuge. The microarray expression studies were performed using an Affymetrix MG-U74Av2 GeneChips (Affymetrix) for each labeled RNA sample. The microarrays were warmed to room temperature and prehybridized in 1x hybridization buffer for 10-20 minutes at 45ºC. The prehybridization solution was removed and 150 µL of the hybridization mix was added to each array. The array and probe fragments were incubated at 45ºC overnight (16-20 hours). Following hybridization, non-specifically bound probe was removed by washing using the GeneChip Fluidics Station 400 (Affymetrix).  In total, ten low stringency washes (6x SSPE, 0.01% Tween-20, 0.005% Antifoam) and four high stringency washes (100 mM MES, 0.1 M NaCl, 0.01% Tween-20, 50ºC) were performed (all reagents from Sigma). Detection of specifically bound probe was performed by incubating the arrays with SAPE (streptavidin phycoerthryin)(Molecular Probes) and biotinylated anti-streptavidin antibody (Vector Laboratories) and scanning the chips using a Gene Array Scanner (Agilent).

scan_protocol: The Chips were analyzed with an Affymetrix Gene Array Scanner (Agilent) controled by the Microarray Analysis Suite 5.0 (Affymetrix).

data_processing: The R software package was used for all analyses. Custom CDFv12 was used on the raw expression data to deal with problem probesets. Expression values were normalized using the Robust Multi-array Analysis (RMA) for Affymetrix gene chips. To define the association between differentially expressed genes and genotypes, ANOVA was conducted on a per-gene basis using the linear model Expression ~ DSO + BG + DSO*BG, where background (BG) and donor strain of origin (DSO) were coded as binary phenotypes corresponding to A/J or B6. The cutoff for genome-wide significance was computed using the Benjamini–Hochberg correction.

source_name: AcB54 recombinant congenic mouse whole lung tissue

label_protocol: cRNA probes were prepared from 10 µg of total RNA dissolved in 10 µL of DEPC-treated water and 1 µL (100 pmol) of T7- (T)24 primer (Genosys, GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG- (T)24) was added. The primer-RNA mixture was denatured for 10 minutes at 70C, and then chilled on ice. First strand cDNA synthesis was performed using 2 µL of Superscript II reverse transcriptase (Invitrogen Canada Inc.) in a 20 µL reaction volume containing 10 µM DTT, 500µM each dNTP and 1x First Strand Buffer (all Invitrogen Canada Inc.) for 60 minutes at 42C. Second strand synthesis was performed by adding 40U DNA Polymerase I, 10U E. Coli DNA ligase, 2U RNAse H in a final reaction volume of 150 µL containing 1x Second Strand Buffer (all Invitrogen Canada Inc.). The reaction was incubated at 16C for two hours and stopped by adding 10 µL of 0.5 M EDTA (Sigma). Following second strand synthesis, the probe cDNA was purified by phenol chloroform extraction using Phase-Lock tubes (5’-3’) and redissolved in 20 µL of DEPC-treated water. Biotinylated probe was prepared from the entire cDNA reaction using the ENZO Bioarray High Yield RNA Transcript Labeling Kit (ENZO diagnostics). The probe synthesis reaction was performed at 37C for 5 hours with occasional agitation. The biotinylated probe was purified using an RNeasy spin column (Qiagen), eluted in 80 µL of DEPC-treated water, quantified by spectrophotometry and probe quality was assessed using Agilent BioAnalyser RNA LabChips. The average probe length was reduced by incubating the purified probe in 1x Fragmentation Buffer for 35 minutes at 95C.

extract_protocol:
The mice were housed with free access to food and water under conditions of 12 h of darkness and 12 h of light. After an overnight fast, the animals were killed and the lung tissues were rapidly dissected and flash frozen in liquid nitrogen. Tissue samples were obtained from two adult male mice for each strain in the RCS panel.
The snap frozen tissue samples were homogenized in TRIzol reagent using a polytron, and RNA was prepared according to the manufacturer's instructions.

value: whole lung

tag: genotype/variaton

value: A/J and C57BL/6J

value: 16 wks


title: BcA80, biological replicate 2

source_name: BcA80 recombinant congenic mouse whole lung tissue

tag: tissue


title: CLL10n


title: BcA81, biological replicate 2

source_name: BcA81 recombinant congenic mouse whole lung tissue


title: AcB56, biological replicate 2

source_name: AcB56 recombinant congenic mouse whole lung tissue


title: BcA73, biological replicate 2

source_name: BcA73 recombinant congenic mouse whole lung tissue


title: BcA84, biological replicate 2

source_name: BcA84 recombinant congenic mouse whole lung tissue


title: baseline_volunteer1

description: Human Genome Plus


title: BcA68, biological replicate 2

source_name: BcA68 recombinant congenic mouse whole lung tissue


title: AcB63, biological replicate 2

source_name: AcB63 recombinant congenic mouse whole lung tissue


title: baseline_volunteer6

description: Human Genome Plus


title: baseline_volunteer5

description: Human Genome Plus


title: BcA71, biological replicate 2

source_name: BcA71 recombinant congenic mouse whole lung tissue


title: baseline_volunteer8

description: Human Genome Plus


title: AcB57, biological replicate 2

source_name: AcB57 recombinant congenic mouse whole lung tissue


title: baseline_volunteer4

description: Human Genome Plus


title: baseline_volunteer2

description: Human Genome Plus


title: baseline_volunteer7

description: Human Genome Plus


title: Melanoma Tumor V28, biological rep2

source_name: Melanoma tumor V28-863AR0106

value: Female

value: yes


title: AcB62, biological replicate 2

source_name: AcB62 recombinant congenic mouse whole lung tissue


title: Kartogenin_100nM_24h

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

hyb_protocol: Standard Affymetrix protocols

scan_protocol: standard Affymetrix procedures

data_processing: gcRMA using R version 2.8.0 (2008-10-20).

label_protocol: GeneChip 3' IVT Express kits (Affymetrix) were used to amplify cRNA from 500 ng total RNA.

extract_protocol: Total RNA was isolated from cell pellets using Trizol extraction followed by clean up with an RNeasy kit (Qiagen, Valencia, CA, USA)

treatment_protocol: Bone marrow derived human mesenchymal stem cells were purchased from All Cells (Emeryville, CA, USA). Cells were plated in 6 well dishes in growth media. Once adhered,   the media was changed to serum free DMEM and treated with either DMSO or Kartogenin (100nM, 10nM, or 1nM) for 6 or 24 hours.   At the indicated time points, the media was removed, the cells scraped in PBS, centrifuged briefly, the PBS removed and the pellet frozen at -80C until RNA isolation.

tag: cell type

value: human mesenchymal stem cells


title: baseline_volunteer3

description: Human Genome Plus


title: Prolonged_wakefulness_volunteer4

description: Human Genome Plus


title: Kartogenin_1nM_24h


title: D0 vs D7_2

city: Pathumthani

first: nitsara

last: karoonuthaisiri

state: Pathumthani

address: Paholyothin

department: Central

country: Thailand

institute: BIOTEC

description: D0 vs D7-rep2

hyb_protocol: The Cy3- and Cy5-samples were mixed together, resuspended in hybridization solution (50% Formamide; 5x SSC; 0.1% SDS; 0.2 mg/ml Salmon sperm DNA; 0.2 mg/ml yeast tRNA; 10mM Tris, pH 7.5) and placed onto the post-processed slides.  The slides were hybridized at 42°C for 16 hrs before they were washed with home-made buffers I, II and III.

scan_protocol: The slides were scanned with GenePix 4000B (Molecular Devices, Sunnyvale, CA).  Microarray spots on scanned images are located using GenePix Pro version 6.1.

data_processing: All “empty” and “bad” spots were removed from the analysis.  “Empty” spots were failed PCR products, whereas “bad” spots were flagged by visual inspection of the spot images.  From the remaining spots, only the spots with intensities more than one standard deviation above the background intensity were further analyzed.  The processed data were normalized within each array by the median-nomalization method, and across arrays, using the Aroma package (Bengtsson, available from: http://www.maths.lth.se/help/R/aroma/) run in R project environment (http://cran.r-project.org).  Data from replicated spots were averaged before clustering.  Logarithmic base 2 values of intensities from both Cy3- and Cy5- samples (M values) were used as inputs for clustering.  Cluster program was used to perform hierarchical clustering, and Treeview program was used to visualized the clustered results (Eisen et al., 1998).

organism: Penaeus monodon

source_name: pooled ovaries from domesticated 14-month-old shrimp before eyestalk ablation (Day0)

label_protocol: The RNA from ovaries at day 0 were labeled with Cy3 dye as a reference, and those of ovaries at days 1, 4 and 7 were labeled with Cy5 dye.

extract_protocol: RNA samples were extracted from the ovaries of domesticated 14-month-old shrimp before (day 0, pooled from n=7) and after eyestalk ablation at days 1, 4 and 7 from Shrimp Genetic Improvement Center, Thailand. Contaminated genomic DNA was removed by treatment with DNase I at 0.15 U/μg total RNA at 37°C for 30 min.

value: ovary

value: 14 months

tag: organism type

value: domesticated

tag: treatment duration

value: 0 days

value: pool from 7 shrimp

source_name: individual ovary from domesticated 14-month-old shrimp after eyestalk ablation day7

value: eyestalk ablation

value: 7 days

value: individual from 1 shrimp


title: Astrocyte, 7 days after sham, biological rep3

city: Stanford

first: Jennifer

middle: L

last: Zamanian

address: 299 Campus Drive

department: Neurobiology

institute: Stanford University

description:
Astrocyte_7DS3
Surgery without occlusion.

hyb_protocol: 10 µg of fragmented, labeled cRNA was hybridized in an Affymetrix GeneChip® Hybridization Oven 640 and processed using an Affymetrix GeneChip® Fluidics Station 450.

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

data_processing: CEL files were analyzed wth the Arraystar 4.0 software (DNAstar) using RMA processing with quantile normalization.

source_name: Purified quiescent astrocytes 7 days after sham surgery

label_protocol: Approximately 20 ng of total RNA was amplified and biotin labeled using the Affymetrix Two-cycle target labeling kit.

extract_protocol: Total RNA was extracted from purified cells using the Qiagen RNeasy micro kit following the manufacturer's instructions.

treatment_protocol: Control and injured brains were digested with papain and dissociated to single cells. Astrocytes were isolated by FACS on the basis of their GFP expression.

tag: strain

value: Tg(Aldh1l1-eGFP) OFC789Gsat on Swiss Webster background

value: male

tag: developmental stage

value: young adult

value: FACS-purified astrocytes

tag: treatment

value: sham surgery

tag: time after treatment


title: AcB65, biological replicate 2

source_name: AcB65 recombinant congenic mouse whole lung tissue

value: whole lung

value: A/J and C57BL/6J

tag: age

value: 16 wks


title: Kartogenin_10nM_24h

value: human mesenchymal stem cells


title: Astrocyte, 3 days after sham, biological rep3

description:
Astrocyte_3DS3
Surgery without occlusion.

source_name: Purified quiescent astrocytes 3 days after sham surgery

value: 3 days


title: D0 vs D4_3

description: D0 vs D4-rep3

value: ovary

value: 14 months

tag: sample type

source_name: individual ovary from domesticated 14-month-old shrimp after eyestalk ablation day4

value: 4 days


title: D0 vs D7_1

description: D0 vs D7-rep1

value: domesticated

value: 0 days

value: pool from 7 shrimp


title: D0 vs D4_4

description: D0 vs D4-rep4

value: eyestalk ablation

value: individual from 1 shrimp


title: Astrocyte, 7 days after sham, biological rep2

description:
Astrocyte_7DS2
Surgery without occlusion.

value: Tg(Aldh1l1-eGFP) OFC789Gsat on Swiss Webster background

value: male

value: 7 days


title: Astrocyte, 7 days after sham, biological rep1

description:
Astrocyte_7DS1
Surgery without occlusion.

value: young adult

value: FACS-purified astrocytes

value: sham surgery


title: AcB64, biological replicate 2

source_name: AcB64 recombinant congenic mouse whole lung tissue

value: whole lung

value: A/J and C57BL/6J

value: 16 wks


title: Kartogenin_100nM_6h

value: human mesenchymal stem cells


title: BcA82, biological replicate 2

source_name: BcA82 recombinant congenic mouse whole lung tissue


title: A/J, biological replicate 2

source_name: A/J mouse whole lung tissue

value: A/J


title: AcB64, biological replicate 1


title: Kartogenin_10nM_6h


title: AcB58, biological replicate 2

source_name: AcB58 recombinant congenic mouse whole lung tissue


title: D0 vs D4_2

description: D0 vs D4-rep2

value: ovary

value: 14 months

value: 4 days


title: Astrocyte, 7 days after MCAO, biological rep3

description:
Astrocyte_7DM3
Transient ischemia, 1 hr occlusion with reperfusion.

source_name: Purified reactive astrocytes 7 days after MCAO-induced stroke

value: MCAO-induced stroke


title: Astrocyte, 3 days after sham, biological rep1

description:
Astrocyte_3DS1
Surgery without occlusion.

value: 3 days


title: Astrocyte, 3 days after sham, biological rep2

description:
Astrocyte_3DS2
Surgery without occlusion.


title: D0 vs D4_1

description: D0 vs D4-rep1

value: domesticated

value: 0 days

value: pool from 7 shrimp

value: eyestalk ablation

value: individual from 1 shrimp


title: Astrocyte, 7 days after MCAO, biological rep2

description:
Astrocyte_7DM2
Transient ischemia, 1 hr occlusion with reperfusion.

value: Tg(Aldh1l1-eGFP) OFC789Gsat on Swiss Webster background

value: male

value: young adult

value: FACS-purified astrocytes

value: 7 days


title: AcB52, biological replicate 2

source_name: AcB52 recombinant congenic mouse whole lung tissue

value: whole lung

value: A/J and C57BL/6J

value: 16 wks


title: DMSO

description: DMSO

source_name: DMSO

value: human mesenchymal stem cells


title: MM1S_MLN4924_24H

city: Boston

first: Constantine

middle: S.

last: Mitsiades

state: MA

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: myeloma cells cultured in vitro and treated with MLN4924

hyb_protocol: Following fragmentation, ~5 microg of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus2 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station.

scan_protocol: Standard Affymetrix Scanner

data_processing: CEL files were analyzed using dChip software (www.dchip.org)

source_name: MM1S cells treated with MLN4924 for 24hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from ~5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The human multiple myeloma (MM) cells MM.1S were cultured in vitro in the presence or absence of the NEDD8 activating enzyme (NAE) inhibitor MLN4924 for 8, 16 or 24hrs. The gene expression profiles of drug treated cells were compared with the profiles of control MM.1S cells.

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

treatment_protocol: MM.1S cells were treated with MLN4924 (250 nM for 8, 16, or 24hrs) or DMSO

tag: cell line

value: multiple myeloma (MM) cell line MM.1S

tag: agent

tag: time


title: AcB61, biological replicate 2

source_name: AcB61 recombinant congenic mouse whole lung tissue


title: Kartogenin_1nM_6h


title: BcA79, biological replicate 2

source_name: BcA79 recombinant congenic mouse whole lung tissue


title: D0 vs D1_1

description: D0 vs D1-rep1

value: ovary

value: 14 months

source_name: individual ovary from domesticated 14-month-old shrimp after eyestalk ablation day1

value: 1 day


title: Astrocyte, 7 days after MCAO, biological rep1

description:
Astrocyte_7DM1
Transient ischemia, 1 hr occlusion with reperfusion.

value: MCAO-induced stroke


title: MM1S MLN4924_16H

source_name: MM1S cells treated with MLN4924 for 16hrs


title: Astrocyte, 3 days after MCAO, biological rep3

description:
Astrocyte_3DM3
Transient ischemia, 1 hr occlusion with reperfusion.

source_name: Purified reactive astrocytes 3 days after MCAO-induced stroke

value: 3 days


title: Astrocyte, 3 days after MCAO, biological rep2

description:
Astrocyte_3DM2
Transient ischemia, 1 hr occlusion with reperfusion.


title: D0 vs D1_2

description: D0 vs D1-rep2

source_name: pooled ovaries from domesticated 14-month-old shrimp before eyestalk ablation (Day0)

value: domesticated

value: 0 days

value: pool from 7 shrimp

value: eyestalk ablation


title: BcA78, biological replicate 2

source_name: BcA78 recombinant congenic mouse whole lung tissue


title: BcA77, biological replicate 2

source_name: BcA77 recombinant congenic mouse whole lung tissue


title: MM1S_Control

description: myeloma cells cultured in vitro

source_name: Control MM1S cells

value: control


title: BcA75, biological replicate 2

source_name: BcA75 recombinant congenic mouse whole lung tissue


title: mock rep3

first: Lea

middle: Haarup

last: Gregersen

address: Robert-Rössle-Str. 10

institute: Max-Delbrück-Centrum für Molekulare Medizin (MDC)

hyb_protocol: After fragmentation at 94 °C for 35 min in 40 mM Tris, 30 mM MgOAc, 10 mM KOAc, samples were hybridized for 16 h to Affymetrix HG-U133 2.0 human arrays (Affymetrix, Santa Clara, CA).

scan_protocol: The arrays were washed and stained with phycoerythrin-conjugated streptavidin (SAPE), and the arrays were scanned in the Affymetrix GeneArray  2500 scanner, exactly as described in the Affymetrix GeneChip  protocol.

data_processing: The expression data was processed using the “affy” package in BioConductor in R. Probe set intensities were summarized using the Robust Multichip Average method and then transformed to generalized log values with the variance stable VSN method.

source_name: DLD-1 mock

label_protocol: Total cDNA was used as template for an “in vitro” transcription reaction generating biotin-labeled antisense cRNA (BioArrayTM High Yield RNA Transcript Labeling kit; Enzo Diagnostics, Farmingdale, NY).

growth_protocol: DLD-1 cells were cultured in DMEM GlutaMAX™-I high glucose medium  (31966, Gibco Invitrogen) supplemented with 10% (v/v) fetal bovine serum (FBS, CH30160.03, Hyclone), 50 U/ml penicillin and 50 µg/ml streptomycin (P/S, 15140 Gibco Invitrogen) and incubated in 5% CO2 plus 20% oxygen.

extract_protocol: Total RNA was isolated with TRIZOL 24.

treatment_protocol: Transfected with Lipofectamine™ 2000 Transfection Reagent (11668-019, Invitrogen) according to the manufactures protocol.

value: colon cancer cell line

tag: transfection

value: mock


title: MM1S_MLN4924_08H

source_name: MM1S cells treated with MLN4924 for 8hrs


title: Astrocyte, 1 day after saline, biological rep3

description:
Astrocyte_Sal14
Endotoxin-free saline.

source_name: Purified quiescent astrocytes 1 day after saline injection

value: Tg(Aldh1l1-eGFP) OFC789Gsat on Swiss Webster background

value: male

value: young adult

value: FACS-purified astrocytes

value: saline injection


title: BcA78, biological replicate 1

value: whole lung

value: A/J and C57BL/6J

value: 16 wks


title: IOSE80pc shGFP Ctr at 72h

city: Baltimore

first: Tian-Li

state: MD

address: 1550 Orleans St., CRB II, Rm 376

department: Pathology

institute: Johns Hopkins University School of Medicine

data_processing: The data were normalised using Median log2 normalization

source_name: IOSE80pc Cells

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

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit (DNase I treated) in accordance with the protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: knockdown

value: ovarian surface epithelial cells


title: mock rep4


title: IOSE80pc shARID1A at 72h


title: Astrocyte, 1 day after saline, biological rep4

description:
Astrocyte_Sal16
Endotoxin-free saline.

tag: gender

value: 1 day


title: mock rep1


title: OSE4 shGFP Ctr at 72h

source_name: OSE4 cells


title: AcB55, biological replicate 2

source_name: AcB55 recombinant congenic mouse whole lung tissue

tag: genotype/variaton


title: Astrocyte, 3 days after MCAO, biological rep1

description:
Astrocyte_3DM1
Transient ischemia, 1 hr occlusion with reperfusion.

value: MCAO-induced stroke

value: 3 days


title: Astrocyte, 1 day after saline, biological rep2

description:
Astrocyte_Sal5
Endotoxin-free saline.


title: C57BL/6, biological replicate 2

source_name: C57Bl/6 mouse whole lung tissue

tag: tissue


title: mock rep2

tag: cell type


title: OSE4 shARID1A at 72h


title: miR-143 rep3

source_name: DLD-1 miR-143

value: miR-143 duplex


title: miR-143 rep4


title: Astrocyte, 1 day after LPS, biological rep4

description:
Astrocyte_LPS13
5 mg/kg LPS from Escherichia coli O55:B55  I.P.

source_name: Purified reactive astrocytes 1 day after LPS-induced neuroinflammation

value: LPS-induced neuroinflammation


title: AcB53, biological replicate 2

source_name: AcB53 recombinant congenic mouse whole lung tissue


title: Astrocyte, 1 day after LPS, biological rep3

description:
Astrocyte_LPS6
5 mg/kg LPS from Escherichia coli O55:B55  I.P.


title: BcA69, biological replicate 2

source_name: BcA69 recombinant congenic mouse whole lung tissue


title: BcA86, biological replicate 2

source_name: BcA86 recombinant congenic mouse whole lung tissue


title: BcA75, biological replicate 1


title: Astrocyte, 1 day after LPS, biological rep2

description:
Astrocyte_LPS4
5 mg/kg LPS from Escherichia coli O55:B55 I.P.


title: BcA84, biological replicate 1

description: Gene expression data from mouse whole lung tissue

source_name: BcA84 recombinant congenic mouse whole lung tissue


title: Astrocyte, 1 day after sham, biological rep4

description:
Astrocyte_5S
Surgery without occlusion.

source_name: Purified quiescent astrocytes 1 day after sham surgery

value: sham surgery


title: AcB65, biological replicate 1

source_name: AcB65 recombinant congenic mouse whole lung tissue


title: SCR.9h.3

source_name: L428 scramble LNA

growth_protocol: L428 cells were cultured in RPMI 1640 GlutaMAX medium  (Gibco, Invitrogen) supplemented with 10% (v/v) fetal bovine serum (Hyclone, Thermo Scientific) and incubated in 5% CO2 plus 20% oxygen.

extract_protocol: Total RNA was isolated with TRIZOL.

treatment_protocol: Transfected by nucleofection using solution L and program X-001.

value: scrambled LNA


title: Astrocyte, 1 day after LPS, biological rep5

description:
Astrocyte_LPS15
5 mg/kg LPS from Escherichia coli O55:B55  I.P.


title: miR-143 rep1

value: colon cancer cell line


title: AcB55, biological replicate 1


title: AcB61, biological replicate 1

source_name: AcB61 recombinant congenic mouse whole lung tissue


title: Astrocyte, 1 day after saline, biological rep1

description:
Astrocyte_Sal3
Endotoxin-free saline.

value: Tg(Aldh1l1-eGFP) OFC789Gsat on Swiss Webster background


title: Astrocyte, 1 day after LPS, biological rep1

description:
Astrocyte_LPS3
5 mg/kg LPS from Escherichia coli O55:B55  I.P.

value: male


title: Astrocyte, 1 day after MCAO, biological rep5

description:
Astrocyte_5I
Transient ischemia, 1 hr occlusion with reperfusion.

source_name: Purified reactive astrocytes 1 day after MCAO-induced stroke

value: young adult


title: miR-143 rep2


title: SCR.9h.2


title: Astrocyte, 1 day after sham, biological rep3

description:
Astrocyte_4S
Surgery without occlusion.

value: FACS-purified astrocytes


title: AcB54, biological replicate 1

source_name: AcB54 recombinant congenic mouse whole lung tissue


title: Astrocyte, 1 day after sham, biological rep2

description:
Astrocyte_3S
Surgery without occlusion.


title: SCR.9h.1


title: miR9.9h.3

source_name: L428 miR-9 LNA

value: LNA inhibitor


title: miR9.9h.2


title: Astrocyte, 1 day after MCAO, biological rep4

description:
Astrocyte_4I
Transient ischemia, 1 hr occlusion with reperfusion.


title: miR9.9h.1


title: AcB58, biological replicate 1

source_name: AcB58 recombinant congenic mouse whole lung tissue

value: whole lung


title: BcA68, biological replicate 1

source_name: BcA68 recombinant congenic mouse whole lung tissue

value: A/J and C57BL/6J


title: AcB52, biological replicate 1

source_name: AcB52 recombinant congenic mouse whole lung tissue

value: 16 wks


title: BcA86, biological replicate 1


title: AcB57, biological replicate 1

source_name: AcB57 recombinant congenic mouse whole lung tissue


title: BcA71, biological replicate 1

source_name: BcA71 recombinant congenic mouse whole lung tissue


title: Astrocyte, 1 day after MCAO, biological rep2

description:
Astrocyte_2I
Transient ischemia, 1 hr occlusion with reperfusion.


title: AcB56, biological replicate 1

source_name: AcB56 recombinant congenic mouse whole lung tissue


title: HMDM+C1q-LAL+LPS rep 3

city: Irvine

first: Marie

middle: Emeline

last: Benoit

address: 2419 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: UC Irvine

description:
0410F-08_18_(HuGene-1_0-st-v1)
gene expression data from C1q-LAL+LPS-stimulated HMDM
QLAL3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the GeneChip Fluidics Stations 450

scan_protocol: GeneChips were scanned using the GeneChip 3000 Scanner 7G with Autoloader

data_processing: The data were analyzed with JMP genomics (v5.0) using the basic expression workflow and median signal intensity as normalization method.

source_name: HMDM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (performed by the personnel of the microarray facility at University of California Irvine)

growth_protocol: Lymphocytes were maintained for 7 days in RPMI1640, 10% FCS, 2 mM L-Glutamine and 1% penicillin/streptomycin (complete media) containing 50 U/ml rhIL-2. HMDM were generated from human peripheral monocytes, isolated by counter flow elutriation, by culture for 8 days in complete media containing 25 ng/ml rhM-CSF

extract_protocol: total RNA was extracted using the Illustra RNAspin Mini Isolation Kit

treatment_protocol: Apoptosis of lymphocytes was induced by g-irradiation (10Gy). HMDM were stimulated with 10 ng/ml ultra-pure LPS.

tag: targets

tag: stimulus

value: LPS


title: BcA79, biological replicate 1

source_name: BcA79 recombinant congenic mouse whole lung tissue

tag: strain


title: Astrocyte, 1 day after sham, biological rep1

description:
Astrocyte_2S
Surgery without occlusion.

tag: developmental stage

value: 1 day


title: Astrocyte, 1 day after MCAO, biological rep1

description:
Astrocyte_1I
Transient ischemia, 1 hr occlusion with reperfusion.

tag: treatment

value: MCAO-induced stroke


title: Astrocyte, 1 day after MCAO, biological rep3

description:
Astrocyte_3I
Transient ischemia, 1 hr occlusion with reperfusion.

tag: time after treatment


title: BcA77, biological replicate 1

source_name: BcA77 recombinant congenic mouse whole lung tissue

tag: age


title: AcB62, biological replicate 1

source_name: AcB62 recombinant congenic mouse whole lung tissue


title: AcB63, biological replicate 1

source_name: AcB63 recombinant congenic mouse whole lung tissue


title: C57BL/6, biological replicate 1

source_name: C57Bl/6 mouse whole lung tissue


title: AcB53, biological replicate 1

source_name: AcB53 recombinant congenic mouse whole lung tissue


title: HMDM+C1q-LAL+LPS rep 2

description:
0410F-08_17_(HuGene-1_0-st-v1)
gene expression data from C1q-LAL+LPS-stimulated HMDM
QLAL2


title: HMDM+LAL+LPS rep 3

description:
0410F-08_15_re_(HuGene-1_0-st-v1)
gene expression data from LAL+LPS-stimulated HMDM
LAL3

value: LAL


title: HMDM+C1q-EAL+LPS rep 2

description:
0410F-08_11_(HuGene-1_0-st-v1)
gene expression data from C1q-EAL+LPS-stimulated HMDM
QEAL2


title: HMDM+C1q-LAL+LPS rep 1

description:
0410F-08_16_(HuGene-1_0-st-v1)
gene expression data from C1q-LAL+LPS-stimulated HMDM
QLAL1


title: HMDM+LAL+LPS rep 1

description:
0410F-08_13_(HuGene-1_0-st-v1)
gene expression data from LAL+LPS-stimulated HMDM
LAL1


title: HMDM+C1q-EAL+LPS rep 1

description:
0410F-08_10_(HuGene-1_0-st-v1)
gene expression data from C1q-EAL+LPS-stimulated HMDM
QEAL1


title: HMDM+EAL+LPS rep 2

description:
0410F-08_8_(HuGene-1_0-st-v1)
gene expression data from EAL+LPS-stimulated HMDM
EAL2

value: EAL


title: HMDM+LAL+LPS rep 2

description:
0410F-08_14_re_(HuGene-1_0-st-v1)
gene expression data from LAL+LPS-stimulated HMDM
LAL2


title: BcA80, biological replicate 1

description: Gene expression data from mouse whole lung tissue

source_name: BcA80 recombinant congenic mouse whole lung tissue


title: BcA82, biological replicate 1

source_name: BcA82 recombinant congenic mouse whole lung tissue


title: HMDM+C1q-EAL+LPS rep 3

description:
0410F-08_12_re_(HuGene-1_0-st-v1)
gene expression data from C1q-EAL+LPS-stimulated HMDM
QEAL3


title: HMDM+LPS rep 3

description:
0410F-08_6_(HuGene-1_0-st-v1)
gene expression data from LPS-stimulated HMDM
LPS3


title: HMDM+EAL+LPS rep 1

description:
0410F-08_7_(HuGene-1_0-st-v1)
gene expression data from EAL+LPS-stimulated HMDM
EAL1


title: BcA81, biological replicate 1

source_name: BcA81 recombinant congenic mouse whole lung tissue


title: A/J, biological replicate 1

source_name: A/J mouse whole lung tissue

value: A/J


title: BcA69, biological replicate 1

source_name: BcA69 recombinant congenic mouse whole lung tissue


title: BcA73, biological replicate 1

source_name: BcA73 recombinant congenic mouse whole lung tissue


title: HMDM+LPS rep 1

description:
0410F-08_4_re_(HuGene-1_0-st-v1)
gene expression data from LPS-stimulated HMDM
LPS1


title: ConA-activated CD8+ Central memory T cells at T24, biological rep1

city: New York

first: Alan

middle: B

last: Frey

state: NY

address: 550 First Avenue

department: Cell Biology

institute: NYUMC

description: Gene expression data from CD8+ Central memory T cells after activation with Con A

hyb_protocol: 0.01 mg of labeled and fragmented cRNA were hybridized to the mouse genome MOE430 2.0 array (Affymetrix).

scan_protocol: Raw expression data were analyzed using GCOS 1.4 (Affymetrix). Data were normalized to a target intensity of 500 to account for differences in global chip intensity.

data_processing: MAS 5.0

source_name: CD8+ Central memory T cells after activation with 0.005 ugr Con A

label_protocol: Samples with a RNA Integrity Number (RIN) >7.0 were considered suitable for labeling and 20 ng were labeled using the GeneChip two-cycle target labeling kit (Affymetrix).

growth_protocol: Ten spleens were pooled from 62 week old C57BL/6 male mice and enriched for CD8+ T cells by negative selection using a cocktail of biotinylated antibodies to deplete CD4, CD11c, CD11b, MHC-II, B220, and NK cells.  Cells were then stained for CD8, CD44, CD62L, and CD127 and sorted (using a iCyt Reflection parallel cell sorter).

extract_protocol: TRIzol Reagent (Invitrogen) followed by RNeasy clean-up kit (Invitrogen) and Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were collected and cultured (0.5 x106 cells/well) in 10% complete RPMI media supplemented with 0.005 ugr Con A.

tag: source tissue

value: Spleen

value: CD8+ Central memory T

value: ConA

value: 62 wk


title: HMDM+LPS rep 2

description:
0410F-08_5_(HuGene-1_0-st-v1)
gene expression data from LPS-stimulated HMDM
LPS2


title: wild type, rosette leaves, biological rep2

city: Loughborough

first: Neil

last: Graham

state: Leicestershire

address: Sutton Bonington Campus

department: Plant and Crop Sciences

country: United Kingdom

institute: University of Nottingham

hyb_protocol: Samples were hybridised at the NASC microarray core facility according to manufactures' instructions. GeneChips were washed and stained in the Affymetrix Fluidics station 450.

scan_protocol: Scanning was performed accordinf to manufactures' instruction using an Affymetrix 3000 7G scanner

data_processing: RNA data was analysed using Genespring GX 11 software (Agilent technologies) using the RMA probe sumarisation algorithm. Each gene signal was then normalised to the median of the gene signal across all samples

organism: Arabidopsis thaliana

source_name: 3 week old rosette leaves from WT plants

label_protocol: Labelling was performed using the Affymetrix 3' IVT express kit as per manufactures' instructions

growth_protocol: Plants were grown in a growth chamber with 20 hr light, 4 hr dark cycle at 20 degree C.

extract_protocol: RNA was extracted using the QIAGEN Rneasy kit

value: Rosette leaves

value: 3 week old

tag: line

value: wild type


title: A6, rosette leaves, biological rep3

source_name: 3 week old rosette leaves from A6 plants


title: wild type, rosette leaves, biological rep3


title: ConA-activated CD8+ Central memory T cells at T16, biological rep1

value: male


title: HMDM+EAL+LPS rep 3

description:
0410F-08_9_(HuGene-1_0-st-v1)
gene expression data from EAL+LPS-stimulated HMDM
EAL3


title: ConA-activated CD8+ Central memory T cells at T8, biological rep1

value: 8 h


title: ConA-activated CD8+ Central memory T cells at T6, biological rep1

value: 6 h


title: HMDM rep 3

description:
0410F-08_3_(HuGene-1_0-st-v1)
gene expression data from unstimulated HMDM
UT3


title: HMDM rep 1

description:
0410F-08_1_(HuGene-1_0-st-v1)
gene expression data from unstimulated HMDM
UT1


title: HMDM rep 2

description:
0410F-08_2_(HuGene-1_0-st-v1)
gene expression data from unstimulated HMDM
UT2


title: wild type, rosette leaves, biological rep1


title: A6, rosette leaves, biological rep2


title: Rapamycin treatment, Rep1

status: Public on May 01 2012

city: Albuquerque

first: Jun

last: Chen

state: NM

address: 2325 Camino de Salud NE

department: Health Science Center

institute: University of New Mexico

description: Gene expression data from BY4741 cells treated with Rapamycin

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using fludics script FS450_0004.

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

data_processing: The RMA algorithm of Expression Consol (v1.1, Affymetric, Santa Clara, CA) was used to generate and normalize signal intensities.

organism: Saccharomyces cerevisiae

source_name: Rapamycin treatment

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix 3' IVT Express protocol from 100ng of total RNA .

growth_protocol: Overnight BY4741 cultures were diluted to 0.05 OD600 in 10 mLYPD media and grown to 0.2 OD600.

extract_protocol: Cells were collected and RNA were isolated with MasterPure RNA purification kit (Epicentre, Madison, WI).

treatment_protocol: Cells were treated with1% DMSO, 20 uM CID 3528206 and 200 nM rapamycin in duplicate for 3hrs.

value: Rapamycin


title: Rapamycin treatment, Rep2


title: ConA-activated CD8+ Central memory T cells at T4, biological rep1

value: 4 h


title: ConA-activated CD8+ Central memory T cells at T20, biological rep1


title: DMSO treatment, Rep2

description: Gene expression data from BY4741 cells treated with DMSO

source_name: DMSO treament

value: DMSO treament


title: CID 3528206 treatment, Rep1

description: Gene expression data from BY4741 cells treated with CID 3528206

source_name: CID 3528206 treatment


title: PMCAO control (Cy5) x PMCAO+PACAP (Cy3) Pooled 2 at 24 h

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scaner

data_processing: Software: Feature Extraction ver 9.5.3.1

source_name: PMCAO+PACAP (Cy3)_24h

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Thirty male mice (8 to 12-weeks-old, 25 ~ 35 g body weight) were housed at the Animal Institution in Showa University in acrylic cages (8 mice / cage) at 23ºC, and maintained with a standard 12 h light/dark cycle with optimum humidity and temperature control. All animals were given access to tap water and laboratory chow ad libitum.

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: Control Saline 24 h

tag: strain background

tag: variation

value: permanent middle cerebral artery occlusion (PMCAO) model

value: 8-12 weeks

value: brain

tag: treated with

value: PACAP38 (1 µl containing 1 pmol)

source_name: PMCAO control (Cy5)_24h

treatment_protocol: Control PACAP 24 h

value: 1 µl of saline (0.9% NaCl)


title: Control+Saline (Cy5) x Control+PACAP (Cy3) Pooled 2 at 6h

source_name: Control+PACAP (Cy3)_6h

treatment_protocol: Control Saline 6 h

value: sham control mice

source_name: Control+Saline (Cy5)_6h

treatment_protocol: Control PACAP 6 h


title: CD8+ Central memory T cells before treatment with Con A, biological rep1

description: Gene expression data from CD8+ Central memory T cells before activation

value: Spleen

value: CD8+ Central memory T

value: untreated

tag: time

value: 0 h


title: Control+Saline (Cy5) x Control+PACAP (Cy3) Pooled 2 at 24 h

source_name: Control+PACAP (Cy3)_24h

tag: gender

source_name: Control+Saline (Cy5)_24h


title: PMCAO control (Cy5) x PMCAO+PACAP (Cy3) Pooled 2 at 6 h

source_name: PMCAO+PACAP (Cy3)_6h

source_name: PMCAO control (Cy5)_6h


title: A6, rosette leaves, biological rep1

value: Rosette leaves

value: 3 week old


title: DMSO treatment, Rep1


title: PMCAO control (Cy3) x PMCAO+PACAP (Cy5) Pooled 1 at 24 h

source_name: PMCAO control (Cy3)_24h

value: male

source_name: PMCAO+PACAP (Cy5)_24h


title: CID 3528206 treatment, Rep2


title: Leaf of TTR04, biological rep1

city: changchun

first: bao

last: qi

address: 5268 Renmin Street

country: China

institute: chinese academy of science

description: Gene expression data from leaf

hyb_protocol: According to the standard Affymetrix protocol(Expression Analysis Technical Manual, Affymetrix).

data_processing: The raw CEL data were normalized with the Robust Multichip Average (RMA)method using the R software 'limma' package. To identify differentially expressed genes, we used an empirical Bayesian based method to construct statistics and compute the relative p-values.Genes that were differentially expressed among genotypes were identified by a cut-off P value<0.05.  The present (P) or absent (A) calls of each probeset was carried out by the MAS5 method using GCOS (Affymetrix Technologies) with default parameters.  The differently expressed genes which did not show both present calls (P) in the two biological replications in at least one of the genotypes of each comparison were excluded from further analysis.

organism: Triticum turgidum subsp. durum

source_name: Leaf of TTR04

growth_protocol: All plants, including the two synthetic lines and their respective parental lines, were grown in controlled growth chambers at 22/20°C day/night of 12 h day length.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogene) and purified through RNeasy Mini Spin Columns (Qiagen). The integrity of RNA was determined with an Agilent Bioanalyser 2100 Eukaryote Total RNA Nano Series II system.  The 2nd leaf of 3-leaf-stage seedlings was the source tissue for all RNA isolations.

treatment_protocol: The 2nd leaf of 3-leaf-stage seedlings was the source tissue for all RNA isolations.Pooled seedlings (10 plants for each replication) were used to represent each sample, with two biological replications.

tag: genotype/variation

value: parental lines

value: The 2nd leaf of 3-leaf-stage seedlings


title: Leaf of TTR04, biological rep2

description: Gene expression data from leaf

scan_protocol: According to the standard Affymetrix protocol(Expression Analysis Technical Manual, Affymetrix).

tag: tissue


title: Leaf of TTH01, biological rep2

description: Gene expression data from leaf

organism: Triticum carthlicum

source_name: Leaf of TTH01

label_protocol: According to the standard Affymetrix protocol(Expression Analysis Technical Manual, Affymetrix).


title: PMCAO control (Cy3) x PMCAO+PACAP (Cy5) Pooled 1 at 6 h

source_name: PMCAO control (Cy3)_6h

source_name: PMCAO+PACAP (Cy5)_6h


title: Leaf of TTH01, biological rep1

description: Gene expression data from leaf


title: Leaf of MPV9, biological rep2

description: Gene expression data from leaf

organism: Triticum aestivum

source_name: Leaf of MPV9

value: synthetic allopolyploid lines


title: Leaf of TQ27, biological rep2

description: Gene expression data from leaf

organism: Aegilops tauschii

source_name: Leaf of TQ27


title: Leaf of TQ27, biological rep1

description: Gene expression data from leaf


title: Leaf of MPV5, biological rep1

description: Gene expression data from leaf

source_name: Leaf of MPV5


title: Leaf of MPV5, biological rep2

description: Gene expression data from leaf


title: Leaf of MPV9, biological rep1

description: Gene expression data from leaf


title: Naut1SalsC_3

city: Urbana

first: Katy

middle: D

last: Heath

state: IL

address: 1201 W. Gregory Dr

department: Plant Biology

institute: University of Illinois

description: gene expression data for plant Naut1 innoculated with rhizobium SalsC (bot1496)

hyb_protocol: Following labeling, 12 ug of cDNA were hybridized for 16 hr at 48C on GeneChip Medicago Genome Array in an Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G  with GCOS v1.1.1 software.

data_processing: Data import into JMP Genomics software (Version 5, SAS Instute, Cary, NC), quality control, and analysis were performed separately for M. truncatula and S. meliloti probe sets. Both datasets were subjected to median polish summarization, log2-transformation, RMA background correction, and quantile normalization of raw probe intensity values present in .CEL files

organism:
Sinorhizobium meliloti
Medicago truncatula

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol from 12 ug fragmented cDNA but with 2x labeling (Expression Analysis Technical Manual, 2005-2009, Affymetrix).

growth_protocol: The greenhouse experiment consisted of two plant and two rhizobium genotypes, grown in a fully factorial experiment with 24 replicates of each genotype combination, for a total of 96 plants. Plants were innoculated with 10^5 rhizobium cells and fed weekly with N-free 2X Fahreus nutrient solution.

extract_protocol: TRI Reagent extraction of total RNA was performed according to the manufacturer's instructions (Molecular Research Center, Inc) using nodules from two plants.

treatment_protocol: At 10 weeks, 64 plants were harvested. Roots were shaken free of loose soil and nodules were counted, excised at the nodule-root junction, and immediately frozen in liquid nitrogen.

value: root nodule


title: Leaf of AT9 at selfed generation 5, biological rep2

description: Gene expression data from leaf

source_name: Leaf of AT9 at selfed generation 5


title: Sals4SalsB_3

description: gene expression data for plant Sals4 innoculated with rhizobium SalsB (bot1495)


title: Leaf of AT5 at selfed generation 4, biological rep1

description: Gene expression data from leaf

source_name: Leaf of AT5 at selfed generation 4


title: Naut1SalsB_2

description: gene expression data for plant Naut1 innoculated with rhizobium SalsB (bot1489)


title: Sals4SalsB_2

description: gene expression data for plant Sals4 innoculated with rhizobium SalsB (bot1491)


title: Sals4SalsC_1

description: gene expression data for plant Sals4 innoculated with rhizobium SalsC (bot1449)


title: Leaf of AT9 at selfed generation 5, biological rep1

description: Gene expression data from leaf


title: Naut1SalsB_3

description: gene expression data for plant Naut1 innoculated with rhizobium SalsB (bot1493)


title: Leaf of AT5 at selfed generation 5, biological rep2

description: Gene expression data from leaf

source_name: Leaf of AT5 at selfed generation 5


title: Leaf of AT5 at selfed generation 5, biological rep1

description: Gene expression data from leaf


title: Sals4SalsC_3

description: gene expression data for plant Sals4 innoculated with rhizobium SalsC (bot1494)


title: Leaf of AT5 at selfed generation 4, biological rep2

description: Gene expression data from leaf


title: Leaf of AT9 at selfed generation 4, biological rep1

description: Gene expression data from leaf

source_name: Leaf of AT9 at selfed generation 4


title: Sals4SalsC_2

description: gene expression data for plant Sals4 innoculated with rhizobium SalsC (bot1492)


title: Sals4SalsB_1

description: gene expression data for plant Sals4 innoculated with rhizobium SalsB (bot1448)


title: Naut1SalsC_2

description: gene expression data for plant Naut1 innoculated with rhizobium SalsC (bot1490)


title: Cd10_R3

city: Ispra (VA)

first: marco

last: fabbri

address: Via E. Fermi, 2749

department: Institute for Health and Consumer Protection

country: Italy

institute: European Commission - Joint Research Centre

description: Gene expression after treatment with 10 μM Cd

hyb_protocol: standard Agilent protocol

scan_protocol: Scanned with the Agilent G2565BA Microarray Scanner (Agilent)

data_processing: The fluorescence intensities on scanned images were extracted and preprocessed by Agilent Feature Extraction Software (v10.5.1.1).

source_name: HepG2 in medium and 10 μM Cd

label_protocol: standard Agilent protocol

growth_protocol: HepG2 cells were routinely cultured in Opti-MEM medium (Invitrogen9, supplemented with 10% fetal bovine serum, and 1% antibiotics. Cells were kept in incubator at constant 37°C under a humidified 5% CO2 atmosphere.

extract_protocol: After 24h of treatment, the cells were washed with cold PBS and lysed in 350 µl of RLT lysis buffer (Qiagen) following manufacturer instructions

treatment_protocol: Cells were plated on day onto 100 mm diameter Petri dishes (Corning) at a concentration of 1.5×106 cells/dish. Twenty four hours after seeding, the medium was removed and the cells were either treated with fresh medium added with CdCl2 (Cd) at a concentration of 2 µM and 10 µM, or with complete medium (control) for 24 h.

tag: cell line

tag: growth condition

value: 10 μM Cd


title: Cd10_R2


title: Ctrl_R3

description: Gene expression control

source_name: HepG2 in normal medium

value: normal medium


title: Naut1SalsB_1

description: gene expression data for plant Naut1 innoculated with rhizobium SalsB (bot1446)


title: Cd2_R1

description: Gene expression after treatment with 2 μM Cd

source_name: HepG2 in medium and 2 μM Cd

value: 2 μM Cd


title: Ctrl_R2

description: Gene expression control


title: Naut1SalsC_1

description: gene expression data for plant Naut1 innoculated with rhizobium SalsC (bot1447)


title: Cd2_R2


title: Cd10_R1


title: Control+Saline (Cy3) x Control+PACAP (Cy5) Pooled 1 at 24 h

source_name: Control+Saline (Cy3)_24h

value: 8-12 weeks

value: brain

source_name: Control+PACAP (Cy5)_24h

value: PACAP38 (1 µl containing 1 pmol)


title: Cd2_R3


title: Control+Saline (Cy3) x Control+PACAP (Cy5) Pooled 1 at 6 h

source_name: Control+Saline (Cy3)_6h

value: sham control mice

value: 1 µl of saline (0.9% NaCl)

source_name: Control+PACAP (Cy5)_6h


title: 7_83

city: Bethesda

first: WeiPing

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: The sorted cell subpopulations

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

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

data_processing: RMA by software Partek

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: All animal studies were approved by the NIDDK/NIH Animal Care and Use Committee.

treatment_protocol: The Mx1-Cre transgene was activated by intraperitoneal injection of PolyIC (polyinosinic: polycytidylic acid) as described (Kimura et al., 2009).  To obtain hematologic data, peripheral blood was collected in heparinized capillary tubes (Drummond Scientific Co., Broomall, PA) by retro-orbital puncture and complete blood counts (CBCs) were determined with HEMAVET HV950FS (Drew Scientific, Dallas, TX).

tag: background strain

value: mixed background of C57BL/6, FVB, and 129


title: 12_959

description: The sorted cell subpopulations


title: IR64_Rep3

city: makati

first: Raveendran

last: Muthurajan

state: manila

address: Metro Manila

department: Entomology and Plant Pathology

country: Philippines

institute: International Rice Research Institute

description:
Keyword = rice
Keyword = Drought stress

hyb_protocol: Standard protocol of Gene Expression Hybridization Kit from Agilent Technologies.

scan_protocol: Standard protocol of Agilent DNA Microarray Scanner

data_processing: Feature Extraction software Version 8.1 from Agilent Technologies

organism: Oryza sativa

label_protocol: Standard Protocol of Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Plants were grown under green house conditions and leaf samples were harvested on 37DAS.

extract_protocol: TRIZOL Reagent method

treatment_protocol: No treatment; Well-watered control

tag: Leaf samples from well-watered plants

growth_protocol: Plants were grown under green house conditions and drought stress was started on 33DAS by withholding water. Leaf samples were harvested after 5 days of drought stress.

treatment_protocol: Drought stressed for 5 days

tag: Leaf samples from drought stressed plants


title: 5-AAB7

description: The sorted cell subpopulations


title: Apo_Rep3

description:
Keyword = rice
Keyword = Drought stress

tag: Leaf samples from well-watered control plants


title: WT

city: frederick

first: Qun

last: Jiang

state: Maryland

address: 1050 boyles street

institute: NCI-Frederick

hyb_protocol: Four replicates of cDNA sample were hybridized to Affymetrix Mouse Genome Mo430 2.0 GeneChips, using Affymetrix GeneChip Hybridization, Wash, and Stain Kit following manufacturer’s protocol.

scan_protocol: GeneChips were scanned on Affymetrix GeneChip scanner 3000.  Data were collected using Affymetrix AGCC software.

data_processing: Analysis was performed by using standard Partek Genomics Gene expression analysis workflow as well as using R package PUMA.

source_name: wild type mouse

label_protocol: RNA (100 ng) was reverse transcribed and labeled with biotin using Affymetrix 3’ IVTexpress Labeling kit following manufacturer’s protocol.

extract_protocol: Total RNA was isolated from lung homogenates by using TRIzol (Invitrogen). RNA quality was checked on Agilent Bioanalyzer.  All samples used for microarray analysis have high quality score (RIN >9).

treatment_protocol: Fresh lungs were harvested into RNA later (Ambion).

value: wild type

value: 16 weeks old

value: normal lung tissue


title: 11_958

description: The sorted cell subpopulations


title: Leaf of AT9 at selfed generation 4, biological rep2

description: Gene expression data from leaf


title: 6-AAB8

description: The sorted cell subpopulations


title: Ctrl_R1

description: Gene expression control


title: 8_909

description: The sorted cell subpopulations


title: IR64_Rep1

description:
Keyword = rice
Keyword = Drought stress


title: 1-ABB2

description: The sorted cell subpopulations


title: 4-AAB6

description: The sorted cell subpopulations


title: IR64_Rep2

description:
Keyword = rice
Keyword = Drought stress

tag: Leaf samples from well-watered control Plants


title: 2-ABB3

description: The sorted cell subpopulations


title: P29-BPD-lung3

city: Rochester

first: Jie

last: Dong

state: MN

address: 200 1st SW

department: Thoracic Surgery

institute: Mayo Clinic

description: Gene expression data from P29 BPD lung.

hyb_protocol: Labeled cRNA was fragmented and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays at 45°C for 16 hr, and then washed and stained using the GeneChip Fluidics.

scan_protocol: The arrays were scanned by a GeneArray Scanner, and the patterns of hybridization were detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes.

data_processing: The data were analyzed with Partek Genomics Suite 6.4 using Affymetrix default analysis settings and GC-RMA as the normalization method.

source_name: lung, P29, BPD

label_protocol: Biotin-labeled cRNA was produced by in vitro transcription according to the Affymetrix Gene Chip technical manual.

growth_protocol: Time-pregnant mice were maintained on an ad libitium diet of standard chow and water. Within 12 hr of birth, pups were pooled and then randomized into four experimental groups: mice would be exposed to either hyperoxic (80%) or room air conditions for either 14 or 29 days. Nursing dams were rotated between exposure groups every 24 hours to prevent oxygen toxicity in the dams and mitigate maternal effects between the experimental groups.

treatment_protocol: Lungs were isolated by manual dissection with the aid of a dissecting microscope where necessary. Lungs were washed twice with PBS before total RNA extraction.

tag: strain

value: ICR

value: lung

tag: age

value: postnatal day 29

tag: treatment

value: hyperoxia

tag: disease state


title: KAT

source_name: KA/KA-Lori-Ikkα mouse with macrophage depletion treatment

value: KA/KA-Lori-Ikkα

value: lung tissue with some inflammation and no tumor observed


title: 9_913

description: The sorted cell subpopulations


title: 10_957

description: The sorted cell subpopulations


title: P29-BPD-lung1

description: Gene expression data from P29 BPD lung.


title: Apo_Rep1

description:
Keyword = rice
Keyword = Drought stress

tag: Leaf samples from well- watered control plants of Apo

tag: Leaf samples from drought stressed plants of Apo


title: P29-WT-lung2

description: Gene expression data from P29 WT lung.

source_name: lung, P29, WT

value: room air

value: normal


title: Apo_Rep2

description:
Keyword = rice
Keyword = Drought stress


title: 3-ABB4

description: The sorted cell subpopulations


title: KA2

source_name: KA/KA-Lori-Ikkα mouse

value: mixture tissue of lung SCC and tumor neighbor


title: exposure to Zn

city: Padua

first: Karina

last: Fincati

address: V.le G. Colombo, 3

department: Department of Biology, University of Padua

institute: CNR-Institute for Biomedical Technologies

description: In all hybridizations SH-SY5Y cell culture was used as control for direct comparison to the experimental conditions: expoure to  Zn

hyb_protocol: Labeled aRNA was dissolved in 90 ul of hybridization buffer, denaturated at 90ºC for 3 min and applied directly to microarray slides. Microarray hybridization was carried out in an ArrayBooster Hybridization Station. The reaction was carried out overnight at 42ºC. Posthybridization washing was performed according to the microarray slides manufacturer’s instructions.

scan_protocol: The microarrays slides were scanned using a GenePix 4000B laser scanner  and images were processed using Genepix 6.0 software.

data_processing: Data analysis  were performed using Acuity 4.0 software. Initial results were normalized using Lowess algorithm and filtered to exclude extreme outliers and flags. We also excluded any spots that had no detectable response on all slides. The log-ratios of expression were calculated as the base 2 logarithm of the ratios of background-corrected intensity medians of red dye over green dye intensities. In order to obtain a single expression value for each gene, the internal replicates (1 to 14) were plotted versus the technical replicates (6 for exposure to AB and 2 for exposure to AB-metal complex and metal). The X-Y scatterplot confirmed that the data were generally reproducible but we observed the presence of extreme outliers values. Then we excluded the outliers and the values of spots replicates within and among arrays were averaged using a trimmed mean. We excluded any spot that had no detectable response in all three treatments.

label: Alexa Fluor 555, Alexa Fluor 647

source_name: human neuroblastoma cells culture

label_protocol: 1 ug of total RNA was amplified following the SuperscriptTM Indirect RNA Amplification System Kit (InvitrogenTM): total RNA was reverse transcribed into single-stranded complementary DNA (cDNA) using oligo(dT) primer containing a T7 promoter and Superscript III reverse transcriptase. RNase H was then added together with E. coli DNA polymerase I and E. coli DNA ligase, followed by a short incubation in order to achieve synthesis of the second-strand cDNA. The purified double-strand cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7-RNA polymerase. This step generated antisense RNA (aRNA) molecules complementary to the original mRNA targets, incorporating amino-allyl UTP (aa-UTP) into the aRNA. 10 ug of purified aRNA was coupled with Alexa Fluor 555 or Alexa Fluor 647 dyes (Invitrogen) according to the manufacturer’s instructions.

growth_protocol: SH-SY5Y human neuroblastoma cells were purchased from ECACC. SH-SY5Y human neuroblastoma cells were maintained in Dulbecco’s modified Eagle’s medium (1: 1) with L-Glutamine and 15 mM Hepes at 37 °C with 5% CO2 in a humidified atmosphere (90 % humidity). The medium was replaced every 2 days. Penicillin (100 units/ml) and streptomycin (100 ug/ml), 15 % fetal bovine serum, and MEM non-essential amino acids (100x) were added to the medium. 0.25% Trypsin-EDTA solution and phosphate buffered saline (PBS) were obtained from Sigma Aldrich. SHSY5Y cells were plated onto 6-well plates.

extract_protocol: Total RNA of SH-SY5Y human neuroblastoma cells exposed to AB,  AB-metal complexes (AB-Cu or AB-Zn) and Cu or Zn was isolated using the Qiagen RNA/DNA Mini Kit following the manufacturer’s instructions.

treatment_protocol: The day after this plating, the culture medium was replaced with the same medium with 2 % FBS containing AB or AB-metal complexes at 0.5 uM peptide concentration. The cells were incubated with different AB or AB-metal complexes for 24h. The cell treatment was also performed in the presence of metals (Cu or Zn) at a concentration 10-fold higher than the peptide concentration.

value: Zn

source_name: human neuroblastoma cells exposed to Zn

value: control


title: sh JMJD3 + TGFb, replicate 2

city: Barcelona

first: Conchi

last: EI

address: Baldiri Reixac 15

country: Spain

institute: IBMB

description: dissected out  from  embrionic cerebral cortex (E12.5). Cells are stably transfected with a JMJD3 shRNA.

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 110%PMT The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: sh2 JMJD3 + TGFb

label_protocol: 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol

tag: cell type

value: neural stem cells

tag: knockdown

value: sh2 JMJD3

value: TGFb


title: sh JMJD3 + TGFb, replicate 3


title: sh JMJD3 - TGFb, replicate 1

source_name: sh2 JMJD3 - TGFb


title: sh JMJD3 + TGFb, replicate 1


title: P29-BPD-lung2

description: Gene expression data from P29 BPD lung.


title: exposure to AB-Cu complex

description: In all hybridizations SH-SY5Y  cell  culture was used as control for direct comparison to the experimental  conditions: expoure to AB-Cu

value: AB-Cu complex

source_name: human neuroblastoma cells exposed to AB-Cu complex


title: sh control + TGFb, replicate 3

description: dissected out  from  embrionic cerebral cortex (E12.5). Cells are stably transfected with a random shRNA.

source_name: sh control + TGFb


title: sh control - TGFb, replicate 3

source_name: sh control - TGFb


title: sh control + TGFb, replicate 1


title: sh control - TGFb, replicate 2


title: P14-WT-lung1

description: Gene expression data from P14 WT lung.

source_name: lung, P14, WT

value: postnatal day 14


title: sh control - TGFb, replicate 1


title: exposure to AB-Zn complex

description: In all hybridizations SH-SY5Y cell culture was used as control for direct comparison to the experimental conditions: expoure to AB-Zn

value: AB-Zn complex

source_name: human neuroblastoma cells exposed to AB-Zn complex


title: P29-WT-lung1

description: Gene expression data from P29 WT lung.

value: ICR


title: sh JMJD3 - TGFb, replicate 3


title: sh JMJD3 - TGFb, replicate 2


title: exposure to Cu

description: In all hybridizations SH-SY5Y  cell  culture was used as control for direct comparison to the experimental  conditions: expoure to  Cu

value: Cu

source_name: human neuroblastoma cells exposed to Cu


title: P14-BPD-lung3

description: Gene expression data from P14 BPD lung.

source_name: lung, P14, BPD

value: lung


title: P14-WT-lung2

description: Gene expression data from P14 WT lung.


title: P14-BPD-lung2

description: Gene expression data from P14 BPD lung.

value: hyperoxia


title: P14-BPD-lung1

description: Gene expression data from P14 BPD lung.