title: MCF7-155m1-21a

city: Cambridge

first: Anna

last: Git

state: Cambs

address: Robinson Way

department: CRUK Cambridge Institute

institute: University of Cambridge

hyb_protocol: Standard Illumina hybridization protocol; HumanHT-12 v4.0

scan_protocol: Standard Illumina scan protocol

data_processing: The raw data was processed and normalised as in Curtis et al. Nature 2012

source_name: MCF-7 breast cancer cell line transfected with 21mer miR-155 mut1 mimic

label_protocol: Standard Illumina labelling protocol

growth_protocol: Cell lines were maintained and split regularly at 90% confluence, see Goldgraben et al. 2015

extract_protocol: RNA was collected in QIAZOL and extracted with QIAGEN miRNeasy kit as per the manufacturers instructions. Quality control was performed with Agilent Bioanalyser before running on microarray

treatment_protocol: Cells were seeded on day prior to transfection, transfected with miRNA mimic or controls and submitted for cell density growth curve readings (Incucyte) [see Goldgraben et al. 2015]


title: B cell lymphoma 28545 - PCI-32765 treated 1 hr - mAdbID:127905

status: Public on Dec 09 2015

type: RNA

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

country: USA

institute: National Cancer Institute

description: mAdb experiment ID: 127905

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 3 Scan_MicronsPerPixelY: 3 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888

data_processing:
Data Processing Protocol
Calculation Method: Expression data (Cy5/Cy3 ratios) were extracted using Agilent Technologies Feature Extraction software (v. 9.1). Raw data were normalized with LIMMA package in R.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

molecule: total RNA

organism: Mus musculus

label_protocol:
Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
TRIzol Extraction
Other: Total RNA was extracted using TRIzol reagent (Invitrogen).

treatment_protocol:
Agent: PCI-32765
Treatment dose: 100 nM
Treatment time: 1 hour
In-vitro treatment: B cell lymphoma cells were treated with the BTK inhibitor (100 nM), PCI-32765 (ChemieTek), for 1 hour.

tag: strain

tag: tissue

value: spleen

tag: cell line

tag: cell type

value: B cell lymphoma

tag: disease state

value: lymphoma

tag: genotype/variation

value: gene knock out

source_name: B cell lymphoma 28545 - DMSO treated 1 hr

label_protocol:
Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

treatment_protocol:
Agent: DMSO
Treatment time: 1 hour
In-vitro treatment: B cell lymphoma cells were treated with DMSO for one hour.


title: MCF7-155m1-21b

country: United Kingdom

label: biotin

organism: Homo sapiens


title: MCF7-155m2-21b

source_name: MCF-7 breast cancer cell line transfected with 21mer miR-155 mut2 mimic


title: MCF7-155w-23a

source_name: MCF-7 breast cancer cell line transfected with 23mer miR-155 wild type mimic


title: B cell lymphoma 178119 - PCI-32765 treated 24 hr - mAdbID:127904

description: mAdb experiment ID: 127904

treatment_protocol:
Agent: PCI-32765
Treatment dose: 100 nM
Treatment time: 24 hours
In-vitro treatment: B cell lymphoma cells were treated with the BTK inhibitor (100 nM), PCI-32765 (ChemieTek), for 24 hours.

source_name: B cell lymphoma 178119 - DMSO treated 24 hr

treatment_protocol:
Agent: DMSO
Treatment time: 24 hours
In-vitro treatment: B cell lymphoma cells were treated with DMSO for 24 hours.


title: TBX3_KO_IPS_2

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

hyb_protocol: Samples were hybridized using Agilent standard hybridization protocol

scan_protocol: Slides were scanned using a microarray scanner (Agilent Technologies).

data_processing: Raw data were pre-processed and quantile normalized using R/Bioconductor. The expression level of individual gene was then calculated by averaging the signal intensities of all corresponding probe sets.

label_protocol: 50 ng of each sample was labelled with the Low Input Quick Amp Kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: RNA was extracted according to manufacturer’s instructions using the RNeasy Mini or Micro Kits (Qiagen) and eluted in 40 or 15 μl RNAse-free H2O.

value: Induced pluripotent stem cells (iPSCs)

tag: phenotype

value: Tbx3 null


title: MCF7-155w-21b

source_name: MCF-7 breast cancer cell line transfected with 21mer miR-155 wild type mimic


title: TBX3_WT_IPS_2

value: Tbx3 wildtype


title: MCF7-Neg23a

source_name: MCF-7 breast cancer cell line transfected with 23mer negative control mimic


title: 199_03

source_name: MCF-7 breast cancer cell line transfected with miR-199a-5p mimic


title: B cell lymphoma 28545 - PCI-32765 treated 6 hr - mAdbID:127907

description: mAdb experiment ID: 127907

treatment_protocol:
Agent: PCI-32765
Treatment dose: 100 nM
Treatment time: 6 hours
In-vitro treatment: B cell lymphoma cells were treated with the BTK inhibitor (100 nM), PCI-32765 (ChemieTek), for 6 hours.

source_name: B cell lymphoma 28545 - DMSO treated 6 hr

treatment_protocol:
Agent: DMSO
Treatment time: 6 hours
In-vitro treatment: B cell lymphoma cells were treated with DMSO for 6 hours.


title: Neg_03

source_name: MCF-7 breast cancer cell line transfected with negative control mimic


title: MCF7-Neg21b

source_name: MCF-7 breast cancer cell line transfected with 21mer negative control mimic


title: B cell lymphoma 28545 - PCI-32765 treated 24 hr - mAdbID:127908

description: mAdb experiment ID: 127908

source_name: B cell lymphoma 28545 - DMSO treated 24 hr


title: TBX3_KO_IPS_1


title: MCF7-155m2-21a


title: TBX3_WT_IPS_1


title: TBX3_high4

value: embryonic stem cell (mESC)


title: B cell lymphoma 178119 - PCI-32765 treated 3 hr - mAdbID:127902

description: mAdb experiment ID: 127902

treatment_protocol:
Agent: PCI-32765
Treatment dose: 100 nM
Treatment time: 3 hours
In-vitro treatment: B cell lymphoma cells were treated with the BTK inhibitor (100 nM), PCI-32765 (ChemieTek), for 3 hours.

source_name: B cell lymphoma 178119 - DMSO treated 3 hr

treatment_protocol:
Agent: DMSO
Treatment time: 3 hours
In-vitro treatment: B cell lymphoma cells were treated with DMSO for 3 hours.


title: Empty_03

source_name: MCF-7 breast cancer cell line mock-transfected


title: B cell lymphoma 28545 - PCI-32765 treated 3 hr - mAdbID:127906

description: mAdb experiment ID: 127906

source_name: B cell lymphoma 28545 - DMSO treated 3 hr


title: TBX3_high3


title: 155_03

source_name: MCF-7 breast cancer cell line transfected with miR-155-5p mimic


title: B cell lymphoma 178119 - PCI-32765 treated 6 hr - mAdbID:127903

description: mAdb experiment ID: 127903

source_name: B cell lymphoma 178119 - DMSO treated 6 hr


title: MCF7-Neg21a


title: B cell lymphoma 178119 - PCI-32765 treated 1 hr - mAdbID:127901

description: mAdb experiment ID: 127901

source_name: B cell lymphoma 178119 - DMSO treated 1 hr


title: MCF7-155w-21a


title: TBX3_low4


title: TBX3_high2


title: 155_02


title: Neg_01


title: 7G8_12hr

city: New York

first: David

last: Fidock

state: NY

address: 701 W. 168th Street

institute: Columbia University

description: 7G8 parental line time series - TP2

hyb_protocol: Equal amounts of labeled samples from each time point and reference pool were subjected to array hybridization for 16-18 hours at 65ºC on a 70-mer P. falciparum microarray chips that contained 10,416 features and represented all 5,363 coding genes as previously reported (Bozdech et al., PLos Biol. 2003)

scan_protocol: Data were acquired using a GenePix 4000B scanner and analyzed with the GenePix Pro 4 software (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The Cy5 and Cy3 intensity channels were separately normalized using the mean difference between the median foreground intensity and the median background intensity of a set of representative probes. This set included probes that contained more than 50% of the pixels with intensities higher than 2 standard deviations above the background pixel intensity for both Cy5 and Cy3 signals, displayed at least 200 expression units and a regression correlation coefficient greater than or equal to 0.75.

organism: Plasmodium falciparum

source_name: parent chloroquine-resistant at 12hr post-invasion

label_protocol: Each reaction was concentrated on a Zymo DNA clean and concentrator-5 column (Zymo Research, Irvine, CA, USA) and labeled with Cy5 dye (GE Healthcare, Piscataway, NJ, USA). The reference RNA pool was labeled with Cy3.

growth_protocol: All parasite lines were propagated in a bioreactor under standard conditions in RPMI-1640 medium with L-glutamine, supplemented with 50 mg/l hypoxanthine, 25 mM HEPES, 0.25% sodium bicarbonate, 0.01 mg/ml gentamicin and 0.5% Albumax II. Equal parasite samples were harvested every 6 hours throughout the 48-hour IDC.

extract_protocol: Pellets of parasitized erythrocytes were directly stored in Trizol® for subsequent RNA extraction and cDNA synthesis.Total RNA was isolated and synthesis of first strand amino-allyl cDNA was performed as previously reported (Kyes et al, MBP 2000, Bozdech et al. PLos Biol. 2003) using 125U of Superscript II reverse transcriptase.

tag: developmental stage

value: rings

source_name: 3D7 reference pool

tag: developmental stages

value: pool of all developmental stages at 6-hour intervals


title: 7G8_18r

description: 7G8 parental line time series - TP3

source_name: parent chloroquine-resistant at 18hr post-invasion

value: trophoizoites


title: 7G8_6hr

description: 7G8 parental line time series - TP1

source_name: parent chloroquine-resistant at 6hr post-invasion


title: 7G8_24hr

description: 7G8 parental line time series - TP4

source_name: parent chloroquine-resistant at 24hr post-invasion


title: Empty_02


title: 199_02


title: 155_01


title: TBX3_high1


title: 7G8_30hr

description: 7G8 parental line time series - TP5

source_name: parent chloroquine-resistant at 30hr post-invasion


title: Empty_01


title: 106/1_30hr

description: 106/1 wild-type line time series - TP5

source_name: wild-type strain chloroquine sensitive at 30hr post-invasion


title: 106/1_42hr

description: 106/1 wild-type line time series - TP7

source_name: wild-type strain chloroquine sensitive at 42hr post-invasion

value: schizonts


title: TBX3_low3


title: 199_01

source_name: MCF-7 breast cancer cell line transfected with miR-199a-5p mimic


title: Medium Control Replicate 2

city: Amsterdam

first: Jessica

last: Legradi

address: De Boelelaan 1087

department: IVM

country: Netherlands

institute: VU Amsterdam

hyb_protocol: After hybridization, the microarrays were washed using Gene Expression Wash Buffer Kit (Agilent Technologies),

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies).

data_processing: The data was normalized using quantile-normalization. Control spots as well as not uniform spots were removed. The solvent control was averaged and the M value (log2FoldChange) calculated. Duplicated spots on the array were averaged before exposure replicates were averaged using the median.

source_name: C3A cells medium control

label_protocol: For Microarray analysis, Agilent SurePrint G3 Human Gene Expression Microarrays (8x60K) were used in combination with a one-color based hybridization protocol (OneColor RNA Spike-In Mix, Agilent Technologies, number 51885282). All steps were carried out according to the manufacturer´s instructions.

growth_protocol: C3A cells were grown in 75 cm2 culture flasks until approx. 80% confluency. Cells were then subcultured as quoted above until the uptake of trypsinised cells in media. C3A cells were diluted to reach a final density of 250 000 cells/ml. 200 µl of cell suspension were seeded in the inner 60 wells of a black 96-well plate with clear bottom (Greiner bio-one, Product 655906, Reinach, Switzerland). The outer rows were filled with 200 µl 1x PBS (phosphate buffered saline, Sigma-Aldrich, Buchs, Switzerland).  Cells were pre-incubated at 37°C for 24 h. After pre-incubation cells were dosed with the test chemicals.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (QUIAGEN, Product 74104, Hombrechtikon, Switzerland) according to manufacturers’ instructions. DNA was digested using the RNeasy Mini Kit optional on-column DNase digestion. Quality of extracted RNA was checked via the Nanodrop 1000 spectraphotomoeter V3.7, as well as running the samples on a 1.5% agarose gel.

treatment_protocol: C3A cells were exposed for 2 hours to substances. For microarray analysis, 6 replicate wells per concentration were pooled. DMSO (0.1%) was used as solvent control.


title: 106/1_36hr

description: 106/1 wild-type line time series - TP6

source_name: wild-type strain chloroquine sensitive at 36hr post-invasion


title: Medium Control Replicate 3


title: TBX3_low1


title: Medium Control Replicate 1


title: TBX3_low2


title: DMSO Control Replicate 2

source_name: C3A cells DMSO control


title: DMSO Control Replicate 1


title: DMSO Control Replicate 3


title: MCF7_Akti1/2 (Antibody Arrays (L-507))

type: protein

city: Boston

first: Ben

middle: S

last: Wittner

state: MA

address: 185 Cambridge Street

department: Cancer Center

institute: Massachusetts General Hospital

description: Supernatant protein profiling after treatment with Akti-1/2 for 6 days.

hyb_protocol: Place each membrane printed side up into a Plastic Incubation Tray. One membrane per tray. Note: The printed membrane will have a “1” mark (for all L-507 membranes) “2” (for all L-493 membranes) in the upper left corner of the membrane. Add 8 ml of Blocking Buffer to each membrane and cover with the lid. Incubate at room temperature with gentle shaking for 1 hour. Aspirate Blocking Buffer from each tray. Add 8 ml of diluted or undiluted sample onto each membrane and cover with the lid. Incubate at room temperature with gentle shaking for 2 hours. Dilute 20X Wash Buffer 1 with deionized or distilled water to prepare the 1X Wash Buffer 1. Aspirate the samples from each tray and then wash by adding 20 ml of 1X Wash Buffer I at room temperature with gentle shaking (5 min per wash). Repeat the wash 2 more times for a total of 3 washes. Aspirate the 1X Wash Buffer 1 from each tray. Dilute 20X Wash Buffer 2 with deionized or distilled water to prepare the 1X Wash Buffer 2. Wash 3 times with 20 ml of 1X Wash Buffer 2 at room temperature with gentle shaking. Aspirate the 1X Wash Buffer 2 from each tray. Dilute the 500X HRP-Conjugated Streptavidin with Blocking Buffer to prepare the 1X HRP-Conjugated Streptavidin. Add 8 ml of 1X HRPConjugated Streptavidin to each membrane. Incubate at room temperature with gentle shaking for 2 hours. Wash as previously directed.

scan_protocol: For detection of 2 membranes, add 4.2 ml of Detection Buffer C and 4.2 ml of Detection buffer D into a tube and mix both solutions. Drain off excess wash buffer. Place membrane antibody side up (“1” or “2” symbol is marked in the top left corner of each membrane) on a clean plastic plate or its cover. Pipette 4 ml of the mixed Detection Buffers on to each membrane and incubate at room temperature for 2 minutes with gentle shaking. Ensure that the detection mixture is evenly covering the membrane without any air bubbles. Gently place the membrane with forceps (antibody side up) on a plastic sheet (provided) and cover the membrane with another plastic sheet. Gently smooth out any air bubbles. Avoid using pressure on the membrane. Work as quickly as possible. The signal can be detected directly from the membrane using a chemiluminescence imaging system or by exposing the array to x-ray film (we recommend using Kodak X-Omat™ AR film) with subsequent development. Expose the membranes for 40 seconds. Then re-expose the film according to the intensity of signals. If the signals are too strong (background too high), reduce exposure time (eg, 5–30 seconds). If the signals are too weak, increase exposure time (eg, 5–20 min or overnight). Or re-incubate membranes overnight with 1X HRP-Conjugated Streptavidin, and repeat detection on the second day. Save membranes at -20 °C to -80 °C for future reference.

data_processing: The manufacturer provided background-subtracted, positive-control normalized intensities for both L-507 and L-493 antibody arrays. For each one of the subarrays, all samples were mean-centered to a log2 value of 4.5. Data from both subarrays were combined after normalization.

molecule: protein

source_name: MCF7 breast adenocarcinoma cells, Akti-1/2 treated

label_protocol: Immediately before use, prepare 1X Labeling Reagent by briefly centrifuging down the Labeling Reagent vial and add 100 µl 1X PBS (pH=8.0) into the vial. Pipette up and down or vortex briefly to dissolve the powder. Add an appropriate amount of 1X Labeling Reagent into the tube containing the sample and immediately mix the reaction solution. Incubate the reaction solution at room temperature for 30 minutes with gentle shaking. Gently tap the tube to mix the reaction solution every 5 minutes. Add 5 µl Stop Solution (Item D) into the reaction solution and then use the Spin Column to remove any unbound biotin. a). Twist off the bottom closure of the Spin Column and loosen the cap (but keep the cap on). Place the Spin Column into a 50 ml conical collection tube. b). Centrifuge the Spin Column at 1,000 g for 3 minutes to remove storage solution. c). Add 5 ml 1X PBS (pH=8.0) into the Spin Column and centrifuge at 1,000 x g for 3 minutes to remove the 1X PBS. Repeat an additional 2 times to wash the Spin Column. d). Place the Spin Column in a new 50 ml conical collection tube and slowly load 3.5 ml of sample to the center of the compact resin bed. e). Centrifuge the Spin Column at 1,000 x g for 3 minutes. The sample should filter through the resin and deposit into the 50 ml conical collection tube. Store at -80 ºC until needed. Discard the Spin Column after use.

growth_protocol: MCF7 was maintained in DMEM, 10% FCS, 40mM glutamine, 100 U/mL penicillin, and 100µg/mL streptomycin; HCT116 was maintained in McCoy’s 5α medium supplemented with 10% FCS, 100U/mL penicillin, and 100µg/mL streptomycin. All cells were grown at 37ºC and 5% CO2.

extract_protocol: Prepare dialysis buffer (1X PBS) by dissolving 0.6 g KCl, 24 g NaCl, 0.6 g KH2PO4 and 3.45 g Na2HPO4 in 2500 ml de-ionized or distilled water. Adjust to a pH of 8.0 with 1M NaOH and adjust final volume to 3000 ml with de-ionized or distilled water. Load each sample into 2 separate Dialysis Vials, 2.5-3.0 ml of sample per vial, total 5-6 ml per sample) for dialyzing. Carefully place all Dialysis Vials into the Floating Rack. Place the Floating Rack into ≥500 ml dialysis buffer in a large beaker. Place beaker on a stir plate and dialyze for at least 3 hours at 4 °C, occasionally gently stirring the dialysis buffer. Then exchange the dialysis buffer with fresh buffer and repeat dialysis for at least 3 hours at 4 °C. Transfer dialyzed samples into a clean eppendorf tube. Centrifuge dialyzed samples for 5 minutes at 10,000 rpm to remove B24any particulates or precipitates and then transfer and combine each sample into one clean eppendorf tube. Mix well by gently pipetting.

treatment_protocol: MCF7 and HCT116 cells were treated either with DMSO or Akti-1/2 for 6 days and culture supernatant were collected and frozen at -80°C until analysis.

value: breast adenocarcinoma

tag: cell state

value: AKT1 Low


title: 106/1_48hr

description: 106/1 wild-type line time series - TP8

source_name: wild-type strain chloroquine sensitive at 48hr post-invasion

value: schizont/merozoites


title: Neg_02

source_name: MCF-7 breast cancer cell line transfected with negative control mimic


title: 106/1_6hr

description: 106/1 wild-type line time series - TP1

source_name: wild-type strain chloroquine sensitive at 6hr post-invasion


title: FCBpfmdr1_3KD_36hr

description: FCB recombinant line with pfmdr1 knockdown time series - TP6

source_name: recombinant pfmdr1 knockdown in the FCB background at 36hr post-invasion


title: 106/1_12hr

description: 106/1 wild-type line time series - TP2

source_name: wild-type strain chloroquine sensitive at 12hr post-invasion


title: FCBpfmdr1_3KD_48hr

description: FCB recombinant line with pfmdr1 knockdown time series - TP8

source_name: recombinant pfmdr1 knockdown in the FCB background at 48hr post-invasion

source_name: 3D7 reference pool


title: 106/1_24hr

description: 106/1 wild-type line time series - TP4

source_name: wild-type strain chloroquine sensitive at 24hr post-invasion


title: FCBpfmdr1_3KD_24hr

description: FCB recombinant line with pfmdr1 knockdown time series - TP4

source_name: recombinant pfmdr1 knockdown in the FCB background at 24hr post-invasion


title: FCBpfmdr1_3KD_30hr

description: FCB recombinant line with pfmdr1 knockdown time series - TP5

source_name: recombinant pfmdr1 knockdown in the FCB background at 30hr post-invasion


title: CCCP Replicate 2

source_name: C3A cells exposed 2h


title: FCBpfmdr1_3KD_18r

description: FCB recombinant line with pfmdr1 knockdown time series - TP3

source_name: recombinant pfmdr1 knockdown in the FCB background at 18hr post-invasion


title: FCBpfmdr1_3KD_12hr

description: FCB recombinant line with pfmdr1 knockdown time series - TP2

source_name: recombinant pfmdr1 knockdown in the FCB background at 12hr post-invasion


title: FCBpfmdr1_3KD_6hr

description: FCB recombinant line with pfmdr1 knockdown time series - TP1

source_name: recombinant pfmdr1 knockdown in the FCB background at 6hr post-invasion


title: FCCP Replicate 1


title: Dinoterb Replicate 2


title: 106/1_18r

description: 106/1 wild-type line time series - TP3

source_name: wild-type strain chloroquine sensitive at 18hr post-invasion


title: FCCP Replicate 2


title: TCP Replicate 2


title: TCP Replicate 1


title: FCB_48hr

description: FCB parental line time series - TP8

source_name: parent multidrug resistant at 48hr post-invasion


title: CCCP Replicate 1


title: FCB_42hr

description: FCB parental line time series - TP7

source_name: parent multidrug resistant at 42hr post-invasion


title: FCBpfmdr1_3KD_42hr

description: FCB recombinant line with pfmdr1 knockdown time series - TP7

source_name: recombinant pfmdr1 knockdown in the FCB background at 42hr post-invasion


title: FCB_36hr

description: FCB parental line time series - TP6

source_name: parent multidrug resistant at 36hr post-invasion


title: Benzoapyrene Replicate1


title: Benzoapyrene Replicate2


title: CCCP Replicate 3

scan_protocol: Arrays were scanned using the Scan Control Software A8.5 with the feature extraction 10.X Software (Agilent technologies) on the DNA microarray scanner G2505C (Agilent Technologies).

data_processing: M values (log2FoldChange) were calculated and LOEWESS and centering normalization applied. Non uniform and control spots were removed from the data set before duplicated spots on the array were averaged (Median). Then exposure replicates were averaged using median. To identify Significantly regulated genes genes expressed |M|>2 were selected and at-test performed. Adjusted p-values were calculated using the Bonferroni-Hochberg correction and a cut-off of 0.1 applied.

label_protocol: The RNA 6000 NanoChip kit (Agilent Technologies, number 506791511) was used with the Agilent 2100 Bioanalyzer for analysis of total RNA samples following the manual instructions. Samples with a RIN (RNA integrity number) above 7 were considered appropriate for consequent microarray testing. For Microarray analysis Agilent SurePrint G3 Human Gene Expression Microarrays (8x60K) were used. All replicates of the same treatment were labeled with the same dye (either Cy3 or Cy5). Each dye (Cy3/Cy5) had its own DMSO control.

source_name: C3A cells control


title: Dinoterb Replicate 1


title: Aniline Replicate 3


title: TCP Replicate 3


title: FCCP Replicate 3


title: PCP Replicate 3


title: FCB_30hr

description: FCB parental line time series - TP5

source_name: parent multidrug resistant at 30hr post-invasion


title: FCB_18r

description: FCB parental line time series - TP3

source_name: parent multidrug resistant at 18hr post-invasion


title: FCB_12hr

description: FCB parental line time series - TP2

source_name: parent multidrug resistant at 12hr post-invasion


title: Chloro-Aniline Replicate 3


title: 7G8pfcrt_T76K_36hr

description: 7G8 pfcrt backmutant line time series - TP6

source_name: pfcrt backmutant in the 7G8 background at 36hr post-invasion

source_name: 3D7 reference pool


title: 6OH-BDE90 Replicate 3


title: 7G8pfcrt_T76K_30hr

description: 7G8 pfcrt backmutant line time series - TP5

source_name: pfcrt backmutant in the 7G8 background at 30hr post-invasion


title: 7G8pfcrt_T76K_42hr

description: 7G8 pfcrt backmutant line time series - TP7

source_name: pfcrt backmutant in the 7G8 background at 42hr post-invasion


title: 7G8pfcrt_T76K_48hr

description: 7G8 pfcrt backmutant line time series - TP8

source_name: pfcrt backmutant in the 7G8 background at 48hr post-invasion


title: 7G8pfcrt_T76K_12hr

description: 7G8 pfcrt backmutant line time series - TP2

source_name: pfcrt backmutant in the 7G8 background at 12hr post-invasion


title: CCCP Replicate 2

source_name: C3A cells exposed 2h


title: FCCP Replicate 2


title: Ethylenglycol Replicate 3


title: 7G8pfcrt_T76K_18r

description: 7G8 pfcrt backmutant line time series - TP3

source_name: pfcrt backmutant in the 7G8 background at 18hr post-invasion


title: Aniline Replicate 2


title: 7G8pfcrt_CTL_48hr

description: 7G8 pfcrt recombinant control line time series - TP8

source_name: recombinant control in the 7G8 background at 48hr post-invasion


title: 7G8pfcrt_T76K_6hr

description: 7G8 pfcrt backmutant line time series - TP1

source_name: pfcrt backmutant in the 7G8 background at 6hr post-invasion


title: PCP Replicate 2


title: 7G8pfcrt_CTL_42hr

description: 7G8 pfcrt recombinant control line time series - TP7

source_name: recombinant control in the 7G8 background at 42hr post-invasion


title: 6OH-BDE90 Replicate 2


title: Chloro-Aniline Replicate 2


title: TCP Replicate 1


title: CCCP Replicate 1


title: TCP Replicate 2


title: 7G8pfcrt_T76K_24hr

description: 7G8 pfcrt backmutant line time series - TP4

source_name: pfcrt backmutant in the 7G8 background at 24hr post-invasion


title: Ethylenglycol Replicate 2


title: 7G8pfcrt_CTL_18r

description: 7G8 pfcrt recombinant control line time series - TP3

source_name: recombinant control in the 7G8 background at 18hr post-invasion


title: 7G8pfcrt_CTL_24hr

description: 7G8 pfcrt recombinant control line time series - TP4

source_name: recombinant control in the 7G8 background at 24hr post-invasion


title: Aniline Replicate 1

source_name: C3A cells control


title: 7G8pfcrt_CTL_30hr

description: 7G8 pfcrt recombinant control  line time series - TP5

source_name: recombinant control in the 7G8 background at 30hr post-invasion


title: 7G8pfcrt_CTL_36hr

description: 7G8 pfcrt recombinant control line time series - TP6

source_name: recombinant control in the 7G8 background at 36hr post-invasion


title: 6OH-BDE90 Replicate 1


title: 7G8pfcrt_CTL_12hr

description: 7G8 pfcrt recombinant control line time series - TP2

source_name: recombinant control in the 7G8 background at 12hr post-invasion


title: 7G8pfcrt_CTL_6hr

description: 7G8  pfcrt recombinant control line time series - TP1

source_name: recombinant control in the 7G8 background at 6hr post-invasion

source_name: 3D7 reference pool


title: 7G8_48hr

description: 7G8 parental line time series - TP8

source_name: parent chloroquine-resistant at 48hr post-invasion


title: 7G8_36hr

description: 7G8 parental line time series - TP6

source_name: parent chloroquine-resistant at 36hr post-invasion


title: 7G8_42hr

description: 7G8 parental line time series - TP7

source_name: parent chloroquine-resistant at 42hr post-invasion


title: FCCP Replicate 1

source_name: C3A cells exposed 2h


title: Ethylenglycol Replicate 1


title: PCP Replicate 1


title: WA01 (H1)_p43_0_exp2, 2

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Gene expression in human embryonic stem cell

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray Kit (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software GX12.0 (Agilent) using default parameters.

source_name: WA01 (H1), passage 43, untreated, experiment 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng of total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human iPSCs and ESCs were maintained in an undifferentiated state in the presence of bFGF. The cultures were incubated at 37 ºC in a humidified incubator with 3 or 5% CO2.

extract_protocol: Total RNA was prepared using ISOGEN (Nippon Gene) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: human embryonic stem cell

tag: passage number

tag: lectin treatment

tag: treatment period


title: WA01 (H1)_p43_10_rBC2LCN_exp2

source_name: WA01 (H1), passage 43, 10ug/ml of rBC2LCN treatment, experiment 2

value: 10ug/ml of rBC2LCN

value: 3 days


title: WA01 (H1)_p43_10_rBC2LCN_exp2, 2


title: WA01 (H1)_p43_0_exp2


title: WA01 (H1)_p43_1_rBC2LCN_exp2, 2

source_name: WA01 (H1), passage 43, 1ug/ml of rBC2LCN treatment, experiment 2

value: 1ug/ml of rBC2LCN


title: WA01 (H1)_p43_1_FITC-rBC2LCN_exp2, 2

source_name: WA01 (H1), passage 43, 1ug/ml of FITC-rBC2LCN treatment, experiment 2

value: 1ug/ml of FITC-conjugated rBC2LCN


title: HDF_p7

description: Gene expression in human dermal fibroblast

source_name: HDF, passage 7, untreated

value: Dermal Fibroblasts; Normal, Human, Adult


title: 201B7_p45, 2

description: Gene expression in human iPS cell

source_name: 201B7, passage 45, untreated

value: human HDF-derived iPS cell


title: WA01 (H1)_p43_1_FITC-rBC2LCN_exp2


title: 253G1_p37, 2

description: Gene expression in human iPS cell

source_name: 253G1, passage 37, untreated


title: 201B7_p45

description: Gene expression in human iPS cell


title: WA01 (H1)_p43_1_rBC2LCN_exp2


title: HDF_p7, 2


title: KhES-3_p28

source_name: KhES-3, passage 28, untreated


title: WA01 (H1)_p43_100_rBC2LCN_exp2

source_name: WA01 (H1), passage 43, 100ug/ml of rBC2LCN treatment, experiment 2

value: 100ug/ml of rBC2LCN


title: WA01 (H1)_p43_100_rBC2LCN_exp2, 2


title: KhES-1_p38, 2

source_name: KhES-1, passage 38, untreated


title: KhES-3_p28, 2


title: 253G1_p37

description: Gene expression in human iPS cell


title: FCB_6hr

description: FCB parental line time series - TP1

source_name: parent multidrug resistant at 6hr post-invasion


title: KhES-1_p38


title: WA01 (H1)_p40_1_FITC-rBC2LCN_exp1, 2

source_name: WA01 (H1), passage 40, 1ug/ml of FITC-rBC2LCN treatment, experiment 1

value: 1ug/ml of FITC-conjigated rBC2LCN


title: WA01 (H1)_p40_100_rBC2LCN_exp1, 2

source_name: WA01 (H1), passage 40, 100ug/ml of rBC2LCN treatment, experiment 1


title: WA01 (H1)_p40_100_rBC2LCN_exp1


title: WA01 (H1)_p40_1_FITC-rBC2LCN_exp1


title: WA01 (H1)_p40_10_rBC2LCN_exp1

source_name: WA01 (H1), passage 40, 10ug/ml of rBC2LCN treatment, experiment 1


title: RNA isolated from Cpeb4 immunoprecipitation, biological replica 1

city: Rochester

first: Wenqian

last: Hu

state: Minnesota

address: 200 First St SW, GU16-01A

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

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

data_processing: RIP-Chip Data from Affymetrix Mouse Gene ST Arrays were normalized by RMA using the affy package from Bioconductor.  A custom probeset definition was used for processing the arrays as defined by Dai M et. al.(PMID:16284200) such that there is one probeset per Entrez Gene ID.

source_name: E14.5 fetal liver erythroblasts

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

growth_protocol: Mouse fetal liver Ter119+ cells were isolated from E14.5 mouse fetal livers using anti-Ter119 magnetic beads

extract_protocol: The extraction protocol was in accordance with the protocol provided in the Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore)

treatment_protocol: The RNA immunoprecipitation was performed using the Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore). Anti-Cpeb4 antibody (ab83009 from Abcam) was used for the immunoprecipitation, and rabbit IgG was used as control

tag: antibody

tag: antibody catalog

tag: antibody vendor

value: Abcam

value: E14.5 fetal liver


title: HCT116_DMSO (Antibody Arrays (L-493))

description: Supernatant protein profiling after treatment with DMSO for 6 days.

source_name: HCT116 colon carcinoma cells, Akti-1/2 treated

value: colon carcinoma

value: AKT1 WT


title: WA01 (H1)_p40_10_rBC2LCN_exp1, 2


title: WA01 (H1)_p40_1_rBC2LCN_exp1

source_name: WA01 (H1), passage 40, 1ug/ml of rBC2LCN treatment, experiment 1


title: shRNA3_Dox3

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

description: SFRP3 sh3 (tet-14460-puro) Dox treated

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA express was used to generate the RMA file

source_name: Rh28 cells

label_protocol: Affymetrix standard protocol

growth_protocol: Human aRMS cell line Rh28 cells described previously (Naini et al., 2008), and were maintained in RPMI + 10% tetracycline-screened FBS (Hyclone).

extract_protocol: RNA was isolated using an RNeasy kit according to the manufacturer’s protocol

treatment_protocol: Rh28 cells transduced with indicated empty vector or SFRP3 shRNAs. One million PD18 cells were plated on day 0, treated with growth media (RPMI + 10% tet-screened FBS) or growth media supplemented with 4 ug/ul doxycyline on days 1-5, and harvested on day 6.  Growth media or growth media supplemented with doxycyline was replaced daily.

tag: sample type

value: human cancer cell line, 4mM glutamine

tag: treatment

value: 4mM glutamine

tag: knockdown

value: SFRP3 sh3


title: shRNA3_Dox1

description: SFRP3 sh3 (tet-14460-puro) Dox treated

tag: cell line


title: WA01 (H1)_p40_0_exp1, 2

source_name: WA01 (H1), passage 40, untreated, experiment 1

tag: cell type


title: shRNA3_Dox2

description: SFRP3 sh3 (tet-14460-puro) Dox treated


title: shRNA5_Dox4

description: SFRP3 sh5 (tet-14462-puro) Dox treated

value: SFRP3 sh5


title: shRNA5_Dox3

description: SFRP3 sh5 (tet-14462-puro) Dox treated


title: RNA isolated from IgG control

value: IgG control

tag: tissue


title: RNA isolated from total Input


title: WA01 (H1)_p40_1_rBC2LCN_exp1, 2

value: human embryonic stem cell


title: V3 iPSC BAP

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

hyb_protocol: Purified cRNA (1 µg) was fragmented to uniform size and applied to Agilent 4x44K v2 microarrays (Design ID 026655, Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 h on a rotating incubator and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner at 5 µm resolution.

data_processing:
Data was analyzed with Agilent Feature Extraction and GeneSpring GX v7.3.1 software packages.
Intensity values are normalized to the median intensity of each array.

source_name: V3 iPSC BAP

label_protocol: First and second strand cDNA was prepared from the total RNA samples. cRNA target was prepared from the DNA template and verified on the Bioanalyzer.

growth_protocol: H1 ESC and all iPSC lines were propagated doxycycline-free standard hESC medium containing FGF2 (10 ng/ml) or mTeSR1 (StemCell Technologies) with daily refreshment.

extract_protocol: RNAs were extracted with STAT60 (Tel-Test, Friendswood, TX) and 1-bromo-3-chloro-propane (Sigma) and were purified using Ribopure (Ambion) RNA isolation kit.

treatment_protocol: To study the effects of BMP4 and BAP to the PSC, respective reagents were added to FGF2-free MEF-CM from the second day culture of following passage. Cells were cultured in MEF-CM+FGF2 (10 ng/ml) (control condition, FGF2),  MEF-CM+BMP4 (10 ng/ml) (BMP4) and MEF-CM+BMP4 (10 ng/ml) +A83-01 (1 μM) +PD173074 (0.1 μM) (BAP) which were replaced daily and up to 6 additional days.

value: iPSC derived with lentiviral transduction (V) from human umbilical cords of control male infant, gestational age 39 weeks

value: after 6 days in MEF-CM+BAP (BMP4;10 ng/ml, A83-01;1 μM, PD173074;0.1 μM)


title: shRNA5_Dox1

description: SFRP3 sh5 (tet-14462-puro) Dox treated


title: HCT116_Akti1/2 (Antibody Arrays (L-493))

description: Supernatant protein profiling after treatment with Akti-1/2 for 6 days.

value: AKT1 Low


title: RNA isolated from Cpeb4 immunoprecipitation, biological replica 2


title: H1 ESC BMP4 [re-analysis]

description: H1 ESC BMP4

source_name: H1 ESC BMP4

value: ESC derived from human male blastocysts (H1, NIH code WA01)

value: after 6 days in MEF-CM+BMP4 (10 ng/ml)


title: P2 iPSC BAP

source_name: P2 iPSC BAP

value: iPSC derived with episomal plasmids (P) from human umbilical cords of male infant whose mother suffered early onset severe type of preeclampsia and delivered gestational age 30 weeks.


title: V3 iPSC FGF2 [re-analysis]

description: V iPSC FGF2


title: MCF7_DMSO (Antibody Arrays (L-493))

source_name: MCF7 breast adenocarcinoma cells, Akti-1/2 treated

value: breast adenocarcinoma


title: P2 iPSC BMP4

source_name: P2 iPSC BMP4


title: WA01 (H1)_p40_0_exp1


title: FCB_24hr

description: FCB parental line time series - TP4

source_name: parent multidrug resistantat 24hr post-invasion

value: trophoizoites

source_name: 3D7 reference pool

value: pool of all developmental stages at 6-hour intervals


title: Vector_Dox2

description: Empty vector (tet-pLKO-puro) Dox treated

value: human cancer cell line, no glutamine

value: no glutamine

value: Empty vector


title: P2 iPSC FGF2

source_name: P2 iPSC FGF2

value: after 6 days in MEF-CM+FGF2 (10 ng/ml)


title: H1 ESC BAP

source_name: H1 ESC BAP


title: Chloro-Aniline Replicate 1

source_name: C3A cells exposed 2h

source_name: C3A cells control


title: Vector_Dox3


title: MCF7_Akti1/2 (Antibody Arrays (L-493))


title: P3 iPSC BMP4

source_name: P3 iPSC BMP4

value: iPSC derived with episomal plasmids (P) from human umbilical cords of control male infant, gestational age 39 weeks


title: P3 iPSC BAP

source_name: P3 iPSC BAP


title: V2 iPSC FGF2

source_name: V2 iPSC FGF2

value: iPSC derived with lentiviral transduction (V) from human umbilical cords of male infant whose mother suffered early onset severe type of preeclampsia and delivered gestational age 30 weeks.


title: Vector_no_Dox3

description: Empty vector (tet-pLKO-puro) No Dox treatment

value: human cancer cell line, 4mM glutamine

value: 4mM glutamine


title: Vector_Dox1


title: P3 iPSC FGF2

source_name: P3 iPSC FGF2


title: V2 iPSC BMP4

source_name: V2 iPSC BMP4


title: Vector_no_Dox1

source_name: Rh28 cells


title: V2 iPSC BAP

source_name: V2 iPSC BAP


title: H1 ESC FGF2

source_name: H1 ESC FGF2


title: Vector_no_Dox2


title: Heart_early exercise_24wk_rep8

city: Burwood

first: Glenn

middle: David

last: Wadley

state: Victoria

address: 221 Burwood Highway

country: Australia

institute: Deakin University

description: group4 rat 8

hyb_protocol: A total hybridisation volume of 15ul was prepared for each sample and 15ul loaded into a single array on the Ilumina RatRef-12 BeadChip.  The chip was then hybridised at 58C for 16 hours in an oven with a rocking platform.  Following hybridisation, the chip was washed using the appropriate protocols as outlined in the Illumina manual.

scan_protocol: Upon completion of the washing, the chips were then coupled with Cy3 and scanned in the Illumina iScan Reader.  The scanner operating software, BeadStudio, converts the signal on the array into a TXT file for analysis.

data_processing: The sample probe profile and control probe profile files were read into R (v3.2.2), and underwent normexp background correction  with limma (v3.24.15) using negative control probes and quantile normalization using negative and positive control probes.

organism: Rattus norvegicus

source_name: Heart_early exercise_24wk

label_protocol: Microarray gene expression analysis was performed by the Australian Genome Research Facility (AGRF, Melbourne, Australia). The quality and quantity of human total RNA was ascertained on the Agilent Bioanalyser 2100 using the NanoChip protocol.  A total of 500 ng of total RNA was then prepared for hybridisation to the Ilumina RatRef-12_V1_0_R4

extract_protocol: Total RNA was extracted from frozen heart using the Micro-to-Midi Total RNA Purification System kit with Trizol and DNase on-column digestion (Invitrogen, Melbourne, Australia). RNA integrity was verified and the concentration determined on the Experion Automated Electrophoresis System (Bio-Rad Laboratories, NSW, Australia).

tag: strain

value: Wistar Kyoto

tag: age

value: 24 weeks old

tag: Sex

value: male

tag: sample group

value: treadmill running from 5-9 weeks of age (early exercise)

value: heart

tag: chip batch id

value: chip 1


title: Heart_later exercise_24wk_rep1

description: group5 rat 1

source_name: Heart_later exercise_24wk

value: treadmill running from 20-24 weeks of age

value: chip 2


title: Primary Human Cardiomyoctes exposed to T. cruzi for 120 mins replicate 2

city: Nashville

first: Pius

middle: N

last: Nde

state: TN

address: 1005 Dr. D.B. Todd Jr. Blvd

department: Microbiology and Immunology

institute: Meharry Medical College

description: Gene expression data from Primary Human cardiomyoctes exposed to T. cruzi for 120 mins

hyb_protocol: Labeled cDNA Microarray hybridizations were performed on HG-ST 1.1 ST v1 arrays (Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Partek Genomic Suite 6.x uisng default settings and RMA as normalization method.

label: Biotin

source_name: Primary Human Cardiomyoctes

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

growth_protocol: The Primary Human Cardiomyoctes were cultured in myocytes basal growth medium supplemented with the supplemental mix (PromoCell, Heidelberg, Germany) containing fetal calf serum (0.05ml/ml), recombinant human epidermal growth factor (0.5ng/ml), recombinant human basic fibroblast growth factor (2ng/ml) and recombinant human insulin (5ug/ml).

extract_protocol: At the end of each experiment the Primary Human Cardiomyoctes cells were lysed in RNA extraction lysis buffer as described by the manufacturer. Total RNA was purified with the RNAeasy RNA purification kit (Qiagen, Valencia, CA, USA). The RNA purification step included an on column DNase treatment step to eliminate traces of genomic DNA as described by the manufacturer (Qiagen). The quality of the purified RNA was analyzed using the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). The quality of purified RNA was assessed by RNA Integrity Number (RIN) and samples with a RIN of at least 7 were used for further analysis.

treatment_protocol: Primary Human Cardiomyoctes confluent monolayers were starved in HBSS containing 30 mM HEPES followed by addition of invasive T. cruzi trypomastigotes in myocyte basal growth medium without supplements at a ratio of 10 parasites per cell. The cells challenged with the parasites were incubated for different time points 60, 90 and 120 minutes. The control cells were not challenged with parasites.

value: Human heart


title: Heart_later exercise_24wk_rep5

description: group5 rat 5

value: chip 3


title: Heart_later exercise_24wk_rep6

description: group5 rat 6


title: Heart_later exercise_24wk_rep7

description: group5 rat 7


title: Heart_later exercise_24wk_rep4

description: group5 rat 4


title: Primary Human Cardiomyoctes exposed to T. cruzi for 120 mins replicate 1


title: Primary Human Cardiomyoctes exposed to T. cruzi for 60 mins replicate 1

description: Gene expression data from Primary Human cardiomyoctes exposed to T. cruzi for 60 mins


title: H0046690

city: Framingham

last: Zuk

address: 49 New York Ave

department: R&D

institute: Genzyme

description:
Sorted cells collected from_58_Sham
Gene expression data from 58_Sham

hyb_protocol: following fragmentation,5 ug of cDNA were hybridized for 18 hours ± 2 hours at 45C on by hybridization to Affymetrix GeneChip Mouse Genome 430 2.0 array

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

data_processing: Raw CEL files were RMA preprocessed in Affymetrix Expression Console, and imported into Array Studio v5.2 (Omicsoft) for further downstream statistical analysis.

label_protocol: Samples were linearly amplified with NuGen Ovation Pico WTA v2 (cat# 3302) to obtain sufficient quantity for downstream microarray application.The amplified cDNA library was further fragmented and labeled with NuGen Encore Biotin Module (cat#4200)

growth_protocol: C57BL/6 male mice (8–10 weeks, Taconic, Germantown, NY)

extract_protocol: Total RNA was extracted with RNeasy Micro kit (Qiagen) with on-column DNaseI digest. RNA was eluted in nuclease free water followed by QC with Bioanalyzer’s RNA Pico assay

treatment_protocol: bilateral renal IRI for 28 min or sham surgery followed by reperfusion for various times; After surgery, animals were hydrated with intraperitoneal injection of 1 ml sterile saline. Pain medication (buprenorphine, 0.05 mg/kg, SC) was administered before surgery and then again at 12-hr intervals for 2 days starting 24 hours later. Sham surgeries were identical without the bilateral clamping; Macrophage populations were sorted by Flow Cytometry into low and intermediate populations by Itgam(Cd11b) and Ly6c markers

tag: gender

value: 8-10 weeks

value: kidneys

value: macrophage


title: Primary Human Cardiomyoctes exposed to T. cruzi for 60 mins replicate 2


title: Heart_later exercise_24wk_rep2

description: group5 rat 2


title: Heart_early exercise_24wk_rep6

description: group4 rat 6


title: Primary Human Cardiomyoctes exposed to T. cruzi for 90 mins replicate 1

description: Gene expression data from Primary Human cardiomyoctes exposed to T. cruzi for 90 mins


title: Heart_later exercise_24wk_rep3

description: group5 rat 3


title: Heart_early exercise_24wk_rep7

description: group4 rat 7


title: H0046691

description:
Mouse Ref_RNA
Gene expression data from Mouse Ref_RNA

value: reference RNA


title: Primary Human Cardiomyoctes exposed to T. cruzi for 90 mins replicate 2


title: RC2-SM vs. all1all2 mutant

city: St. Louis

first: Jinsheng

last: Yu

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description:
SM-A_vs_All1all2-A
Samples in minimal media.

hyb_protocol: Each sample pair (~20ul) is suspended in Formamide-based hybridization buffer (vial 7-Genisphere) (26ul), Array 50dT blocker (Genisphere) (2ul), and RNase/DNase-free water (4ul). Two hybridizations are carried out in a sequential manner. The primary hybridization is performed by adding 48ul of sample to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity. Prior to the secondary hybridization, slides are gently submerged into 2X SSC, 0.2% SDS (at 43C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. Secondary hybridization is carried out using the complimentary capture reagents provided in the 3DNA Array 350 kit (Genisphere). For each reaction, the following are added: 3DNA capture reagent with Cy3 (2.5ul), 3DNA capture reagent with Cy5 (2.5ul), SDS-based hybridization buffer (vial 6-Genisphere) (26ul), and RNase/DNase-free water (21ul). The secondary hybridization solution is incubated in the dark at 80C for 10 min. then 50C for 15 min. Hybridization is performed by adding 48ul secondary hybridization solution to the slide under a supported glass coverslip at 65C for 3 hr at high humidity in the dark. At hybridization termination, arrays are gently submerged into 2X SSC, 0.2% SDS (at 65C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. To prevent fluorophore degradation, the arrays are treated with Dyesaver (Genisphere).

scan_protocol: Slides are scanned on a Molecular Devices GenePix 4000B microarray scanner to detect Cy3 fluorescence. Laser power is kept constant and PMT voltage is established for all 12 arrays on the glass such that each array has less than 1% signal saturation in either dye. Images were quantitated with GenePix Pro, v6.1 (Molecular Devices).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of test/reference. Partek Genomics Suite v6.5 (St. Louis, MO, USA) was used for normalization.

organism: Cryptococcus neoformans

source_name: RC2 yeast cells, growth at 37C in minimal media

label_protocol: First strand cDNA is generated by polyT primed reverse transcription (Superscript II; Invitrogen) utilizing the 3DNA Array350 kit (Genisphere). For cDNA synthesis, 1ul of fluorophore specific oligo-dT primer is added to 8ug of total RNA and the solution is incubated at 80C for 10 minutes then cooled on ice for 2 minutes. To each sample are added RNase inhibitor (Superase-In; Ambion) (1ul), 5X first strand buffer (4ul), dNTP mix (10mM each dATP, dCTP, dGTP, and dTTP) (1ul), 0.1M DTT (2ul), and Superscript II RNase H- Reverse Transcriptase (1ul). Reverse transcription is carried out at 42C for 2 hours. The reaction is terminated by adding 0.5M NaOH/ 50mM EDTA (3.5ul) and incubation at 65C for 15 minutes then neutralized with 1M Tris-HCL, pH 7.5 (5ul). For RNA expression level comparison, samples are paired and concentrated using Microcon YM30 microconcentrators (Millipore) according to the manufacturer's protocol.

growth_protocol: Yeast cells were grown in minimal media for 16 hours at 37C prior with agitation at 150rpm.

extract_protocol: RNA extraction using a QIAGEN RNeasy column.

treatment_protocol: Not applicable.

value: RC2-Serotype D

tag: genotype/variation

value: WT

tag: growth medium

value: minimal media

source_name: all1all2 mutant yeast cells, growth at 37C in minimal media

value: all1all2 mutant


title: H0046688


title: V3 iPSC BMP4 [re-analysis]

description: V iPSC BMP4

source_name: V3 iPSC BMP4

value: iPSC derived with lentiviral transduction (V) from human umbilical cords of control male infant, gestational age 39 weeks

value: after 6 days in MEF-CM+BMP4 (10 ng/ml)


title: all1all2 mutant vs. RC2-SM

description:
All1all2-B_vs_SM-B
Samples in minimal media.


title: Primary Human Cardiomyoctes control replicate 1

description: Gene expression data from control Primary Human cardiomyoctes


title: H0046689

value: male


title: Primary Human Cardiomyoctes control replicate 2


title: RC2-SM vs. all2 mutant

description:
SM-A_vs_all2-A
Samples in minimal media.

source_name: all2 mutant yeast cells, growth at 37C in minimal media

value: all2 mutant


title: Heart_early exercise_24wk_rep3

description: group4 rat 3

value: Wistar Kyoto

value: 24 weeks old

value: treadmill running from 5-9 weeks of age (early exercise)

value: heart


title: H0046687

description:
Sorted cells collected from Sham surgery  2( without  the bilateral clamping)
Gene expression data from Sham 2


title: PAO1 GA, rep 2

city: Atlanta

first: Han Ting

last: Chou

state: GA

address: 1 University Park Drive

department: Biology

institute: Georgia State University

description: Gene expression data from PAO1 wild type strain

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Pseudomonas aeruginosa Array [Pae_G1a]. 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: Data collection was carried out using GCOS 1.4 software (Affymetrix). analysis was performed using GeneSpring GX 11 Software (Aglient, Palo Alto,CA), and probe intensity values were normalized using Robust Multichip Average (RMA)-algorithm.

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 grown on glutaric acid

growth_protocol: Two independent sets of P. aeruginosa PAO1 cultures were grown aerobically to exponential phase in minimal medium P with 350 rpm shaking at 37C

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

treatment_protocol: Cultures in MMP were supplemented with 10mM L-glutamate with the addition of 10 mM L-lysine, cadaverine, 5-amino valerate, glutaric acid, D-lysine or 5mM L-pipecolate.

tag: tgt value

tag: nf value

tag: supplements

value: 10mM L-glutamate with the addition of 10 mM glutaric acid

tag: growth phase

value: exponential


title: H0046686

value: 8-10 weeks

value: kidneys


title: Heart_early exercise_24wk_rep5

description: group4 rat 5

value: chip 1


title: Heart_early exercise_24wk_rep4

description: group4 rat 4

value: chip 3


title: Heart_early exercise_24wk_rep2

description: group4 rat 2


title: H0046683

description:
Sorted cells collected from Sham surgery  1( without  the bilateral clamping)
Gene expression data from Sham 1

value: macrophage


title: Heart_sedentary_24wk_rep5

description: group3 rat 5

value: sedentary


title: H0046685


title: Heart_sedentary_24wk_rep6

description: group3 rat 6

value: chip 2


title: PAO1 L-pip, rep 2

source_name: PAO1 grown on L-pipecolate

value: 10mM L-glutamate with the addition of 10 mM L-pipecolate


title: Heart_early exercise_24wk_rep1

description: group4 rat 1


title: Heart_sedentary_24wk_rep7

description: group3 rat 7


title: H0046682


title: H0046684


title: H0046681

description:
Sorted cells collected_4 hrs postperfusion after IRI(Renal ischemia-reperfusion injury)
Gene expression data from 4 hrs postperfusion after IRI(Renal ischemia-reperfusion injury)


title: Cu2-REF-2

city: Recife

first: Marcos

middle: Antonio

last: Morais

state: Pernambuco

address: Av. Moraes Rego, 1235

department: Department of Genetics

country: Brazil

institute: Federal University of Pernambuco

hyb_protocol: RNA from the cells fermented with reference medium were labelled with Cy3 and mixed with Cyb5-labelled RNA from the cells fermented with Mg2+ medium and Cu2+ medium. Target and reference cRNA samples were mixed and the hybridizations were performed on yeast gene expression 8x15K spots slides (cat. nr. G4813A-016322, Agilent, USA) at 65 ºC for 17 hours at 10 r.pm. in the Microarray Hybridization Oven (cat. nr. G2545A, Agilent, USA).

scan_protocol: The slides were placed into the High-Resolution Microarray Scanner (cat. nr. G2505-60502, Agilent, USA). The fluorescence data were extracted (.txt files) for each spot  by using Scan Control 8.5.1 software (Agilent, USA)

data_processing: Data were then analyzed using specific packages from the R statistical language with the specific LIMMA and MArray  packages. Background correction was done with normexp method. Robust spline and quantile methods were used for normalization within and between arrays, respectively. A list of differentially expressed genes was generated by applying adjusted p-values for multiple tests. Groups of genes with statistical significance (Adj.p<0.05) were utilized.

organism: Saccharomyces cerevisiae

source_name: yeast cells

label_protocol: Synthesis of cDNA and labelling was performed by Two-Color Low Input Quick Amp Labeling Kit (cat. nr. 5190-2306, Agilent, USA), with Two-Color RNA spike-in kit for internal control (cat. nr. 5188-5279, Agilent, USA). For yeast samples, 100 ng of purified RNA was used for labelling.

growth_protocol: The cell was growth in YPD medium at 30ºC and 150 rpm in a rotatory shaker until a cell concentration of 25g/L to start the fermentation assay.

extract_protocol: The total RNA extraction was carried out with the rupture of the yeast cells with AE buffer and SDS10% in 65ºC and purified with the Maxwell 16LEV simplyRNA blood Kit.

treatment_protocol: Fermentation assays was performed with the industrial yeast S. cerevisiae JP1 in reference medium (mineral concentration balanced), in the medium supplemented with 500 mg/L of magnesium (Mg2+ medium) and in the medium supplemented with 1 mg/L of copper (Cu2+ medium).

tag: treatment

value: 1 mg/L of copper (Cu2+ medium)

tag: sample type

value: reference


title: PAO1 GA, rep 1


title: Primary Human Cardiomyoctes control replicate 3

value: Human heart


title: PAO1 L-pip, rep 1


title: Cu1-REF-2


title: PAO1 AMV, rep 1

source_name: PAO1 grown on 5-amino valerate

value: 10mM L-glutamate with the addition of 10 mM 5-amino valerate


title: PAO1 AMV, rep 2


title: H0046679

value: male


title: Mg1-REF-2

value: 500 mg/L of magnesium (Mg2+ medium)


title: Heart_sedentary_24wk_rep4

description: group3 rat 4

value: Wistar Kyoto

value: 24 weeks old

value: heart


title: H0046680

value: 8-10 weeks


title: Heart_sedentary_24wk_rep3

description: group3 rat 3


title: Heart_early exercise_9wk_rep7

description: group2 rat 7

source_name: Heart_early exercise_9wk

value: 9 weeks old

value: treadmill running from 5-9 weeks (early exercise)


title: H0046678

value: kidneys


title: Cu2-REF-1


title: Heart_sedentary_24wk_rep2

description: group3 rat 2


title: H0046676

description:
Sorted cells collected_4 hrs postperfusion after IRI(Renal ischemia-reperfusion injury)
Gene expression data from 9 days  postperfusion after IRI(Renal ischemia-reperfusion injury)

value: macrophage


title: PAO1 Cad, rep 1

source_name: PAO1 grown on cadaverine

value: 10mM L-glutamate with the addition of 10 mM cadaverine

value: exponential


title: all2 mutant vs. RC2-SM

description:
all2-B_vs_SM-B
Samples in minimal media.

value: RC2-Serotype D

value: all2 mutant

value: minimal media

value: WT


title: Cu1-REF-1

value: 1 mg/L of copper (Cu2+ medium)

value: reference


title: Heart_early exercise_9wk_rep6

description: group2 rat 6

value: male

value: chip 2


title: H0046677


title: Mg2-REF-1

value: 500 mg/L of magnesium (Mg2+ medium)


title: H0046674

description:
Sorted cells collected 9 days  postperfusion after IRI(Renal ischemia-reperfusion injury)
Gene expression data from 9 days  postperfusion after IRI(Renal ischemia-reperfusion injury)


title: PAO1 D-lys, rep 2

source_name: PAO1 grown on D-lysine

value: 10mM L-glutamate with the addition of 10 mM D-lysine


title: Mg2-REF-2


title: Mg1-REF-1


title: PAO1 D-lys, rep 1


title: PAO1 Cad, rep 2


title: Heart_early exercise_9wk_rep5

description: group2 rat 5

value: Wistar Kyoto

value: heart

value: chip 1


title: Heart_sedentary_24wk_rep1

description: group3 rat 1

value: 24 weeks old

value: sedentary


title: PAO1 L-lys, rep 1

source_name: PAO1 grown on L-lysine

value: 10mM L-glutamate with the addition of 10 mM L-lysine


title: H0046673

value: 8-10 weeks

value: kidneys

value: macrophage


title: PAO1 L-lys, rep 2

value: exponential


title: H0046672


title: Heart_early exercise_9wk_rep3

description: group2 rat 3

value: 9 weeks old

value: treadmill running from 5-9 weeks (early exercise)


title: Heart_early exercise_9wk_rep1

description: group2 rat 1

value: chip 3


title: Heart_early exercise_9wk_rep4

description: group2 rat 4

value: male


title: Heart_early exercise_9wk_rep2

description: group2 rat 2

value: chip 2


title: H0046671


title: H0046675


title: H0046669

description:
Sorted cells collected 24 hrs postperfusion after IRI(Renal ischemia-reperfusion injury)
Gene expression data from 24 hrs postperfusion after IRI(Renal ischemia-reperfusion injury)


title: FOP_TGF-B3_3

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

institute: Kyoto University

description: Gene expression data from human induced mesenchymal stromal cells (iMSCs).

hyb_protocol: Hybridisations were carried out with GeneChip® Hybridisation, Wash, and Stain Kit, with subsequent washing and staining of arrays on GeneChip® Fluid Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G

data_processing: Analysis was performed using GeneSpring 12.6.1 software. Data were normalized with the MAS5 algorithm.

label_protocol: 100ng of total RNA from samples were amplified, reverse-transcribed and then labeled according to the Affymetrix GeneChip® 3' IVT Express Kit protocol.

growth_protocol: iMSCs were induced and maintained in a minimum essential medium alpha modification supplemented with 10% FBS, 5 ng/mL FGF2 and 0.5% penicillin and streptomycin

extract_protocol: RNA was isolated with RNeasy mini kit (QIAGEN).

treatment_protocol: Several ligands were treated 16h in in a minimum essential medium alpha modification supplemented with 0.5% FBS


title: FOP_TGF-B3_2

value: human induced mesenchymal stromal cells (iMSCs)


title: Heart_sedentary_9wk_rep7

description: group1 rat 7


title: H0046668


title: H0046667


title: H0046670


title: Heart_sedentary_9wk_rep6

description: group1 rat 6


title: Heart_sedentary_9wk_rep5

description: group1 rat 5


title: Heart_sedentary_9wk_rep4

description: group1 rat 4


title: resFOP_TGF-B3_2


title: TabbyfootpadAdult-rep1

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description:
Biological replicate 1 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
Footpad skin was taken from wild-type and Tabby mutant mice at E17.5, P1, P3, P5 and P56 (adult) under a dissection microscope, and frozen immediately on dry ice, and stored in -80C freezer.

hyb_protocol: Slides were hybridized to Agilent-015087 arrays according to the manufacturer's protocol (Two-Color Microarray-Based Gene Expression Analysis Protocol, Product # G4140-90050, Version 5.0.1)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software. The data were further processed with NIA ANOVA tool utilities. See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal, rDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri, where i is array number.
(2) Take average of Xri's for the oligo among 28 arrays in the series: AverXr = average(Xri).
(3) For each array, estimate Yi = Xgi-Xri+AverXr (adjust to UMR).
(4) Remove outliers. Each cell/treatment type (CTT) is characterized by 2 replications, all are log-transformed (log10). Here we check if any of these values is an outlier.
First we estimate the average square difference (ASD) between replication pairs:
ASD = SUM[(x(i,1)-x(i,2))^2]/N/2
where x(i,j) is log intensities for i-th CTT and replication j, N = number of CTT. Then we estimate z-value for each CTT: z = (x(i,1)-x(i,2))/sqrt(ASD). If abs(z) > 4, then one of the replications is an outlier. The value that is farther away from the median expression value is considered an outlier and it is replaced with the value from another replication.
The result is used as the normalized VALUE. More detailed information with error correction can be found at: http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: Tabby footpad Adult

label_protocol: Total RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit according to the manufacturer's instructions.

extract_protocol: 1ml of TRIzol reagent was added to each sample, and homogenized immediately. They were then transferred to Phase Lock Gel Heavy tubes (eppendorf) and 0.2 volumes of chloroform (Sigma-Aldrich) was added to each sample. They were mixed by hand and allowed to stand for 2-5 min at room temperature. The samples were then separated by centrifugation for 5 minutes at 13,000 rpm on an eppendorf centrifuge at 4C. The aqeous phase was transferred to another eppendorf tube, and 0.8 volumes of ice-cold isopropanol was added. They were allowed to incubate for a minimum of 10 minutes at room temperature. If longer, they were placed at 4C. The sample was centrifuged again at the same conditions for 15 minutes. After centrifugation, the liquid was dumped out of the tubes and the pellet was washed with 1 mL of ice-cold 70% ethanol. The tube was spun for 5 minutes, then the ethanol was dumped out. Excess was removed with a pipette and the pellet was allowed to air dry until no liquid remained, but no longer. ddH2O was then added in the appropriate volume, the sample was allowed to dissolve for 5 minutes at 55C and then transferred to -80C for storage.

value: Adult footpads

tag: individual identifier

source_name: Universal Mouse Reference

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting UMR RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

value: Referecne


title: TabbyfootpadAdult-rep2

description:
Biological replicate 2 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
Footpad skin was taken from wild-type and Tabby mutant mice at E17.5, P1, P3, P5 and P56 (adult) under a dissection microscope, and frozen immediately on dry ice, and stored in -80C freezer.


title: FOP_TGF-B3_1

tag: cell type


title: Heart_sedentary_9wk_rep3

description: group1 rat 3

value: Wistar Kyoto

tag: tissue

value: heart


title: Heart_sedentary_9wk_rep2

description: group1 rat 2

tag: strain


title: Right region at stage 12HH chicken somite1

city: BOSTON

first: Masayuki

last: Oginuma

state: MASSACHUSETTS

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description: Gene expression data from stage 12 chicken somite

hyb_protocol: Following fragmentation, cRNAs were hybridized for 16 hours at 45oC on GeneChip® Chicken Genome arrays. Each microarray was then washed and stained on a GeneChip® fluidics station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G. Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.1.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0)

organism: Gallus gallus

label_protocol: Biotinylated cRNA targets were prepared from total RNA using a double amplification protocol according to the GeneChip® Expression Analysis Technical Manual: Two-Cycle Target Labeling Assay (P/N 701021 Rev.5, Affymetrix, Santa Clara, USA).

growth_protocol: Stage 12HH chicken embryos were pinned on a silicon-coated petri dish in PBS. After removing the endoderm and the ectoderm, both the left and right posterior paraxial mesoderm from the same embryo were dissected into 10 pieces each.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen)

tag: Stage

value: Stage 12HH

value: paraxial mesoderm


title: Left region at stage 12HH chicken somite1


title: WTfootpadAdult-rep2

source_name: WT footpad Adult


title: TabbyfootpadP5-rep2

source_name: Tabby footpad P5

value: Young pup footpads


title: Right region at stage 12HH chicken PSM8

description: Gene expression data from stage 12 chicken PSM8


title: resFOP_TGF-B3_3


title: FOP_BMP-7_1


title: Heart_sedentary_9wk_rep1

description: group1 rat 1

tag: age

tag: Sex

value: sedentary


title: FOP_BMP-7_2


title: resFOP_TGF-B3_1


title: FOP_BMP-7_3


title: Podocytes - with High Glucose 48h rep3

city: Toronto

first: Andrew

last: Advani

state: Ontario

address: 6-151 61 Queen Street East

department: Medicine

country: Canada

institute: St. Michael's Hospital

description:
HG 3
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using average normalization (background subtracted) with Illumina GenomeStudio.

source_name: Cell Line

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

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

tag: dznep time exposure (hrs)

tag: glucose time exposure (hrs)

value: cultured podocytes


title: Right region at stage 12HH chicken PSM7

description: Gene expression data from stage 12 chicken PSM7


title: WTfootpadAdult-rep1


title: Left region at stage 12HH chicken PSM8


title: resFOP_BMP-7_3


title: Right region at stage 12HH chicken PSM6

description: Gene expression data from stage 12 chicken PSM6


title: resFOP_BMP-7_2


title: TabbyfootpadP3-rep2

source_name: Tabby footpad P3


title: TabbyfootpadP5-rep1


title: Podocytes - with High Glucose + DZNep 48h rep3

description:
HG+DZNEP 3
replicate 3


title: resFOP_BMP-7_1


title: Podocytes - with High Glucose 48h rep1

description:
HG 1
replicate 1


title: WTfootpadP5-rep1

source_name: WT footpad P5


title: Left region at stage 12HH chicken PSM5

description: Gene expression data from stage 12 chicken PSM5


title: WTfootpadP5-rep2


title: Left region at stage 12HH chicken PSM6


title: FOP_Activin-A_3


title: Podocytes - with High Glucose 48h rep2

description:
HG 2
replicate 2


title: Left region at stage 12HH chicken PSM7


title: TabbyfootpadP3-rep1


title: Podocytes - with High Glucose + DZNep 48h rep2

description:
HG+DZNEP 2
replicate 2


title: WTfootpadP3-rep2

source_name: WT footpad P3


title: Podocytes - with DZNep + No High Glucose 48h rep2

description:
DZNEP 2
replicate 2


title: Podocytes - with High Glucose + DZNep 48h rep1

description:
HG+DZNEP 1
replicate 1


title: Right region at stage 12HH chicken PSM4

description: Gene expression data from stage 12 chicken PSM4


title: Left region at stage 12HH chicken PSM4


title: FOP_Activin-A_2


title: resFOP_Activin-A_3


title: Podocytes - with DZNep + No High Glucose 48h rep3

description:
DZNEP 3
replicate 3


title: WTfootpadP3-rep1


title: Right region at stage 12HH chicken PSM3

description: Gene expression data from stage 12 chicken PSM3


title: resFOP_Activin-A_2


title: FOP_Activin-A_1


title: Podocytes - with DZNep + No High Glucose 48h rep1

description:
DZNEP 1
replicate 1


title: FOP_Control_3


title: WTfootpadP1-rep2

source_name: WT footpad P1

value: Newborn footpads


title: TabbyfootpadP1-rep1

source_name: Tabby footpad P1


title: Podocytes - No DZNep + No High Glucose 48h rep3

description:
CONTROL 3
replicate 3


title: resFOP_Activin-A_1


title: Left region at stage 12HH chicken PSM3


title: Right region at stage 12HH chicken PSM2

description: Gene expression data from stage 12 chicken PSM2


title: Left region at stage 12HH chicken PSM2


title: Podocytes - No DZNep + No High Glucose 48h rep2

description:
CONTROL 2
replicate 2


title: TabbyfootpadP1-rep2


title: Podocytes - No DZNep + No High Glucose 48h rep1

description:
CONTROL 1
replicate 1


title: FOP_Control_1


title: TabbyfootpadE17.5-rep2

source_name: Tabby footpad E17.5

value: embryonic footpads


title: FOP-iMSCs (+ActA)

description: Gene expression data of induced chondrocyte derived from induced mesenchymal stromal cells (iMSCs)

data_processing: Analysis was performed using GeneSpring 12.6.1 software. Data were normalized with the RMA algorithm.

source_name: FOP-iMSCs (+ActA)

label_protocol: 500ng of total RNA from samples were reversed transcribed according to the Ambion® WT Expression Kit Protocol. Synthesized cDNA was then Labeled with GeneChip® Terminal Labeling Kit.

treatment_protocol: iMSCs were chondrogenic differentiated  for 7 days with or without Activin-A.

value: induced chondrocyte


title: FOP-iMSCs (-ActA)

source_name: FOP-iMSCs (-ActA)


title: Right region at stage 12HH chicken PSM1

description: Gene expression data from stage 12 chicken PSM1


title: resFOP_Control_3


title: FOP_Control_2


title: TabbyfootpadE17.5-rep1


title: WTfootpadP1-rep1


title: resFOP_Control_2


title: WTfootpadE17.5-rep2

source_name: WT footpad E17.5


title: resFOP-iMSCs (+ActA)

source_name: resFOP-iMSCs (+ActA)


title: mirPCL.039

status: Public on Dec 08 2015

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: microRNA expression data from plasma cell leukemia primary tumor.

hyb_protocol: Biotin-labeled RNA samples were hybridized for 16 hours  at 48°C on GeneChip miRNA 3.0 array, according to the standard manufacturer's protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning  of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Raw data were extracted from CEL files and then normalized using robust multi-array average (RMA) procedure in the affy package for Bioconductor and the miRBase Release 18 annotations included in the corresponding cdf definition files available at the University of Michigan Brainarray portal at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/mirbaseg.asp. Annotations were then updated to miRBase Release 20 definition using the mirna.diff files available at the MiRBase website.

source_name: Plasma cell leukemia patient 039

label_protocol: 500 ng of total RNA were converted to biotin-labeled RNA using the FlashTag Biotin HSR Labeling kit, according to Affymetrix protocol.

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

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: disease status

value: plasma cell leukemia (PCL)

tag: pcl type

value: sPCL

value: plasma cells

tag: patient


title: mirPCL.043

source_name: Plasma cell leukemia patient 043

value: pPCL


title: mirPCL.042

source_name: Plasma cell leukemia patient 042


title: mirPCL.046

source_name: Plasma cell leukemia patient 046


title: mirPCL.044

source_name: Plasma cell leukemia patient 044


title: mirPCL.038

source_name: Plasma cell leukemia patient 038


title: resFOP-iMSCs (-ActA)

source_name: resFOP-iMSCs (-ActA)


title: mirPCL.033

source_name: Plasma cell leukemia patient 033


title: mirPCL.035

source_name: Plasma cell leukemia patient 035


title: WTfootpadE17.5-rep1

source_name: Universal Mouse Reference


title: mirPCL.037

source_name: Plasma cell leukemia patient 037


title: Left region at stage 12HH chicken PSM1


title: Left region at stage 12HH chicken tailbud

description: Gene expression data from stage 12 chicken tailbud

source_name: tailbud


title: mirPCL.032

source_name: Plasma cell leukemia patient 032


title: Right region at stage 12HH chicken tailbud


title: mirPCL.031

source_name: Plasma cell leukemia patient 031


title: mirPCL.020

source_name: Plasma cell leukemia patient 020


title: mirPCL.026

source_name: Plasma cell leukemia patient 026


title: mirPCL.021

source_name: Plasma cell leukemia patient 021


title: mirPCL.029

source_name: Plasma cell leukemia patient 029


title: mirPCL.027

source_name: Plasma cell leukemia patient 027


title: mirPCL.028

source_name: Plasma cell leukemia patient 028


title: resFOP_Control_1

value: human induced mesenchymal stromal cells (iMSCs)


title: mirPCL.018

source_name: Plasma cell leukemia patient 018


title: mirPCL.036

source_name: Plasma cell leukemia patient 036


title: mirPCL.019

source_name: Plasma cell leukemia patient 019


title: mirPCL.017

source_name: Plasma cell leukemia patient 017


title: mirPCL.034

source_name: Plasma cell leukemia patient 034


title: mirPCL.030

source_name: Plasma cell leukemia patient 030


title: mirPCL.011

source_name: Plasma cell leukemia patient 011


title: mirPCL.016

source_name: Plasma cell leukemia patient 016


title: mirPCL.007

source_name: Plasma cell leukemia patient 007


title: mirPCL.006

source_name: Plasma cell leukemia patient 006


title: mirPCL.005

source_name: Plasma cell leukemia patient 005


title: mirMM.281-MM96db

description: microRNA expression data from multiple myeloma newly-diagnosed primary tumor.

hyb_protocol: Byotin-labeled RNA samples were hybridized for 16 hours  at 48°C on GeneChip miRNA 3.0 array, according to the standard manifacturer's protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Raw data were extracted from CEL files and then normalized using robust multi-array average (RMA) procedure in the affy package for Bioconductor and the miRbase Release 18 annotations included in the corresponding cdf definition files available at the University of Michigan Brainarray portal at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/version.html). Annotations were then updated to miRBase Release 20 definition using the mirna.diff files available at the miRbase website

source_name: Newly-diagnosed MM patient 281

label_protocol: 500 ng of total RNA were converted to biotin-labeled RNA using the FlashTag Biotin HSR Labeling kit, according to Affimetrix protocol.

tag: translocation

tag: disease state

value: multiple myeloma primary tumor


title: cKO_Day2_rep1

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
251486834674_1_1
Gene expression of oviduct from cKO at day 2 of pregnancy (1.5 dpc)

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

data_processing: The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise.

source_name: Oviduct from cKO at day 2 of pregnancy (1.5 dpc)

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: WT and cKO females at the age of 8 to 10 weeks were used in the experiment.

extract_protocol: The oviducts were collected at 0.5 and 1.5 dpc, respectively and were immediately frozen in liquid nitrogen. RNA was extracted by using RNeasy Mini Kit (Qiagen, Valencia, CA) and treated with DNaseI (Qiagen) according to the manufacture’s protocol.

treatment_protocol: WT and cKO females were naturally mated with WT male. The presence of a copulatory plug was determined the next morning as 0.5 dpc.

tag: strain background

tag: genotype/variation

value: conditional knockout of epithelial ERα (cKO)

tag: gender

value: female

value: 8-10 weeks

value: oviduct

tag: days post coitum

value: 1.5 dpc


title: cKO_Day1_rep1

description:
251486834805_1_1
Gene expression of oviduct from cKO at day 1 of pregnancy (0.5 dpc)

source_name: Oviduct from cKO at day 1 of pregnancy (0.5 dpc)

value: 0.5 dpc


title: WT_Day2_rep4

description:
251486834806_1_4
Gene expression of oviduct from WT at day 2 of pregnancy (1.5 dpc)

source_name: Oviduct from WT at day 2 of pregnancy (1.5 dpc)

value: WT control littermate

value: Wnt7aCre-:Esr1fl/fl, Wnt7aCre+:Esr1+/+, Wnt7aCre-, Esr1+/+


title: cKO_Day1_rep2

description:
251486834805_1_2
Gene expression of oviduct from cKO at day 1 of pregnancy (0.5 dpc)


title: WT_Day2_rep3

description:
251486834806_1_3
Gene expression of oviduct from WT at day 2 of pregnancy (1.5 dpc)


title: cKO_Day2_rep3

description:
251486834674_1_3
Gene expression of oviduct from cKO at day 2 of pregnancy (1.5 dpc)


title: cKO_Day2_rep2

description:
251486834674_1_2
Gene expression of oviduct from cKO at day 2 of pregnancy (1.5 dpc)


title: cKO_Day2_rep4

description:
251486834674_1_4
Gene expression of oviduct from cKO at day 2 of pregnancy (1.5 dpc)


title: cKO_Day1_rep3

description:
251486834805_1_3
Gene expression of oviduct from cKO at day 1 of pregnancy (0.5 dpc)


title: WT_Day1_rep1

description:
251486834803_1_1
Gene expression of oviduct from WT at day 1 of pregnancy (0.5 dpc)

source_name: Oviduct from WT at day 1 of pregnancy (0.5 dpc)


title: WT_Day2_rep2

description:
251486834806_1_2
Gene expression of oviduct from WT at day 2 of pregnancy (1.5 dpc)


title: mirPCL.013

source_name: Plasma cell leukemia patient 013

tag: cell type


title: WT_Day1_rep3

description:
251486834803_1_3
Gene expression of oviduct from WT at day 1 of pregnancy (0.5 dpc)

tag: tissue


title: WT_Day1_rep2

description:
251486834803_1_2
Gene expression of oviduct from WT at day 1 of pregnancy (0.5 dpc)


title: cKO_Day1_rep4

description:
251486834805_1_4
Gene expression of oviduct from cKO at day 1 of pregnancy (0.5 dpc)


title: WT_Day2_rep1

description:
251486834806_1_1
Gene expression of oviduct from WT at day 2 of pregnancy (1.5 dpc)


title: 5594-5

city: Raleigh

first: Callie

middle: Virginia

last: Barnwell

address: North Carolina State University

department: Animal Science

institute: North Carolina State University

hyb_protocol: Following fragmentation, the aRNA was prepared for hybridization according to the GeneChip 3' IVT Express Kit User Manual. The arrays were washed with the Affymetrix Fluidics Station 450 wash stations.

scan_protocol: The arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G Plus with Autoloader.

data_processing: The data were analyzed using Affymetrix Expression Console software, using the Robust Multi-array Average algorithm.

organism: Bos taurus

source_name: Day 15 bovine conceptus, Grade 1, short length

label_protocol: Biotin-labeled aRNA was prepared according to the standard Affymetrix protocol from 250ng of total RNA

growth_protocol: Synchronized and superovulated donor Holstein cows were artificially inseminated using frozen semen from a single Holstein bull. Embryos were recovered by non-surgical uterine lavage from donor cows at Day 6.5 of gestation and evaluated for stage of development and morphological grade. Embryos were grouped by grade and transferred to recipient Holstein heifers in groups of 2-6 embryos per recipient based. Conceptuses were then non-surgically flushed from the recipients at Day 15 of gestation.

extract_protocol: Total RNA was isolated according to manufacturer's instructions

treatment_protocol: Bovine conceptuses were identified/separated by embryo grade at transfer, then measured for length and width, and snap frozen at -80C.

tag: strain

value: Holstein

tag: grade

value: Grade 1

tag: length

value: Short

value: Female


title: 5613-2


title: 5610-3

source_name: Day 15 bovine conceptus, Grade 1, long length

value: Long


title: 5594-3


title: WT_Day1_rep4

description:
251486834803_1_4
Gene expression of oviduct from WT at day 1 of pregnancy (0.5 dpc)

tag: age


title: 5604-2

source_name: Day 15 bovine conceptus, Grade 3

value: Grade 3

value: Male


title: 5610-4


title: 5575-15


title: 5588-7


title: 5604-1


title: 5575-16


title: 5594-2


title: 5575-13

source_name: Day 15 bovine conceptus, Grade 1


title: MSC co-cultured in transwell with activated T cells,  biological repetition 2

city: Genoa

first: Tiziana

last: Vigo

address: Largo Daneo

institute: University of Genoa

description: Gene expression data from MSC exposed to activated Tcell

hyb_protocol: Following fragmentation cRNA were hybridized for 16 hr at 45C on Gene Chip Mouse Genome 430 2.0 array

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

data_processing: Data was normalized using RMA and filtered to keep genes showing at least 1.5-fold difference from the median in at least 20% of the samples

source_name: MSC-Trans-II

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

growth_protocol: Mouse bone marrow derived MSC purified and cultured in vitro in Mesencult medium (Zappia et al., 2005)

treatment_protocol: MSC cultured for 48 hrs in a transwell system (Corning) with purified T cells activated in vitro with anti CD3/CD28. MSC:Tcell ratio 1:10

value: bone marrow

value: primary culture of mouse bone marrow MSC


title: MSC, biological repetition 1

description: Gene expression data from MSC

source_name: MSC-I


title: MSC,  biological repetition 2

description: Gene expression data from MSC

source_name: MSC-II


title: MSC,  biological repetition 3

description: Gene expression data from MSC

source_name: MSC-III


title: 5575-14


title: WT1M2, biological replicate 1

city: Columbus

first: Mireia

last: Guerau

state: OH

address: 453 W 10th Ave

department: HRS-Medical Laboratory Science

institute: The Ohio State University

description: Sample Expr WT1M2

hyb_protocol: Samples were hybridized to Affymetric 430_2 array using Herring sperm DNA, acetlylated BSA (50 mg/ml) and, Bioarray Eukaryotic Hybridization controls (Enzo Life Sciences), heated 650C 5 minutes, 990C 5 minutes, 450C 5 minutes, centrifuge top speed for 5 minutes, hybridize 16 hours at 450C at 60 rpm; Fluidics script EukGE-WS2v4_450

scan_protocol: Affymetrix Gene ChIP scanner 30007G using Command Console

data_processing: Raw data were normalized with the RMA algorithm implemented in the ‘‘Expression File Creator’’ module from the GenePattern software package. Data were visualized with the Multiplot modules from GenePattern.

source_name: Bone Marrow Derived Macrophages

label_protocol: Samples were enzymatically labeled using BioArray HighYield RNA Transcript Labeling kit (Enzo)

growth_protocol: To generate BMDM, the bone marrow cells from femurs and tibias from mice were harvested and cultured. Briefly, isolated cells were incubated in Dulbecco’s Modified Eagle Media (DMEM, Mediatech, Herndon, VA) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Life Technologies, Grand Island, NY)), 1% penicillin/streptomycin, 1% glutamine, and 20% L929 cell supernatant (containing macrophage colony stimulating factor).

extract_protocol: To examine mRNA expression, cells were isolated using the miRVana isolation kit (Life Technologies) according to manufacturer specifications.

treatment_protocol: On day 7 in culture the cells were washed, counted and replated in DMEM media (without L929 supernatant) at a density of 6-8^6 cells/well (6-well plate, Falcon polystyrene). Cells were classically activated (M1 condition) with LPS (100 ng/ml, Sigma-Aldrich) + IFN-γ (20ng/mL, E-bioscience, San Diego, CA) or alternatively activated (M2 condition) with IL-4 (20ng/mL, E-bioscience) or received media alone (M0 condition). Cells were harvested at 24 hours post-stimulation, by washing in phosphate buffered saline (PBS) before cell lysis in miRVana Lysis buffer (Life Technologies) for total RNA isolation.

value: BMDM

tag: treatment


title: WT2M2, biological replicate 2

description: Sample Expr WT2M2

value: alternatively activated (M2 condition) with IL-4


title: WT2M1, biological replicate 2

description: Sample Expr WT2M1

value: classically activated (M1 condition) with LPS + IFN-gamma


title: WT1M1, biological replicate 1

description: Sample Expr WT1M1


title: WT3M1, biological replicate 3

description: Sample Expr WT3M1


title: WT3M0, biological replicate 3

description: Sample Expr WT3M0

value: received media alone (M0 condition)


title: WT2M0, biological replicate 2

description: Sample Expr WT2M0


title: WT1M0, biological replicate 1

description: Sample Expr WT1M0


title: P84, MC, HC, biological rep3

city: Shinagawa-ku

first: KATSUHIDE

last: IGARASHI

state: Tokyo

department: Life Science Tokyo Advanced Research center (L-StaR)

institute: Hoshi University School of Pharmacy and Pharmaceutical Science

hyb_protocol: For hybridization to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix), 15 µg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 1x eukaryotic hybridization control, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, and 1x hybridization buffer in a 45°C rotisserie oven for 16 h. Washing and staining were performed by using a GeneChip Fluidic Station (Affymetrix) according to the manufacturer's protocol (Fluidics Protocol: EuKGE-WS2v4).

scan_protocol: Phycoerythrin-stained arrays were scanned as digital image files with GeneChip Scanner 3000 7G with AutoLoader.

data_processing:
Data transformation algorithm and normalization was done by Affymetrix GCOS.
Scaling: All Probe Sets, Target Signal=500
Normalization value: 1
Parameters: default settings

source_name: MC administered mouse brain hippocampus at P84

label_protocol: Total RNA was purified by using an RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. First-strand cDNA was synthesized from 5 µg of RNA by using 200 units of SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), 100 pmol T7- (dT)24 primer [5'-GGCCAGTGA AT TGTA ATACGACTCACTATAGGGAGGCGG- (dT)24-3'], 1x first-strand buffer, and 0.5 mM dNTPs at 42°C for 1 h. Second-strand synthesis was performed by incubating first-strand cDNA with 10 units of Escherichia coli ligase (Invitrogen), 40 units of DNA polymerase I (Invitrogen), 2 units of RNase H (Invitrogen), 1x reaction buffer, and 0.2 mM dNTPs at 16°C for 2 h, followed by 10 units of T4 DNA polymerase (Invitrogen) and incubation for another 5 min at 16°C. Double-stranded cDNA was purified by using the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions and labeled by in vitro transcription by using a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY). Briefly, dsDNA was mixed with 1x HY reaction buffer, 1x biotin-labeled ribonucleotides (NTPs with Bio-UTP and BioCTP), 1x DTT, 1x RNase inhibitor mix, and 1x T7 RNA polymerase and incubated at 37°C for 4 h. Labeled cRNA was then purified by using the GeneChip Sample Cleanup Module and fragmented in 1x fragmentation buffer at 94°C for 35 min.

growth_protocol: Pregnant C57BL/6 mice were individually housed in plastic breeding cages with free access to water and pellet diet in a 12 h light-dark cycle. At three consecutive embryonic days (E) 12.5, E13.5, and E14.5, all mice received an oral administration of the chemicals and were reared in the same condition until being sacrificed for sample preparation. For the analysis of voluntary running effect, the running wheel was put in the cages after mice were weaned.

extract_protocol: Brain samples were prepared from E14.5 (3 h after oral treatment), E18.5, and 12-week-old mice of the MC, VPA, and VPM groups. Samples were homogenized and lysed in 500 ul of RLT buffer (QIAGEN, Valencia, CA), and total RNA was extracted according to the manufacturer's instructions using the RNeasy Kit (QIAGEN) for GeneChip analysis.

treatment_protocol: Three groups were designated as valproic acid (VPA), valpromide (VPM) and methylcellulose (MC) on gestation period. The VPA and VPM groups received an oral administration of 300 mg/kg VPA (Sigma) and VPM (Wako), respectively, once a day on three consecutive embryonic days (E) 12.5, E13.5, and E14.5. The MC group received an oral administration of identical volumes of 0.5% (w/v) MC (Wako) once a day on the same days.

value: male

value: hippocampus

value: methylcellulose


title: 4_LS_Week_0

city: New York

first: Mayte

last: Suarez-Farinas

address: One Gustave L. Levy Place, Box 1077

department: Population Health Science and Policy

institute: Icahn School of Medicine at Mount Sinai

description: 7_HGU133 plus 2.0_Susan_04242015_(HG-U133_Plus_2).CEL

hyb_protocol: RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: Data was preprocessed using GCRMA package (version 2.40.0) in R (version 3.2.1) and Bioconductor (version 3.1)

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion

tag: subject status

value: Alopecia areata (AA) patient

tag: subject id

tag: age (yrs)

tag: area/tissue

value: Scalp

tag: tissue type

value: lesional

tag: time point

value: Pre-treatment; baseline


title: Adult (12-13w old), VPA, CX (Cortex), biological rep3

description:
AdRW-VPA-CX-3
Mouse without behavioral test.

source_name: VPA administered mouse brain cortex at 12-13w old

value: 12-13 weeks

value: cortex

value: valproic acid


title: P84, VPA, HC, biological rep2

source_name: VPA administered mouse brain hippocampus at P84


title: P84, VPA, HC, biological rep3


title: 4_LS_Week_20

description: 8_HGU133 plus 2.0_Susan_04242015_(HG-U133_Plus_2).CEL

value: Post-treatment with 90 mg ustekinumab treatment


title: P84, MC, HC, biological rep1


title: 7_Normal_Week_0

description: 11_HGU133 plus 2.0_Susan_04242015_(HG-U133_Plus_2).CEL

value: healthy individual

value: Normal


title: P84, MC, HC, biological rep2


title: P84, MC, HC, biological rep4


title: 4_NL_Week_0

description: 6_HGU133 plus 2.0_Susan_04242015_(HG-U133_Plus_2).CEL

value: non-lesional


title: 5_Normal_Week_0

description: 9_HGU133 plus 2.0_Susan_04242015_(HG-U133_Plus_2).CEL


title: 3_LS_Week_20

description: 5_HGU133 plus 2.0_Susan_04242015_(HG-U133_Plus_2).CEL

value: female


title: 6_Normal_Week_0

description: 10_HGU133 plus 2.0_Susan_04242015_(HG-U133_Plus_2).CEL


title: Adult (12-13w old), VPA+RW (running wheel), CX (Cortex), biological rep3

description:
AdRW-VPARW-CX-3
Mouse without behavioral test.

source_name: VPA administered + RW mouse brain cortex at 12-13w old

value: valproic acid + running wheel


title: P84, VPA, HC, biological rep4


title: Adult (12-13w old), VPA+RW (running wheel), CX (Cortex), biological rep2

description:
AdRW-VPARW-CX-2
Mouse without behavioral test.


title: Adult (12-13w old), VPA+RW (running wheel), CX (Cortex), biological rep1

description:
AdRW-VPARW-CX-1
Mouse without behavioral test.


title: Adult (12-13w old), MC+RW (running wheel), CX (Cortex), biological rep3

description:
AdRW-MCRW-CX-3
Mouse without behavioral test.

source_name: MC administered + RW mouse brain cortex at 12-13w old

value: methylcellulose + running wheel


title: 3_NL_Week_0

description: 3_HGU133 plus 2.0_Susan_04242015_(HG-U133_Plus_2).CEL


title: 1_LS_Week_20

description: 2_HGU133 plus 2.0_Susan_04242015_(HG-U133_Plus_2).CEL

value: male


title: P84, VPA, HC, biological rep1

value: hippocampus


title: 3_LS_Week_0

description: 4_HGU133 plus 2.0_Susan_04242015_(HG-U133_Plus_2).CEL


title: Adult (12-13w old), VPA, CX (Cortex), biological rep2

description:
AdRW-VPA-CX-2
Mouse without behavioral test.


title: Adult (12-13w old), MC+RW (running wheel), CX (Cortex), biological rep2

description:
AdRW-MCRW-CX-2
Mouse without behavioral test.


title: 1_LS_Week_0

description: 1_HGU133 plus 2.0_Susan_04242015_(HG-U133_Plus_2).CEL


title: Adult (12-13w old), VPA, CX (Cortex), biological rep1

description:
AdRW-VPA-CX-1
Mouse without behavioral test.


title: Adult (12-13w old), VPA+RW (running wheel), HC (Hippocampus), biological rep3

description:
AdRW-VPARW-HC-3
Mouse without behavioral test.

source_name: VPA administered + RW mouse brain hippocampus at 12-13w old


title: Adult (12-13w old), MC, CX (Cortex), biological rep1

description:
AdRW-MC-CX-1
Mouse without behavioral test.

source_name: MC administered mouse brain cortex at 12-13w old

value: methylcellulose