title: hiPSCCM_CVB3_IFNB1_Rep1

city: Stanford

first: Jared

last: Churko

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford

description: Interferon beta-treated, CVB3-infected hiPSC-CMs (sample 1)

hyb_protocol: Performed at the Pan facility @ http://cmgm.stanford.edu

data_processing:
Data were processed using Affymetrix expression console
HuGene-2_0-st.pgf
HuGene-2_0-st.mps

source_name: hiPSC-CMs

growth_protocol: hiPSC-CMs after 30 days of differentiation (see Lian et al 2012) were purified and replated into 96 wells at a density of 40,000 cells per well.

extract_protocol: All samples were harvested in Trizol. RNA was extracted with the miRNeasy kit (Qiagen). cDNA was synthesized using a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, CA)

treatment_protocol: Two treatment groups were established: 1 receiving interferon beta and 1 untreated control group. Interferon-treatment group received 8ng/mL interferon beta 1 treatment for 12 hours prior to coxsackievirus B3 infection. Both groups were infected with CVB3 at MOI 5. Cells were harvested at 8 hours after infection.

value: hiPSC-CMs (human induced pluripotent stem cell-derived cardiomyocytes)

tag: infection

value: coxsackievirus CVB3

value: 8 ng/mL interferon beta 1, 12 hour pretreatment


title: MSC alone_21% Oxygen_s2

status: Public on May 19 2014

type: RNA

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

country: USA

institute: MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MSC alone_21% Oxygen

label_protocol: 200 ng total RNA was amplified and biotin-labeled through a Eberwine procedure using Illumina TotalPrep RNA Amplification kits (Ambion).

growth_protocol: BM-MSC isolated from BM of healthy donors, expanded with pooled human platelet lysate and cryopreserved, were thawed and plated for triplicate cultures in RPMI with 10% FBS at 37°C in 5% CO2/air. After 24 hours, medium was replaced with RPMI/FBS alone, for BM-MSC alone, or with RPMI/FBS containing pre-B REH cells for REH/BM-MSC co-cultures, at an REH/BM-MSC ratio of ~2. In parallel, monocultures of REH cells and BM-MSC were similarly prepared and seeded at the same density as co-cultures.

extract_protocol: Total RNA was isolated by using TRIzol reagent (life Technologies), then further purified using the RNeasy plus Mini kit (Qiagen).

treatment_protocol: All cultures were maintained for 48 hours. To harvest co-cultured cells for analysis, medium and nonattached REH cells were removed and discarded, and attached REH cells and BM-MSC were mobilized with EDTA and collected. Monocultured BM-MSC were similarly harvested, and all cells from REH monocultures were collected. All cell suspensions were stained with anti-human CD90 (Thy-1) antibody as the BM-MSC marker, and anti-human CD45 antibody as the REH cell marker, and then separated with a FACSAria II flow cytometer. Sorted cells were pelleted and lysed with QIAzol lysis reagent for total RNA extraction.

tag: tissue source

value: BM of healthy donors

tag: cell type

value: Human bone marrow mesenchymal stromal cells (BM-MSCs)

tag: culture type

value: cultured alone (monoculture)


title: hiPSCCM_CVB3_Rep2

state: CA

description: CVB3-infected hiPSC-CMs (sample 2)

scan_protocol: Performed at the Pan facility @ http://cmgm.stanford.edu

tag: treatment

value: Untreated


title: MSC coculture_21% Oxygen_s1

source_name: MSC coculture_21% Oxygen

value: co-cultured with the pre-B ALL REH cells


title: D2947_Saliva_Affected_rep1

type: genomic

city: Montreal

first: Philippe

last: Lemay

state: Quebec

address: 3175 Chemin de la Côte-Sainte-Catherine

country: Canada

institute: Université de Montréal

description:
Genotyping batch2
raw data file: Batch2_RAW.txt

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a iScan Autoloader 2X (Illumina).

data_processing: Genomic DNA extracted from saliva was genotyped using Infinium CanineHD Genotyping BeadChips (Illumina).

label: Cy3 and Cy5

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: saliva (mouth swap)_affected

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-MA1, WG-MA2) and primer/neutralization mix (WG-MSM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: DNA was extracted from blood or saliva using the ORAGENE Animal kit (DNAgenotek)

tag: breed

value: Griffon Bruxellois

tag: Sex

value: Male

tag: age

tag: diameter f

tag: line ab

tag: angle 1 (abc)

tag: line bc

tag: line cd

tag: line bd

tag: line be

tag: line ae

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)

tag: line fg


title: IMR32, CDK2 shRNA, t=72, rep3

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description: Neuroblastoma were transfected with CDK2 shRNA.

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.

data_processing: Expression data (CEL files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

source_name: IMR32, CDK2 shRNA, time 72

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

treatment_protocol: The IMR32 clone capable of inducible CDK2 shRNA expression was generated in a step-wise process. First, IMR32 cells were transfected with the pcDNA6/TR vector (Invitrogen) encoding the tetracycline/doxycycline repressor behind a constitutive CMV promoter, using Lipofectamine 2000®. Clones were selected using 5µg/ml Blasticidin-S (Invitrogen), resulting in the isolation of IMR32-pcDNA6. The CDK2 shRNA expression constructs were prepared as follows: Oligonucleotides targeting CDK2 on nucleotide 546-566 in NM_001798.2 (GenBank) were annealed and ligated into pTER restricted with BglII and HindIII as described [34,35], creating pTER/CDK2. This construct was used for transfection of IMR32-pcDNA6 using Lipofectamin 2000®. Clones were again selected using 5µg/ml Blasticidin-S and 10µg/ml Zeocine resulting in the isolation of IMR32-pcDNA6-CDK2sh. For induction of the shRNA expression vector, doxycycline was added to the culture medium to a concentration of 100ng/ml.

tag: cell line

tag: cell type

value: neuroblastoma

tag: cdk2 shrna expression

value: inducible


title: D2936_Saliva_Affected_rep1

tag: breed

tag: Sex

value: Female

tag: age

tag: diameter f


title: hiPSCCM_CVB3_Rep1

description: CVB3-infected hiPSC-CMs (sample 1)

label_protocol: Performed at the Pan facility @ http://cmgm.stanford.edu

tag: infection

tag: treatment


title: D2932_Saliva_Affected_rep1

tag: line ab

tag: angle 1 (abc)

tag: line bc

tag: line cd

tag: line bd

tag: line be


title: D2941_Saliva_Affected_rep1

tag: line ae

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: D2935_Saliva_Affected_rep1

tag: breed

tag: Sex

tag: line fg


title: D2928_Saliva_Affected_rep1

tag: age

tag: diameter f


title: D2927_Saliva_Affected_rep1

tag: line ab


title: IMR32, CDK2 shRNA, t=0, rep3

source_name: IMR32, CDK2 shRNA, time 0

tag: cell line

tag: cell type

tag: cdk2 shrna expression


title: IMR32, CDK2 shRNA, t=8, rep3

source_name: IMR32, CDK2 shRNA, time 8


title: IMR32, CDK2 shRNA, t=48, rep3

source_name: IMR32, CDK2 shRNA, time 48


title: D2924_Saliva_Affected_rep1

tag: angle 1 (abc)

tag: line bc

tag: line cd

tag: line bd


title: D2923_Saliva_Affected_rep1

tag: line be

tag: line ae

tag: angle 2(caf)

tag: angle 3 (dla)


title: D3050_Saliva_Unaffected_rep1

source_name: saliva (mouth swap)_unaffected (control)

tag: breed

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: T250_12h_control_rep3

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

description:
T250_12h_-N_3
T250 roots sampled at 12h after KCl treatment. It is the third of 12h T250 control biological replicates used in this experiment.

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Zea mays

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: Maize (Zea mays L.) seeds of two inbred lines (T250 e Lo5), previously soaked in running water for 24 h, were allowed to germinate in the dark at 28°C for 72 h over an aerated solution of 0.5 mM CaSO4. Seedlings with roots were transferred to plastic pots containing 2.2 L of 0.5 mM CaSO4 solution (12 seedlings in each pot) and were grown for 48 h under 200 μmol m-2 s-1 PPF with a 14h/10h day/night regime (27/20°C day/night temperature cycling; 80% relative humidity).

extract_protocol: Total RNA was isolated using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich).

treatment_protocol:
Seedlings were then transferred to a nutrient solution (NS) containing 100 μM MgSO4, 200 μM K2SO4, 400 μM CaSO4, 175 μM KH2PO4, 25 μM NH4H2PO4, 0.05 μM NaMoO4, 2.5 μM H3BO3, 0.2 μM MnSO4, 0.2 μM ZnSO4, 0.05 μM CuSO4 and 2 μM Fe-EDTA.
For N treated samples (+NO3-) NS contained 200 μM of KNO3 while for control samples (-NO3-) contained an appropriate amounts of the corresponding chloride salt (KCl) to keep K+concentration balanced.

tag: inbred line

tag: tissue

value: root (2d-old seedlings)

tag: treated with

value: chloride salt (KCl) for 12h (control, -NO3-)


title: IMR32, CDK2 shRNA, t=72, rep2

tag: cell line

tag: cell type


title: IMR32, CDK2 shRNA, t=24, rep3

source_name: IMR32, CDK2 shRNA, time 24

tag: cdk2 shrna expression


title: hiPSCCM_CVB3_IFNB1_Rep2

description: Interferon beta-treated, CVB3-infected hiPSC-CMs (sample 2)

tag: infection

tag: treatment


title: T250_12h_N treated_rep3

description:
T250_12h_+N_3
T250 roots sampled at 12h after KNO3 treatment. It is the third of 12h T250 N treated biological replicates used in this experiment.

source_name: T250_12h_N treated

value: 200 μM of KNO3 for 12h (+NO3-)


title: T250_12h_control_rep1

description:
T250_12h_-N_1
T250 roots sampled at 12h after KCl treatment. It is the first of 12h T250 control biological replicates used in this experiment.


title: D2922_Saliva_Affected_rep1

tag: Sex

tag: age

tag: diameter f

tag: line ab

tag: angle 1 (abc)

tag: line bc

tag: line cd

tag: line bd

tag: line fg


title: T250_12h_N treated_rep2

description:
T250_12h_+N_2
T250 roots sampled at 12h after KNO3 treatment. It is the second of 12h T250 N treated biological replicates used in this experiment.

tag: inbred line


title: IMR32, CDK2 shRNA, t=24, rep2


title: IMR32, CDK2 shRNA, t=48, rep1


title: IMR32, CDK2 shRNA, t=48, rep2


title: T250_12h_N treated_rep1

description:
T250_12h_+N_1
T250 roots sampled at 12h after KNO3 treatment. It is the first of 12h T250 N treated biological replicates used in this experiment.

tag: tissue


title: T250_11h_control_rep3

description:
T250_11h_-N_3
T250 roots sampled at 11h after KCl treatment. It is the third of 11h T250 control biological replicates used in this experiment.

tag: treated with

value: chloride salt (KCl) for 11h (control, -NO3-)


title: IMR32, CDK2 shRNA, t=8, rep2

tag: cell line


title: IMR32, CDK2 shRNA, t=0, rep2

tag: cell type


title: T250_12h_control_rep2

description:
T250_12h_-N_2
T250 roots sampled at 12h after KCl treatment. It is the second of 12h T250 control biological replicates used in this experiment.


title: IMR32, CDK2 shRNA, t=72, rep1

tag: cdk2 shrna expression


title: T250_11h_control_rep2

description:
T250_11h_-N_2
T250 roots sampled at 11h after KCl treatment. It is the second of 11h T250 control biological replicates used in this experiment.


title: D2919_Saliva_Affected_rep1

tag: breed

tag: line be

tag: line ae

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: T250_11h_control_rep1

description:
T250_11h_-N_1
T250 roots sampled at 11h after KCl treatment. It is the first of 11h T250 control biological replicates used in this experiment.


title: D2911_Saliva_Unaffected_rep1

tag: Sex

tag: age

tag: diameter f

tag: line ab

tag: angle 1 (abc)

tag: line bc

tag: line cd


title: D2807_Saliva_Affected_rep1

tag: line bd

tag: line fg


title: D2921_Saliva_Affected_rep1

tag: breed


title: D2806_Saliva_Affected_rep1

tag: line be


title: IMR32, CDK2 shRNA, t=8, rep1

tag: cell line

tag: cell type

tag: cdk2 shrna expression


title: T250_11h_N treated_rep2

description:
T250_11h_+N_2
T250 roots sampled at 11h after KNO3 treatment. It is the second of 11h T250 N treated biological replicates used in this experiment.

source_name: T250_11h_N treated

tag: inbred line

tag: tissue

tag: treated with

value: 200 μM of KNO3 for 11h (+NO3-)


title: T250_11h_N treated_rep1

description:
T250_11h_+N_1
T250 roots sampled at 11h after KNO3 treatment. It is the first of 11h T250 N treated biological replicates used in this experiment.


title: IMR32, CDK2 shRNA, t=0, rep1


title: T250_5h_control_rep3

description:
T250_5h_-N_3
T250 roots sampled at 5h after KCl treatment. It is the third of 5h T250 control biological replicates used in this experiment.

value: chloride salt (KCl) for 5h (control, -NO3-)


title: D2809_Saliva_Affected_rep1

tag: Sex

tag: line ae

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: D2856_Saliva_Affected_rep1

tag: age

tag: diameter f

tag: line ab

tag: angle 1 (abc)

tag: line bc

tag: line cd

tag: line bd


title: Patient 6_H_FAT_Fast

first: Mahmoud

middle: Ali

last: Mohammad

state: Texas

address: 1100 Bates St.

department: Pediatrics-Nutrition

institute: Baylor College of Medicine

description: Patient 6_ 36h post delivery

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using  Cubic Spline normalisation and substracted for background with  GenomeStudio version 1.9.0, Illumina Inc.

label: Biotin-labeled & Cy3 stained

source_name: Milk Fat Globule

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

extract_protocol: Total RNA was extracted with Trizol reagent according to manufacturer specifications. Total RNA concentration was measured using NanoDrop spectrophotometer. Quality control was performed using the Experion RNA StdSens Analysis Kit, Bio-Rad Laboratories.concentration was measured using NanoDrop spectrophotometer (NanoDrop Technologies,   Wilmington, DE). RNA quality was assessed using the ExperionTMRNA StdSens Analysis Kit (Bio-Rad Laboratories, Hercules, CA).

tag: gener

tag: bmi

value: Lean

tag: condition

value: Fast

tag: diet

value: high fat


title: Patient 7_H_FAT_Fast

description: Patient 7_ 36h post delivery


title: D2810_Saliva_Affected_rep1

tag: breed

tag: Sex

tag: line be

tag: line ae

tag: line fg


title: T250_5h_control_rep1

description:
T250_5h_-N_1
T250 roots sampled at 5h after KCl treatment. It is the first of 5h T250 control biological replicates used in this experiment.

tag: inbred line

tag: tissue

tag: treated with


title: D2910_Saliva_Affected_rep1

tag: age

tag: diameter f

tag: line ab

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: T250_5h_N treated_rep3

description:
T250_5h_+N_3
T250 roots sampled at 5h after KNO3 treatment. It is the third of 5h T250 N treated biological replicates used in this experiment.

source_name: T250_5h_N treated

value: 200 μM of KNO3 for 5h (+NO3-)


title: Patient 5_H_FAT_Fast

description: Patient 5_ 36h post delivery

tag: gener

tag: bmi

tag: condition

tag: diet


title: Patient 4_H_FAT_Fast

description: Patient 4_ 36h post delivery


title: IMR32, CDK2 shRNA, t=24, rep1

tag: cell line

tag: cell type

tag: cdk2 shrna expression


title: D2808_Saliva_Affected_rep1

description:
Genotyping batch2
raw data file: Batch2_RAW.txt

tag: breed

tag: Sex

tag: angle 1 (abc)

tag: line bc

tag: line cd

tag: line bd

tag: line be

tag: line ae

tag: line fg


title: Patient 3_H_FAT_Fast

description: Patient 3_ 36h post delivery


title: T250_5h_control_rep2

description:
T250_5h_-N_2
T250 roots sampled at 5h after KCl treatment. It is the second of 5h T250 control biological replicates used in this experiment.

tag: inbred line

tag: tissue

tag: treated with


title: Chironomus riparius whole genome

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

hyb_protocol: The 1 M probe-selection microarray was subsequently hybridized with 10 µg of Cy3 labelled C. riparius gDNA and 10 µg Cy5 labelled A. gambiae gDNA according to the Oligonucleotide Array-Based CGH for Genomic DNA Analysis manual (Agilent Technologies version 6.3).

scan_protocol: The microarray was scanned in an ozone-free room on an Agilent G2505CA scanner at 3 µm resolution and the data was extracted with Feature Extraction version 10.7.3.1 (Protocol CGH_107_Sep09).

data_processing: The log2 transformed median signals were analysed in R.

organism: Chironomus riparius

source_name: C. riparius gDNA

label_protocol: 200 ng DNA was amplified and labelled by strand displacement amplification. Concentrations of amplified products were measured on the NanoDrop ND-1000 and qualified on the BioAnalyzer with the DNA 1000 Kit (Agilent Technologies). Yield and CyDye incorporation of the final labelled products were measured with the NanoDrop ND-1000 in the Microarray Measurement Mode.

growth_protocol: The Chironomus riparius specimens originated from the University of Amsterdam’s in-house laboratory culture and were maintained on artificial sediment at 20±1°C, 65% humidity and a 16:8 h light: dark photoperiod. The genetic fidelity of this C. riparius laboratory culture was previously confirmed by mitochondrial cytochrome oxidase I (COI) gene sequencing. Each sample was immediately snap frozen in liquid nitrogen and stored at –80°C until processing.

extract_protocol: gDNA was extracted from 30 pooled fertilized C. riparius egg ropes, respectively, 30 pooled unfed A. gambiae adults. To keep contamination of the C. riparius gDNA sample to an absolute minimum the midges were allowed to deposit the egg ropes in petri dishes filled with clean water. Egg ropes not older than 30 minutes were collected, stringently rinsed with clean water and immediately flash frozen in liquid nitrogen. After pooling, gDNA was extracted using a CTAB DNA extraction method that included a RNAse A (Sigma-Aldrich) digestion step for removal of residual RNA. gDNA quality and quantity were determined with gel electrophoresis (0.5% agarose in TAE buffer) and NanoDrop ND-1000 measurements.

tag: genome

value: C. riparius


title: Anopheles gambiae whole genome

organism: Anopheles gambiae

source_name: A. gambiae gDNA

value: A. gambiae


title: T250_5h_N treated_rep2

description:
T250_5h_+N_2
T250 roots sampled at 5h after KNO3 treatment. It is the second of 5h T250 N treated biological replicates used in this experiment.


title: T250_5h_N treated_rep1

description:
T250_5h_+N_1
T250 roots sampled at 5h after KNO3 treatment. It is the first of 5h T250 N treated biological replicates used in this experiment.


title: D2805_Saliva_Affected_rep1

value: Griffon Bruxellois

tag: age

tag: diameter f

tag: line ab

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: D2801_Saliva_Affected_rep1

tag: breed

tag: Sex

tag: angle 1 (abc)

tag: line bc

tag: line cd


title: Patient 7_H_FAT_Fed

description: Patient 7_ 24h post delivery

tag: gener

tag: bmi

tag: condition

value: Fed

tag: diet


title: T250_0h_rep2

description:
T250_0h_2
T250 roots sampled at 0h. It is the second of T250 0h biological replicates used in this experiment.

tag: inbred line

tag: tissue

tag: treated with

value: none (0h sample)


title: Patient 1_H_FAT_Fast

description: Patient 1_ 36h post delivery


title: T250_0h_rep3

description:
T250_0h_3
T250 roots sampled at 0h. It is the third of T250 0h biological replicates used in this experiment.


title: Patient 2_H_FAT_Fast

description: Patient 2_ 36h post delivery


title: Patient 5_H_FAT_Fed

description: Patient 5_ 24h post delivery


title: Patient 6_H_FAT_Fed

description: Patient 6_ 24h post delivery


title: Patient 4_H_FAT_Fed

description: Patient 4_ 24h post delivery


title: D2775_Saliva_Affected_rep1

tag: age

tag: diameter f

tag: line ab

tag: line bd

tag: line be

tag: line ae

tag: angle 2(caf)

tag: line fg


title: D2803_Saliva_Affected_rep1

tag: breed

tag: Sex

tag: angle 1 (abc)

tag: line bc

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: D2777_Saliva_Affected_rep1

value: Male

tag: line cd


title: Lo5_4h_control_rep3

description:
Lo5_4h_-N_3
Lo5 roots sampled at 4h after KCl treatment. It is the third of 4h Lo5 control biological replicates used in this experiment.

tag: inbred line

tag: tissue

tag: treated with

value: chloride salt (KCl) for 4h (control, -NO3-)


title: T250_11h_N treated_rep3

description:
T250_11h_+N_3
T250 roots sampled at 11h after KNO3 treatment. It is the third of 11h T250 N treated biological replicates used in this experiment.

value: root (2d-old seedlings)


title: D2754_Saliva_Affected_rep1

value: Female

tag: age

tag: diameter f

tag: line ab

tag: line bd


title: Lo5_4h_control_rep2

description:
Lo5_4h_-N_2
Lo5 roots sampled at 4h after KCl treatment. It is the second of 4h Lo5 control biological replicates used in this experiment.


title: Lo5_4h_control_rep1

description:
Lo5_4h_-N_1
Lo5 roots sampled at 4h after KCl treatment. It is the first of 4h Lo5 control biological replicates used in this experiment.


title: Patient 2_H_FAT_Fed

description: Patient 2_ 24h post delivery

tag: gener

tag: bmi

tag: condition

tag: diet


title: Patient 3_H_FAT_Fed

description: Patient 3_ 24h post delivery


title: Lo5_4h_N treated_rep3

description:
Lo5_4h_+N_3
Lo5 roots sampled at 4h after KNO3 treatment. It is the third of 4h Lo5 N treated biological replicates used in this experiment.

source_name: Lo5_4h_N treated

value: 200 μM of KNO3 for 4h (+NO3-)


title: T250_0h_rep1

description:
T250_0h_1
T250 roots sampled at 0h. It is the first of T250 0h biological replicates used in this experiment.


title: D2753_Saliva_Affected_rep1

tag: breed

tag: Sex

tag: angle 1 (abc)

tag: line bc

tag: line be

tag: line ae

tag: angle 2(caf)

tag: line fg


title: Patient 1_H_FAT_Fed

description: Patient 1_ 24h post delivery


title: D2804_Saliva_Affected_rep1

tag: line cd

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: Patient 6_H_CHO_Fast

description: Patient 6_ 12h post delivery

tag: gener

value: high carbohydrate


title: Patient 7_H_CHO_Fast

description: Patient 7_ 12h post delivery

tag: bmi


title: D2752_Saliva_Affected_rep1

tag: age

tag: diameter f

tag: line ab

tag: line bd


title: Patient 5_H_CHO_Fast

description: Patient 5_ 12h post delivery

tag: condition

tag: diet


title: D2662_Saliva_Affected_rep1

tag: breed

tag: Sex

tag: angle 1 (abc)

tag: line bc

tag: line be


title: Lo5_4h_N treated_rep1

description:
Lo5_4h_+N_1
Lo5 roots sampled at 4h after KNO3 treatment. It is the first of 4h Lo5 N treated biological replicates used in this experiment.

tag: inbred line

tag: tissue

tag: treated with


title: Lo5_2h_control_rep1

description:
Lo5_2h_-N_1
Lo5 roots sampled at 2h after KCl treatment. It is the first of 2h Lo5 control biological replicates used in this experiment.

value: chloride salt (KCl) for 2h (control, -NO3-)


title: Patient 4_H_CHO_Fast

description: Patient 4_ 12h post delivery


title: Lo5_2h_control_rep3

description:
Lo5_2h_-N_3
Lo5 roots sampled at 2h after KCl treatment. It is the third of 2h Lo5 control biological replicates used in this experiment.


title: D2750_Saliva_Affected_rep1

tag: line cd

tag: line ae

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)

tag: line fg


title: Lo5_2h_control_rep2

description:
Lo5_2h_-N_2
Lo5 roots sampled at 2h after KCl treatment. It is the second of 2h Lo5 control biological replicates used in this experiment.


title: D2978_Saliva_Affected_rep1

description:
Genotyping batch1 Whole genome amplified using the Repli-g kit
raw data file: Batch1_whole_genome_amplified_RAW.txt

tag: age

tag: diameter f

tag: line ab

tag: line bd


title: Lo5_2h_N treated_rep3

description:
Lo5_2h_+N_3
Lo5 roots sampled at 2h after KNO3 treatment. It is the third of 2h Lo5 N treated biological replicates used in this experiment.

source_name: Lo5_2h_N treated

value: 200 μM of KNO3 for 2h (+NO3-)


title: D2909_Saliva_Unaffected_rep1

tag: breed

tag: Sex

tag: angle 1 (abc)

tag: line bc


title: Lo5_4h_N treated_rep2

description:
Lo5_4h_+N_2
Lo5 roots sampled at 4h after KNO3 treatment. It is the second of 4h Lo5 N treated biological replicates used in this experiment.

tag: inbred line

tag: tissue

tag: treated with


title: Patient 2_H_CHO_Fast

description: Patient 2_ 12h post delivery

tag: gener

tag: bmi

value: Lean

tag: condition

tag: diet


title: Lo5_2h_N treated_rep2

description:
Lo5_2h_+N_2
Lo5 roots sampled at 2h after KNO3 treatment. It is the second of 2h Lo5 N treated biological replicates used in this experiment.


title: Lo5_1h_control_rep3

description:
Lo5_1h_-N_3
Lo5 roots sampled at 1h after KCl treatment. It is the third of 1h Lo5 control biological replicates used in this experiment.

value: chloride salt (KCl) for 1h (control, -NO3-)


title: D2826_Saliva_Affected_rep1

tag: line cd

tag: line be

tag: line ae

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: Patient 1_H_CHO_Fast

description: Patient 1_ 12h post delivery

value: Fast


title: D2825_Saliva_Unaffected_rep1

tag: breed

tag: Sex

tag: age

tag: diameter f

tag: line ab

tag: angle 1 (abc)

tag: line bd

tag: line fg


title: D2851_Saliva_Affected_rep1

tag: line bc


title: D2751_Saliva_Affected_rep1

description:
Genotyping batch2
raw data file: Batch2_RAW.txt

tag: line cd


title: D2815_Saliva_Unaffected_rep1

tag: line be


title: Patient 4_H_CHO_Fed

description: Patient 4_ 6h post delivery

tag: gener

tag: bmi

tag: condition

tag: diet


title: Lo5_2h_N treated_rep1

description:
Lo5_2h_+N_1
Lo5 roots sampled at 2h after KNO3 treatment. It is the first of 2h Lo5 N treated biological replicates used in this experiment.

tag: inbred line

tag: tissue

tag: treated with


title: D2137_Saliva_Affected_rep1

tag: breed

tag: Sex

tag: line ae

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: Patient 7_H_CHO_Fed

description: Patient 7_ 6h post delivery


title: Patient 3_H_CHO_Fed

description: Patient 3_ 6h post delivery


title: D2880_Saliva_Affected_rep1

description:
Genotyping batch1 regular
raw data file: Batch1_RAW.txt

tag: age

tag: diameter f

tag: line ab

tag: angle 1 (abc)

tag: line bc

tag: line cd

tag: line bd

tag: line fg


title: Patient 3_H_CHO_Fast

description: Patient 3_ 12h post delivery

tag: gener

tag: bmi

tag: condition

tag: diet


title: Patient 5_H_CHO_Fed

description: Patient 5_ 6h post delivery


title: D2976_Saliva_Affected_rep1

tag: breed

tag: Sex

tag: line be

tag: line ae

tag: angle 2(caf)


title: D2797_Saliva_Unaffected_rep1

tag: age

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: Patient 6_H_CHO_Fed

description: Patient 6_ 6h post delivery


title: D2139_Saliva_Unaffected_rep1

tag: diameter f

tag: line ab

tag: angle 1 (abc)

tag: line bc

tag: line cd


title: Patient 1_H_CHO_Fed

description: Patient 1_ 6h post delivery

tag: gener

tag: bmi

tag: condition


title: Patient 2_H_CHO_Fed

description: Patient 2_ 6h post delivery

tag: diet


title: D2811_Saliva_Unaffected_rep1

tag: breed

tag: Sex

tag: line bd

tag: line be

tag: line fg


title: Danio rerio Male, rep6

description:
371306A12
Unspecified strain.

hyb_protocol: Each hybridization mixture was made up from 1 µg test material (Cy3) and 1 µg reference material (Cy5). The D. rerio experiments were performed according to a common reference design, with twelve individuals as test samples and a pool as common reference. Details for the D. rerio microarray can be found in Rauwerda et al., 2010 (PMID 20626891). It is a three prime biased expression microarray with 63,751 target probes and 7,742 probes with random sequences not targeting to the Danio rerio genome, which we used as negative-control probes.

scan_protocol: The slides were washed according to the NimbleGen Arrays User's Guide (Gene Expression Arrays Version 5.0) and scanned in an ozone-free room with an Agilent DNA microarray scanner G2565CA.

data_processing: Selection of probes matching the D. rerio genome (bitscore 119), and not matching the genome (bitscore < 40).

organism: Danio rerio

source_name: Danio rerio male

label_protocol: Genomic DNA was amplified and labeled by strand displacement amplification. 200 ng genomic DNA was combined with 5 µg random octamers (Biolegio). The DNA was partly fragmented by heat at 99°C for 10 min. and allowed to cool on an ice/water bath for 5 min. The DNA/octamer mix was made on ice to 50 mM Tris-Cl (pH 7.5), 5 mM MgCl2, 1 mM DTT, 1 mM dGAC (GE Healthcare), 0.6 mM dTTP (GE Healthcare), 0.4 mM aminoallyl dUTP (TriLink Biotechnologies) and finally 10U Klenow exo- (Jena Bioscience) was added. After gentle vortexing, the samples were placed at 37°C for 8h. and subsequently incubated for 15 min. at 75°C to inactivate the enzyme. Each reaction was made to 1.5M sodium acetate (pH 5.2) and the amplified DNA was purified with the QIAquick PCR Purification Kit (Qiagen) according to the manufacturer's instructions with the exception that 7 volumes of buffer PB were used instead of 5 to increase the recovery of smaller fragments. Concentrations of amplified products were measured on the NanoDrop ND-1000 (Thermo Scientific) and quality assessed on the BioAnalyzer (Agilent Technologies) with the DNA 1000 Kit (Agilent Technologies). From each sample, 5 µg was taken, dried down and dissolved in 50 mM carbonate buffer (pH 8.5). Individual vials of Cy3/Cy5 from the mono-reactive dye packs (GE Healthcare) were dissolved in 200 µl DMSO. To each sample, 10 µl of the appropriate CyDye dissolved in DMSO was added and the mixture was incubated for 1h. Reactions were quenched with the addition of 5 µl 4M hydroxylamine (Sigma-Aldrich). This mixture was made to 0.75M Ammonium acetate and 0.2 µg/µl glycogen (Ambion). After mixing, 2.5 vol. of 100% EtOH was added and mixed. All samples were incubated for at least 60 min. at -20°C to enhance precipitation and centrifuged for 30 min. at 13.000xg. The supernatants were carefully removed by pipetting and 1 vol. of 80% EtOH was added to the pellets. After brief vortexing, the labeled DNA was pelleted once more by centrifugation for 10 min. at 13.000xg. The supernatants were removed by pipetting and the pellets were dried by vacuum concentrating. Final labeled pellets were dissolved in 30 µl H2O, and the yield and CyDye incorporation were measured with the NanoDrop ND-1000.

extract_protocol: Genomic DNA was extracted using a CTAB DNA extraction method that included an RNAse A (Sigma-Aldrich) digestion step for removal of residual RNA.

tag: genotype/variation

value: wild type

tag: gender

value: male

source_name: Common reference

value: male, female

tag: content

value: pooled samples

tag: sample type

value: reference


title: D2776_Saliva_Unaffected_rep1

value: Griffon Bruxellois

tag: age

tag: diameter f

tag: line ab

tag: line ae

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: Lo5_1h_control_rep2

description:
Lo5_1h_-N_2
Lo5 roots sampled at 1h after KCl treatment. It is the second of 1h Lo5 control biological replicates used in this experiment.

tag: inbred line

tag: tissue

tag: treated with


title: Danio rerio Female, rep6

description:
371306A11
Unspecified strain.

source_name: Danio rerio female

value: female


title: Lo5_1h_control_rep1

description:
Lo5_1h_-N_1
Lo5 roots sampled at 1h after KCl treatment. It is the first of 1h Lo5 control biological replicates used in this experiment.


title: Lo5_0h_rep3

description:
Lo5_0h_3
Lo5 roots sampled at 0h. It is the third of Lo5 0h biological replicates used in this experiment.

value: none (0h sample)


title: Danio rerio Male, rep4

description:
371306A08
Unspecified strain.


title: Danio rerio Female, rep4

description:
371306A07
Unspecified strain.


title: Danio rerio Male, rep5

description:
371306A09
Unspecified strain.


title: Danio rerio Female, rep5

description:
371306A10
Unspecified strain.


title: Lo5_0h_rep2

description:
Lo5_0h_2
Lo5 roots sampled at 0h. It is the second of Lo5 0h biological replicates used in this experiment.

value: root (2d-old seedlings)


title: Lo5_0h_rep1

description:
Lo5_0h_1
Lo5 roots sampled at 0h. It is the first of Lo5 0h biological replicates used in this experiment.


title: Lo5_1h_N treated_rep1

description:
Lo5_1h_+N_1
Lo5 roots sampled at 1h after KNO3 treatment. It is the first of 1h Lo5 N treated biological replicates used in this experiment.

source_name: Lo5_1h_N treated

value: 200 μM of KNO3 for 1h (+NO3-)


title: Lo5_1h_N treated_rep3

description:
Lo5_1h_+N_3
Lo5 roots sampled at 1h after KNO3 treatment. It is the third of 1h Lo5 N treated biological replicates used in this experiment.


title: Lo5_1h_N treated_rep2

description:
Lo5_1h_+N_2
Lo5 roots sampled at 1h after KNO3 treatment. It is the second of 1h Lo5 N treated biological replicates used in this experiment.


title: D2400_Saliva_Unaffected_rep1

tag: breed

tag: Sex

value: Male

tag: angle 1 (abc)

tag: line bc

tag: line cd

tag: line bd

tag: line be

tag: line fg


title: D2175_Saliva_Unaffected_rep1

value: Female

tag: age

tag: diameter f

tag: line ab

tag: line ae


title: Danio rerio Female, rep3

description:
371306A06
Unspecified strain.

tag: genotype/variation

tag: gender

tag: content

tag: sample type


title: D2430_Saliva_Affected_rep1

source_name: saliva (mouth swap)_affected

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: D2399_Saliva_Affected_rep1

tag: breed

tag: Sex

tag: angle 1 (abc)

tag: line bc

tag: line cd


title: Danio rerio Male, rep3

description:
371306A05
Unspecified strain.


title: D2398_Saliva_Affected_rep1

tag: age

tag: diameter f

tag: line bd

tag: line be

tag: line fg


title: D2384_Saliva_Unaffected_rep1

tag: line ab

tag: line ae


title: Danio rerio Male, rep2

description:
371306A04
Unspecified strain.

tag: genotype/variation

tag: gender

tag: content

tag: sample type


title: BMDM(KO)_24h LPS_rep2

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

country: Germany

institute: Medical School Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were also carried-out exactly as recommended: “One-Color Microarray-Based Gene Expression Analysis Protocol V5.7”.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing: Data extraction was performed with the “Feature Extraction Software V10.7.3.1” by using the recommended default extraction protocol file: GE1_107_Sep09.xml. The single channel data generated by the Feature Extraction software were normalized and analyzed in Genespring GX software, version 12.0 (Agilent Technologies). Low expression values were raised to the constant value 15 (defined as threshold) to minimize false positive ratios. Data were log2 transformed, normalized to 75th percentile of each array according to the standard procedure in Genespring GX.

organism: Mus musculus

source_name: BMDM(KO)_24h LPS

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the “Quick Amp Labeling kit, one color” (#5190-0442, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: BMDMs were generated by isolation of bone marrow cells from long bones, which were cultured in RPMI supplemented with 10% FCS, antibiotics (penicillin G 100μg/mL and streptomycin 100μg/mL) and Fungizone (Fisher), in the presence of GM-CSF (20ng/ml, Peprotech). Myeloid differentiation was allowed to proceed for 10 days.

extract_protocol: Total RNA was prepared by use of RNeasy Mini Kit (Qiagen).

treatment_protocol: Cells were treated with LPS (10ng/mL, Escherichia coli 026:B6, Sigma).

tag: individual

tag: genotype

value: Commd1 knockout

tag: treatment

value: 24 hr LPS

tag: cell type

value: Bone marrow derived macrophages


title: BMDM(KO)_24h LPS_rep1


title: BMDM(WT)_24h LPS_rep2

source_name: BMDM(WT)_24h LPS

value: Commd1 wildtype


title: D2397_Saliva_Affected_rep1

tag: breed

tag: Sex

tag: angle 1 (abc)

tag: line bc

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: D2375_Saliva_Affected_rep1

tag: age

tag: diameter f

tag: line ab

tag: line cd

tag: line bd

tag: line be

tag: line ae

tag: line fg


title: Danio rerio Female, rep1

description:
371306A02
Unspecified strain.

tag: genotype/variation

tag: gender

tag: content

tag: sample type


title: BMDM(KO)_3h LPS_rep2

source_name: BMDM(KO)_3h LPS

tag: individual

tag: genotype

tag: treatment

value: 3hr LPS

tag: cell type


title: D2396_Saliva_Affected_rep1

tag: breed

tag: Sex

tag: angle 1 (abc)

tag: line bc

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: Danio rerio Female, rep2

description:
371306A03
Unspecified strain.

tag: genotype/variation

value: wild type


title: D2429_Saliva_Affected_rep1

tag: age

tag: diameter f

tag: line ab

tag: line cd

tag: line bd

tag: line be

tag: line ae

tag: line fg


title: D2174_Saliva_Unaffected_rep1

source_name: saliva (mouth swap)_unaffected (control)

tag: breed

tag: Sex


title: D2173_Saliva_Unaffected_rep1

tag: angle 1 (abc)

tag: line bc


title: BMDM(WT)_24h LPS_rep1

tag: individual

tag: genotype

tag: treatment

tag: cell type


title: D2372_Saliva_Unaffected_rep1

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: D2176_Saliva_Unaffected_rep1

tag: age

tag: diameter f

tag: line ab

tag: line cd

tag: line bd


title: BMDM(KO)_3h LPS_rep1


title: D2157_Saliva_Affected_rep1

tag: breed

tag: Sex

tag: line be

tag: line ae

tag: line fg


title: D2141_Saliva_Unaffected_rep1

tag: angle 1 (abc)

tag: line bc


title: D2661_Saliva_Affected_rep1

tag: angle 2(caf)


title: BMDM(WT)_3h LPS_rep1

source_name: BMDM(WT)_3h LPS

tag: individual

tag: genotype

tag: treatment

tag: cell type


title: BMDM(KO)_untreated_rep2

value: untreated


title: BMDM(WT)_3h LPS_rep2


title: BMDM(KO)_untreated_rep1


title: D2152_Saliva_Affected_rep1

tag: age

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: BMDM(WT)_untreated_rep2


title: D2138_Saliva_Affected_rep1

tag: breed

tag: diameter f

tag: line ab

tag: line cd

tag: line bd


title: D2154_Saliva_Unaffected_rep1

tag: Sex

tag: angle 1 (abc)

tag: line be

tag: line ae

tag: line fg


title: WT_Tfh.2

status: Public on May 18 2014

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: replicate 2 (9259611043_E)

hyb_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization Assay system  was used to hybridize Biotin -aRNA to the Illumina Mouse WG-6 v 2 Expression Beadchip

scan_protocol: Illumina BeadArray Reader  with Illumina BeadScan

data_processing: Illumina GenomeStudio software was used to export expression levels and detection p-values for each probe of each sample. Signal intensity data was log2 transformed and quantile normalized. Only genes that showed significant detection p-value (p<0.05) in at least one of six samples were considered.

source_name: CXCR5highPD-1high Follicular helper T cells (Tfh)

label_protocol: Total RNA was labeled with Epicentre TargetAmp™- Nano Labeling Kit for Illumina® Expression BeadChip

extract_protocol: RNA was extracted with Trizol reagent according to manufacturer’s protocol. Quality control was performed with Agilent Bioanalyser.

tag: donor mouse stain

value: OT-II TCR transgenic mice

tag: donor mouse age

value: 6-8 weeks

tag: recipient mouse stain

value: SMARTA mice

tag: recipient mouse age

tag: genotype/variation

value: Foxp1 wild type


title: D2151_Saliva_Affected_rep1

value: Griffon Bruxellois

tag: age

tag: line bc

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)


title: Exp_Tfh.1

description: replicate 1 (9259611043_C)

value: Foxp-conditional knockout


title: Exp_Non.1

description: replicate 1 (9259611043_D)

source_name: CXCR5- PD-1- Non-Tfh cells


title: Exp_Tfh.2

description: replicate 2 (9259611043_F)


title: D2136_Saliva_Unaffected_rep1

tag: breed

tag: diameter f

tag: line ab

tag: line cd

tag: line bd

tag: angle 5 (afh)


title: D2132_Saliva_Unaffected_rep1

tag: Sex

tag: angle 1 (abc)

tag: line be

tag: line ae

tag: line fg


title: WT_Non.1

description: replicate 1 (9259611043_B)

tag: donor mouse stain

tag: donor mouse age

tag: recipient mouse stain

tag: recipient mouse age

tag: genotype/variation


title: Epi4_capsaicin_3

status: Public on May 17 2014

city: Niigata

first: Naoki

last: Takahashi

address: 2-5274 Gakko-cho, Chuo-ku

department: Oral Biological Science

country: Japan

institute: Niigata University Faculty of Dentistry

hyb_protocol: The Cy3-labelled cRNA was fragmented at 60°C for 30 minutes using Agilent fragmentation buffer (Agilent). On completion of the fragmentation reaction, the samples were competitively hybridized onto the Agilent 4 × 44K whole human genome oligo microarray slide (Agilent) for 17 hours at 65C°in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting.

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

label_protocol: The RNA samples were amplified and labeled with Cy3 by use of the Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA), followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer (Agilent Technologies).

growth_protocol: Epi4 cells were seeded into a 12-well culture plate at a concentration of 2 × 105 cells in Epilife medium (Cascade Biologics, Portland, OR) supplemented with S7 (Cascade Biologics).

extract_protocol: Total RNA was isolated from the cells using TRI Reagent (Molecular Research Center, Cincinnati, OH, USA) following the manufacturer's recommendations.

treatment_protocol: After incubation for 24 hours at 37 ºC in a humidified incubator with 5% CO2, epi4 cells were stimulated with 1 μM capsaicin for 4 hours.

tag: tissue

value: Gingiva

tag: cell line

tag: cell type

value: Epithelial


title: BMDM(WT)_untreated_rep1

tag: individual

tag: genotype

tag: treatment


title: Epi4_capsaicin_2


title: Epi4_capsaicin_4


title: WT_Tfh.1

description: replicate 1 (9259611043_A)


title: D2129_Saliva_Unaffected_rep1

tag: breed

value: Male

tag: age

tag: diameter f

tag: line ab

tag: line bc

tag: line cd

tag: line bd

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: D2130_Saliva_Unaffected_rep1

tag: Sex

tag: angle 1 (abc)

tag: line be

tag: line ae

tag: line fg


title: Epi4_capsaicin_1

tag: tissue

tag: cell line

tag: cell type


title: Epi4_control_2


title: Epi4_control_1


title: Danio rerio Male, rep1

description:
371306A01
Unspecified strain.

tag: genotype/variation

tag: gender

value: male

value: male, female

tag: content

value: pooled samples

tag: sample type

value: reference


title: Wounded Leaves_rep3

city: Grossbeeren

first: Philipp

last: Franken

address: Theodor-Echtermeyer-Weg 1

institute: Leibniz Institute of Vegetable and Ornamental Crops - IGZ EV

description: To provide control tissues, the uppermost fully developed leaves of axillary shoots still attached at the stock plant were transversely pinched and used as wounded leaves.  It is the third of four biological replicates used in this experiment.

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

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

data_processing:
Data processing and normalization were performed by NimbleGen Systems Inc., Switzerland, following their standard operating protocol. See www.nimblegen.com.
Normalized expression values of different time points (0 hpe - 192 hpe) were compared with 0 hpe. Significantly up- or down-regulated genes were recognized via Rank Product (RP) analysis using MeV (MultiExperiment Viewer, version 4.4.1.) software. For each individual time point, the expression values of each replicate were divided by expression values of all four replicates at 0 hpe, followed by a log2-transformation for the Rank Product analysis (to generate M-values). Then, median values of these paired log-fold changes were calculated for each gene-related sequence identifier. Finally, the median values were back-transformed by a power of two in order to obtain the real expression ratios. The same procedure was carried out for the comparison of control tissues. To extract up or down-regulated genes, median ratios with values above two (>2) were determined as up-regulated and median ratios with values below 0.5 (<0.5) were determined as down-regulated. Putative genes showing expression value ratios more than 2 or less than 0.5 were considered as induced or repressed genes respectively (M-value > 1 or < 1). Based on the RP statistical analysis for each gene, using 1000 permutations, P-values below (≤0.01) were considered as significant differentially expressed. Cluster analyses (K-means clustering method) and preparation of expression graphs were performed using Genesis software version 1.7.6.

organism: Petunia x hybrida

source_name: P. hybrida pinched leaf

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

growth_protocol: Leafy stem cuttings of Petunia hybrida cv. Mitchell were used for all experiments. Cuttings were produced on donor plants which were kept in short day condition with 10 hours light per day. All samples were collected at the same time of the day (2 h after the onset of light). Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays with a size of 38×58 cm containing perlite (Perligran A, particle size 0-6 mm, Knauf Perlite GmbH, Dortmund, Germany). Perlite is an aluminium silicate, which has been expanded by heating to ca. 1000 °C. The substrate is chemically inert and does not contain mineral nutrients. Trays containing cuttings were watered and covered completely with a light-permeable top to maintain a humid environment. Cuttings were put in a phytotron and cultivated under the following growth conditions: temperature 20°C (night) and 22°C (day), humidity 60% (night) and 85% (day), time regime 10 h light and 14 h dark and a light intensity of 250 µmol x m-2 x s-1.

extract_protocol: Total RNA was extracted from petunia cutting base as described by Logemann et al. (1987).

tag: cultivar

value: Mitchell

value: Leaf

tag: developmental stage

value: 2 hours post wounding


title: Wounded Leaves_rep4

description: To provide control tissues, the uppermost fully developed leaves of axillary shoots still attached at the stock plant were transversely pinched and used as wounded leaves.  It is the fourth of four biological replicates used in this experiment.


title: Epi4_control_4


title: Epi4_control_3


title: Roots_rep2

description: To provide control tissues, petunia adventitious root system harvested 24 days post excision of cuttings (begin of lateral root formation) was used as fully developed root system.  It is the second of four biological replicates used in this experiment.

source_name: P. hybrida leafy cutting_root system

value: Root

value: 24 days post excision of cuttings


title: Roots_rep4

description: To provide control tissues, petunia adventitious root system harvested 24 days post excision of cuttings (begin of lateral root formation) was used as fully developed root system.  It is the fourth of four biological replicates used in this experiment.


title: Roots_rep3

description: To provide control tissues, petunia adventitious root system harvested 24 days post excision of cuttings (begin of lateral root formation) was used as fully developed root system.  It is the third of four biological replicates used in this experiment.


title: Roots_rep1

description: To provide control tissues, petunia adventitious root system harvested 24 days post excision of cuttings (begin of lateral root formation) was used as fully developed root system.  It is the first of four biological replicates used in this experiment.


title: Wounded Leaves_rep2

description: To provide control tissues, the uppermost fully developed leaves of axillary shoots still attached at the stock plant were transversely pinched and used as wounded leaves.  It is the second of four biological replicates used in this experiment.


title: D2124_Saliva_Affected_rep1

tag: breed

tag: age

tag: diameter f

tag: line ab

tag: line bc

tag: line cd

tag: line bd

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag


title: Leaves_rep4

description: To provide control tissues, the uppermost fully developed leavesof axillary shoots attached at the stock plant  were harvested.  It is the fourth of four biological replicates used in this experiment.

source_name: P. hybrida leaf

tag: tissue

value: Control (no specific stage)


title: Wounded Leaves_rep1

description: To provide control tissues, the uppermost fully developed leaves of axillary shoots still attached at the stock plant were transversely pinched and used as wounded leaves.  It is the first of four biological replicates used in this experiment.


title: Leaves_rep3

description: To provide control tissues, the uppermost fully developed leavesof axillary shoots attached at the stock plant  were harvested.  It is the third of four biological replicates used in this experiment.


title: Stem Base_192h_rep2

description: Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays containing perlite. 192 hours post excision, five mm of each cutting base (rooting zone) were harvested, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the second of four biological replicates used in this experiment.

source_name: P. hybrida leafy cutting_5 millimeter of stem base

value: Stem

value: 192 hours post excision of cuttings


title: Leaves_rep1

description: To provide control tissues, the uppermost fully developed leavesof axillary shoots attached at the stock plant  were harvested.  It is the first of four biological replicates used in this experiment.


title: Stem Base_192h_rep3

description: Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays containing perlite. 192 hours post excision, five mm of each cutting base (rooting zone) were harvested, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the third of four biological replicates used in this experiment.


title: Stem Base_192h_rep4

description: Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays containing perlite. 192 hours post excision, five mm of each cutting base (rooting zone) were harvested, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the fourth of four biological replicates used in this experiment.


title: Stem Base_72h_rep2

description: Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays containing perlite. 72 hours post excision, five mm of each cutting base (rooting zone) were harvested, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the second of four biological replicates used in this experiment.

value: 72 hours post excision of cuttings


title: Stem Base_72h_rep3

description: Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays containing perlite. 72 hours post excision, five mm of each cutting base (rooting zone) were harvested, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the third of four biological replicates used in this experiment.


title: D2123_Saliva_Affected_rep1

description:
Genotyping batch1 regular
raw data file: Batch1_RAW.txt

value: Griffon Bruxellois

tag: Sex

value: Female

tag: angle 1 (abc)

tag: line be

tag: line ae

tag: angle 4 (ahg)

tag: angle 5 (afh)

tag: line fg


title: Stem Base_72h_rep4

description: Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays containing perlite. 72 hours post excision, five mm of each cutting base (rooting zone) were harvested, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the fourth of four biological replicates used in this experiment.

tag: cultivar

tag: developmental stage


title: Stem Base_6h_rep2

description: Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays containing perlite. Six hours post excision, five mm of each cutting base (rooting zone) were harvested, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the second of three biological replicates used in this experiment.

value: 6 hours post excision of cuttings


title: Stem Base_6h_rep3

description: Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays containing perlite. Six hours post excision, five mm of each cutting base (rooting zone) were harvested, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the third of three biological replicates used in this experiment.


title: Stem Base_72h_rep1

description: Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays containing perlite. 72 hours post excision, five mm of each cutting base (rooting zone) were harvested, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the first of four biological replicates used in this experiment.


title: CHIKV infected larvae against control 3

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

hyb_protocol: The dual-color hy- bridization of the microarray chips was performed at ServiceXS according to Agilent protocol G4140-90050 version 5.7 (www.Agilent.com) for two- color microarray-based gene expression analysis.

scan_protocol: standard Agilent protocol

data_processing: A loess normalization was operated for each micro-array using Limma R package.

source_name: Larvae infected by CHIKV

label_protocol: 6 micrograms of amino-allyl-modified aRNA was used for coupling of monoreactive Cy3 and Cy5 dyes (GE Healthcare) and column purified.

growth_protocol: Wild-type zebrafish (AB strain) were raised under standard conditions at 28°C to be infected at 3 days post-fertilization.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, from pools of 24 to 70 larvae per sample.

treatment_protocol: IHNV infection : intravenous microinjection of ~65pfu of IHNV25-70, followed by incubation at 24°C for 48h. CHIKV infection was performed by injection within the yolk cell of ~200pfu of CHIKV-GFP, followed by incubation at 28° for 48h. Control samples were either uninjected or injected with PBS.

tag: strain

value: strain AB

source_name: non infected larvae


title: Stem Base_24h_rep1

description: Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays containing perlite. 24 hours post excision, five mm of each cutting base (rooting zone) were harvested, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the only biological replicates used in this experiment.

value: 24 hours post excision of cuttings


title: B pumilus [control III] - [pool]

city: Greifswald

first: Birgit

last: Voigt

address: F.-L.-Jahnstr. 15

department: Institute for Microbiology

description: Sample 7

hyb_protocol: Hybridization was done according to the two-Color Microarray-Based Gene Expression Analysis Protocol of Agilent Technologies

scan_protocol: Agilent scanner Type G2565CA with high resolution upgrade G2539A and the software Scan Control 8.4.1

data_processing: Agilent's Feature Extraction Software (version 10.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Bacillus pumilus

source_name: reference pool

label_protocol: Synthesis and purification of fluorescently labeled cDNA was done according to Schroeter et al 2011, Proteomics 11, p. 2851-66

growth_protocol: B. pumilus was grown in Belitsky minimal medium

extract_protocol: Total RNA of B. pumilus was prepared by the acid phenol method with modofication according to Homuth et al. 1997, J. Bacteriol. 179, p. 1153-64

treatment_protocol: 2 mM hydrogen peroxide was added to growing cells (OD500 0.6), samples taken after 3 and 8 min

tag: sample type

value: mix of t=0 min samples (reference)

source_name: Bacillus pumilus control

tag: treated with

value: none (control)


title: Stem Base_192h_rep1

description: Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays containing perlite. 192 hours post excision, five mm of each cutting base (rooting zone) were harvested, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the first of four biological replicates used in this experiment.


title: Stem Base_2h_rep1

description: Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays containing perlite. Two hours post excision, five mm of each cutting base (rooting zone) were harvested, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the first of two biological replicates used in this experiment.

value: 2 hours post excision of cuttings


title: Stem Base_0h_rep2

description: Excised leafy cuttings harboring four to five leaves of similar size were harvested and five mm of each cutting base (rooting zone) were collected, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the second of two biological replicates used in this experiment.

value: Mitchell

value: 0 hour post excision of cuttings


title: Stem Base_2h_rep2

description: Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays containing perlite. Two hours post excision, five mm of each cutting base (rooting zone) were harvested, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the second of two biological replicates used in this experiment.


title: B pumilus [stress 8 min III] - [pool]

description: Sample 9

source_name: Bacillus pumilus stress 8 min

value: 2 mM hydrogen peroxide for 8min


title: LT-HSC_WASH-KO_rep1

city: Beijing

first: Pengyan

last: Xia

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

country: China

institute: Institute of biophysics, Chinese Academy of Sciences

description: LT-HSC profiling

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

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

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

source_name: Mouse LT-HSC KO

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

growth_protocol: Mouse strain were fed in SPF conditions.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with NanoDrop ND-1000 (Institute of Biophysics, Chinese Academy of Sciences).

treatment_protocol: Bone marrow cells were isolated form mouse femurs, followed by LT-HSC purification through flow cytometry.

tag: cell type

value: LT-HSC

tag: genotype/variation

value: knock out


title: CD138low RPMI-8226 rep 2

city: Salamanca

first: Teresa

last: Paíno

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de investigación del cáncer

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions (Affymetrix)

scan_protocol: The arrays were processed using the Fluidics Station 450, GeneChip Scanner 3000 7 G and AGCC (AffymetrixGeneChip Command Console Software)

data_processing: .CEL files were generated from the scanned array image files by the Affymetrix GeneChip Command Console Software and were imported into the Affymetrix Chromosome Analysis Suite v1.2.2 Software.  Copy number data files (.CYCHP files) were generated using the ChAS Analysis Files for the CytoScan HD Array version NA32.1 as a reference

source_name: RPMI-8226 cell line

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: cells were cultured in RPMI-1640 medium supplemented with 2 mM L-glutamine, 100 U/mL penicillin, 100 mg/mL streptomycin and 10% fetal bovine serum at 37°C and 5% CO2/95% air

extract_protocol: DNA was isolated from CD138++ (n=3) and CD138low (n=3) RPMI-8226 cells using a GenElute Mammalian Genomic DNA Miniprep Kit (Sigma-Aldrich) following the manufacturer’s protocol

treatment_protocol: not applicable

tag: cell line

tag: subpopulation

tag: disease

value: multiple myeloma


title: IHNV infected larvae against control 2

source_name: Larvae infected by IHNV


title: Stem Base_6h_rep1

description: Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays containing perlite. Six hours post excision, five mm of each cutting base (rooting zone) were harvested, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the first of three biological replicates used in this experiment.

tag: tissue

value: Stem


title: B pumilus [control II] - [pool]

description: Sample 4


title: IHNV infected larvae against control 3


title: CD138low RPMI-8226 rep 3


title: Leaves_rep2

description: To provide control tissues, the uppermost fully developed leavesof axillary shoots attached at the stock plant  were harvested.  It is the second of four biological replicates used in this experiment.

value: Leaf

value: Control (no specific stage)


title: B pumilus [stress 8 min I] - [pool]

description: Sample 3


title: CD138++ RPMI-8226 rep 3


title: CD138low RPMI-8226 rep 1


title: B pumilus [stress 3 min I] - [pool]

description: Sample 2

source_name: Bacillus pumilus stress 3 min

value: 2 mM hydrogen peroxide for 3min


title: Stem Base_0h_rep1

description: Excised leafy cuttings harboring four to five leaves of similar size were harvested and five mm of each cutting base (rooting zone) were collected, immediately frozen in liquid N2 and stored at -80°C for further analyses.  It is the first of two biological replicates used in this experiment.


title: CD138++ RPMI-8226 rep 1


title: CD138++ RPMI-8226 rep 2


title: B pumilus [control I] - [pool]

description: Sample 1


title: B pumilus [stress 8 min II] - [pool]

description: Sample 6


title: IHNV infected larvae against control 1


title: Control matched sample pair amygdala MD3_AMY #34

status: Public on May 16 2014

city: Pittsburgh

first: Etienne

last: Sibille

address: 450 Technology Drive, Suite 231

department: Psychiatry

institute: University of Pittsburgh

description: dissected from frozen coronal blocks ~2 cm caudal to the temporal pole

hyb_protocol: The sections were then hybridized with [35S]-labeled riboprobes (10^6 cpm/uL) in hybridization buffer at 56 °C for 16h. The hybridization buffer contained 50% formamide, 0.75 M NaCl, 20 mM 1,4-piperazine diethane sulfonic acid, pH 6.8, 10 mM ethylenediaminetetraacetic acid (EDTA), 10% dextran sulfate, 5X Denhardt’s solution (0.2 mg/mL Ficoll, 0.2 mg/mL polyvinylpyrrolidone, 0.2 mg/mL bovine serum albumin), 50 mM dithiothreitol, 0.2% sodium dodecyl sulfate, and 100 ug/mL yeast transfer RNA.

scan_protocol: DirecHyb Gene Expression. iScan Control Software 1.3.10+

data_processing:
Probeset signals were extracted with the Beadarray software following the default quality control parameters and batch-normalized.
GenomeStudio Gene Expression Module v1.6+

source_name: Control sample, brain amygdala

label_protocol: standard Illumina protocol

growth_protocol: not applicable

extract_protocol: 1µg of total high quality total RNA was reverse transcribed into single stranded cDNA, that was then converted into double stranded cDNA and purified using the Illumina TotalPrep RNA Amplification Kit. An in vitro transcription reaction was carried out overnight in the presence of biotinylated UTP and CTP to obtain biotin-labeled cRNA from the double stranded cDNA. The cRNA was purified using the same Amplification Kit, and quality control was assessed.

value: brain amygdala

tag: disease state

value: Control


title: CHIKV infected larvae against control 1

value: strain AB


title: B pumilus [stress 3 min III] - [pool]

description: Sample 8


title: Control matched sample pair amygdala MD3_AMY #29


title: LT-HSC_WASH-control_rep1

description: LT-HSC profiling

source_name: Mouse LT-HSC control

value: wild type control


title: Control matched sample pair amygdala MD3_AMY #24


title: Control matched sample pair amygdala MD3_AMY #28


title: Control matched sample pair amygdala MD3_AMY #23


title: Control matched sample pair amygdala MD3_AMY #25


title: Control matched sample pair amygdala MD3_AMY #31


title: Control matched sample pair amygdala MD3_AMY #32


title: Control matched sample pair amygdala MD3_AMY #35


title: B pumilus [stress 3 min II] - [pool]

description: Sample 5

value: mix of t=0 min samples (reference)


title: Control matched sample pair amygdala MD3_AMY #19


title: Control matched sample pair amygdala MD3_AMY #16


title: Control matched sample pair amygdala MD3_AMY #15


title: Control matched sample pair amygdala MD3_AMY #20


title: Control matched sample pair amygdala MD3_AMY #17


title: Control matched sample pair amygdala MD3_AMY #26


title: Control matched sample pair amygdala MD3_AMY #33


title: Control matched sample pair amygdala MD3_AMY #14


title: Control matched sample pair amygdala MD3_AMY #27


title: Control matched sample pair amygdala MD3_AMY #22


title: Control matched sample pair amygdala MD3_AMY #18


title: Control matched sample pair amygdala MD3_AMY #30


title: CHIKV infected larvae against control 2


title: MDD matched sample pair amygdala MD3_AMY #34

source_name: MDD sample, brain amygdala

value: MDD case


title: MDD matched sample pair amygdala MD3_AMY #35


title: MDD matched sample pair amygdala MD3_AMY #30


title: MDD matched sample pair amygdala MD3_AMY #33


title: MDD matched sample pair amygdala MD3_AMY #32


title: MDD matched sample pair amygdala MD3_AMY #29


title: MDD matched sample pair amygdala MD3_AMY #27


title: MDD matched sample pair amygdala MD3_AMY #28


title: MDD matched sample pair amygdala MD3_AMY #31


title: MDD matched sample pair amygdala MD3_AMY #26


title: MDD matched sample pair amygdala MD3_AMY #20


title: MDD matched sample pair amygdala MD3_AMY #24


title: MDD matched sample pair amygdala MD3_AMY #22


title: MDD matched sample pair amygdala MD3_AMY #23


title: MDD matched sample pair amygdala MD3_AMY #17


title: MDD matched sample pair amygdala MD3_AMY #15


title: MDD matched sample pair amygdala MD3_AMY #16


title: MDD matched sample pair amygdala MD3_AMY #25


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #32

source_name: MDD sample, brain anterior cingulate cortex

value: brain anterior cingulate cortex


title: MDD matched sample pair amygdala MD3_AMY #19


title: MDD matched sample pair amygdala MD3_AMY #18


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #35


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #30


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #34


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #29


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #31


title: MDD matched sample pair amygdala MD3_AMY #14


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #13


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #26


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #33


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #28


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #11


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #22


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #21


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #25


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #3


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #23


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #20


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #24


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #19


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #27


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #17


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #16


title: MDD matched sample pair anterior cingulate cortex MD2_ACC #10


title: MDD matched sample pair anterior cingulate cortex MD2_ACC #12


title: MDD matched sample pair anterior cingulate cortex MD2_ACC #9


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #15


title: MDD matched sample pair anterior cingulate cortex MD2_ACC #5


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #14


title: MDD matched sample pair anterior cingulate cortex MD2_ACC #6


title: MDD matched sample pair anterior cingulate cortex MD3_ACC #18


title: Control matched sample pair anterior cingulate cortex MD2_ACC #12

source_name: Control sample, brain anterior cingulate cortex


title: MDD matched sample pair anterior cingulate cortex MD2_ACC #2


title: MDD matched sample pair anterior cingulate cortex MD2_ACC #8


title: MDD matched sample pair anterior cingulate cortex MD2_ACC #7


title: Control matched sample pair anterior cingulate cortex MD2_ACC #10


title: Control matched sample pair anterior cingulate cortex MD2_ACC #7


title: Control matched sample pair anterior cingulate cortex MD2_ACC #5


title: Control matched sample pair anterior cingulate cortex MD2_ACC #6


title: Control matched sample pair anterior cingulate cortex MD2_ACC #8


title: Control matched sample pair anterior cingulate cortex MD2_ACC #9


title: MDD matched sample pair anterior cingulate cortex MD2_ACC #4


title: MDD matched sample pair anterior cingulate cortex MD2_ACC #1


title: Control matched sample pair anterior cingulate cortex MD2_ACC #2


title: Control matched sample pair anterior cingulate cortex MD2_ACC #4


title: Control matched sample pair anterior cingulate cortex MD2_ACC #1


title: 31928_EGFR WT +DMSO HCC78 HCC78 SAM819902

city: South San Francisco

first: Ho-June

last: Lee

address: 1 DNA way

department: Discovery Oncology

institute: Genentech

description: EGFR WT +DMSO

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

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

data_processing: Data was preprocessed and normalized using RMA method in the Bioconductor affy package

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

growth_protocol: Cell lines were grown in RPMI 1640 or DMEM/F12 (GIBCO) supplemented with 10% FBS, 50 units/mL penicillin, 50 units/mL streptomycin and 2mM L-glutamine.

extract_protocol: Total RNA was extracted with RNAeasy kit according to the manufacturer's instructions.

treatment_protocol: Cells were treated with DMSO or erlotinib (1 mM) for 24 hr

tag: genotype

value: EGFR WT

tag: treatment

value: DMSO


title: 31929_EGFR WT +Erlotinib NCI-H1648 NCI-H1648 SAM819900

description: EGFR WT +Erlotinib

value: Erlotinib


title: 31929_EGFR WT +Erlotinib HCC78 HCC78 SAM819904

description: EGFR WT +Erlotinib


title: 31928_EGFR WT +DMSO NCI-H1648 NCI-H1648 SAM819897

description: EGFR WT +DMSO


title: 31929_EGFR WT +Erlotinib HCC78 HCC78 SAM819903

description: EGFR WT +Erlotinib


title: 31928_EGFR WT +DMSO HCC78 HCC78 SAM819901

description: EGFR WT +DMSO


title: 31928_EGFR WT +DMSO NCI-H838 NCI-H838 SAM819893

description: EGFR WT +DMSO


title: 31929_EGFR WT +Erlotinib NCI-H838 NCI-H838 SAM819896

description: EGFR WT +Erlotinib


title: 31929_EGFR WT +Erlotinib NCI-H838 NCI-H838 SAM819895

description: EGFR WT +Erlotinib


title: 31928_EGFR WT +DMSO NCI-H23 NCI-H23 SAM819890

description: EGFR WT +DMSO


title: 31929_EGFR WT +Erlotinib NCI-H23 NCI-H23 SAM819892

description: EGFR WT +Erlotinib


title: 31927_EGFR Mutant +Erlotinib HCC2279 HCC2279 SAM819876

description: EGFR Mutant +Erlotinib

value: EGFR Mutant


title: 31928_EGFR WT +DMSO NCI-H1648 NCI-H1648 SAM819898

description: EGFR WT +DMSO


title: 31926_EGFR Mutant +DMSO HCC2935 HCC2935 SAM819877

description: EGFR Mutant +DMSO


title: 31928_EGFR WT +DMSO NCI-H23 NCI-H23 SAM819889

description: EGFR WT +DMSO


title: 31929_EGFR WT +Erlotinib NCI-H1648 NCI-H1648 SAM819899

description: EGFR WT +Erlotinib


title: 31929_EGFR WT +Erlotinib NCI-H23 NCI-H23 SAM819891

description: EGFR WT +Erlotinib


title: 31927_EGFR Mutant +Erlotinib HCC2279 HCC2279 SAM819875

description: EGFR Mutant +Erlotinib


title: 31927_EGFR Mutant +Erlotinib PC-9 PC-9 SAM819867

description: EGFR Mutant +Erlotinib


title: 31926_EGFR Mutant +DMSO HCC4006 HCC4006 SAM819870

description: EGFR Mutant +DMSO


title: 31928_EGFR WT +DMSO NCI-H838 NCI-H838 SAM819894

description: EGFR WT +DMSO


title: 31927_EGFR Mutant +Erlotinib HCC2935 HCC2935 SAM819879

description: EGFR Mutant +Erlotinib


title: 31926_EGFR Mutant +DMSO HCC2279 HCC2279 SAM819873

description: EGFR Mutant +DMSO


title: 31926_EGFR Mutant +DMSO HCC2935 HCC2935 SAM819878

description: EGFR Mutant +DMSO


title: 31927_EGFR Mutant +Erlotinib HCC2935 HCC2935 SAM819880

description: EGFR Mutant +Erlotinib


title: 31926_EGFR Mutant +DMSO HCC2279 HCC2279 SAM819874

description: EGFR Mutant +DMSO


title: 31927_EGFR Mutant +Erlotinib HCC4006 HCC4006 SAM819871

description: EGFR Mutant +Erlotinib


title: 31927_EGFR Mutant +Erlotinib HCC4006 HCC4006 SAM819872

description: EGFR Mutant +Erlotinib


title: 31927_EGFR Mutant +Erlotinib PC-9 PC-9 SAM819868

description: EGFR Mutant +Erlotinib


title: 31926_EGFR Mutant +DMSO HCC4006 HCC4006 SAM819869

description: EGFR Mutant +DMSO


title: 31926_EGFR Mutant +DMSO PC-9 PC-9 SAM819866

description: EGFR Mutant +DMSO


title: MDD matched sample pair brain anterior cingulate cortex BA25_M #30

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials: • Heat the hybridization cocktail to 99°C for 5 minutes in a heat block • Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation • Transfer the hybridization cocktail that has been heated at 99°C, to a 45°C heat block for 5 minutes • Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture • Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube • Place probe array into the hybridization oven, set to 45°C • To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm • Hybridize for 16 hours • During the latter part of the 16-hour hybridization, proceed to the GeneChip® Expression Wash, Stain and Scan User Manual, P/N 702731, to prepare reagents for the washing and staining steps required immediately after completion of hybridization

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G

data_processing: Probeset signals (i.e., transcript levels) were extracted with the Affymetrix GCOS software. For statistical analysis, log2- transformed probeset signal intensities were extracted and normalized with the robust multiarray average (GC-RMA) algorithm

label_protocol: According to standard affymetrix protocol: • 10ul  Purified cDNA10ul • DEPC H2O • 4ul  10x IVT Labeling Buffer • 12ul  IVT Labeling NTP mix • 4ul  IVT Labeling Enzyme mix - Incubate at 37C 16 hour in an incubating oven or thermal cycler with heated lid to avoid condensation. - Purify labeled cRNA generated from either IVT labeling reaction using RNeasy RNA Purification Mini kit (Qiagen) using the RNA Cleanup Protocol according to manufacturers instructions. - Quantitate Biotin labeled cRNA using 260nm/280nm spectrophotometric assay.

extract_protocol: Total RNA was extracted from frozen samples stored in TRIzol (Invitrogen, Carlsbad, Calif.) and processed for microarray analysis according to the microarray manufacturer’s protocol (Affymetrix, Santa Clara, Calif.)


title: Serum starved MCF7 cells, Rep1

city: Lyon

first: Olivier

last: Peyruchaud

state: Rhone Alpes

address: UFR de medicine Lyon Est (Domaine Laennec), 7-11 Rue Guillaume Paradin

institute: INSERM U1033

description:
Transcriptomic data from Serum starved MCF7 cells (Without LPA stimulation)
MCF7-LPA_1

hyb_protocol: Hybridization was performed following Affymetrix protocol. 10µg of labeled cRNA was fragmented and denatured in hybridization buffer, then hybridized on chip during 16h at 45°C with contant mixing by rotation at 60 rpm in an Genechip hybridization oven 640 (Affymetrix)

scan_protocol: The arrays were scanned using the confocal laser (Genechip scanner 3000, Affymetrix)

data_processing: The CEL files were generated using the Affymetrix GeneChip Command Console (AGCC) software 3.0. The obtained data were normalized with affymetrix Expression Console software using MAS5 statistical algorithm

label: Biotin

source_name: MCF7 cells, Serum starved

label_protocol: Total RNA (250ng) was amplified and biotin-labeled using GeneChip® 3' IVT Express target labeling kit as per the protocol from Affymetrix

growth_protocol: The MDA-MB-231, MCF7, PC3 cells were cultured in DMEM, EMEM, F-12K Nutrient Medium respectively, suplemented with 10% FBS and 1% Penicillin/streptomycin at 37°C in a 5% CO2 incubator

extract_protocol: Total RNA was extracted using the RNeasy kit (QIAGEN) as per manufacturer's protocol

treatment_protocol: The cells were serum starved for 24h and then stimulated with LPA (1µM) for 45min.

value: MCF7 cells (obtained from ATCC)

tag: agent

value: control


title: MDD matched sample pair brain anterior cingulate cortex BA25_M #26


title: 31926_EGFR Mutant +DMSO PC-9 PC-9 SAM819865

description: EGFR Mutant +DMSO


title: MCF7 cells stimulated with LPA, Rep1

description:
Transcriptomic data from MCF7 cells stimulated with LPA
MCF7+LPA_1

source_name: MCF7 cells stimulated with LPA

value: LPA


title: MDD matched sample pair brain anterior cingulate cortex BA25_M #15


title: Serum starved MCF7 cells, Rep2

description:
Transcriptomic data from Serum starved MCF7 cells (Without LPA stimulation)
MCF7-LPA_2


title: MDA-MB-231 cells stimulated with LPA, Rep1

description:
Transcriptomic data from MDA-MB-231 cells stimulated with LPA
MDA-MB-231+LPA_1

source_name: MDA-MB-231 cells stimulated with LPA

value: MDA-MB-231 cells (obtained from ATCC)


title: PC3 cells stimulated with LPA, Rep2

description:
Transcriptomic data from PC3 cells stimulated with LPA
PC3+LPA_2

source_name: PC3 cells stimulated with LPA

value: PC3 cells (obtained from ATCC)


title: MDA-MB-231 cells stimulated with LPA, Rep2

description:
Transcriptomic data from MDA-MB-231 cells stimulated with LPA
MDA-MB-231+LPA_2


title: MDD matched sample pair brain anterior cingulate cortex BA25_M #20


title: PC3 cells stimulated with LPA, Rep1

description:
Transcriptomic data from PC3 cells stimulated with LPA
PC3+LPA_1


title: Control matched sample pair brain anterior cingulate cortex BA25_M #26


title: MDD matched sample pair brain anterior cingulate cortex BA25_M #25


title: MDD matched sample pair brain anterior cingulate cortex BA25_M #2


title: MCF7 cells stimulated with LPA, Rep2

description:
Transcriptomic data from MCF7 cells stimulated with LPA
MCF7+LPA_2


title: MDD matched sample pair brain anterior cingulate cortex BA25_M #11


title: MDD matched sample pair brain anterior cingulate cortex BA25_M #7


title: Control matched sample pair brain anterior cingulate cortex BA25_M #29


title: MDD matched sample pair brain anterior cingulate cortex BA25_M #18


title: MDD matched sample pair brain anterior cingulate cortex BA25_M #22


title: Serum starved PC3 cells, Rep2

description:
Transcriptomic data from Serum starved PC3 cells (Without LPA stimulation)
PC3-LPA_2

source_name: PC3 cells, Serum starved


title: Serum starved PC3 cells, Rep1

description:
Transcriptomic data from Serum starved PC3 cells (Without LPA stimulation)
PC3-LPA_1


title: MDD matched sample pair brain anterior cingulate cortex BA25_M #4


title: Serum starved MDA-MB-231 cells, Rep1

description:
Transcriptomic data from Serum starved MDA-MB-231 cells (Without LPA stimulation)
MDA-MB-231-LPA_1

source_name: MDA-MB-231 cells, Serum starved


title: MDD matched sample pair brain anterior cingulate cortex BA25_M #29


title: Serum starved MDA-MB-231 cells, Rep2

description:
Transcriptomic data from Serum starved MDA-MB-231 cells (Without LPA stimulation)
MDA-MB-231-LPA_2


title: Control matched sample pair brain anterior cingulate cortex BA25_M #22


title: Control matched sample pair brain anterior cingulate cortex BA25_M #25


title: Control matched sample pair brain anterior cingulate cortex BA25_M #30


title: Control matched sample pair brain anterior cingulate cortex BA25_M #11


title: Control matched sample pair brain anterior cingulate cortex BA25_M #4


title: Control matched sample pair brain anterior cingulate cortex BA25_M #20


title: MDD matched sample pair brain anterior cingulate cortex BA25_F #17


title: Control matched sample pair brain anterior cingulate cortex BA25_M #15


title: Control matched sample pair brain anterior cingulate cortex BA25_M #7


title: MDD matched sample pair brain anterior cingulate cortex BA25_F #21


title: MDD matched sample pair brain anterior cingulate cortex BA25_F #24


title: MDD matched sample pair brain anterior cingulate cortex BA25_F #14


title: MDD matched sample pair brain anterior cingulate cortex BA25_F #13


title: MDD matched sample pair brain anterior cingulate cortex BA25_F #10


title: MDD matched sample pair brain anterior cingulate cortex BA25_F #19


title: MDD matched sample pair brain anterior cingulate cortex BA25_F #12


title: Control matched sample pair brain anterior cingulate cortex BA25_M #18


title: MDD matched sample pair brain anterior cingulate cortex BA25_F #5


title: MDD matched sample pair brain anterior cingulate cortex BA25_F #9


title: MDD matched sample pair brain anterior cingulate cortex BA25_F #16


title: Control matched sample pair brain anterior cingulate cortex BA25_M #2


title: MDD matched sample pair brain anterior cingulate cortex BA25_F #8


title: Control matched sample pair brain anterior cingulate cortex BA25_F #24


title: MDD matched sample pair brain anterior cingulate cortex BA25_F #3


title: Control matched sample pair brain anterior cingulate cortex BA25_F #14


title: Control matched sample pair brain anterior cingulate cortex BA25_F #17


title: Control matched sample pair brain anterior cingulate cortex BA25_F #19


title: Control matched sample pair brain anterior cingulate cortex BA25_F #21


title: Control matched sample pair brain anterior cingulate cortex BA25_F #10


title: Control matched sample pair brain anterior cingulate cortex BA25_F #12


title: Control matched sample pair brain anterior cingulate cortex BA25_F #9


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #16

source_name: MDD sample, brain dorsolateral prefrontal cortex

value: brain dorsolateral prefrontal cortex


title: Control matched sample pair brain anterior cingulate cortex BA25_F #16


title: Control matched sample pair brain anterior cingulate cortex BA25_F #8


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #13


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #17


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #28


title: Control matched sample pair brain anterior cingulate cortex BA25_F #13


title: Control matched sample pair brain anterior cingulate cortex BA25_F #5


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #21


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #24

source_name: Control sample, brain dorsolateral prefrontal cortex


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #28


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #3


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #10


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #9


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #5


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #19


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #14


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #8


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #12


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #24


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #6


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #21


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #19


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #16


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #12


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #17


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #13


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #14


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #10


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #9


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #6


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #3


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_M #30


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #8


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_M #29


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_M #26


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_M #27


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_M #4


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_M #2


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_M #20


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_F #5


title: Control matched sample pair brain anterior cingulate cortex BA25_F #3


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_M #15


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_M #11


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_M #1


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_M #25


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_M #7


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_M #25


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_M #30


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_M #22


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_M #29


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_M #22


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_M #27


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_M #1


title: MDD matched sample pair amygdala MD1_AMY #17

value: brain amygdala


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_M #7

value: Control


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_M #18


title: MDD matched sample pair amygdala MD1_AMY #18


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_M #26


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_M #15


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_M #4


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_M #2


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_M #20


title: MDD matched sample pair amygdala MD1_AMY #19


title: Control matched sample pair brain dorsolateral prefrontal cortex BA9_M #11


title: MDD matched sample pair brain dorsolateral prefrontal cortex BA9_M #18


title: MDD matched sample pair amygdala MD1_AMY #20


title: MDD matched sample pair amygdala MD1_AMY #1


title: MDD matched sample pair amygdala MD1_AMY #11


title: Control matched sample pair amygdala MD1_AMY #19


title: MDD matched sample pair amygdala MD1_AMY #12


title: Control matched sample pair amygdala MD1_AMY #13


title: MDD matched sample pair amygdala MD1_AMY #9


title: MDD matched sample pair amygdala MD1_AMY #15


title: MDD matched sample pair amygdala MD1_AMY #5


title: Control matched sample pair amygdala MD1_AMY #20


title: MDD matched sample pair amygdala MD1_AMY #2


title: MDD matched sample pair amygdala MD1_AMY #10


title: Control matched sample pair amygdala MD1_AMY #18


title: Control matched sample pair amygdala MD1_AMY #17


title: Control matched sample pair amygdala MD1_AMY #15


title: Control matched sample pair amygdala MD1_AMY #12


title: Control matched sample pair amygdala MD1_AMY #9


title: Control matched sample pair amygdala MD1_AMY #1


title: Control matched sample pair amygdala MD1_AMY #4


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #17


title: Control matched sample pair amygdala MD1_AMY #5


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #20


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #18


title: Control matched sample pair amygdala MD1_AMY #11


title: Control matched sample pair amygdala MD1_AMY #10


title: MDD matched sample pair amygdala MD1_AMY #13


title: Control matched sample pair amygdala MD1_AMY #2


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #15


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #13


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #12


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #19


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #7


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #9


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #11


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #6


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #5


title: Control matched sample pair anterior cingulate cortex MD1_ACC #19


title: Control matched sample pair anterior cingulate cortex MD1_ACC #18


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #4


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #2


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #1


title: Control matched sample pair anterior cingulate cortex MD1_ACC #20


title: Control matched sample pair anterior cingulate cortex MD1_ACC #15


title: MDD matched sample pair anterior cingulate cortex MD1_ACC #10


title: Control matched sample pair anterior cingulate cortex MD1_ACC #13


title: Control matched sample pair anterior cingulate cortex MD1_ACC #12


title: Control matched sample pair anterior cingulate cortex MD1_ACC #10


title: Control matched sample pair anterior cingulate cortex MD1_ACC #7


title: Control matched sample pair anterior cingulate cortex MD1_ACC #5


title: Control matched sample pair anterior cingulate cortex MD1_ACC #4


title: Control matched sample pair anterior cingulate cortex MD1_ACC #9


title: Control matched sample pair anterior cingulate cortex MD1_ACC #11