title: iDCs_GM-CSF and curdlan_48h

city: Changchun

first: Yinghua

last: Zhao

address: Dongminzhu street 519

institute: 1st hosptal of Jinli University

description: immature DCs (iDCs) were matured with GM-CSF (10ng/mL) and curdlan (5μg/mL).

hyb_protocol: MOA v2.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: MOA v2.1 The arrays were scanned by Agilent Microarray Scanner (G2505C)  0.1 XDR protocol and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

source_name: Mice bone marrow

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: Bone marrow cells were cultured in RPMI 1640 complete medium supplemented with GM-CSF (20ng/mL) and IL-4 (10ng/mL). At day 4, culture medium was removed and replaced with fresh GM-CSF/IL-4–containing medium. At day 7, semi-adherent cells were collected as immature DCs (iDCs) and matured.

extract_protocol: RNA extraction by Trizol Reagent ((Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

value: Balb/c

value: 6-8 weeks

value: bone marrow

value: dendritic cells


title: bone marrow_wildtype_no Dox_rep3

status: Public on May 05 2016

type: RNA

city: Cincinnati

first: Marc

middle: E

last: Rothenberg

state: OH

address: 3333 Burnet Ave. MLC-7028

department: Allergy

country: USA

institute: Cincinnati Children's Hospital Medical Center

description: PirB WT3 no Dox BM

hyb_protocol: 3.85ug of fragmented cDNA were hybridized to a Mouse Gene 2.0 ST arrays (Affymetrix).  Probe arrays were incubated at 45C for 17 hours in the Hybridization Oven 640 (Affymetrix) rotating at 60 rpm.  Probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix), utilizing the fluidics protocol FS450-0002.  The Stain and Antibody solutions are produced by Affymetrix and contained in the Genechip Hybridization Wash and Stain Kit.

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

data_processing: The .cel were created by Common Console (Affymetrix).  The .cel files were analyzed by Expression Console (Affymetrix) to create the .chp files.  The Data were analyzed using Genespring software with a fold-change cutoff of 2 (FC>2) and unpaired Student's t test (P>0.05).  Heat plots and Venn diagrams were generated according to gene lists that were generated by GeneSpring software (Agilent, Santa Clara, CA).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: bone marrow, wildtype, no Dox

label_protocol: The resulting cDNA was fragmented and labeled with the Nugen Encore Biotin Module (cat#4200) per manufacturers instructions.

growth_protocol: Male and females 6-8 week old CC10-IL13Tg/Pirb-/- and littermate control CC10-IL13Tg/Pirb+/+ mice were used.

extract_protocol: The esophagus was removed from the mice and digested with Collagenase to form a single cell suspension.  The bone marrow was also removed from the mice and passed through a needle to form a single cell suspension.  The cells were sorted by flow cytometry, CD45+/SiglecF+/CCR3+, to isolate the eosinophils.  RNA was then extracted from the eosinophils per manufacturers instructions with a Qiagen RNeasy Mini kit (cat#74106).  The RNA was then amplified using Nugen Ovation One-Direct system (cat#3500) per manufacturers instructions.

treatment_protocol: IL13 transgene expression was induced by feeding the CC10-IL13 Tg mice doxycycline-impregnated food (DOX) for two weeks.

tag: tissue

value: Bone marrow

tag: cell type

value: Eosinophils

tag: genotype/variation

value: wildtype

tag: treatment

value: no Dox


title: H37Rv_1.5BDQ_0Hr_rep1

city: Seattle

first: Shuyi

last: Ma

state: Washington

address: 1900 9th Avenue

department: Department of Pediatrics

institute: University of Washington

description:
raw data file: 20150206_EP-D1T0_1-5_v_MS-D1T0_1-5.txt
EP-D1T0_1.5

hyb_protocol: Each pair of differentially labeled probes was resuspended in 45μL of hybridization buffer (4.5 μL Agilent 10x blocking agent, 22.5μL Agilent 2x hybridization buffer, Dnase/Rnase-free water) and hybridized to the microarray slide overnight in a 42C incubator.

scan_protocol: Slides were washed in increasingly stringent wash conditions using Agilent Wash Buffers I and II.

data_processing:
Arrays were scanned and spots were quantified using PerkinElmer ScanArray Express scanner.
These data were exported to ArrayStar DNASTAR software (version 4.1.0) for RMA normalization and analysis. Paired samples were processed as though they are single channels (no Cy3/Cy5 ratios calculated). Spots flagged as ‘Not Found’ by the ScanArray software algorithms were excluded from downstream analysis.

organism: Mycobacterium tuberculosis

source_name: H37Rv_1.5 μM Bedaquiline for 0hr

label_protocol: Up to 3μg of total RNA was used to create cDNA labeled with aminoallyl dUTP (Fermentas). Fluores- cent Cy3 and Cy5 dyes (Amersham) were then covalently attached to the aminoallyl tags.

growth_protocol: Mycobacteria tuberculosis strain H37Rv (ATCC 27294) were grown on Middlebrook 7H9 medium (Difco) with 0.05% Tween 80 and ADC supplement.

extract_protocol: RNA was isolated and applied to custom tiled Agilent arrays using published protocols (Rustad TR, Harrell MI, Liao R, Sherman DR (2008) The Enduring Hypoxic Response of Mycobacterium tuberculosis. PLoS ONE 3(1): e1502). In summary, frozen cell pellets Pellets were resuspended in Trizol, transferred to a tube containing Lysing Matrix B (QBiogene, Inc.), and vigorously shaken at max speed for 30 sec in a FastPrep 120 homogenizer (Qbiogene) three times, with cooling on ice between steps. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a tube containing 300 mL chloroform and Heavy Phase Lock Gel (Eppendorf North America, Inc.), inverted for one minute, and centrifuged at max speed. The aqueous phase was then precipitated with 270 mL isopropanol and 270 mL high salt solution (0.8M Na citrate, 1.2M NaCl). RNA was cleaned using an RNeasy kit following manufacturer’s recommendations (Qiagen).

treatment_protocol: Bacteria were harvested at 1, 6, 24, 48, 96 hrs after being exposed to concentrations of bedaquiline (no drug, 1.5M, 15M) during a 7-day drug exposure time course experiment (as indicated in each sample title).

tag: strain

tag: bedaquiline dose

tag: exposed to

value: 1.5 μM Bedaquiline for 0hr


title: bone marrow_wildtype_no Dox_rep1

description: PirB WT1 no Dox BM


title: iDCs_GM-CSF,TNF-α and IL-1β_48h

country: China

description: immature DCs (iDCs) were matured with GM-CSF (10ng/mL),TNF-α (10ng/mL) and IL-1β (10ng/mL) .

tag: age


title: MC1-ZE16, RA50 day4 rep1

status: Public on May 04 2016

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

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

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 14 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr (adjust to UMR)
(4) Remove outliers. Each cell/treatment type (CTT) is characterized by 2 replications, all are log-transformed (log10). Here we check if any of these values is an outlier.
First we estimate the average square difference (ASD) between replication pairs:
ASD = SUM[(x(i,1)-x(i,2))^2]/N/2
where x(i,j) is logintensities for i-th CTT and replication j, N = number of CTT. Then we estimate z-value for each CTT:  z =  (x(i,1)-x(i,2))/sqrt(ASD). If abs(z) > 4 then one of the replications is an outlier. The value that is farther away from the median expression value is considered an outlier and it is replaced with the value from another replication.
The result is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: TrizolTM (Invitrogen) was added to picked pooled colonies. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 15ul of DEPC dH2O.

treatment_protocol: 129 MC1 ES cells were plated into 6-well gelatinized plates in LIF+ standard ES medium supplemented with 50nM retinoic acid (RA). On the day4 of culture Trizol was added and RNA extracted

value: ES

tag: gender

value: male

tag: individual identifier

tag: cell line

tag: protocol

value: RA50 day4

source_name: Universal Mouse Reference 129ES Cell

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

value: Universal Mouse Reference


title: MC1-ZE-3 LY294002 48h rep2

treatment_protocol: 129 MC1 ES cells were plated into 6-well gelatinized plates in LIF+ standard ES medium and cultured for 24 hrs. After 24 hrs standard ES medium with 10nM LY294002 was added for 48 hrs. Fresh medium was replaced every day.

value: unknown sex


title: MC1-ZE-3 LY294002 48h rep1


title: H37Rv_0BDQ_0Hr_rep1

description:
raw data file: 20150206_EP-D1T0_WT_v_MS-D1T0_WT.txt
EP-D1T0_WT

source_name: H37Rv_0 μM Bedaquiline for 0hr

value: 0 μM

value: 0 μM Bedaquiline for 0hr


title: MC1-ZE3 day3 2nd replication P10 day3 rep2

treatment_protocol: cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in ES medium .

value: RA for 7days, 10 passages in standard conditions (without RA). RNA collected on day 3.


title: MC1-ZE3 day3 rep2

value: standard conditions, day3


title: MC1-ZE16, RA50 day4 rep2


title: MC1-ZE-3 control day3 rep1

description: control(GrowthFactors)

source_name: control(GrowthFactors)

treatment_protocol: 129 MC1 ES cells were grown for 3 days in LIF+ standard ES medium. Fresh medium was replaced every day.

value: control, day3


title: MC1-ZE-3 control day3 rep2

description: control(GrowthFactors)


title: MC1-ZE-3 atRA50 48h rep1

treatment_protocol: 129 MC1 ES cells were plated into 6-well gelatinized plates in LIF+ standard ES medium and cultured for 24 hrs. After 24 hrs standard ES medium with 50nM atRA was added for 48 hrs . Fresh medium was replaced every day.


title: ES MC1 Intact Lif+ RA rep1

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 50ul of DEPC dH2O.

value: ES MC1

value: RA, day7


title: ES MC1 Intact Lif+ RA rep2


title: MC1-ZE-3 atRA50 48h rep2


title: Hypothalamus_LUN_biorep5

city: Olsztyn

first: Monika

middle: M

last: Kaczmarek

address: Tuwima 10

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

description:
5130701018_E_LUN3
Biological replicate 5

hyb_protocol: Illumina Whole Genome Expression Direct Hybridization Assay Guide - 750 ng labeled cRNA hybridized to array.

scan_protocol: Standard Illumina scanning protocol was used.

data_processing: Scanned images were analyzed using Illumina GenomeStudio Gene Expression Module v 1.9.0 for background subtraction. Baseline transformation to the median of all samples was applied, and then data were normalized among the samples by quantile method (GeneSpring GX 10 Software, Agilent). The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring GX 10 Software.

source_name: Hypothalamus, lactation under-nourished mouse

label_protocol: Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for Illumina (TAN07924) - Manufacturer's protocol 400ng input total RNA.

extract_protocol: Total RNA from the hypothalamus of 8 LUN and 8 CON mice was isolated using TRI Reagent and BCP phase separation reagent (Molecular Research Center Inc. Cincinnati, OH, United States). RNA was further purified using the RNeasy minikit (QIAGEN, Valencia, CA, United States) and stored at -80°C in RNase-free H2O with addition of SUPERase-In (Ambion, Austin, TX, United States) for RNA protection. Quality and quantity of RNA were determined using UV spectrophotometry (NanoDrop). RNA with RNA Integrity number higher than 7.9 (Agilent 2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA) was used for microarray analysis of each individual mouse.

treatment_protocol: Newborn F1 C57BL/6J mice were raised from birth to weaning with one of two sets of nutritional conditions: 1) the control condition (CON) fed ad libitum, 2) lactation under-nutrition condition (LUN) fed 50% of the food consumed by the control mice the previous 24 hr. Female mice were used for the analysis at 21 days of post-natal development.

tag: strain/background

value: female

value: 21 days

value: hypothalamus

tag: nutrition

value: lactation under-nutrition


title: Hypothalamus_LUN_biorep8

description:
5130701018_H_LUN9
Biological replicate 8


title: MC1-ZE3 day3 rep1


title: Hypothalamus_LUN_biorep6

description:
5130701018_F_LUN5
Biological replicate 6


title: Hypothalamus_LUN_biorep7

description:
5130701018_G_LUN7
Biological replicate 7


title: Hypothalamus_LUN_biorep4

description:
5130701017_H_LUN8
Biological replicate 4


title: Hypothalamus_LUN_biorep1

description:
5130701017_E_LUN2
Biological replicate 1


title: Hypothalamus_LUN_biorep2

description:
5130701017_F_LUN11
Biological replicate 2


title: MC1-ZE3 day3 2nd replication P10 day3 rep1


title: Hypothalamus_CON_biorep8

description:
5130701018_D_CON10
Biological replicate 8

source_name: Hypothalamus, control mouse

value: ad libitum


title: Hypothalamus_CON_biorep5

description:
5130701018_A_CON3
Biological replicate 5


title: Hypothalamus_CON_biorep7

description:
5130701018_C_CON7
Biological replicate 7


title: Hypothalamus_CON_biorep3

description:
5130701017_C_CON6
Biological replicate 3


title: Hypothalamus_CON_biorep6

description:
5130701018_B_CON5
Biological replicate 6


title: A_T1_D2_025

city: Ottawa

first: Vinita

last: Chauhan

state: Ontario

address: 775 Brookfield Rd

country: Canada

institute: Health Canada

hyb_protocol: Samples were hybridized on Illumina human-12 v3 RNA BeadChips.

scan_protocol: BeadChips were imaged and quantified with the Illumina iScan scanner.

data_processing: Data pre-processing was carried out within GenomeStudio v2010.2.2. The data was median normalized (50th percentile) where the intensities were averaged per probe/gene. Normalization of dataset was conducted in GeneSpring (version GX 11.5).

organism: Homo sapiens

source_name: human cell cultures

label_protocol: cRNA was labeled using biotin following protocols  in Genome Expression Profiling Assay Guide (11317302 Rev. A).

growth_protocol: Cells were maintained in a humidified incubator (37oC, 5% CO2/95% air) in 75 cm2 tissue culture flasks (Costar, Cambridge, MA, USA). The cells were grown to confluence for 2-3 days in Royal Park Medical Institute-1640 (RPMI-1640) (Invitrogen Canada, Burlington, ON Canada) medium, containing 10% fetal bovine serum (FBS) (Sigma-Aldrich Canada, Oakville, ON, Canada).  A total of 1.0x106 cells were seeded into 5 mL of culture media containing 100 units/mL of penicillin and 100 µg/mL of streptomycin (Invitrogen Canada Inc.).

extract_protocol: The pelleted cells were resuspended in 350 µL of Buffer RLT containing 1% β-Mercaptoethanol (Qiagen’s RNeasy Mini kit; Qiagen Inc, Mississauga, ON) then frozen at -80oC until processed.   Frozen THP-1 cells were thawed on ice and mixed well by pipetting. The lysate was transferred directly onto a QIAshredder spin column (Qiagen Inc), placed in a 2 mL collection tube and centrifuged for 2 min at ~12,000 g. A volume of 350 µL of 70% ethanol was added. Total RNA was then extracted using the RNeasy Mini kit according to the manufacturer’s instructions (Qiagen Inc), with the addition of Qiagen’s On-Column RNase-free DNase (Qiagen Inc) to eliminate any remaining DNA contamination. All total RNA sample concentrations and RNA quality were determined using both an Agilent 2100 Bioanalyzer and RNA Nanochips (Agilent Technologies Canada Inc., Mississauga, ON) and spectrophotometrically using an Ultrospec 2100 (Fisher Scientific) (OD ratio of A260:A280). All extracted RNA samples were determined to be of good quality (RNA Integrity Number=10) with minimal degradation and stored at -80oC until further analysis.  The pelleted cells were resuspended in 350 µL of Buffer RLT containing 1% β-Mercaptoethanol (Qiagen’s RNeasy Mini kit; Qiagen Inc, Mississauga, ON) then frozen at -80oC until processed.   Frozen THP-1 cells were thawed on ice and mixed well by pipetting. The lysate was transferred directly onto a QIAshredder spin column (Qiagen Inc), placed in a 2 mL collection tube and centrifuged for 2 min at ~12,000 g. A volume of 350 µL of 70% ethanol was added. Total RNA was then extracted using the RNeasy Mini kit according to the manufacturer’s instructions (Qiagen Inc), with the addition of Qiagen’s On-Column RNase-free DNase (Qiagen Inc) to eliminate any remaining DNA contamination. All total RNA sample concentrations and RNA quality were determined using both an Agilent 2100 Bioanalyzer and RNA Nanochips (Agilent Technologies Canada Inc., Mississauga, ON) and spectrophotometrically using an Ultrospec 2100 (Fisher Scientific) (OD ratio of A260:A280). All extracted RNA samples were determined to be of good quality (RNA Integrity Number=10) with minimal degradation and stored at -80oC until further analysis.

treatment_protocol: The cells were exposed to α-particle radiation at doses ranging from 0.0 (control) to 1.5 Gy, using 241Americium (241Am) electroplated discs (Eckert and Ziegler Isotope Products Ltd, Valencia, CA, USA) having an activity level of 66.0 kBq ± 3% (dose rate of 0.98 ± 0.01 Gy/h, LET of 127.4±0.4 keV/m).

value: Alpha

tag: dose (gy)

tag: time point (h) 1=24h 2=72h


title: Hypothalamus_CON_biorep2

description:
5130701017_B_CON4
Biological replicate 2


title: A_A1_D1_012


title: Hypothalamus_LUN_biorep3

description:
5130701017_G_LUN6
Biological replicate 3


title: A_T2_D2_054


title: A_P1_D1_086

value: HPEAC


title: A_A1_D3_015


title: SSF CP (11c+)

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: CD11c positive, replicate 2

hyb_protocol: Hybridization of Affymetrix Mouse Genome 430 PM Strip arrays were performed following the manufacturer’s recommendations.

scan_protocol: Staining and scanning of Affymetrix Mouse Genome 430 PM Strip arrays were performed following the manufacturer’s recommendations.

data_processing: Images intensities were extracted using GeneAtlas System software (Affymetrix), normalized and summarized using Robust Multi-array Average algorithm. Differential gene expression analysis assessed by fitting to an empirical Bayesian linear model. Statistical significance in differential gene expression was computed with a false discovery rate multiple testing adjustment correction. For this analysis we used the Limma package and the R statistical programming environment (Smyth, 2005).

label: Biotin

source_name: Effector lymphocytes

label_protocol: Biotinylated cRNA was prepared by terminal transferase from the GeneChip Mapping 250K Nsp Assay Kit (AffymetrixInc, Santa Clara, CA, USA).

growth_protocol: 6 to 8-week-old female C57BL/6 mice were bred in house. Mice were kept in ventilated cages with sterile food and water ad libitum, under specific-pathogen-free (SPF) conditions at the animal facility for experimental models of the Germans Trias i Pujol Health Science Research Institute (IGTP), Spain. All experimental proceedures were approved and supervised by the Animal Care Committee of the Germans Trias i Pujol University Hospital and by the Department of Environment of the Catalan Government in agreement with the European Union Laws for the protection of experimental animals. A group of six females was treated subcutaneously with 3 mg of Depo-Provera five days prior to euthanasia in order to synchronize their menstrual cycle and thus homogenize the endocrine effects on immunity. All mice were euthanized with isoflurane (inhalation excess) and blood was immediately obtained by cardiac puncture.

extract_protocol: RNA isolation and cDNA amplification were performed as described in Gonzalez-Roca et al. (2010). In brief, 300 cells were sorted into lysis buffer and RNA was purified using magnetic beads (RNAClean XP beads, Agencourt). RNA was reverse transcribed and cDNA was amplified using Whole Transcriptome Amplification chemistry (WTA2, Sigma Aldrich). For monitoring amplification, SYBR Green was added to the reaction; it was stopped after 24 cycles when SYBR Green signal reached a plateau. cDNA was purified using GenElute PCR Clean up kit (Sigma).

treatment_protocol: Blood samples were immediately lysed using a RBC lysis buffer (containing 20.75 g/l NH4Cl, 2.5 g/l NaHCO3 and 0.093 g/l EDTA in distillated water). After washing twice, cells were stained with following cocktail of pre-titrated anti-mouse Abs: CD3-Vioblue (145-2C11), CD4-Allophycocyanin (APC)-H7 (GK1.5), CD62L-PE (MEL-14-H2.100) (MiltenyiBiotec, Madrid, Spain), CD44-Brilliant Violet 570  (IM7) (BioLegend, San Diego, CA) and CD11c-PE-Cy7 (HL3) (BD Biosciences, San Jose, CA), for 20 mins. Cells suspended in cold FACS flow buffer  (0,5% FBS-PBS with 0.5mM EDTA) were immediately sorted into 350μl of chilled RLT buffer (QIAGEN, Valencia, CA) using a BD FACSAriaTM Cell Sorter.

value: CD11c positive T cells

tag: individual

value: mouse C

tag: Sex

value: 6-8 weeks-old


title: Hypothalamus_CON_biorep4

description:
5130701017_D_CON8
Biological replicate 4

tag: tissue


title: Hypothalamus_CON_biorep1

description:
5130701017_A_CON2
Biological replicate 1


title: X_A1_D3_104

value: X-Ray

tag: cell type


title: A_T2_D3_047

tag: treatment


title: A_A1_D2_013


title: SSF AP (11c+)

description: CD11c positive, replicate 1

tag: strain

value: mouse A


title: SSF CN (11c-)

description: CD11c negative, replicate 2

value: CD11c negative T cells


title: SSF DP (11c+)

description: CD11c positive, replicate 3

value: mouse D


title: SSF AN (11c-)

description: CD11c negative, replicate 1


title: A_A1_D1_004


title: A_T2_D3_048


title: SSF DN (11c-)

description: CD11c negative, replicate 3


title: A_T1_D2_026


title: A_T2_D2_046


title: C4HD_premiR16_Rep2

city: Ciudad Autónoma de Buenos Aires

first: Patricia

middle: Virginia

last: Elizalde

state: Ciudad Autónoma de Buenos Aires

address: Vuelta de Obligado 2490

country: Argentina

institute: Instituto de Biología y Medicina Experimental

description: Gene expression in C4HD primary tumor culture after 48hr transfection with pre-miR-16 30nM

hyb_protocol: For each sample, 1.65 µg of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven. Slides were washed and then scanned with an Agilent Scanner

scan_protocol: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

data_processing: The Agilent Feature Extraction software performed error modeling, adjusting for additive and multiplicative noise. Pre-processing of the data and quality control were conducted using R statistical software via the Agi4x44PreProcess (Pedro Lopez-Romero; PreProcessing of Agilent 4x44 array data. R package version 1.22.0) Bioconductor package. Extracted intensities were background-corrected using the normexp method and were then quantile normalized and log2 transformed.

source_name: C4HD primary tumor culture, pre-miR-16 30nM transfected, Replicate 2

label_protocol: Starting with 300 ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Hormone-dependent ductal tumors (C4HD) originated in mice treated with 40 mg medroxyprogesterone acetate (MPA) every 3 months for a year, and have been maintained by serial transplantation in animals treated with 40 mg s.c. MPA depot on the opposite flank to tumor inoculum. Primary cultures of epithelial cells from C4HD tumors, growing in MPA-treated mice, were performed as previously described. In brief, tumors were aseptically removed, minced and washed with DMEM/F12 (Dulbecco's modified Eagle's medium: Ham's F12, 1:1, without phenol red, 100 U/ml penicillin and 100 μg/ml Streptomycin). The tissue was suspended in 5 ml of enzymatic solution [trypsin: 2.5 mg/ml, albumin: 5 mg/ml and collagenase type II (Gibco-BRL, Gaithersburg, MD): 239 U/ml] in phosphate buffered saline (PBS) and incubated at 37°C for 20 min, under continuous stirring. The liquid phase of the suspension was then removed and the undigested tissue was incubated with fresh enzymatic solution for 20 min. Enzyme action was stopped by adding DMEM/F12+5% heat inactivated fetal calf serum (FCS) (Gen S.A., Buenos Aires). Epithelial and fibroblastic cells were separated as already described. Briefly, the cell suspension was resuspended in 15 ml of DMEM/F12+10% FCS and allowed to sediment for 20 min. The upper 5 ml, corresponding to the fibroblastic fraction, was seeded in flasks, and the cells were allowed to attach during 1 - 2 h after which the medium containing unattached cells was removed and replaced by fresh DMEM/F12+10% FCS. The sedimented cells, corresponding to the epithelial enriched fraction, were resuspended again in 15 ml of DMEM/F12+5% FCS and allowed to sediment for another 20 min. The upper 15 ml were discarded and this procedure was repeated until no fibroblasts were observed in the supernatant. Cells were plated in culture flasks with DMEM/F12+5% steroid-stripped FCS (ChFCS) and allowed to attach for 24 - 48 h.

extract_protocol: Total RNA was extracted using the miRVANA Paris RNA Extraction Kit (Ambion, Austin, TX), following the manufacturer's instructions. RNA was quantified using a NanoDrop-2000 (Thermo Fisher Scientific) spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: miRNA precursors were obtained from Life Technologies and were used in accordance with the manufacturer's instructions. Briefly, 30 nM pre-miR-16 (AM17100) or a pre-miR-Control (AM17110) that does not form any known mammalian miRNA were transfected for 48hs using the siPORT NeoFx transfection reagent (Ambion).

value: BALB/c

value: Female

tag: transfection

value: primary cultures of the C4HD murine breast tumor


title: A_T2_D1_052


title: S14_Pre_normoxic bedrest (NBR)

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: Subject 14, First Intervention: normoxic bedrest (NBR), Pre

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix miRNA_4.1 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Not provided

data_processing: The probe-set level intensities of the arrays were normalized using the Robust Multi-array Analysis method (RMA) implemented withinAffymetrix Expression Console version 1.4.1.

source_name: Human skeletal muscle, Vastus lateralis

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

extract_protocol: Biopsies were obtained from the vastus lateralis muscle using the Bergström needle technique. The biopsies were immediately stored in liquid nitrogen until processing. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Vastus lateralis

value: Male

tag: condition

value: normoxic bedrest (NBR)

tag: subject

value: First

tag: time

value: Pre


title: S14_Post_normoxic bedrest (NBR)

description: Subject 14, First Intervention: normoxic bedrest (NBR), Post

tag: gender

value: Post


title: A_H1_D1_063

value: Alpha

value: HLF


title: C4HD_premiR16_Rep1

source_name: C4HD primary tumor culture, pre-miR-16 30nM transfected, Replicate 1


title: A_P1_D2_091

value: HPEAC


title: A_A1_D2_005


title: A_A1_Co_009


title: A_P1_D1_089


title: S14_Post_hypoxic bedrest (HBR)

description: Subject 14, Second Intervention: hypoxic bedrest (HBR), Post

value: hypoxic bedrest (HBR)

value: Second


title: C4HD_premiRCtrl_Rep3

description: Gene expression in C4HD primary tumor culture after 48hr transfection with pre-miR-Control 30nM

source_name: C4HD primary tumor culture, pre-miR-Ctrl 30nM transfected, Replicate 3

value: pre-miR-Control


title: C4HD_premiRCtrl_Rep2

source_name: C4HD primary tumor culture, pre-miR-Ctrl 30nM transfected, Replicate 2


title: C4HD_premiR16_Rep3

source_name: C4HD primary tumor culture, pre-miR-16 30nM transfected, Replicate 3


title: S14_Post_hypoxic ambulatory confinement (HAMB)

description: Subject 14, Third Intervention: hypoxic ambulatory confinement (HAMB), Post

value: hypoxic ambulatory confinement (HAMB)

value: Third


title: S14_Pre_hypoxic bedrest (HBR)

description: Subject 14, Second Intervention: hypoxic bedrest (HBR), Pre


title: C4HD_premiRCtrl_Rep1

source_name: C4HD primary tumor culture, pre-miR-Ctrl 30nM transfected, Replicate 1

value: BALB/c


title: S14_Pre_hypoxic ambulatory confinement (HAMB)

description: Subject 14, Third Intervention: hypoxic ambulatory confinement (HAMB), Pre


title: S13_Pre_normoxic bedrest (NBR)

description: Subject 13, First Intervention: normoxic bedrest (NBR), Pre


title: A_A1_D1_003


title: A_H1_D3_080


title: A_A1_Co_001


title: A_H1_Co_061


title: A_T2_D3_060


title: X_A1_Co_110

value: X-Ray


title: S13_Post_hypoxic bedrest (HBR)

description: Subject 13, Second Intervention: hypoxic bedrest (HBR), Post


title: S13_Post_normoxic bedrest (NBR)

description: Subject 13, First Intervention: normoxic bedrest (NBR), Post


title: S13_Pre_hypoxic bedrest (HBR)

description: Subject 13, Second Intervention: hypoxic bedrest (HBR), Pre


title: S13_Pre_hypoxic ambulatory confinement (HAMB)

description: Subject 13, Third Intervention: hypoxic ambulatory confinement (HAMB), Pre


title: S13_Post_hypoxic ambulatory confinement (HAMB)

description: Subject 13, Third Intervention: hypoxic ambulatory confinement (HAMB), Post


title: S12_Post_normoxic bedrest (NBR)

description: Subject 12, First Intervention: normoxic bedrest (NBR), Post


title: S11_Post_normoxic bedrest (NBR)

description: Subject 11, First Intervention: normoxic bedrest (NBR), Post


title: A_T2_Co_050


title: S12_Post_hypoxic bedrest (HBR)

description: Subject 12, Second Intervention: hypoxic bedrest (HBR), Post


title: S12_Pre_normoxic bedrest (NBR)

description: Subject 12, First Intervention: normoxic bedrest (NBR), Pre


title: S12_Pre_hypoxic bedrest (HBR)

description: Subject 12, Second Intervention: hypoxic bedrest (HBR), Pre


title: A_T1_D1_031


title: A_P1_Co_081


title: X_A1_Co_106


title: A_H1_D2_065


title: S11_Pre_hypoxic bedrest (HBR)

description: Subject 11, Second Intervention: hypoxic bedrest (HBR), Pre


title: S11_Post_hypoxic bedrest (HBR)

description: Subject 11, Second Intervention: hypoxic bedrest (HBR), Post


title: A_A1_Co_010


title: S11_Pre_normoxic bedrest (NBR)

description: Subject 11, First Intervention: normoxic bedrest (NBR), Pre


title: S9_Pre_normoxic bedrest (NBR)

description: Subject 9, Third Intervention: normoxic bedrest (NBR), Pre


title: S9_Post_normoxic bedrest (NBR)

description: Subject 9, Third Intervention: normoxic bedrest (NBR), Post


title: A_T1_D1_023


title: CSB deficient cell line expressing CSB-K991R mutant, biological replicate2

city: London

first: Yuming

last: Wang

address: South Mimms

department: Mechanisms of Transcription Laboratory

country: United Kingdom

institute: Cancer Research UK

hyb_protocol: Following labelling, 4ug of Cy3-cDNA were hybridized for 16 hr at 42ºC on Nimblegen 12 x 135K human expression array by using Nimblegen hybridization kit. The array was washed using Nimblegen washing buffers followed by drying on a microarray dryer.

scan_protocol: The array was scanned using NimbleGen MS 200 Microarray scanner.

data_processing: Data was analyzed using Biocondutor 2.12 running on R3.0.0. Probe set expression measures were calculated using quantile normalization of log2 transformed data.

label: Cyanine 3

label_protocol: Double-stranded cDNA was synthesized using Nimblegen cDNA synthesis kit from 10-20 μg total RNA, up to 1 μg cDNA was labelled with Cy3 according to the standard Nimblegen protocol by using Nimblegen labeling kit.

growth_protocol: Transformed fibroblast cells were maintained in DMEM + 10% FBS. Cell lines for the tetracycline-inducible systems were cultured in DMEM + 10% Tet-free FBS, 5-10 ng ml-1 doxycycline was added to the cells 48 hr before total RNA isolation.

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) as per the manufacturer's instructions.

tag: cell line

value: human fibroblast derived from CS patient and transformed with SV40 T-antigen

tag: genotype/variation

value: expressing CSB-K991R


title: A_T2_D2_059


title: A_T2_Co_042


title: A_P1_D3_100


title: A_T1_D1_024


title: A_P1_D3_096


title: A_P1_D2_095


title: A_T1_D3_040


title: S8_Post_hypoxic bedrest (HBR)

description: Subject 8, First Intervention: hypoxic bedrest (HBR), Post

value: Vastus lateralis

value: Male


title: S8_Pre_hypoxic bedrest (HBR)

description: Subject 8, First Intervention: hypoxic bedrest (HBR), Pre

value: First


title: S8_Post_hypoxic ambulatory confinement (HAMB)

description: Subject 8, Second Intervention: hypoxic ambulatory confinement (HAMB), Post


title: S9_Pre_hypoxic ambulatory confinement (HAMB)

description: Subject 9, Second Intervention: hypoxic ambulatory confinement (HAMB), Pre

value: Pre


title: S9_Post_hypoxic ambulatory confinement (HAMB)

description: Subject 9, Second Intervention: hypoxic ambulatory confinement (HAMB), Post

value: Post


title: S9_Post_hypoxic bedrest (HBR)

description: Subject 9, First Intervention: hypoxic bedrest (HBR), Post


title: S7_Post_hypoxic bedrest (HBR)

description: Subject 7, First Intervention: hypoxic bedrest (HBR), Post


title: S9_Pre_hypoxic bedrest (HBR)

description: Subject 9, First Intervention: hypoxic bedrest (HBR), Pre


title: S8_Pre_hypoxic ambulatory confinement (HAMB)

description: Subject 8, Second Intervention: hypoxic ambulatory confinement (HAMB), Pre


title: S7_Pre_normoxic bedrest (NBR)

description: Subject 7, Third Intervention: normoxic bedrest (NBR), Pre

value: normoxic bedrest (NBR)


title: S7_Post_normoxic bedrest (NBR)

description: Subject 7, Third Intervention: normoxic bedrest (NBR), Post


title: A_T2_Co_041

value: Alpha


title: S7_Pre_hypoxic ambulatory confinement (HAMB)

description: Subject 7, Second Intervention: hypoxic ambulatory confinement (HAMB), Pre


title: S7_Post_hypoxic ambulatory confinement (HAMB)

description: Subject 7, Second Intervention: hypoxic ambulatory confinement (HAMB), Post


title: A_A1_D3_008


title: EBV-tumor 4

city: Boston

first: Gerburg

last: Wulf

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

description: gene expression data from described sample

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip庐Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and hybridized for 16 hr in the Affymetrix Hybridization Oven 640.

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

data_processing: Data were analyzed with Expression Console (Affymetrix) and normalized by RMA method.

source_name: breast tumor

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

growth_protocol: Cells were cultured in MCF-10A medium with Insulin, EGF, Hydrocortisone, Cholera Toxin, 5% hores serum

extract_protocol: RNA was extracted using the total RNA isolation mini kit (Agilent),  RNA quality and concentration were assessed using Nanodrop 1000 and agarose gel electrophoresis. Only RNA samples with absorbance ratio 260/280 > 1.8, preserved rRNA ratio (28S/18S) and no signs of degradation were used.

treatment_protocol: Growth the cell in MCF-10A medium or generate the tumor using EBV-HMEC-R or GFP-HMEC-R

value: xenograft


title: A_T2_D1_043


title: A_P1_D3_097

value: HPEAC


title: A_T2_D1_044


title: A_T2_D2_053


title: A_P1_Co_082


title: EBV-tumor 2


title: EBV-tumor 3


title: GFP-tumor 3


title: A_H1_D3_068

value: HLF


title: GFP-tumor 2


title: GFP-tumor 4


title: EBV-tumor 1


title: S5_Pre_normoxic bedrest (NBR)

description: Subject 5, Second Intervention: normoxic bedrest (NBR), Pre

value: Second


title: S5_Post_hypoxic ambulatory confinement (HAMB)

description: Subject 5, First Intervention: hypoxic ambulatory confinement (HAMB), Post

value: hypoxic ambulatory confinement (HAMB)


title: S5_Post_normoxic bedrest (NBR)

description: Subject 5, Second Intervention: normoxic bedrest (NBR), Post


title: GFP-HMEC

source_name: immortalized mammary epithelial cells

value: HMEC

value: mammary epithelial cells


title: S6_Pre_hypoxic ambulatory confinement (HAMB)

description: Subject 6, First Intervention: hypoxic ambulatory confinement (HAMB), Pre


title: EBV-HMEC


title: GFP-HMEC-R


title: EBV-MCF-10A-R


title: GFP-MCF-10A-R


title: GFP-MCF-10A


title: EBV-HMEC-R


title: S6_Post_normoxic bedrest (NBR)

description: Subject 6, Second Intervention: normoxic bedrest (NBR), Post


title: S6_Pre_normoxic bedrest (NBR)

description: Subject 6, Second Intervention: normoxic bedrest (NBR), Pre


title: S7_Pre_hypoxic bedrest (HBR)

description: Subject 7, First Intervention: hypoxic bedrest (HBR), Pre

value: hypoxic bedrest (HBR)


title: S5_Pre_hypoxic ambulatory confinement (HAMB)

description: Subject 5, First Intervention: hypoxic ambulatory confinement (HAMB), Pre


title: GFP-tumor 1


title: A_H1_Co_069


title: A_T1_D2_034


title: A_P1_D3_098


title: S6_Post_hypoxic bedrest (HBR)

description: Subject 6, Third Intervention: hypoxic bedrest (HBR), Post

value: Third


title: S6_Pre_hypoxic bedrest (HBR)

description: Subject 6, Third Intervention: hypoxic bedrest (HBR), Pre


title: A_T2_D2_045


title: A_T1_Co_022


title: S6_Post_hypoxic ambulatory confinement (HAMB)

description: Subject 6, First Intervention: hypoxic ambulatory confinement (HAMB), Post


title: A_H1_D1_070


title: X_A1_Co_108

value: X-Ray


title: EBV-MCF-10A


title: A_P1_D1_088


title: S4_Post_hypoxic bedrest (HBR)

description: Subject 4, Third Intervention: hypoxic bedrest (HBR), Post

value: Vastus lateralis


title: S4_Post_normoxic bedrest (NBR)

description: Subject 4, Second Intervention: normoxic bedrest (NBR), Post

value: Male


title: A_T1_D2_033


title: A_H1_D2_077


title: S4_Pre_hypoxic ambulatory confinement (HAMB)

description: Subject 4, First Intervention: hypoxic ambulatory confinement (HAMB), Pre

value: First


title: S4_Pre_hypoxic bedrest (HBR)

description: Subject 4, Third Intervention: hypoxic bedrest (HBR), Pre

value: Pre


title: A_T1_Co_037


title: S4_Post_hypoxic ambulatory confinement (HAMB)

description: Subject 4, First Intervention: hypoxic ambulatory confinement (HAMB), Post

value: Post


title: ABYPM2

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
raw data file: ABYPM12_252828211746_2.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with infantile spasms_postnatally treated with PMX53 P15_Replicate 2

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two rats were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 10.7.3.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.  Raw data files are available in a tar archive on the series record.
Data table contains normalized log2 ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

organism: Rattus norvegicus

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Time-pregnant Sprague-Dawley rats were purchased from approved source (Taconic Farms, Germantown, NY). The rats were housed individually during the remainder of their pregnancy in the animal facility with free access to standard rat chow and water on the regular 12 hour light-dark cycle with the lights on at 07:00 am.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE).

treatment_protocol: On G15, some pregnant rats received 2 injections of betamethasone (Sigma-Aldrich, St. Louis, MO) at 0.4 mg/kg each at 08:30 and 18:30; controls received vehicle (normal saline) instead. Delivery was consistent on G23, considered as postnatal day (P) 0 for the offspring. On P1, the offspring were identified and marked, and litters were culled down to four males. The rats prenatally exposed (G15) to betamethasone had repeated adiministration of N-Methyl-D-Aspartic acid on postnatal days 12, 13 and 15 which triggered infantile spasms. Pups were treated with either ATCH, PMX53 (a potent C5ar1 antagonist) or saline to act as a control, on days 13, 14 and 15 prior to NMDA administration to determine what effects each treatment had on transcriptome recovery.

value: male

value: Sprague-Dawley

value: hypothalamic arcuate nucleus

tag: developmental stage


title: S4_Pre_normoxic bedrest (NBR)

description: Subject 4, Second Intervention: normoxic bedrest (NBR), Pre

value: normoxic bedrest (NBR)


title: ABYPM3

description:
raw data file: ABYPM34_252828211746_1.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with infantile spasms_postnatally treated with PMX53 P15_Replicate 3


title: A_P1_D2_093

value: Alpha

value: HPEAC


title: ABYAM4

description:
raw data file: ABYAM34_252828211747_1.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with infantile spasms_postnatally treated with ACTH P15_Replicate 4


title: SNU-5

type: genomic

city: Thousand Oaks

first: Dan

last: Baker

state: CA

address: 1 Amgen Center Drive

department: Molecular Sciences

institute: Amgen Inc.

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to 2x400K microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed according to the manufacturer's instructions

scan_protocol: Scanned on an Agilent G2565A scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11), normalized log2 ratios were generated by OmicSoft ArrayStudio V8.1

molecule: genomic DNA

source_name: Cultured Cell Line

label_protocol: 250ng of purified genomic DNA was labeled with Cy-labeled primers using Exo- Klenow, according to the Roche Nimblegen dual color labeling protocol, with modifications

growth_protocol: Individual cell lines were cultured according to source guidelines

extract_protocol: Genomic DNA extracted using Qiagen Dneasy Blood and Tissue Kit, according the manufacturer's instructions

source_name: pooled genomic DNA from 40 healthy males

tag: sample type


title: ABYAM3

description:
raw data file: ABYAM34_252828211747_1.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with infantile spasms_postnatally treated with ACTH P15_Replicate 3


title: A_P1_D2_092

tag: dose (gy)


title: A_A1_D2_019

tag: time point (h) 1=24h 2=72h


title: ABYPM1

description:
raw data file: ABYPM12_252828211746_2.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with infantile spasms_postnatally treated with PMX53 P15_Replicate 1


title: OE33

value: pooled genomic DNA from 40 healthy males


title: ABYAM2

description:
raw data file: ABYAM12_252828211747_2.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with infantile spasms_postnatally treated with ACTH P15_Replicate 2


title: A_A1_Co_002


title: ABYPM4

description:
raw data file: ABYPM34_252828211746_1.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with infantile spasms_postnatally treated with PMX53 P15_Replicate 4


title: SNU-620


title: A_T1_D3_035


title: SNU-638


title: ABYAM1

description:
raw data file: ABYAM12_252828211747_2.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with infantile spasms_postnatally treated with ACTH P15_Replicate 1


title: S3_Pre_normoxic bedrest (NBR)

description: Subject 3, Second Intervention: normoxic bedrest (NBR), Pre

value: Second


title: ABYSM4

description:
raw data file: ABYSM34_252828211743_1.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with infantile spasms_postnatally treated with saline P15_Replicate 4


title: S3_Post_hypoxic bedrest (HBR)

description: Subject 3, Third Intervention: hypoxic bedrest (HBR), Post


title: S3_Pre_hypoxic bedrest (HBR)

description: Subject 3, Third Intervention: hypoxic bedrest (HBR), Pre


title: NCI-H2342


title: S2_Post_normoxic bedrest (NBR)

description: Subject 2, Second Intervention: normoxic bedrest (NBR), Post


title: NCI-H1993


title: S2_Pre_normoxic bedrest (NBR)

description: Subject 2, Second Intervention: normoxic bedrest (NBR), Pre


title: S2_Post_hypoxic bedrest (HBR)

description: Subject 2, Third Intervention: hypoxic bedrest (HBR), Post


title: A_T1_D1_032


title: ABYSM2

description:
raw data file: ABYSM12_252828211743_2.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with infantile spasms_postnatally treated with saline P15_Replicate 2


title: ABYSM1

description:
raw data file: ABYSM12_252828211743_2.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with infantile spasms_postnatally treated with saline P15_Replicate 1


title: NUGC-4


title: A_T2_D3_055


title: NCI-H1648


title: NCI-H820


title: A_T1_D1_038


title: ABYSM3

description:
raw data file: ABYSM34_252828211743_1.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with infantile spasms_postnatally treated with saline P15_Replicate 3


title: A_A1_D2_014


title: X_A1_Co_107


title: MKN-45


title: ABNSM4

description:
raw data file: ABNSM34_252828211745_1.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 4


title: S3_Post_normoxic bedrest (NBR)

description: Subject 3, Second Intervention: normoxic bedrest (NBR), Post


title: NCI-H1573


title: S2_Pre_hypoxic bedrest (HBR)

description: Subject 2, Third Intervention: hypoxic bedrest (HBR), Pre


title: S2_Post_hypoxic ambulatory confinement (HAMB)

description: Subject 2, First Intervention: hypoxic ambulatory confinement (HAMB), Post

value: hypoxic ambulatory confinement (HAMB)


title: ABNSM3

description:
raw data file: ABNSM34_252828211745_1.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 3


title: Malme-3M


title: HOP-92


title: ABNSM1

description:
raw data file: ABNSM12_252828211745_2.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 1


title: S2_Pre_hypoxic ambulatory confinement (HAMB)

description: Subject 2, First Intervention: hypoxic ambulatory confinement (HAMB), Pre


title: S1_Pre_normoxic bedrest (NBR)

description: Subject 1, Second Intervention: normoxic bedrest (NBR), Pre


title: S1_Post_hypoxic bedrest (HBR)

description: Subject 1, Third Intervention: hypoxic bedrest (HBR), Post

value: hypoxic bedrest (HBR)


title: S1_Post_normoxic bedrest (NBR)

description: Subject 1, Second Intervention: normoxic bedrest (NBR), Post


title: A_T1_D3_028


title: ASNSM4

description:
raw data file: ASNSM34_252828211742_1.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to saline_no infantile spasms_postnatally treated with saline P15_Replicate 4


title: A_H1_D2_078

value: HLF


title: ASNSM3

description:
raw data file: ASNSM34_252828211742_1.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to saline_no infantile spasms_postnatally treated with saline P15_Replicate 3


title: Hs 746T

value: Hs 746T


title: S1_Pre_hypoxic bedrest (HBR)

description: Subject 1, Third Intervention: hypoxic bedrest (HBR), Pre

value: Vastus lateralis

value: Third


title: A_P1_D1_090


title: SJ_liver, control diet, biological rep2

city: Shanghai

first: FUYI

last: XU

state: Shanghai

address: 2999 NORTH RENMING ROAD, SONGJIANG DISTRICT

department: College of Chemistry, Chemical Engineering, and Biotechnology

institute: Donghua University

description: Gene expression data from liver tissue of SJ mice fed with control diet

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on  Affymetrix GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: liver from SJ mice fed with control diet

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (WT PLUS Reagent Manual, 2013, Affymetrix).

extract_protocol: Liver tissues from each mice were collected and total RNAs were immediately extracted with RNAiso Plus reagent (Takara Biotechnology (Dalian) Co., Ltd, China) according to the manufacturer’s protocol, followed by quantification with NanoDrop 2000c. They had an A260/A280 of 1.8-2.0.

value: liver


title: ASNSM2

description:
raw data file: ASNSM2-ABYAF4_252828211750_1.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to saline_no infantile spasms_postnatally treated with saline P15_Replicate 2


title: A_H1_D1_076


title: A_H1_Co_073


title: EBC-1


title: SJ_liver, control diet, biological rep1


title: ABNSM2

description:
raw data file: ABNSM12_252828211745_2.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 2


title: S1_Post_hypoxic ambulatory confinement (HAMB)

description: Subject 1, First Intervention: hypoxic ambulatory confinement (HAMB), Post

value: Male

value: First


title: G-361


title: A_A1_D3_007


title: CAL-54


title: X_A1_Co_109

value: X-Ray


title: HCC1395


title: A_T1_D3_027


title: A_T1_Co_021


title: SJ_liver, high fat diet, biological rep1

description: Gene expression data from liver tissue of SJ mice fed with high fat diet

source_name: liver from SJ mice fed with high fat diet


title: X_A1_D3_101


title: SJ_liver, high fat diet, biological rep2


title: KM_liver, control diet, biological rep1

description: Gene expression data from liver tissue of KM mice fed with control diet

source_name: liver from KM mice fed with control diet


title: A_A1_D3_016


title: Proliferating Tregs 2

city: Chiciago

first: Prabhakaran

last: Kumar

state: Illinois

address: 835 S Wolcott Ave.

department: Microbiology and Immunology

institute: UIC

hyb_protocol: The GeneChip® Hybridization, Wash, and Stain Kit was used as per manufacturer’s protocols. The GeneChip® Fluidics Station 450 was used for washing and staining using fluidics script FS450_0002.

scan_protocol: Microarray chips were read on the GeneChip® Scanner 3000 7G with AGCC version 4.0.0.1567.

data_processing: RMA method in Partek Genomics Suite 6.6

source_name: Prikuferating Tregs

label_protocol: Samples were labeled using the Affymetrix GeneChip® WT PLUS Kit as per manufacturer's protocols.

growth_protocol: Cells were we co-cultured in RPMI 1640 medium containg 10% FBS and 1X Penicillin/Streptomycin.

extract_protocol: Total RNA was isolated by using Qiagen's RNAeasy coulums as per manufacturer's protocol.

treatment_protocol: Regulatory T-cells and GM-CSF treated bone marrow derived dendritic cells were we co-cultured in complete RPMI 1640 medium for 5 days. Post-cultures resting and proliferating regulatory T-cells were sorted out by FACS based on CFSE dilution.

value: Treg


title: Proliferating Tregs 1

source_name: Proliferating Tregs


title: Resting Tregs 2

source_name: Resting Tregs


title: KM_liver, high fat diet, biological rep2

description: Gene expression data from liver tissue of KM mice fed with high fat diet

source_name: liver from KM mice fed with high fat diet


title: Resting Tregs 1


title: C32


title: AU565


title: KM_liver, control diet, biological rep2


title: Alexander cells

value: Alexander cells


title: S1_Pre_hypoxic ambulatory confinement (HAMB)

description: Subject 1, First Intervention: hypoxic ambulatory confinement (HAMB), Pre

source_name: Human skeletal muscle, Vastus lateralis

value: Pre


title: KM_liver, high fat diet, biological rep1


title: A_H1_D1_075

source_name: human cell cultures

value: Alpha


title: A_H1_D3_072


title: HZ_liver, control diet, biological rep2

description: Gene expression data from liver tissue of HZ mice fed with control diet

source_name: liver from HZ mice fed with control diet


title: A_P1_Co_085

value: HPEAC


title: A_H1_D2_071


title: HZ_liver, control diet, biological rep1


title: A_H1_D2_066


title: aCGH_krt18-/- liver tissue 18 months_male_non-tumor_1

city: Graz

first: Vendula

last: Svendova

address: Auenbruggerplatz 2

country: Austria

institute: Medical University Graz

hyb_protocol: Samples were hybridized according to the Agilents protocol;hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: The slides were scanned using Agilent Scanner (Agilent Microarray Scanner G2505C) using the programme Agilent Scan Controlwhich generates a tiff file of the array slide. This tiff file was further extracted with the Agilent Feature Extraction Software which generates a txt.* file

data_processing:
After data extraction the data visualisation was done with Agilent Genomic Workbench 6.5 using different settings (see the filter settings below):
Aberration Algorithm: ADM-2
Threshold: 6.0
GC Correction: ON
Window Size: 2Kb
Centralization: ON
Bin Size: 10
Centralization Threshold: 6.0
Fuzzy Zero: OFF
Nesting Level: OFF
Combine Replicates (Intra Array): ON
Combine Replicates (Inter Array): OFF
Genome: mm9
Aberration Filters:   minProbes = 20 AND minAvgAbsLogRatio = 0.1 AND maxAberrations = 100 AND percentPenetrance = 0
Feature Level Filters:   gIsSaturated = true OR rIsSaturated = true OR gIsFeatNonUnifOL = true OR rIsFeatNonUnifOL = true; Include matching values=false
Design Level Filters: NONE
Array Level Filters: NONE
Genomic Boundaries: Not Applied

source_name: liver tissue, aged 18 month

label_protocol: 500 ng genomic DNA were primed with random primers,denatured and cooled down for 10 min on ice;Nucleotide mix, dye and ExoKlenow was added according to the manufacturer`s protocoll; samples were incubated at 37°C, 2 h for amplifieing and labeling

extract_protocol: Genomic DNA was isolated using the Qiagen Dneasy Blood and Tissue Kit following manufacturer's instructions;instead of washing buffer2, 80% ETOH was used. 500ng DNA was digested using the restriction enzymes RsaI and AluI to obtain shorter DNA fragments according to the manufacturer’s protocol. The DNA concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer. To assess the completeness of the digestion the length of digested DNA fragments was analysed using gel electrophoresis (1% agarose).

tag: age

value: 18 months

tag: background strain

value: male

tag: genotype

source_name: healthy liver tissue, aged 3 month

value: 3 months

value: wt


title: A_H1_D3_067

tag: cell type

value: HLF


title: A_T2_D3_056

tag: treatment


title: HZ_liver, high fat diet, biological rep1

description: Gene expression data from liver tissue of HZ mice fed with high fat diet

source_name: liver from HZ mice fed with high fat diet

tag: tissue


title: HZ_liver, high fat diet, biological rep2


title: B6_liver, control diet, biological rep2

description: Gene expression data from liver tissue of B6 mice fed with control diet

source_name: liver from B6 mice fed with control diet


title: B6_liver, control diet, biological rep1


title: ASNSM1

description:
raw data file: ASNSM1-ABYAF3_252828211742_2.txt
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to saline_no infantile spasms_postnatally treated with saline P15_Replicate 1

tag: Sex

tag: strain

value: Sprague-Dawley

value: hypothalamic arcuate nucleus


title: B6_liver, high fat diet, biological rep1

description: Gene expression data from liver tissue of B6 mice fed with high fat diet

source_name: liver from B6 mice fed with high fat diet


title: aCGH_WT_liver tissue 18 months_male_non-tumor_2


title: aCGH_WT_liver tissue 18 months_female_non-tumor_1

value: female


title: A_A1_D1_018


title: A_H1_Co_062


title: aCGH_krt18-/- liver tissue 18 months_male_non-tumor_2

value: liver


title: A_P1_D2_094


title: A_T2_Co_049


title: aCGH_krt18+/- liver tissue 18 months_male_non-tumor_2


title: aCGH_krt18+/- liver tissue 18 months_male_non-tumor_3


title: aCGH_WT_liver tissue 18 months_male_non-tumor_1


title: aCGH_krt18-/- liver tissue 12 months_female_non-tumor_4

source_name: liver tissue, aged 12 month

value: 12 months


title: aCGH_krt18-/- liver tissue 18 months_male_non-tumor_3


title: B6_liver, high fat diet, biological rep2


title: A_T1_Co_029


title: aCGH_krt18-/- liver tissue 12 months_female_non-tumor_3


title: A_P1_Co_084


title: A_A1_D3_020


title: aCGH_krt18+/- liver tissue 18 months_male_non-tumor_1


title: A_T2_D1_051


title: aCGH_krt18-/- liver tissue 12 months_female_non-tumor_2


title: A_A1_D2_006


title: HCT116 E11 CPT rep3

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: SAMPLE 12

hyb_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer's protocol.

data_processing: The data were processed and normalised using Illumina GenomeStudio.

source_name: HCT116 E11, CPT

growth_protocol: HCT116 cells (WT and E11) were cultured in McCoy's 5A medium supplemented with 10% fetal bovine serum.

extract_protocol: Total RNAs were extracted using Agilent Total RNA Isolation Mini Kit (cat# 5185-6000) following the manufacturer's protocol. The quantity and quality of isolated RNAs were determined using ND-1000 Spectrophotometer.

treatment_protocol: Cells were treated with DMSO or 1.5 uM of camptothecin for 4 h, and then collected for RNA extraction and microarray profiling.

value: colon cancer cell line

value: camptothecin


title: aCGH_krt18-/- liver tissue 12 months_male_non-tumor_5


title: HCT116 WT DMSO rep3

description: SAMPLE 9

scan_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer's protocol.

source_name: HCT116 WT, DMSO

value: DMSO


title: A_H1_Co_074


title: A_P1_D1_087


title: aCGH_krt18-/- liver tissue 12 months_female_non-tumor_1


title: A_H1_D1_064


title: HCT116 E11 CPT rep2

description: SAMPLE 8

label_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer's protocol.


title: aCGH_krt18-/- liver tissue 12 months_male_non-tumor_4


title: HCT116 E11 DMSO rep3

description: SAMPLE 11

source_name: HCT116 E11, DMSO


title: aCGH_krt18-/- liver tissue 12 months_male_non-tumor_1


title: X_A1_D3_105

value: X-Ray


title: A_T1_D3_036


title: aCGH_krt18-/- liver tissue 12 months_male_non-tumor_2


title: HCT116 WT CPT rep3

description: SAMPLE 10

source_name: HCT116 WT, CPT


title: aCGH_krt18+/- liver tissue 12 months_female_non-tumor_6


title: aCGH_krt18+/- liver tissue 12 months_female_non-tumor_5


title: HCT116 E11 CPT rep1

description: SAMPLE 4


title: A_H1_D3_079


title: HCT116 WT CPT rep2

description: SAMPLE 6


title: HCT116 WT DMSO rep2

description: SAMPLE 5


title: A_A1_Co_017


title: HCT116 E11 DMSO rep2

description: SAMPLE 7


title: HCT116 E11 DMSO rep1

description: SAMPLE 3


title: siCAF1_3 [exon-level]

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: MCF7 stable cell lines were routinely maintained in DMEM supplemented with 10% foetal bovine serum, penicillin/streptomycin ,blasticidin 3µg/mL in a humidified atmosphere of 5% CO2 at 37°C

extract_protocol: total RNA purified using TRI-Reagent (Sigma),

tag: sirna


title: X_A1_D3_102


title: A_T2_D1_058


title: siCAF1_2 [exon-level]


title: A_T1_D2_039


title: siCAF1_1 [exon-level]


title: aCGH_krt18+/- liver tissue 12 months_female_non-tumor_4


title: A_P1_D3_099


title: siCTRL_3 [exon-level]

value: CTRL


title: aCGH_krt18+/- liver tissue 12 months_female_non-tumor_2


title: A_A1_D1_011

value: Alpha


title: A_T1_Co_030


title: SCG GFP- Rep6

city: PITTSBURGH

first: John

middle: P.

last: Horn

state: PA

address: 3500 Terrace Street

department: Neurobiology

institute: University of Pittsburgh

description:
Sample name: JH23
9445918042_E_Grn

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with Illumina BeadStudio.

source_name: Superior cervical ganglia, neuron, GFP negative

label_protocol: Biotinylated samples were prepared with the Encore BiotinIL Module (NuGen) for Illumina arrays.

growth_protocol: Mouse SCG's were dissociated into single-cell preparations via treatment with collagenase and trypsin, followed by trituration. Single cells were incubated in growth media containing MEM, FBS, pen-strep, NGF, and ara-C for 1 hour at 37oC preceding manual cell sorting.

extract_protocol: Samples were prepared according to the Ovation One-Direct System (NuGen) protocol. Single cells from dissociated mouse SCG were deposited directly into Direct Lysis Buffer and cDNA was amplified. Amplified cDNA was purified using the MinElute Reaction Cleanup Kit (Qiagen). Quality control was performed with the Agilent Bioanalyser.

tag: strain/background

value: 7 months

value: Male

value: Superior cervical ganglia

value: Neuron

tag: neuropeptide y expression

value: Negative

tag: mouse


title: aCGH_krt18+/- liver tissue 12 months_male_non-tumor_11

tag: gender

value: male

value: 3 months

value: wt


title: HCT116 WT DMSO rep1

description: SAMPLE 1

tag: cell line

tag: genotype/variation


title: LLF biological rep6 vs. HLF biological rep6

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

hyb_protocol: Equal amounts of labeled RNA were then hybridized on the Agilent-032221 chip, per the Agilent protocol, at 60 degrees overnight. The hybridization mixes were prepared using the Gene Expression Hybridization Kit from Agilent following the manufacturer's protocol. After hybridization, the slide was washed first with Gene Expression Wash Buffer 1 (Agilent) and then Gene Expression Wash Buffer 2 (Agilent). This was followed by an acetonitrile wash and finally the slides were placed in Stabilization & Drying Solution (Agilent). The washed slides were scanned on an Agilent G2565BA scanner. Feature extraction was performed using the Feature Extraction software from Agilent.

scan_protocol: Scanned on an Agilent G2565BA microarray scanner.

data_processing: The data from all arrays were first subjected to background correction and LOESS within-array normalization using Agilent Feature Extraction software (version 9.5.1.1 Agilent Technologies, Santa Clara, CA). The rest of the analysis was performed in Partek® Genomics Suite software, version 6.6 Copyright © 2012 Partek Inc., St. Louis, MO, USA.The log expression ratios that were produced during the normalization step were analyzed.

organism: Stylophora pistillata

source_name: LLF

label_protocol: 200 ng of total RNA, in the presence of control RNAs (RNA spike-in kit; Agilent), for each sample was labeled with either Cy-3 or Cy-5 using the Low Input Quick Amp Labeling Kit, two-color (Agilent) following the manufacturer's protocol.

extract_protocol: Total RNA was extracted using Trizol.

treatment_protocol: Conditions were then changed in each aquarium as follow: PAR was increased in two aquaria to 500 µmoles photons m-2 s-1 for 15 days to induce bleaching of the coral colonies. The two other tanks were kept at 200 µmoles photons m-2 s-1. Moreover, in each of the two light conditions, one aquarium was kept starved while the other was fed every day with artemia salina nauplii at repletion. Four conditions were achieved: low light-unfed/starved (LLS), low light fed (LLF), high light unfed/starved (HLS) and high light fed (HLF).

tag: light condition

value: low

tag: feeding condition

value: fed

tag: biological replicate

source_name: HLF

value: high


title: X_A1_D3_103

tag: dose (gy)

tag: time point (h) 1=24h 2=72h


title: A_P1_Co_083

tag: cell type

value: HPEAC


title: aCGH_krt18+/- liver tissue 12 months_female_non-tumor_1

tag: age

value: 12 months

value: liver

tag: background strain

value: female

tag: genotype


title: aCGH_krt18+/- liver tissue 12 months_female_non-tumor_3

tag: tissue


title: aCGH_krt18+/- liver tissue 12 months_male_non-tumor_9


title: SCG GFP- Rep4

description:
Sample name: JH13
9445918042_D_Grn


title: HLS biological rep4 vs. LLS biological rep4

source_name: HLS

value: starved

source_name: LLS


title: aCGH_krt18+/- liver tissue 12 months_male_non-tumor_10


title: LLF biological rep4 vs. HLF biological rep4


title: HLF biological rep5 vs. LLF biological rep5


title: aCGH_krt18+/- liver tissue 12 months_male_non-tumor_8


title: HCT116 WT CPT rep1

description: SAMPLE 2

value: colon cancer cell line

tag: treatment

value: camptothecin


title: aCGH_krt18-/- liver tissue 12 months_male_non-tumor_3


title: SCG GFP- Rep5

description:
Sample name: JH15
9445918042_A_Grn

tag: strain/background

value: 7 months

value: Male


title: A_T2_Co_057

source_name: human cell cultures

value: Alpha


title: siCTRL_2 [exon-level]

tag: sirna

value: CTRL


title: SCG GFP+ Rep2

description:
Sample name: JH3
9419900001_F_Grn

source_name: Superior cervical ganglia, neuron, GFP positive

value: 4 months

value: Superior cervical ganglia

value: Neuron

tag: neuropeptide y expression

value: Positive

tag: mouse


title: SCG GFP+ Rep6

description:
Sample name: JH22
9445918042_B_Grn

tag: gender


title: LLS biological rep6 vs. LLF biological rep6

value: low

value: fed


title: SCG GFP+ Rep5

description:
Sample name: JH14
9445918042_F_Grn


title: siCTRL_1 [exon-level]


title: SCG GFP+ Rep1

description:
Sample name: JH1
9419900001_E_Grn


title: LLF biological rep4 vs. LLS biological rep4


title: LLF biological rep6 vs. LLS biological rep6


title: SCG GFP+ Rep3

description:
Sample name: JH5
9419900001_D_Grn


title: LLS biological rep3 vs. HLS biological rep3, 2

value: high


title: LLS biological rep5 vs. LLF biological rep5


title: LLF biological rep1 vs. HLF biological rep2


title: aCGH_krt18+/- liver tissue 12 months_male_non-tumor_7

value: 12 months

value: male

value: 3 months

value: wt


title: LLF biological rep3 vs. HLF biological rep3


title: HLS biological rep2 vs. LLS biological rep2, 2

value: starved


title: LLS biological rep3 vs. HLS biological rep3


title: aCGH_krt18+/- liver tissue 12 months_male_non-tumor_6

value: liver


title: aCGH_krt18+/- liver tissue 12 months_male_non-tumor_5


title: SCG GFP- Rep3

description:
Sample name: JH6
9419900001_B_Grn

value: Negative


title: aCGH_krt18+/- liver tissue 12 months_male_non-tumor_3


title: LLS biological rep3 vs. LLF biological rep2


title: HLS biological rep1 vs. LLS biological rep1


title: HLS biological rep2 vs. LLS biological rep2


title: aCGH_WT_liver tissue 12 months_male_non-tumor_2


title: aCGH_WT_liver tissue 12 months_female_non-tumor_2

value: female


title: aCGH_WT_liver tissue 12 months_female_non-tumor_1


title: aCGH_WT_liver tissue 12 months_male_non-tumor_3


title: SCG GFP- Rep1

description:
Sample name: JH2
9419900001_A_Grn

value: Male


title: aCGH_WT_liver tissue 12 months_female_non-tumor_3


title: aCGH_krt18+/- liver tissue 12 months_male_non-tumor_2


title: HLF biological rep1 vs. LLF biological rep2


title: aCGH_krt18+/- liver tissue 12 months_male_non-tumor_4


title: aCGH_krt18+/- liver tissue 12 months_male_non-tumor_1


title: aCGH_WT_liver tissue 12 months_male_non-tumor_1


title: LLF biological rep1 vs. LLS biological rep1


title: WERI Infected 2hours rep 2 (outlier)

status: Public on May 03 2016

city: Subiaco

first: Genevieve

last: Syn

state: Western Australia

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

description: T. gondii infected WERI cells

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Analysis was done in R version 3.1.3. using R package RnBeads

label: biotin (C or G base) dinitrophenyl (A and T base)

label_protocol: standard Illumina protocol

growth_protocol: Cells were grown in RPMI-1640 medium supplemented with 100U/ml Penicillin/100ug ug/ml Streptomycin (Gibco), 2mM Glutamax supplement (Gibco) and 10% heat-inactivated fetal calf serum.

extract_protocol: DNA was extracted using GenElute Mammalian Genomic DNA MiniPrep kit (Sigma-Aldrich) following manufacturer's instructions

treatment_protocol: 1 X 10^6 WERI cells were infected with Toxoplasma gondii RH (Type I) strain at a multiplicity of infection of 10 for 2 hours, 6 hours and 24 hours. 1 X 10^6 mock-infected cells were treated exactly the same as infected cells but with the absence of Toxoplasma.

value: Infected

tag: time of infection

value: 2 hours

value: Retinoblastoma

tag: sample type

value: Cell line


title: WERI Mock-infected 6 hours rep 2 (outlier)

description: Mock-infected WERI cells

value: Mock-infected

value: 6 hours


title: Invivo -TSLP BM_9wk_techn_rep3

city: Loma Linda

first: Kimberly

last: Payne

address: 11085 Campus Street, Mortensen Hall, First Floor

institute: Loma Linda University

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays (8x60K v2, Design ID 039494) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing:
The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.
qunatile normalization

source_name: Primary B-ALL cells harvested from –T xenograft

label_protocol: The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. To produce Cy3- labeled cRNA the following RNA amoutns were used: 50 ng RNA for the samples from  groups A, B, E and F; 10 ng RNA for the samples of group C and D, except for the samples C3 and D1 from which the complete available amount was taken.

growth_protocol: Studies were performed on primary human CRLF2 B-ALL cells from a Hispanic patient that had been expanded in xenograft mice for 9 weeks. Xenograft recipient mice were NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice that had been engineered produce human TSLP (+T mice) or mice that did not produce human TSLP.   For samples E and F, frozen bone marrow from xenograft mice was thawed and leukemia cells were isolated by magnetic separation prior to microarray analysis. Microarray was performed on cells harvested directly from one  +T and one  –T mice with 3 technical replicates performed. Cells for Samples A-D came from separate thawed vials from the same xenograft bone marrow samples as those for E and F but were cultured and treated as described below.

extract_protocol: RNA was extracted using NucleoSpin® RNA kit (Macherey & Nagel) following manufacturer's instructions.

treatment_protocol: Freshly thawed bone marrow from xenografts that produced samples E and F described above were placed into culture (in vitro) with TSLP (15 pg/ml) (A,C) or without TSLP (B,D) for 3 days. An  anti-TSLP antibody was added to the cultures without TSLP to neutralize any endogenously produced TSLP.   Cells were harvested after 3 days, and leukemia cells were purified by magnetic separation. Three biological replicates of cultures were performed. Samples A and B came from +T mice and samples C and D came from –T mice. Culture media was as follows:  RPMI, 20% FBS, penicillin, streptomyacin, L-Glutamine and 2-mercaptoethanol at 37oC and 5% CO2.

tag: cell type (xenografted)

value: primary human CRLF2 B-ALL cells

tag: xenograft recipient strain

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG)

tag: strain genotype/variation

value: not producing human TSLP (TSLP-)

value: bone marrow (of xenograft mouse)

value: leukemia cells

tag: treatment group

value: F

tag: replicate

value: 3 (techn.)


title: Invivo -TSLP BM_9wk_techn_rep1

tag: cell type

value: 1 (techn.)


title: Invivo -TSLP BM_9wk_techn_rep2

value: 2 (techn.)


title: Exvivo +/+TSLP BM_3dy_biol_rep3

source_name: Primary B-ALL cells expanded in +T xenograft, 3 day culture, +human TSLP

value: engineered produce human TSLP (TSLP+)

tag: in vitro treatment

value: TSLP (15 pg/ml)

value: A

value: 3 (biol.)


title: Invivo +TSLP BM_9wk_techn_rep2

source_name: Primary B-ALL cells harvested from +T xenograft

value: E


title: Exvivo -/-TSLP BM_3dy_biol_rep2

source_name: Primary B-ALL cells expanded in –T xenograft, 3 day culture, –human TSLP

value: αTSLP (anti-TSLP antibody; control)

value: D

value: 2 (biol.)


title: Exvivo +/-TSLP BM_3dy_biol_rep3

source_name: Primary B-ALL cells expanded in +T xenograft, 3 day culture, –human TSLP

value: primary human CRLF2 B-ALL cells

value: B


title: Invivo +TSLP BM_9wk_techn_rep1

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG)


title: Invivo +TSLP BM_9wk_techn_rep3

value: bone marrow (of xenograft mouse)


title: Exvivo +/-TSLP BM_3dy_biol_rep2

value: leukemia cells


title: Exvivo +/-TSLP BM_3dy_biol_rep1

value: 1 (biol.)


title: Exvivo -/+TSLP BM_3dy_biol_rep1

source_name: Primary B-ALL cells expanded in –T xenograft, 3 day culture, +human TSLP

value: not producing human TSLP (TSLP-)

value: C


title: Exvivo -/+TSLP BM_3dy_biol_rep3


title: Exvivo -/-TSLP BM_3dy_biol_rep1


title: Exvivo -/+TSLP BM_3dy_biol_rep2


title: Exvivo -/-TSLP BM_3dy_biol_rep3


title: Exvivo +/+TSLP BM_3dy_biol_rep1


title: Exvivo +/+TSLP BM_3dy_biol_rep2


title: Parkinson's Disease serum sample 28

type: other

city: Stratford

first: Robert

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

institute: UMDNJ-SOM

scan_protocol: Protein microarrays were scanned using a Genepix 4000B microarray scanner at 635nm using default parameters, PMT of 600, and a pixel size of 5um.

data_processing:
The GPR files were imported into Invitrogen's Prospector v5.2.1 microarray analysis software.  Individual serum results were linearly normalized via internal reference features into diagnostically appropriate disease or control groups  using the "Group Characterization" function.  Group characterized samples were then compared to identify the differential expression of autoantibodies using the "Two Groups Comparison" feature.   More information about this process, and the exact differentiating power being addressed with each comparison, can be found in the accompanying manuscript.  Selected biomarker potential, power, and efficacy was further evaluated using Random Forest (RF) Training and Testing Set analysis and decision-tree logic.
Normalized fluorescence intensities are presented in Relative Fluorescent Units (RFUs).
The RFU values for individual proteins in a sample.  These values are reported for every sample used in any comparison and are subject to a degree of normalized variation depending on group characterization and the exact diagnostic comparison rendered.

label: Alexa Fluor 647

molecule: other

source_name: Parkinson's Disease serum sample 28

label_protocol: Probing and analysis of microarrays was performed with strict adherence to suggested manufacturer protocols.  (See Invitrogen and Molecular Devices online.)

extract_protocol: All serum samples were purchased from commercial biofluid repositiories, drawn and stored under proper conditions, and collected and used with IRB approval.

tag: age

value: Female


title: lame73_ area1_data

city: Québec

first: Anne-Laure

last: Nivet

state: Québec

address: 2440 Hochelaga Blvd

institute: Laval University

description: Array 16

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent  (Agilent-026652 human whole genome) using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray 1.6.1 software used.

source_name: M+

label_protocol:
Amplification protocol:  This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.
The labelling aRNA was done using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: granulosa collected individually in vivo (ovum pick up)

extract_protocol: centrifugation on Qiashredder (Qiagen)  2min 13000 rpm, and total RNA extraction using phenol with miRNeasy kit (Qiagen) according to manufacturer guidlines.

treatment_protocol: freezing in liquid nitrogen until RNA extraction

tag: follicle size

value: M

tag: related embryo development

source_name: M-


title: Parkinson's Disease serum sample 27

source_name: Parkinson's Disease serum sample 27

value: Male


title: Parkinson's Disease serum sample 29

source_name: Parkinson's Disease serum sample 29


title: Parkinson's Disease serum sample 26

source_name: Parkinson's Disease serum sample 26


title: WERI Mock-infected 24 hours rep 1

description: Mock-infected WERI cells

tag: treatment

value: Mock-infected

value: 24 hours

value: Retinoblastoma

value: Cell line


title: WERI Mock-infected 24 hours rep 2

description: Mock-infected WERI cells


title: lame73_ area3_data

description: Array 18


title: lame98_ area3_data

description: Array 11

source_name: L-

value: L


title: lame72_ area2_data

description: Array 14


title: lame72_ area3_data

description: Array 15


title: lame98_ area2_data

description: Array 10


title: WERI Mock-infected 2 hours rep 2

description: Mock-infected WERI cells

value: 2 hours


title: lame98_ area4_data

description: Array 12


title: lame97_ area4_data

description: Array 8


title: lame73_ area2_data

description: Array 17


title: lame98_ area1_data

description: Array 9


title: lame72_ area1_data

description: Array 13


title: lame97_ area2_data

description: Array 6

source_name: S-

value: S


title: Parkinson's Disease serum sample 23

source_name: Parkinson's Disease serum sample 23


title: lame97_ area3_data

description: Array 7


title: Parkinson's Disease serum sample 25

source_name: Parkinson's Disease serum sample 25

value: UNK


title: WERI Mock-infected 6 hours rep 1

description: Mock-infected WERI cells

value: 6 hours


title: Parkinson's Disease serum sample 22

source_name: Parkinson's Disease serum sample 22


title: Parkinson's Disease serum sample 24

source_name: Parkinson's Disease serum sample 24


title: WERI Infected 24 hours rep 2

description: T. gondii infected WERI cells

value: Infected


title: Parkinson's Disease serum sample 21

source_name: Parkinson's Disease serum sample 21


title: WERI Infected 24 hours rep 1

description: T. gondii infected WERI cells


title: Parkinson's Disease serum sample 20

source_name: Parkinson's Disease serum sample 20


title: WERI Infected 6 hours rep 2

description: T. gondii infected WERI cells


title: Parkinson's Disease serum sample 19

source_name: Parkinson's Disease serum sample 19


title: Parkinson's Disease serum sample 14

source_name: Parkinson's Disease serum sample 14


title: Parkinson's Disease serum sample 18

source_name: Parkinson's Disease serum sample 18


title: Parkinson's Disease serum sample 12

source_name: Parkinson's Disease serum sample 12


title: Parkinson's Disease serum sample 11

source_name: Parkinson's Disease serum sample 11


title: Parkinson's Disease serum sample 9

source_name: Parkinson's Disease serum sample 9


title: Parkinson's Disease serum sample 13

source_name: Parkinson's Disease serum sample 13


title: lame96_ area2_data

description: Array 2

source_name: M+


title: WERI Mock-infected 2 hours rep 1

description: Mock-infected WERI cells


title: lame96_ area4_data

description: Array 4


title: Parkinson's Disease serum sample 8

source_name: Parkinson's Disease serum sample 8


title: lame97_ area1_data

description: Array 5


title: Parkinson's Disease serum sample 10

source_name: Parkinson's Disease serum sample 10


title: Parkinson's Disease serum sample 7

source_name: Parkinson's Disease serum sample 7


title: lame96_ area3_data

description: Array 3

source_name: S-


title: Parkinson's Disease serum sample 4

source_name: Parkinson's Disease serum sample 4


title: WERI Infected 6 hours rep 1

description: T. gondii infected WERI cells


title: WERI Infected 2hours rep 1

description: T. gondii infected WERI cells


title: lame96_ area1_data

description: Array 1


title: Parkinson's Disease serum sample 6

source_name: Parkinson's Disease serum sample 6


title: Parkinson's Disease serum sample 2

source_name: Parkinson's Disease serum sample 2


title: Parkinson's Disease serum sample 1

source_name: Parkinson's Disease serum sample 1


title: Multiple Sclerosis serum sample 25

source_name: Multiple Sclerosis serum sample 25


title: Multiple Sclerosis serum sample 22

source_name: Multiple Sclerosis serum sample 22


title: Multiple Sclerosis serum sample 24

source_name: Multiple Sclerosis serum sample 24


title: Multiple Sclerosis serum sample 23

source_name: Multiple Sclerosis serum sample 23


title: Parkinson's Disease serum sample 3

source_name: Parkinson's Disease serum sample 3


title: Multiple Sclerosis serum sample 21

source_name: Multiple Sclerosis serum sample 21


title: Multiple Sclerosis serum sample 20

source_name: Multiple Sclerosis serum sample 20


title: Adults T-cell ALL Bone marrow, sample 259

city: Salamanca

first: Jesús

middle: Maria

last: Hernández-Rivas

state: Salamanca

address: Paseo San Vicente, 88-182

department: Hematology

institute: Hospital Universitario de Salamanca, Universidad de Salamanca-CSIC

hyb_protocol: Hybridization was performed according to the instructions in the NimbleGen Array User Guide

scan_protocol: Scanning was performed according to the instructions in the NimbleGen Array User Guide

data_processing: Arrays were processed using Nimblegen's standard protocol and segmented using the CGHweb tool.

source_name: Bone marrow cells (test)

label_protocol: Samples were denatured and labeled in parallel with Cy3 for the test group and Cy5 for the control group, each through a random priming method, using Klenow fragments (NimbleGen Dual-Color DNA Labeling Kit, Roche NimbleGen, Inc., Madison, WI, USA)

extract_protocol: The genomic DNA was extracted from frozen bone marrow or fixed peripheral blood cell samples with QIAmp DNA Mini Kit (Qiagen,  16 Valencia, CA, USA) following the manufacturer’s instructions

value: Bone marrow cells

tag: disease state

value: T-cell acute lymphoblastic leukemia

tag: age group

value: Adults ≥18 years

tag: genetic subtype

value: Abnormal

value: PETHEMA LAL-AR/2003

source_name: control

value: Not applicable

tag: reference composition

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Adults T-cell ALL Bone marrow, sample 261

tag: gender

value: Male

value: Not evaluable

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Multiple Sclerosis serum sample 17

source_name: Multiple Sclerosis serum sample 17

value: FEMALE


title: Multiple Sclerosis serum sample 18

source_name: Multiple Sclerosis serum sample 18

value: female


title: Adults T-cell ALL Bone marrow, sample 253

value: Female

value: Normal

value: PETHEMA LAL-07FRAIL


title: Adults T-cell ALL Bone marrow, sample 264


title: Adults T-cell ALL Bone marrow, sample 248


title: Multiple Sclerosis serum sample 19

source_name: Multiple Sclerosis serum sample 19


title: Adults T-cell ALL Bone marrow, sample 262

value: PETHEMA LAL-AR/93


title: Adults T-cell ALL Bone marrow, sample 257


title: Adults T-cell ALL Peripheral blood, sample 265

source_name: Peripheral blood cells (test)

value: Peripheral blood cells

value: UNKN


title: Adults T-cell ALL Bone marrow, sample 246

value: Bone marrow cells

value: T-cell acute lymphoblastic leukemia

value: Hoelzer protocol


title: Adults T-cell ALL Peripheral blood, sample 260

value: Adults ≥18 years


title: Adults T-cell ALL Bone marrow, sample 245

value: PETHEMA LAL-AR/2003

value: Not applicable


title: Adults T-cell ALL Bone marrow, sample 249

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Adults T-cell ALL Bone marrow, sample 250


title: Adults T-cell ALL Bone marrow, sample 255

value: Male


title: Adults T-cell ALL Bone marrow, sample 263

value: Not evaluable

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Adults T-cell ALL Bone marrow, sample 247


title: Adults T-cell ALL Bone marrow, sample 258

value: Abnormal


title: Multiple Sclerosis serum sample 16

source_name: Multiple Sclerosis serum sample 16

value: FEMALE


title: Adults T-cell ALL Bone marrow, sample 254

value: Female

value: Normal

value: PETHEMA LAL-07OLD


title: Adults T-cell ALL Bone marrow, sample 251

value: PETHEMA LAL-AR 2011


title: Multiple Sclerosis serum sample 15

source_name: Multiple Sclerosis serum sample 15

value: MALE


title: Adults T-cell ALL Bone marrow, sample 256

value: Bone marrow cells

value: UNKN


title: Adults T-cell ALL Bone marrow, sample 252

value: T-cell acute lymphoblastic leukemia


title: Children T-cell ALL Peripheral blood, sample 239

value: Peripheral blood cells

value: Children <18 years

value: PETHEMA LAL-RI/96


title: Children T-cell ALL Bone marrow, sample 242

value: PETHEMA LAL-AR/2003

value: Not applicable


title: Multiple Sclerosis serum sample 14

source_name: Multiple Sclerosis serum sample 14


title: Adults T-cell ALL Bone marrow, sample 243

value: Male

value: Adults ≥18 years

value: PETHEMA LAL-AR/93


title: Children T-cell ALL Bone marrow, sample 241

value: Not evaluable

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Multiple Sclerosis serum sample 12

source_name: Multiple Sclerosis serum sample 12


title: Adults T-cell ALL Bone marrow, sample 244

value: Normal


title: Children T-cell ALL Bone marrow, sample 240


title: Multiple Sclerosis serum sample 11

source_name: Multiple Sclerosis serum sample 11

value: FEMALE


title: Multiple Sclerosis serum sample 10

source_name: Multiple Sclerosis serum sample 10


title: Multiple Sclerosis serum sample 9

source_name: Multiple Sclerosis serum sample 9


title: Multiple Sclerosis serum sample 13

source_name: Multiple Sclerosis serum sample 13


title: Children T-cell ALL Bone marrow, sample 236

value: Female

value: Abnormal

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Children T-cell ALL Bone marrow, sample 235

value: Bone marrow cells


title: Children T-cell ALL Bone marrow, sample 238

value: T-cell acute lymphoblastic leukemia


title: Children T-cell ALL Bone marrow, sample 237

value: UNKN


title: Children T-cell ALL Peripheral blood, sample 234

value: Peripheral blood cells

value: Children <18 years


title: Multiple Sclerosis serum sample 7

source_name: Multiple Sclerosis serum sample 7


title: Multiple Sclerosis serum sample 8

source_name: Multiple Sclerosis serum sample 8

value: MALE


title: Multiple Sclerosis serum sample 6

source_name: Multiple Sclerosis serum sample 6


title: Children T-cell ALL Bone marrow, sample 230

source_name: Bone marrow cells (test)

value: Not applicable


title: Children T-cell ALL Bone marrow, sample 226

source_name: control


title: Multiple Sclerosis serum sample 5

source_name: Multiple Sclerosis serum sample 5


title: Children T-cell ALL Bone marrow, sample 231

value: Male


title: Children T-cell ALL Bone marrow, sample 229


title: Children T-cell ALL Bone marrow, sample 224

value: PETHEMA LAL-AR/2005


title: Children T-cell ALL Bone marrow, sample 232


title: Children T-cell ALL Bone marrow, sample 221


title: Children T-cell ALL Bone marrow, sample 223

value: PETHEMA LAL-RI/96


title: Children T-cell ALL Peripheral blood, sample 222


title: Multiple Sclerosis serum sample 3

source_name: Multiple Sclerosis serum sample 3


title: Children T-cell ALL Bone marrow, sample 225


title: Children T-cell ALL Bone marrow, sample 233


title: Children T-cell ALL Bone marrow, sample 228

value: PETHEMA LAL-AR/2003


title: Multiple Sclerosis serum sample 4

source_name: Multiple Sclerosis serum sample 4


title: Children T-cell ALL Bone marrow, sample 219

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Multiple Sclerosis serum sample 2

source_name: Multiple Sclerosis serum sample 2


title: Children T-cell ALL Bone marrow, sample 227

value: Normal

value: PETHEMA LAL-AR/93


title: Multiple Sclerosis serum sample 1

source_name: Multiple Sclerosis serum sample 1

value: FEMALE


title: Children T-cell ALL Bone marrow, sample 217


title: Adults B-cell ALL Bone marrow, sample 214

value: Female

value: B-cell acute lymphoblastic leukemia

value: Adults ≥18 years


title: Adults B-cell ALL Bone marrow, sample 213

value: Bone marrow cells

value: PETHEMA LAL-07OLD

value: Human Genomic DNA:Female, Promega, Madison, WI, USA


title: Adults B-cell ALL Bone marrow, sample 215

value: No therapy


title: Normal Control Donor serum sample 50

source_name: Normal Control Donor serum sample 50


title: Normal Control Donor serum sample 49

source_name: Normal Control Donor serum sample 49


title: Normal Control Donor serum sample 48

source_name: Normal Control Donor serum sample 48


title: Children T-cell ALL Bone marrow, sample 220

value: T-cell acute lymphoblastic leukemia

value: Children <18 years

value: UNKN


title: Normal Control Donor serum sample 46

source_name: Normal Control Donor serum sample 46

value: Male


title: Adults B-cell ALL Bone marrow, sample 209

value: PETHEMA LAL-RI/96

value: Not applicable


title: Adults B-cell ALL Bone marrow, sample 208


title: Normal Control Donor serum sample 44

source_name: Normal Control Donor serum sample 44


title: Normal Control Donor serum sample 45

source_name: Normal Control Donor serum sample 45


title: Adults B-cell ALL Bone marrow, sample 206


title: Normal Control Donor serum sample 47

source_name: Normal Control Donor serum sample 47


title: Adults B-cell ALL Bone marrow, sample 199

value: Human Genomic DNA:Male, Promega, Madison, WI, USA


title: Adults B-cell ALL Bone marrow, sample 211

value: Normal


title: Adults B-cell ALL Bone marrow, sample 202


title: Adults B-cell ALL Bone marrow, sample 201

value: PETHEMA LAL-AR/93


title: Adults B-cell ALL Peripheral blood, sample 210

source_name: Peripheral blood cells (test)

value: Peripheral blood cells


title: Children T-cell ALL Bone marrow, sample 218

value: Female

value: PETHEMA LAL-AR/2005


title: Normal Control Donor serum sample 43

source_name: Normal Control Donor serum sample 43


title: Adults B-cell ALL Bone marrow, sample 207

value: B-cell acute lymphoblastic leukemia

value: Adults ≥18 years


title: Adults B-cell ALL Bone marrow, sample 212

value: Bone marrow cells


title: Normal Control Donor serum sample 42

source_name: Normal Control Donor serum sample 42


title: Adults B-cell ALL Peripheral blood, sample 195

value: GMALL