title: Ang II 6

city: Lund

first: Catarina

last: Rippe

address: BMC, D12

department: Experimental Sciences

country: Sweden

institute: Lund University

description:
Angiotensin treatment
3_14

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 Expression Console software. Probe intensities, gene level expression were RMA summarized and then quantile normalized.
Probes with signals lower than median negative control were filtered.

source_name: AngII, aorta

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

extract_protocol: RNA was extracted with Trizol and Rneasy (Qiagen) according to manufacturers instructions

treatment_protocol: vehicle or AngII treatment in vivo for three weeks

tag: strain

tag: agent

value: AngII

value: Aorta


title: Ang II 7

status: Public on May 01 2017

type: RNA

description:
Angiotensin treatment
3_17

label: Biotin

molecule: total RNA

organism: Mus musculus

tag: tissue


title: Proband160

type: genomic

city: New York

first: Andrew

last: Sharp

state: NY

address: 1470 Madison Av

department: Genetics and Genomic Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

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

scan_protocol: Arrays were imaged using standard recommended Illumina scanner protocol

data_processing: The methylation value was set to null for probes with a detection p-value >0.01. Probe sequences (50-mer oligonucleotides) were uniquely mapped to the reference human genome hg19 (GRCh37) using BLAT, allowing up to 2 mismatches and 1 gap. Beta values from the autosomal probes were quantile normalized using lumi package in R.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole Blood

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA was acquired from various labs/consortiums

value: Whole Blood

tag: gender

value: Female

tag: individual


title: Ang II 5

description:
Angiotensin treatment
3_10


title: Ang II 2

description:
Angiotensin treatment
Ang4


title: Ang II 3

description:
Angiotensin treatment
Ang5


title: Vehicle (PBS) aspiration 4days + 24h C2_4d24h

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

hyb_protocol: Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays, , according to the manufacturer's recommendations.

scan_protocol: Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and analyzed with BioConductor package Limma.

label_protocol: Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.

growth_protocol: Female C57BL/6 mice (7-8 weeks old) were housed in groups of four in stainless steel cages, bedded with aspen chip and were provided with standard mouse chow diet and tab water ad lib. 12 h dark/light cycle was used in the animal room temperature being 20-21 degree celcius and humidity of 40-45 %.

extract_protocol: RNA isolation from the lung samples was done with TRIsure (phenol-chloroform extraction) and the quantity and purity was determined by NanoDrop spectrophotometer. Further quality check of the total RNA was performed with the Agilent BioAnalyzer, according to the manufacturer's recommendations.

treatment_protocol: mice lung tissue samples collected 24h after final exposure. Tissue samples stored in RNAlater in -80ºC

tag: exposure

value: 50 ul of PBS

tag: exposure method

value: aspiration

tag: time


title: Ang II 4

description:
Angiotensin treatment
3_6


title: Ang II 1

description:
Angiotensin treatment
Ang3


title: ctrl 7

description:
vehicle control
3_16

source_name: ctrl, aorta

value: vehicle


title: ctrl 5

description:
vehicle control
3_12


title: ctrl 6

description:
vehicle control
3_13


title: Proband257

value: Male


title: ctrl 4

description:
vehicle control
3_4


title: ctrl 3

description:
vehicle control
3_2


title: Ang II 8

description:
Angiotensin treatment
3_18


title: Proband256_sibling


title: Proband255_sibling


title: Proband257_sibling


title: Proband258


title: Proband253_sibling


title: Proband258_sibling


title: Proband159


title: Proband252


title: Proband252_sibling


title: Proband253


title: ctrl 2

description:
vehicle control
C2


title: Proband255


title: Proband251


title: Uninj Low 2209_Replicate3

city: Brussels

first: Simon

middle: Lieven Imanuel Johannes

last: Denil

address: Laarbeeklaan 101

department: University Hospital Brussels

country: Belgium

institute: VUB/ULB

description: non-treated

hyb_protocol: Fragmented,biotin labeled 3.5 ug of cDNA were hybridized for 18 hrs at 45C on Gene Chip Mouse Gene 2.0 ST Array.Gene Chips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The CEL files were processed in R (v3.2.3) with the Bioconductor (v3.2) libraries “oligo” (v1.34.2), “pd.mogene.2.0.st” (v3.14.1) and “limma” (v3.26.8). We used Robust Multi-array Average (RMA) to perform background correction and normalization with the “rma” function implemented in the “oligo” package (“target” parameter was set to “core” to obtain expression values at the gene-level).

label: biotin

source_name: control low Lgr5GFP, replicate 3

label_protocol: 2 ug of purified RNA was used to generate cDNA using Nugen Ovation Pico WTA System V2 kit and 5ug of cDNA was biotinylated using Nugen Encore Biotin Module(4200-12).

extract_protocol: RNA was extracted using Rneasy Micro kit as per supplier instructions

treatment_protocol: injured samples originate from mice injected with tamoxifen (0.27mg/g bodyweight) 24hours before isolation

tag: cell population

value: Lgr5-GFPlow corpus cells

tag: treatment


title: Proband254_sibling


title: Uninj Neg 2209_Replicate3

description: non-treated

value: Lgr5-GFPneg corpus cells


title: Uninj Neg 1809_Replicate2

description: non-treated

source_name: control low Lgr5GFP, replicate 2


title: Uninj Neg 1609_Replicate1

description: non-treated

source_name: control low Lgr5GFP, replicate 1


title: Proband256


title: Proband251_sibling


title: Proband250


title: Proband254


title: Uninj Low 1609_Replicate1

description: non-treated


title: Uninj High 2209_Replicate3

description: non-treated

source_name: control high Lgr5GFP, replicate 3

value: Lgr5-GFPhigh corpus cells


title: Proband250_sibling


title: Uninj High 1809_Replicate2

description: non-treated

source_name: control high Lgr5GFP, replicate 2


title: Uninj High 1609_Replicate1

description: non-treated

source_name: control high Lgr5GFP, replicate 1


title: Proband248


title: Proband249_sibling


title: Inj Neg 4_Replicate3

description: treated with tamoxifen (0.27mg/g bodyweight)

source_name: treated, neg Lgr5GFP, replicate 3

value: tamoxifen


title: Inj Neg 2_Replicate2

source_name: treated, neg Lgr5GFP, replicate 2


title: Proband248_sibling


title: Inj Neg 28_Replicate4

source_name: treated, neg Lgr5GFP, replicate 4


title: Proband247_sibling


title: Proband249


title: ctrl 1

description:
vehicle control
C1


title: Inj Low 29_Replicate4

source_name: treated, low Lgr5GFP, replicate 4


title: Proband247


title: Inj Neg 1_Replicate1

source_name: treated, neg Lgr5GFP, replicate 1


title: Proband158_sibling


title: Proband246_sibling


title: Uninj Low 1809_Replicate2

description: non-treated


title: Inj Low 28_Replicate3

source_name: treated, low Lgr5GFP, replicate 3


title: Proband246


title: Inj Low 4_Replicate2

source_name: treated, low Lgr5GFP, replicate 2


title: Proband158


title: Inj High 29_Replicate4

source_name: treated, high Lgr5GFP, replicate 4


title: Proband244


title: Inj High 28_Replicate3

source_name: treated, high Lgr5GFP, replicate 3


title: Inj High 2_Replicate1

source_name: treated, high Lgr5GFP, replicate 1


title: Inj High 4_Replicate2

source_name: treated, high Lgr5GFP, replicate 2


title: UC_batch2

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description: universal batch control

hyb_protocol: standard Affymetrix protocol

scan_protocol: For each microarrays (Schwann cell, macrophage), Affymetrix GeneChip Command Console (v4.0.0) was used to create .chp files.

data_processing:
All the probe sets on Affymetrix Mouse Gene 2.0 ST array (Mogene-2_0-st-v1.na33.2.mm10) were summarized by Affymetix Expression Console program (v.1.3.1.187) using robust multi-chip average (RMA) method. After preprocessing steps, data from two batches were combined and their batch effects were corrected using ComBat method
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

source_name: universal batch control

label_protocol: standard Affymetrix protocol

growth_protocol: We chopped mouse DRG/neurofibromas into 1-3 mm3 pieces and plated them in dissociation medium containing 20mL L-15 (Mediatech), 0.5 mg/mL collagenase type 1 (Worthington; Lakewood, NJ), and 2.5 mg/mL dispase protease type II (Cambrex; East Rutherford, NJ) at 37°C for 4-6 hours with shaking. The dissociation reaction was stopped by adding DMEM +10%FBS.  Undigested DRG/tumors were excluded by 100µM cell strainer. Cells were collected by centrifugation.

extract_protocol: RNA purification was performed as described (Williams et al, 2008). RNA integrity was determined by Agilent BioAnalyzer. RNAs with RNA integrity number (RIN) ≥9 were processed for Affymetrix. RNA purification was performed as described (Williams et al, 2008). RNA integrity was determined by Agilent BioAnalyzer. RNAs with RNA integrity number (RIN) ≥9 were processed for Affymetrix.

treatment_protocol: We incubated the dissociated mouse DRG/neurofibroma cell suspensions with anti-mouse monoclonal antibodies against CD11b (8G12/HPCA-2, Becton-Dickinson; San Jose, CA) bound to allophycocyanin (APC) anti-p75/NGFR (C40-1457, Becton-Dickinson) bound to phycoerythrin (PE), anti-F4/80 bound to Cy5.5 on ice in a solution containing PBS/0.2 %BSA/0.01 % NaN3 for 30 min. After washing, we resuspended cells in PBS/0.2 %BSA/0.01 % NaN3/2 μg/mL 7-aminoactinomycin D (7-AAD, Invitrogen). We carried out isotopic controls with irrelevant IgG1-APC, IgG1-PE and IgG1-Cy5.5 in parallel. We acquired cell suspensions in a dual-laser (Argon 488 and dye laser 630 or HeNe 633) FACSCanto (Becton-Dickinson) and analyzed on an “alive” gate based on light scatter parameters and 7-AAD staining negativity

tag: strain background

value: C57BL/6 and BALB/c (mixed)

tag: sample type

value: universal batch control


title: Inj Low 2_Replicate1

source_name: treated, low Lgr5GFP, replicate 1


title: Proband240_sibling

source_name: Whole Blood


title: Proband242


title: Proband243_sibling


title: MP_nf1_7m_4486_batch2

description: macrophage, neurofibroma, 7-month-old

source_name: Nf1+/+_7 month_macrophage_neurofibroma

tag: age

value: 7 month

tag: genotype

tag: tissue/cell type

value: macrophage, neurofibroma


title: SC_nf1_7m_4486_batch2

description: Schwann cell, neurofibroma, 7-month-old

value: Schwann cell, neurofibroma


title: Proband245


title: Proband244_sibling


title: Proband245_sibling


title: MP_nf1_7m_s4481_batch2

description: macrophage, neurofibroma, 7-month-old


title: Proband236_sibling


title: Proband241


title: Proband238


title: Proband242_sibling


title: Proband240


title: Proband243


title: MP_nf1_7m_s4448_batch2

description: macrophage, neurofibroma, 7-month-old


title: Proband241_sibling


title: Proband237_sibling


title: Proband238_sibling


title: Proband237


title: Proband239


title: Proband235_sibling


title: Proband234_sibling


title: Proband236


title: MP_nf1_7m_s4441_batch2

description: macrophage, neurofibroma, 7-month-old


title: SC_nf1_1m_s9_batch2

description: Schwann cell, neurofibroma, 1-month-old

value: 1 month


title: SC_nf1_7m_4992_batch2

description: Schwann cell, neurofibroma, 7-month-old


title: SC_nf1_1m_s8_batch2

description: Schwann cell, neurofibroma, 1-month-old


title: Proband235


title: MP_wt_1m_s4_batch2

description: macrophage, wild-type DRG, 1-month-old

source_name: Nf1+/+_1 month_macrophage_wild-type dorsal root ganglia (DRG)

value: macrophage, wild-type dorsal root ganglia (DRG)


title: MP_wt_1m_s6_batch2

description: macrophage, wild-type DRG, 1-month-old


title: MP_wt_1m_s5_batch2

description: macrophage, wild-type DRG, 1-month-old


title: SC_wt_1m_s3_batch2

description: Schwann cell, wild-type DRG, 1-month-old

source_name: Nf1+/+_1 month_Schwann cell_wild-type dorsal root ganglia (DRG)

value: Schwann cell, wild-type dorsal root ganglia (DRG)


title: Proband239_sibling

value: Whole Blood


title: SC_nf1_7m_s4481_batch2

description: Schwann cell, neurofibroma, 7-month-old


title: UC_s16_batch1

description: universal batch control


title: MP_nf1_1m_s15_batch1

description: macrophage, neurofibroma, 1-month-old

source_name: Nf1+/+_1 month_macrophage_neurofibroma


title: SC_wt_1m_s2_batch2


title: Proband234


title: MP_nf1_1m_s13_batch1

description: macrophage, neurofibroma, 1-month-old


title: Proband232_sibling

value: Female


title: Proband181_sibling


title: SC_wt_1m_s1_batch1


title: MP_nf1_1m_s14_batch1

description: macrophage, neurofibroma, 1-month-old


title: MP_nf1_1m_s12_batch1

description: macrophage, neurofibroma, 1-month-old


title: SC_nf1_1m_s10_batch1

description: Schwann cell, neurofibroma, 1-month-old


title: Proband233


title: Proband180


title: Proband181


title: Proband180_sibling


title: Proband232


title: Proband173_sibling


title: Proband178


title: Proband177_sibling


title: MP_nf1_1m_s11_batch1

description: macrophage, neurofibroma, 1-month-old


title: Proband178_sibling


title: Proband172_sibling


title: Proband176_sibling


title: Proband171_sibling


title: Proband176


title: Proband173


title: Proband179


title: Proband175


title: Proband233_sibling


title: Proband179_sibling


title: Proband169


title: Proband172


title: Proband174_sibling


title: Proband175_sibling


title: Proband169_sibling


title: Proband174


title: Proband177


title: Proband167


title: Proband168_sibling


title: Proband182


title: Proband156_sibling


title: Proband171


title: Proband170_sibling


title: Proband170


title: Proband167_sibling


title: Proband168


title: Proband156


title: Proband380


title: Proband477


title: Proband377


title: Proband374


title: Proband469


title: Proband472


title: Proband478


title: Proband375


title: Proband470


title: Proband361


title: Proband368


title: Proband378


title: Proband467


title: Proband468


title: Proband376


title: Proband465


title: Proband471


title: Proband476


title: Proband372


title: Proband370


title: Proband474


title: Proband463


title: Proband461


title: Proband479


title: Proband466


title: Proband462


title: Proband379


title: Proband460


title: Proband367


title: Proband373


title: Proband475


title: Proband371


title: Proband464


title: Proband473


title: Proband369


title: Proband360


title: Proband231_sibling


title: Proband231


title: Proband458


title: Proband230


title: Proband366


title: Proband459


title: Proband456


title: Proband224_sibling


title: Proband457


title: Proband229


title: Proband228_sibling


title: Proband224


title: Proband225


title: Proband222_sibling


title: Proband219


title: Proband222


title: Proband227


title: Proband226_sibling


title: Proband228


title: Proband226


title: Proband221


title: Proband219_sibling


title: Proband220_sibling


title: Proband230_sibling


title: Proband223_sibling


title: Proband220


title: Proband223


title: Proband216


title: Proband217_sibling


title: Proband225_sibling


title: Proband218


title: Proband229_sibling


title: Proband217


title: Proband216_sibling


title: Proband215_sibling


title: Proband218_sibling


title: Proband214


title: Proband215


title: Proband213_sibling


title: Proband211


title: Proband221_sibling


title: Proband209_sibling


title: Proband212_sibling


title: Proband208


title: Proband207_sibling


title: Proband203


title: Proband209


title: Proband206


title: Proband208_sibling


title: Proband214_sibling


title: Proband212


title: Proband210_sibling


title: Proband204_sibling


title: Proband210


title: Proband213


title: Proband207


title: Proband204


title: Proband201


title: Proband200


title: Proband203_sibling


title: Proband206_sibling


title: Proband199_sibling


title: Proband200_sibling


title: Proband202_sibling


title: Proband202


title: Proband211_sibling


title: Proband205


title: Proband201_sibling


title: Proband198_sibling


title: Proband197_sibling


title: Proband199


title: Proband193_sibling


title: Proband193


title: Proband197


title: Proband198


title: Proband196


title: Proband196_sibling


title: Proband190_sibling


title: Proband194


title: Proband187


title: Proband191_sibling


title: Proband189_sibling


title: Proband195_sibling


title: Proband189


title: Proband192_sibling


title: Proband195


title: Proband187_sibling


title: Proband192


title: Proband191


title: Proband186_sibling


title: Proband188


title: Proband157_sibling


title: Proband157


title: Proband186


title: Proband184_sibling


title: Proband185


title: Proband185_sibling


title: Proband184


title: Proband188_sibling


title: Proband205_sibling


title: Proband190


title: Proband183_sibling


title: Proband66


title: Proband182_sibling


title: Proband63


title: Proband64


title: Proband183


title: Proband65


title: Proband62


title: Proband22_father


title: Proband61


title: Proband53_father


title: Proband53_mother


title: Proband9_father


title: Proband60


title: Proband9_mother


title: Proband22_mother


title: Proband402


title: Proband389_father


title: Proband21_father


title: Proband393_mother


title: Proband21_mother


title: Proband57


title: Proband59


title: Proband401


title: Proband389_mother


title: Proband393_father


title: Proband56


title: Proband55


title: Proband58


title: Proband54


title: Proband52


title: Proband389


title: Proband49


title: Proband1


title: Proband53


title: Proband47


title: Proband50


title: Proband48


title: Proband44


title: Proband45


title: Proband36


title: Proband42


title: Proband43


title: Proband38


title: Proband51


title: Proband35


title: Proband32


title: Proband392


title: Proband31


title: Proband26


title: Proband34


title: Proband37


title: Proband41


title: Proband39


title: Proband24


title: Proband27


title: Proband30


title: Proband46


title: Proband33


title: Proband40


title: Proband17


title: Proband28


title: Proband23


title: Proband21


title: Proband19


title: Proband22


title: Proband29


title: Proband14


title: Proband13


title: Proband16


title: Proband20


title: Proband9


title: Proband15


title: Proband10


title: Proband12


title: Proband18


title: Proband7


title: Proband397


title: Proband3


title: Proband4


title: Proband5


title: Proband25


title: Proband394


title: Proband393


title: Proband382


title: Proband398


title: Proband6


title: Proband399


title: Proband400


title: Proband395


title: Proband384


title: Proband388_sibling


title: Proband396


title: Proband386_sibling


title: Proband391


title: Proband383


title: Proband11


title: Proband2


title: Proband387_sibling


title: Proband385


title: Proband386


title: Proband390


title: Proband8


title: Proband387


title: Proband388


title: Proband154


title: Proband153


title: Proband146


title: Proband385_sibling


title: Proband155


title: Proband152


title: Proband151


title: Proband148


title: Proband137


title: Proband141


title: Proband132


title: Proband139


title: Proband142


title: Proband145


title: Proband136


title: Proband135


title: Proband144


title: Proband130


title: TumorTissue262

city: Vilnius

first: Kristina

last: Daniunaite

address: Sauletekio Ave. 7

department: Institute of Biosciences

country: Lithuania

institute: Vilnius University

description: DNA methylation in primary prostate tumor from patient 262

hyb_protocol: All amount of labeled cRNA was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized onto Human Gene Expression 8×60K microarrays for 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies).

scan_protocol: Microarrays were scanned immediately after washing using SureScan microarray scanner (Agilent Technologies).

data_processing: Scanned images were analyzed with Feature Extraction software v10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09, grid 028004_D_F_20120411). Background subtracted and spatially detrended signals were obtained.

source_name: Prostate cancer tissue, donor P262

label_protocol: Cyanine-3 labeled cRNA was prepared from 200 ng of purified RNA using Low Input Quick Amp Labeling Kit, One Color and RNA Spike-In Kit, One Color acording to manufacturer's protocol (Agilent Technologies), followed by purification with RNeasy Mini Kit (Qiagen). Dye incorporation and cRNA yield was measured with NanoDrop 2000.

extract_protocol: Total RNA was extracted from 10-30 ng of mechanically homogenized tissue with mirVana miRNA Isolation Kit according to manufacturer’s protocol (Life Technologies). Extracted RNA was quantified using NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific) and quality was monitored with Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Tissue samples were obtained from radical prostatectomy material of prostate cancer patients. None of the patients had preoperatively received radiotherapy, chemotherapy, or hormone therapy.

tag: biochemical disease recurrence

value: no

tag: pathological tumor stage

tag: gleason score


title: Proband147


title: Proband149


title: Proband150


title: Proband131


title: Proband134


title: Proband143


title: Proband128


title: TumorTissue249

description: DNA methylation in primary prostate tumor from patient 249

source_name: Prostate cancer tissue, donor P249

value: yes


title: TumorTissue225

description: DNA methylation in primary prostate tumor from patient 225

source_name: Prostate cancer tissue, donor P225


title: TumorTissue257

description: DNA methylation in primary prostate tumor from patient 257

source_name: Prostate cancer tissue, donor P257


title: Proband127

value: Male


title: Proband123


title: TumorTissue191

description: DNA methylation in primary prostate tumor from patient 191

source_name: Prostate cancer tissue, donor P191


title: TumorTissue232

description: DNA methylation in primary prostate tumor from patient 232

source_name: Prostate cancer tissue, donor P232


title: Proband126


title: Proband138


title: TumorTissue188

description: DNA methylation in primary prostate tumor from patient 188

source_name: Prostate cancer tissue, donor P188


title: Proband124


title: Proband121


title: TumorTissue169

description: DNA methylation in primary prostate tumor from patient 169

source_name: Prostate cancer tissue, donor P169


title: TumorTissue146

description: DNA methylation in primary prostate tumor from patient 146

source_name: Prostate cancer tissue, donor P146


title: TumorTissue157

description: DNA methylation in primary prostate tumor from patient 157

source_name: Prostate cancer tissue, donor P157


title: Proband133


title: Proband117


title: TumorTissue075

description: DNA methylation in primary prostate tumor from patient 075

source_name: Prostate cancer tissue, donor P075


title: TumorTissue133

description: DNA methylation in primary prostate tumor from patient 133

source_name: Prostate cancer tissue, donor P133


title: TumorTissue162

description: DNA methylation in primary prostate tumor from patient 162

source_name: Prostate cancer tissue, donor P162


title: Proband120

source_name: Whole Blood


title: TumorTissue035

description: DNA methylation in primary prostate tumor from patient 035

source_name: Prostate cancer tissue, donor P035


title: Proband140


title: TumorTissue022

description: DNA methylation in primary prostate tumor from patient 022

source_name: Prostate cancer tissue, donor P022


title: Proband129


title: Proband119


title: TumorTissue021

description: DNA methylation in primary prostate tumor from patient 021

source_name: Prostate cancer tissue, donor P021


title: Proband116


title: Proband125


title: Proband118


title: Proband115


title: Proband122


title: Proband111


title: Proband114


title: Proband112


title: Proband109


title: Proband105


title: Proband108


title: Proband113


title: Proband107


title: SEM_treated_2

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

description:
SEM_treated_2
Replicate_2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol (Hiscan array scanner)

data_processing: Raw idat files were processed using beadarray bioconductor package. Code available here: https://github.com/PoisonAlien/beadAnalyze

source_name: SEM, treated

label_protocol: target probes were labelled with biotin using TargetAmp Nano labelling kit.

growth_protocol: Cells were cultured in RPMI supplemented with 10% FBS, 100 units/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: total RNA was extracted using AxyPrep Multisource Total RNA Miniprep Kits  (Axygen Biosciences).

treatment_protocol: Cells were treated with either KPT-9274 or DMSO diluent control for 48 hours.

tag: cell line

value: SEM B-cell ALL cell line


title: Proband102

tag: tissue


title: Proband106

tag: gender


title: Proband101

tag: individual


title: Proband92


title: Proband99


title: Proband97


title: Proband103


title: Proband98


title: Proband95


title: Proband90


title: Proband94


title: Proband88


title: Proband110


title: Proband93


title: Proband89


title: Proband96


title: Proband100


title: SEM_control_1

description:
SEM_control_1
Replicate_1

source_name: SEM, control

value: DMSO


title: SEM_treated_1

description:
SEM_treated_1
Replicate_1


title: SEM_control_2

description:
SEM_control_2
Replicate_2


title: REH_treated_2

description:
REH_treated_2
Replicate_2

source_name: REH, treated

value: REH B-cell ALL cell line


title: Proband91


title: Proband85


title: Proband104


title: REH_treated_1

description:
REH_treated_1
Replicate_1


title: Proband87


title: Proband86


title: RS4;11_treated_2

description:
RS4_treated_2
Replicate_2

source_name: RS4;11, treated

value: RS4;11 B-cell ALL cell line


title: REH_control_1

description:
REH_control_1
Replicate_1

source_name: REH, control


title: RS4;11_control_2

description:
RS4_control_2
Replicate_2

source_name: RS4;11, control


title: REH_control_2

description:
REH_control_2
Replicate_2


title: Proband84


title: Proband83


title: RS4;11_control_1

description:
RS4_control_1
Replicate_1


title: RS4;11_treated_1

description:
RS4_treated_1
Replicate_1


title: LNCaP_IRF1 siRNA_vehicle treated 2

city: buffalo

first: Dan

last: Wang

address: Elm & Carlton Streets

institute: RPCI

hyb_protocol: The labeled probes were then mixed with hybridization reagents and hybridized overnight to the HumanHT12 v4 BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

data_processing: BeadChip data files are analyzed with Illumina’s GenomeStudio gene expression module (V1.9.0)

source_name: LNCaP_IRF1 siRNA_vehicle treated

label_protocol: Initially, we converted 250-500 ng total RNA to cDNA, followed by in vitro transcription to generate biotin-labeled cRNA (Illumina TotalPrep RNA Amplification Kit, Ambion Inc., Austin, TX).

extract_protocol: Total RNA was isolated from frozen tissue samples using TRIZOL reagent (Invitrogen).

value: LNCaP

tag: cell type

value: prostate cancer cells

tag: transfected with

value: IRF1 siRNA

tag: treated with

value: vehicle


title: LNCaP_STAT3 siRNA_R1881 treated 2

source_name: LNCaP_STAT3 siRNA_R1881 treated

value: STAT3 siRNA

value: 5nM synthetic androgen R1881


title: LNCaP_PGAM5 siRNA_vehicle treated 2

source_name: LNCaP_PGAM5 siRNA_vehicle treated

value: PGAM5 siRNA


title: LNCaP_PGAM5 siRNA_R1881 treated 1

source_name: LNCaP_PGAM5 siRNA_R1881 treated


title: LNCaP_control siRNA_R1881 treated 3

source_name: LNCaP_control siRNA_R1881 treated

value: control siRNA


title: LNCaP_STAT3 siRNA_vehicle treated 1

source_name: LNCaP_STAT3 siRNA_vehicle treated


title: LNCaP_PGAM5 siRNA_R1881 treated 3


title: LNCaP_STAT3 siRNA_vehicle treated 3


title: Proband80

value: Whole Blood


title: Proband81


title: Proband78


title: LNCaP_IRF1 siRNA_R1881 treated 1

source_name: LNCaP_IRF1 siRNA_R1881 treated


title: Proband82

source_name: Whole Blood


title: Proband76


title: Proband68


title: LNCaP_control siRNA_R1881 treated 1


title: LNCaP_IRF1 siRNA_R1881 treated 3


title: LNCaP_STAT3 siRNA_vehicle treated 2


title: Proband77


title: Proband70


title: Proband79

value: Female


title: Proband71


title: Proband74


title: LNCaP_PGAM5 siRNA_vehicle treated 1


title: Proband67


title: LNCaP_STAT3 siRNA_R1881 treated 3


title: Proband72


title: Proband485


title: Proband480


title: LNCaP_PGAM5 siRNA_vehicle treated 3


title: LNCaP_IRF1 siRNA_R1881 treated 2


title: LNCaP_control siRNA_vehicle treated 2

source_name: LNCaP_control siRNA_vehicle treated


title: LNCaP_control siRNA_R1881 treated 2


title: LNCaP_PGAM5 siRNA_R1881 treated 2


title: LNCaP_control siRNA_vehicle treated 3


title: Proband73


title: Proband75


title: LNCaP_IRF1 siRNA_vehicle treated 1


title: LNCaP_STAT3 siRNA_R1881 treated 1


title: Proband484


title: Proband69


title: Proband286


title: Proband285


title: Proband293


title: Proband287


title: LNCaP_IRF1 siRNA_vehicle treated 3


title: Proband294


title: Proband283


title: LNCaP_control siRNA_vehicle treated 1


title: AB ctrl, rep2

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were normalised using quantile normalisation in Partek Genomic Suite. Expression values from different chip types (AB from HG-U133A, CB from HG-U133_Plus_2) were combined, keeping only probes with information from both chip types, resulting in 22277 probes. Further, only one probe per gene symbol was left by selecting the probes with the highest variance among all samples, resulting in 13515 unique transcripts.

source_name: Adult blood monocytes, Ctrl

label_protocol: cRNA were prepared and SAGE-labeled according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA) from 5 ug total RNA.

growth_protocol: Monocytes were isolated by Ficoll-Paque density gradient centrifugation and by using the Monocyte Isolation Kit II (Miltenyi Biotec, Bergisch Gladbach, Germany).

extract_protocol: Total RNA was isolated from monocytes using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: After o/n culture in teflon bags in McCoys modified medium supplemented with 1% glutamine, 1% penicillin-streptomycin and 15% FBS, monocytes were incubated for 4h with 10 ng/ml LPS.

value: Monocytes

tag: tissue source

value: Adult blood

value: Control

tag: array


title: AB ctrl, rep3

tag: treatment


title: Proband292

value: Male


title: Bone metastatic clones 8th generation SPC-A-1

city: Washington, DC

first: Shu

last: Yang

state: District of Columbia

address: SEH, Suite 8840, 800 22nd Street NW

institute: GEORGE WASHINGTON UNIV

hyb_protocol: The probe was dissolved in 20 µl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide]. Microarrays were pre-hybridized with a hybridization solution containing 0.5 mg/ml denatured salmon sperm DNA at 42C for 6 hrs. Fluorescent probe mixtures were denatured at 90C for 5 minutes, and then applied onto the pre-hybridized chip under a cover glass. Chips were hybridized at 42C for 15-17 hours. Next, the hybridized chips were each washed at 60C for 10 min in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS, and 0.1X SSC, then dried at room temperature.

scan_protocol: The chips were scanned with a ScanArray 4000 (GSI Lumonics, Bellerica, MA) at two wavelengths, 635nm and 532 nm, to detect emission from both Cy5 and Cy3 respectively.

data_processing: The intensities of each spot at the two wavelengths represent the quantity of Cy3-dUTP and Cy5-dUTP. Ratios of Cy5 to Cy3 were computed using the GenePix Pro 3.0 median of ratio method. Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged 'Bad' or 'Not Found' by GenePix software was removed from the final data. Only genes with raw intensity values for both Cy3 and Cy5 of >200 counts were selected from each array and used for further analysis.

label_protocol: Total RNA was reverse transcribed using the Superscript III RNase H- Reverse Transcriptase kit (Invitrogen) following the manufacturer’s instructions with Cy3-dUTP or Cy5-dUTP.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

source_name: Chinese lung adenocarcinoma cancer cells (SPC-A-1), parental


title: AB ctrl, rep1


title: Proband288


title: IPSDH-Control-clone3

city: Philadelphia

first: Daniel

last: Rader

state: Pennsylvania

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

hyb_protocol: We use Affymetrix Hybridization Kit for hybridization. Hyb. final labeled DNA concentration is 25ng/uL. Hyb. condition is 45C/16 hours.

scan_protocol: Scanner is Affymetrix 7G (GCS3000 system). Analysis was done by Affemetrix Expression Console software.

data_processing: Raw data is normalized using RMA in the program Partek Genomics Suite (v6.6, Partek, Inc., St. Louis, MO).

source_name: IPSC derived hepatocytes from Healthy Control Patient-

label_protocol: WT Expression-Ambion and WT-Terminal Labeling protocols.

growth_protocol: Cells were maintained in Hepatocyte Culture Medium (Lonza CC-3199 & CC-4182 ) at 37C

extract_protocol: Total RNA was extracted with QIAGEN miRNeasy according to the manufacturer's instructions.

treatment_protocol: Culture medium was aspirated and cells were washed once with 1xPBS. TRIzol reagent (Ambion) was added to harvest RNA.

value: Cultured cells


title: Proband291


title: Proband290


title: AB LPS, rep2

source_name: Adult blood monocytes, LPS

value: Lipopolysaccharide (LPS)


title: Bone metastatic clones 4th generation SPC-A-1

value: Chinese lung adenocarcinoma cancer cells


title: IPSDH-Control-clone2


title: Proband284


title: IPSDH-Tangier-clone2

source_name: IPSC derived hepatocytes from Tangier Disease Patient-

value: Tangier


title: AB LPS, rep3


title: IPSDH-Tangier-clone3


title: Proband289


title: Rv1 pLKO.1_rep1

city: Oxford

first: Natasha

last: Sahgal

address: Old Road Campus

department: Ludwig Institute of Cancer Research

country: United Kingdom

institute: University of Oxford

description: replicate 1

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Affymetrix Gene Chip system 3000 7G

data_processing:
R and Bioconductor packages were used for processing and analyzing raw data to generate RMA normalized intensities
The dataset was filtered to retain only the main probesets followed by further excluding probes with low expression (<4).

source_name: CWR22Rv1 prostate cancer cells expressing control pLKO.1 vector

label_protocol: The samples were labeled, hybridized, wahsed and scanned by by the Biopolymer-Genomics Core Facility (Univeristy of Maryland School of Medicne)

growth_protocol: CWR22Rv1 cells were grown in the RPMI1640 media supplmentd with 10% FBS and antibiotics.

extract_protocol: Total RNA was extracted from cells using the GenElute Mammalian Total RNA Purification Kit (Sigma).

treatment_protocol: Cells were transduced with the lentiviral particles encoding control shRNA (pLKO.1) or AR shRNA (AR-KD) for 48 h.

value: CWR22Rv1 prostate cancer cells

tag: genotye/variation

value: control


title: Rv1 AR-KD_rep2

description: replicate 2

source_name: CWR22Rv1 prostate cancer cells expressing AR shRNA

value: AR depletion


title: Rv1 AR-KD_rep1

description: replicate 1


title: IPSDH-Control-clone1


title: AB LPS, rep1


title: Proband282


title: Rv1 pLKO.1_rep2

description: replicate 2


title: Proband274


title: Proband276


title: Proband271


title: IPSDH-Tangier-clone1


title: Bone metastatic clones 8th generation NCI-H460

value: Human larger cell lung cancer cells

source_name: Human larger cell lung cancer cells (NCI-H460), parental


title: Proband281


title: Proband275


title: Proband279


title: obese insulin sensitive lipogenesis ID48_2656

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

institute: Karolinska

hyb_protocol: The labeled samples were placed in a hybridization cocktail mix containing 4 % formamide and hybridized overnight to Affymetrix GeneChip miRNA 1.0 arrays (Affymetrix Inc., Santa Clara, CA) following the indicated Genisphere protocol.

scan_protocol: The arrays were washed, stained and scanned in an Affymetrix GCS 3000 scanner.

data_processing: Signal intensities and present calls were generated in the miRNA QC tool (by Affymetrix) using default settings, i.e. BC-CG background adjustment, quantile normalization, and median polish summarization.

source_name: Subcutaneous abdominal WAT

label_protocol: One μg of total adipose RNA was labeled using the FlashTag biotin HSR labeling kit (Genisphere Inc., Hatfield, PA) according to the supplier’s protocol.

extract_protocol: Total RNA was extracted from adipose tissue specimens (300 mg) using the miRNeasy kit (Qiagen, Hilden, Germany)

treatment_protocol: Patients came to the laboratory for clinical examination following an overnight fast. An abdominal subcutaneous fat biopsy was obtained by needle biopsy. Tissue pieces were rapidly rinsed in saline. A small part was immediately used for determination of mean fat cell volume and for ex vivo quantification of adipocyte lipogenesis. The rest was frozen in liquid nitrogen and kept at -70 °C for subsequenct RNA preparation.

value: WAT

value: female

tag: age


title: obese insulin sensitive lipogenesis ID47_328

tag: genotype


title: obese insulin resistant lipogenesis ID40_4810


title: obese insulin resistant lipogenesis ID44_4642


title: obese insulin resistant lipogenesis ID45_514


title: obese insulin resistant lipogenesis ID38_4640


title: obese insulin sensitive lipogenesis ID46_4603


title: Proband280


title: obese insulin resistant lipogenesis ID41_4639


title: obese insulin resistant lipogenesis ID39_4910


title: Proband295


title: obese insulin resistant lipogenesis ID42_4275


title: Proband273


title: obese insulin resistant lipogenesis ID36_5171


title: obese insulin resistant lipogenesis ID43_1794


title: Proband278


title: obese insulin resistant lipogenesis ID37_4649


title: Proband333


title: obese insulin resistant lipogenesis ID35_4991


title: obese insulin resistant lipogenesis ID33_2658


title: obese insulin resistant lipogenesis ID31_4957


title: obese insulin resistant lipogenesis ID34_4965


title: Proband277


title: obese insulin resistant lipogenesis ID30_4982


title: obese insulin resistant lipogenesis ID32_4921


title: obese insulin resistant lipogenesis ID29_4967


title: Proband272


title: Proband325


title: obese insulin resistant lipogenesis ID28_4973


title: Proband327


title: Proband311


title: Proband331


title: Proband326


title: Proband329


title: Proband332


title: Proband330


title: obese insulin sensitive lipogenesis ID27_2629


title: obese insulin sensitive lipogenesis ID25_2645


title: Proband328


title: Proband324


title: obese insulin sensitive lipogenesis ID26_2663


title: obese insulin sensitive lipogenesis ID24_4270


title: Proband323


title: obese insulin sensitive lipogenesis ID21_2652


title: Proband316


title: Proband317


title: obese insulin sensitive lipogenesis ID22_3699


title: Proband489


title: obese insulin sensitive lipogenesis ID19_4662


title: obese insulin sensitive lipogenesis ID17_3718


title: Proband321


title: obese insulin sensitive lipogenesis ID18_3713


title: obese insulin sensitive lipogenesis ID23_4594


title: Proband320


title: Proband314


title: obese insulin sensitive lipogenesis ID16_4624


title: Proband315


title: obese insulin sensitive lipogenesis ID15_325


title: Proband322


title: obese insulin sensitive lipogenesis ID20_4281


title: obese insulin sensitive lipogenesis ID13_1529


title: Proband313


title: obese insulin sensitive lipogenesis ID14_3689


title: obese insulin sensitive lipogenesis ID10_2636


title: Proband319


title: lean control ID09_1796


title: Proband56_father


title: Proband56_mother


title: obese insulin sensitive lipogenesis ID11_4589


title: Proband312


title: obese insulin sensitive lipogenesis ID12_2183


title: Proband23_father


title: lean control ID08_1034


title: Proband318


title: Proband34_father


title: lean control ID05_4638


title: Proband54_mother


title: Proband23_mother


title: lean control ID04_791


title: Proband15_mother


title: lean control ID06_1732


title: lean control ID03_1141


title: Proband13_father


title: obese insulin resistant lipogenesis ID01_751


title: lean control ID02_884


title: Proband54_father


title: Proband34_mother


title: Proband11_father


title: 2LPS8

city: New Haven

first: Yajaira

last: Suarez

state: Connecticut

address: 10 Amistad Street

department: Comparative Medicine

institute: Yale University School of Medicine

description: Biological Replicate 2 LPS (8h)

scan_protocol: Standard Illumina scanning protocol

data_processing: Scanned files will be loaded into BeadStudio software for analysis  for analysis

source_name: Bone Marrow derived macrophages (BMDMs

label_protocol: labeled cRNA for hybridization onto Illumina BeadChipsfollowing the recommended Illumina protocol using a TotalPrep RNA Amplification kit (Applied Biosystems).Purification of the cRNA will follow and integrity of the cRNA will be assessed by running aliquots on the Bioanalyzer prior to hybridization.

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

tag: strain

value: 8 weeks


title: Proband11_mother

value: Whole Blood


title: 3C8

description: Biological Replicate 3 mock Control (8h)


title: Proband15_father


title: Proband6_father


title: lean control ID07_4618


title: Proband398_father


title: 1LPS8

description: Biological Replicate 1 LPS (8h)


title: 3LPS8

description: Biological Replicate 3 LPs (8h)


title: Proband13_mother

value: Female


title: Proband25_father


title: LP

city: Tucson

first: Hsin-Jung

last: Wu

state: AZ

address: 1656 E mabel street

department: Immunobiology

institute: University of Arizona

description: Gene expression data from exvivo isolated Th17 cells

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix GeneChip Mouse Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: The data were analyzed with the Robust Multiarray Average (RMA) using the Affymetrix Expression Console.

source_name: small intestine-lamina propria (SI-LP)

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol

growth_protocol: Tissues of SFB+ K/BxN mice were harvest at 6 week old.

extract_protocol: RNA from sorted cells was purified using TriPure (Roche) and further enriched by RNeasy® MinElute® Cleanup Kit (Qiagen).

treatment_protocol: Cells from spleen, lung, and SI-LP of SFB+ IL-17eGFP.K/BxN mice (5-6.5 weeks old) were cultured with 1 mM ionomycin, 50ng/ml PMA, and BD GolgiPlug (1:1000 dilution) for 4 hrs. Cells were stained with Abs recognizing CD4, TCRβ, and CD45 prior to cell sorting (FACSAria). Th17 (CD45+ TCRβ+ CD4+ GFP+) cells from spleen, lung, and SI-LP were sorted.

value: C57BL/6 X NOD

value: SI-LP

value: Th17 cells


title: Proband6_mother


title: Proband397_mother


title: Proband350

value: Male


title: Proband357


title: spleen

source_name: spleen

value: spleen


title: Tnrc6a(GW182)-mutant-E18.5 lung rep2

first: Jining

last: Lu

address: 630 West 168th Street, BB8-801c

department: Medicine

institute: Columbia University Medical Center

description: Tnrc6a(GW182)-mutant-lung-2[log(2) transformed]

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: lung of E18.5 Tnrc6a (GW182) mutant mouse embryo

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

extract_protocol: Trizol extraction of total RNA of E18.5 lung disseected from individual embryo was performed according to the manufacturer's instructions.

tag: strain background

tag: genotype/variation

value: Tnrc6a (GW182) mutant

value: lung


title: 1C8

description: Biological Replicate 1 mock Control (8h)


title: lung

source_name: lung


title: Tnrc6a(GW182)-mutant-E18.5 lung rep1

description: Tnrc6a(GW182)-mutant-lung-1[log(2) transformed]


title: Tnrc6a(GW182)-mutant-E18.5 lung rep3

description: Tnrc6a(GW182)-mutant-lung-3[log(2) transformed]


title: 2C8

description: Biological Replicate 2 mock Control (8h)


title: Proband349


title: Proband397_father


title: Proband351


title: Tnrc6a(GW182)-WT-E18.5 lung rep3

description: Tnrc6a(GW182)-WT-lung-3[log(2) transformed]

source_name: lung of E18.5 wild type mouse embryo

value: wild type


title: Proband25_mother

source_name: Whole Blood


title: Proband356


title: Tnrc6a(GW182)-WT-E18.5 lung rep2

description: Tnrc6a(GW182)-WT-lung-2[log(2) transformed]


title: 72h 4.5nM TNBC MELK Inhibitor vs. DMSO Replicate 2 (SUM159)

city: Houston

first: Cecilia

middle: M.

last: Williams

state: Texas

address: 3605 Cullen Blvd

department: Center for Nuclear Receptors & Cell Signaling

institute: The University of Houston

description: Biological and technical replicate 2 of 2. OTSSP167 Sample labeled with Cy5, DMSO sample labeled with Cy3

hyb_protocol: Human Genome OpArray- custom (Cat No: OPHS4V-25, Microarray, Inc.) were incubated in warm (42 degC) pre-hybridization buffer (1% BSA, 5x SSC, 0.1% SDS) for 30 minutes. Then, they were quickly washed with MilliQ H20 and isopropanol, dried, and placed in hybridization chambers. The Cy5 and Cy3 samples were pooled, and reduced to 13.6µL using a speed vac and then several reagents were added to a final volume of 65.05µL (5x SCC, 50% Formamide, 0.1% SDS, 0.1µg/µL tRNA, and 0.2µg/µL human Cot-1 DNA). The mixture was then heated for 3 minutes at 95 degC , cooled, and loaded under a coverslip onto the pre-hybridized arrays. The hybridization chambers were sealed and placed in a 42 degC water bath for 40 hours. After hybridization, they were washed 3 x 5 minutes in water with decreased concentrations of SSC and SDS each time (2x SSC and 0.1% SDS, then 0.1x SSC and 0.1% SDS, then just 0.1x SSC)

scan_protocol: Slides were scanned on a Gene Pix 4300A machine, and then quantified with GenePix Pro 6.0 software.

data_processing: Array reports were generated within GenePix Pro 6.0 to assess the quality of the arrays. R software was used to generate array comparisons, filter (background, signal-to-noise ratio) and normalize data, perform a dye-swap, generate log2(R/G) values for each slide, and derive B-test and t-test significance for each gene with changed expression. The specific R package used for microarray analysis in R was called the “Limma” package and was obtained from the Karolinska Institutet (Stockholm, Sweden)

source_name: SUM159 TNBC Cells OTSSP167

label_protocol: Samples containing 20 µg of total RNA and 1µL (5µg/µL) of random hexamer primer were diluted to a final volume of 18.4µL using RNase-free H2O, and then incubated for 10 minutes at 70deg C. After cooling for 5 minutes on ice, 11.6µL of cDNA synthesis master mix was added (1x first-strand buffer, 0.01M DTT, 1x-aa-dUTP+dNTP mix, Superscript III). The mixture was first incubated for 10 minutes at 35deg C, and then for 2 hours at 46 degC. The remaining RNA was hydrolyzed by adding 3µL 0.2M EDTA (pH 8.0) and 4.5µL 1M NaOH, incubating for 15 minutes at 70 degC, cooling, and then adding 4.5µL 1M HCL. The cDNA was subsequently purified using Quiagen MinElute columns and buffers, and eluted in 20µL 100mM NaHCO3. Finally, the elute was transferred to dried (speed-vac'd) aliquots of either Cy3 or Cy5 mono-reactive ester, and incubated for 30 minutes in the dark at room temp. The dye-coupled samples were purified, again using Quiagen minElute columns and buffers, and eluted in a final amount of 20µL elution buffer.

growth_protocol: SUM159 cells were grown in DMEM with 10%FBS. No PEST was used.

extract_protocol: TriZOL/ chloroform/ Quiagen Rneasy Kit according to manufacturer's guidelines.

treatment_protocol: 4.5uL of either 10uM OTSSP167 in DMSO or just DMSO in 10mL cell culture media in a 10cm cell culture dish.

value: Mammary gland/ breast

tag: passage

source_name: SUM159 TNBC Cells DMSO


title: Proband348


title: 72h 45nM TNBC MELK Inhibitor vs. DMSO Replicate 2

source_name: MDA-MB-231 TNBC Cells + 45nM OTSSP167 MELK Inhibitor

growth_protocol: MDA-MB-231 cells were grown in 1:1 DMEM/F-12 with 10%FBS. No PEST was used.

treatment_protocol: 4.5uL of either 100uM OTSSP167 in DMSO or just DMSO in 10mL cell culture media in a 10cm cell culture dish.

value: Mammary gland/breast

source_name: MDA-MB-231 TNBC Cells + 0.045% DMSO


title: Proband338


title: 72h 45nM TNBC MELK Inhibitor vs. DMSO Replicate 1 (SUM159)

description: Biological and technical replicate 1 of 2. OTSSP167 Sample labeled with Cy3, DMSO sample labeled with Cy5


title: Tnrc6a(GW182)-WT-E18.5 lung rep1

description: Tnrc6a(GW182)-WT-lung-1[log(2) transformed]


title: 72h 4.5nM TNBC MELK Inhibitor vs. DMSO Replicate 1

source_name: MDA-MB-231 TNBC Cells + 4.5nM OTSSP167 MELK Inhibitor


title: 72h 45nM TNBC MELK Inhibitor vs. DMSO Replicate 2 (SUM159)


title: Proband347


title: Proband344


title: 72h 45nM TNBC MELK Inhibitor vs. DMSO Replicate 1


title: Proband346


title: 72h 4.5nM TNBC MELK Inhibitor vs. DMSO Replicate 2


title: Proband354


title: Proband337


title: 48h TNBC MELK Inhibitor vs. DMSO Replicate 1

treatment_protocol: 4.5uL of either OTSSP167 in DMSO or just DMSO in 10mL cell culture media in a 10cm cell culture dish.


title: Proband345


title: Proband342


title: Proband355


title: Proband353


title: Proband352


title: Proband401_mother


title: 48h TNBC MELK Inhibitor vs. DMSO Replicate 2


title: Proband343


title: Proband365


title: Libusova_NcKI3

city: Freiburg

first: Marc

middle: P.

last: Stemmler

address: Stuebeweg 51

department: Molecular Embryology

institute: Max-Planck Institute of Immunobiology and Epigenetics

description: Gene expression data from intestinal epithelial cells with E-cadherin replacement by N-cadherin

scan_protocol: Standard Affymetrix protocol

data_processing: Data analysis was performed using the R/Bioconductor Limma software. Quality of the data set was controlled by the simpleaffy package and normalized by quantile normalization with the GCRMA alogrithm.

source_name: Epithelial cells with N-cadherin instead of E-cadherin

label_protocol: Standard Affymetrix protocol

growth_protocol: 2 week-old mice were used.

extract_protocol: RNA was prepared from isolated epithelial cells using the Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Rinsed small intestine was cut into small pieces, and epithelial cells were detached from the lamina propria by incubation in isolation buffer (30 mM EDTA in Mg2+-free, Ca2+-free Hank's balanced salt solution) and vigorous vortexing. Suspended cells were collected by brief centrifugation, washed with PBS and immediately used for RNA extraction.

value: 2 weeks-old

value: Ecadflox/Ncad;Vil-Cre

value: intestinal epithelial cells


title: Libusova_NcKI1


title: Proband339

first: Andrew

last: Sharp

address: 1470 Madison Av

institute: Icahn School of Medicine at Mount Sinai

scan_protocol: Arrays were imaged using standard recommended Illumina scanner protocol

data_processing: The methylation value was set to null for probes with a detection p-value >0.01. Probe sequences (50-mer oligonucleotides) were uniquely mapped to the reference human genome hg19 (GRCh37) using BLAT, allowing up to 2 mismatches and 1 gap. Beta values from the autosomal probes were quantile normalized using lumi package in R.

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA was acquired from various labs/consortiums


title: Proband340


title: Proband335


title: Proband334


title: 72h 4.5nM TNBC MELK Inhibitor vs. DMSO Replicate 1 (SUM159)

value: female


title: Proband454


title: control, rep1

city: Shanghai

first: Haixin

last: Zhao

address: Yueyang Road 320

country: China

institute: Institute of Health Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences

description:
Gene expression data from control ESCs with normal Chd4 expression
Chd4i-1 - Dox 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the the Affymetrix Scanner3000.

source_name: Control ESCs

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

growth_protocol: J1 ESCs were cultured on gelatin-coated plates in standard ESC medium consisting of DMEM (Dulbecco’s modified Eagle’s medium) (Gibico) supplemented with 15% fetal bovine serum (Gibico), 2 mM Glutamax (Gibico), 0.1% b-mercaptoethanol (Sigma), 1 mM MEM pyruvate sodium (Gibico), 0.1 mM MEM nonessential amino acid (Gibico), 1% Penicillin/Streptomycin (Hyclone), and 1000 U/ml recombinant leukemia inhibitory factor (Millipore).

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

treatment_protocol: The inducible RNAi cell line Chd4i-1 was treated with 5 ng/ml doxycycline for knocking down Chd4 and the group without doxycycline trearment was taken as the control. After 3 days, ESCs were washed twice with PBS buffer, tryipsinized and washed twice with PBS, and placed on ice in the Trizol solution (Invitrogen).

tag: cell line

value: J1 ESCs

value: control


title: Libusova_NcKI2


title: Proband341

city: New York

tag: tissue

value: Whole Blood


title: Chd4 RNAi, rep2

description:
Gene expression data from control ESCs with deficient Chd4 expression
Chd4i-1 + Dox 2

source_name: Chd4 knockdowm ESCs

value: Chd4 knockdown


title: control, rep2

description:
Gene expression data from control ESCs with normal Chd4 expression
Chd4i-1 - Dox 2


title: Chd4 RNAi, rep1

description:
Gene expression data from control ESCs with deficient Chd4 expression
Chd4i-1 + Dox 1


title: Proband455

tag: gender


title: Proband452

tag: individual


title: Libusova_Ctrl1

description: Gene expression data from control intestinal epithelial cells

source_name: Control epithelial cells

value: Control

tag: cell type


title: Proband336


title: Proband381


title: Proband449

value: Female


title: Proband364

value: Male


title: Libusova_Ctrl2


title: Proband453


title: Proband363


title: Proband433


title: Libusova_Ctrl3


title: Proband446


title: Proband448


title: Proband450


title: Proband443


title: Proband447


title: Proband362


title: Proband441


title: Proband444


title: Proband445


title: Proband442


title: Proband451


title: Proband431


title: Proband436


title: Proband434


title: Proband438


title: Proband437


title: Proband440


title: Proband427


title: Proband435


title: Proband428


title: Sporadic Desmoid Tumor; 6

city: Bari

first: Maria Teresa

last: Rotelli

address: Piazza Giulio Cesare 11

department: DETO

country: Italy

institute: University of Bari

hyb_protocol: Fluorescently-labeled miRNAs were then hybridized for 20 hours at 55°C on Human miRNA Microarray, Release 19.0, 8x60K slides, (Agilent Technologies, Santa Clara, CA). After hybridization the slides were washed according to manufacturer’s protocols.

scan_protocol: The slides were scanned using the High-Resolution Microarray C Scanner (Agilent Technologies).

data_processing: Data extraction was performed using Agilent Feature Extraction software.

source_name: FFPE tumor specimen

label_protocol: Fluorescently-labeled miRNAs were generated using the miRNA Complete Labeling and Hyb kit (Agilent Technologies, Santa Clara, CA), with a sample input of 100 ng of total RNA.

extract_protocol: After deparaffinization, total RNA was extracted by miRNeasy FFPE Kit and miRNeasy mini Kit (Qiagen, Milan, Italy) for FFPE and fresh frozen tissue samples

value: Desmoid tumor


title: Proband429

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


title: Proband359


title: Proband432


title: Proband430


title: Proband439


title: Proband309


title: Proband301


title: Sporadic Desmoid Tumor; 5


title: Proband308


title: MICRO5B

city: LUGO

first: Belen

middle: G

last: Pardo

state: LUGO

address: Avda. Carballo Calero s/n

department: Zoology, Genetics and Physical Anthropology

country: Spain

institute: University of Santiago de Compostela

description: Gene expression at 5 days after injection with antigen and microspheres

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to turbot custom Oligo Microarrays (G2514F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565B) using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Extended dynamic range implemented in the Agilent software was applied to avoid saturation in the highest intensity range. The Agilent feature extraction was used as raw data for further preprocessing. The processed signal (gProcessed-Signal) value was chosen for the statistical analysis.

organism: Scophthalmus maximus

source_name: Antigen and microspheres, 5 day, replicate B

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA  from two  control fishes and two  treatment fishes of each condition and time using the Low Input Quick Amp Labeling Kit, One-Color (Cy3) (Agilent Technologies, USA)  according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Specimens of turbot Scophthalmus maximus (L.), of approximately 30 g body weight, were obtained from a local fish farm. The fish were maintained in 250-L tanks with aerated and recirculated sea water at 16°C and were fed daily with commercial pellets. Fish were acclimatized to laboratory conditions for two weeks before the experiments began.

extract_protocol: To avoid the presence of erythrocytes in the peritoneal cavity, fish were bled as much as possible by caudal vein puncture. The peritoneal cavity was washed carefully with 5 mL of cold PBS and the cells counted with an haemocytometer. The cell suspensions were washed twice with cold PBS by centrifugation at 300 x g for 5 min and the tubes with the pellets were frozen in liquid nitrogen and kept at -80 oC until RNA extraction using the RNAeasy Mini kit (Qiagen) according to manufacturer's recommendations. All extractions were performed by the same researcher. RNA quality and quantification were evaluated respectively in a Bioanalyzer (Bonsai Technologies) and in a NanoDrop® ND-1000 spectrophotometer (NanoDrop® Technologies Inc.), prior to labelling and hybridization.

treatment_protocol: Six groups of fish (per duplicate, 114 fish in total) were used. The control group was injected intraperitoneally (i.p.) with 0.1 ml of phosphate-buffered saline (PBS). The remained groups were injected with 230 μg of antigen in PBS, with 5 mg of MS containing 230 μg of covalently linked antigen to their surface in PBS (Noia et al., 2014), or with a mixture of antigen and the following adjuvants (1:1, v:v): Montanide Isa 763 A (Seppic, Paris, France), aluminium  hydroxide gel (Alhydrogel, Sigma) or Matrix-Q (Isconova, Sweden) (5 µg/fish). Five fish in the case of control groups and three fish in each of the rest of duplicate groups were then sampled at days 1, 3 and 5 after injection.

value: peritoneal cells


title: Proband310


title: Proband300


title: Proband307


title: Proband306


title: PBS5B2

description: Gene expression at 5 days after injection with PBS

source_name: PBS, 5 day, replicate B


title: FAP associated Desmoid Tumor; 25

value: male


title: Proband298


title: Proband304


title: Control; 24

source_name: FFPE  tissue specimen

value: normal fibrous tissue


title: Control; 23


title: ALUM5B

description: Gene expression at 5 days after injection with Alhydrogel

source_name: Antigen and aluminium  hydroxide gel  , 5 day, replicate B


title: Proband305


title: Proband296


title: Proband299


title: MATRIX-Q5B

description: Gene expression at 5 days after injection with Matrix-Q

source_name: Antigen and Matrix-Q, 5 day, replicate B


title: Proband426


title: Control; 22


title: Proband425


title: FAP associated Desmoid Tumor; 2


title: Control; 21


title: Sporadic Desmoid Tumor; 20


title: Sporadic Desmoid Tumor; 4


title: FAP associated Desmoid Tumor; 19


title: FREUND'S5B

description: Gene expression at 5 days after injection with Freund´s

source_name: Antigen and Freund´s, 5 day, replicate B


title: ANTIG5B

description: Gene expression at 5 days after injection with antigen

source_name: Antigen, 5 day, replicate B


title: PBS5B


title: MATRIX-Q5A

description: Gene expression at 5 days after injection with antigen and Matrix-Q

source_name: Antigen and Matrix-Q, 5 day, replicate A


title: MICRO5A

source_name: Antigen and microspheres, 5 day, replicate A


title: Proband302

source_name: Whole Blood


title: PBS5A2

source_name: PBS, 5 day, replicate A


title: ALUM5A

description: Gene expression at 5 days after injection with antigen and Alhydrogel

source_name: Antigen and aluminium  hydroxide gel  , 5 day, replicate A


title: Sporadic Desmoid Tumor; 18


title: Proband420


title: FAP associated Desmoid Tumor; 15


title: Proband423


title: Sporadic Desmoid Tumor; 13


title: Proband424


title: Proband488


title: Sporadic Desmoid Tumor; 16


title: PBS5A


title: MATRIX-Q3B

description: Gene expression at 3 days after injection with antigen and Matrix-Q

source_name: Antigen and Matrix-Q, 3 day, replicate B


title: Proband419


title: Daphnias exposed to Cbz_F12 generation_replica3

city: Aveiro

first: Ana

last: Soares

address: Campus de Santiago

country: Portugal

institute: University of Aveiro

hyb_protocol: Hybridizations were carried out using Agilent gasket slides in a rotating oven for 17hr at 65ºC. After hybridization, microarrays were washed using the wash procedure with stabilization and drying solution following the manufacturer recommendations (Agilent).

scan_protocol: Agilent DNA microarray scanner G2505B (Agilent Technologies) was used for scanning. Probes signal values were extracted from microarray scan data using Agilent Feature Extraction Software (Agilent).

data_processing:
Data was median normalized using BrB-Array tools v4.4.1 software.
Differentially expressed genes in F0 and F12 generations were identified using the Multiple Experiment Viewer Mev software v4.9. An unpaired t-test (p < 0.05) with standard Bonferroni correction was performed to identify genes that demonstrated statistically significant differences in expression between clean medium and carbendazim exposed daphnids for both F0 and F12 generations; in addition, differences between F0 and F12 daphnids in clean medium and between F0 and F12 of daphnids in carbendazim were also assessed using the same methodology. Genes were considered up-regulated when the fold change was higher than 1.5 and were considered down-regulated when the fold change was lower than -1.5.

organism: Daphnia magna

label_protocol: Following RNA extraction, samples were prepared for labeling and hybridization on the microarray. The custom D. magna microarrays used in this work were manufactured for EcoArray by Agilent Technologies, Inc (8 individual arrays per slide) and was composed by 7370 probes. A total of three replicates per treatment were used and each biological replicate was individually hybridized on the array. A single-color design was used, using the Agilent one-color RNA Spike-In Kit (AgilentTechnologies, Santa Clara, CA, USA), following the manufacturers protocol. Gene expression profiling was performed using the Agilent protocol for One-Color Microarray-Based Gene Expression Analysis Quick Amp Labeling v5.7 (Agilent Technologies). Briefly, cDNA was synthesized from 100ng of total RNA using Agilent T7 Promoter Primer and T7 RNA Polymerase Blend and labeled with Cyanine 3-CTP. Labeled cDNA was purified with RNAeasy mini spin columns (QIAGEN) to remove residual Cyanine 3-CTP. Dye incorporation and quantification was monitored using the Nanodrop 1000 Spectrophotometer.

growth_protocol: D. magna Straus clone K6 (originally from Antwerp, Belgium) were maintained at a temperature between 20±1⁰C and a 16h light-8h dark photoperiod. The medium was renewed three times a week and daphnids were fed with Raphidocelis subcapitata (formerly known as Pseudokirchneriella subcapitata) at a concentration of 3x105 cells/mL and supplemented with an organic extract (Marinure seaweed extract, supplied by Glenside Organics Ltd.).

extract_protocol:
For the microarray experiment, neonates with less than 24h were picked from the F0 and F12 generations from both clean medium and carbendazim. Three replicates per each treatment were used and consisted of 5 daphnids aging 10 days old. Organisms were collected, shock-frozen with liquid nitrogen and stored at -80ºC until RNA extractions were performed.
RNA was extracted using the Trizol® method followed by a column purification step using the RNAeasy kit® and stored at -80 °C. Prior to the storage, the purity of the RNA samples (A260/280 and A260/230 ratios) was analysed using Nanodrop® 2000c spectrophotometer (Nanodrop Technologies, USA) and checked for integrity in an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Based on the reproduction test results, daphnids were exposed throughout the twelve generations to the NOEC (no observed effect concentration) value of carbendazim, corresponding to 5 µg/L (Silva et al., 2015). During the multigenerational experiment, D. magna populations consisted on three replicates of 1 L glass vessel containing 1L of culture medium and 20 daphnids, for both clean medium and carbendazim (5 µg/L) exposures. Each replicate consisted in ASTM medium with R. subcapitata (concentration of 3x105 cells/mL) and was supplemented with an organic extract. D. magna neonates of the third brood of the previous generation were used to start the next generation under the same conditions, consisting therefore in a continuous exposure trail. Daphnids kept throughout generations in control conditions (ASTM, R. subcapitata and organic extract) will be designated in the paper as daphnids in clean medium and daphnids that were exposed to carbendazim (ASTM, R. subcapitata, organic extract and carbendazim) designated as daphnids in carbendazim.

tag: developmental stage

value: neonate

value: Cbz

tag: generation


title: Sporadic Desmoid Tumor; 11


title: PBS3B2

description: Gene expression at 3 days after injection with PBS

source_name: PBS, 3 day, replicate B


title: ANTIG5A

source_name: Antigen, 5 day, replicate A


title: FREUND'S5A

description: Gene expression at 5 days after injection with antigens and  Freund´s

source_name: Antigen and Freund´s, 5 day, replicate A


title: Daphnias exposed to Cbz_F12 generation_replica2


title: MICRO3B

description: Gene expression at 3 days after injection with antigen and microspheres

source_name: Antigen and microspheres, 3 day, replicate B


title: ALUM3B

description: Gene expression at 3 days after injection with antigen and Alhydrogel

source_name: Antigen and aluminium  hydroxide gel  , 3 day, replicate B


title: Proband297


title: Proband418


title: Proband303


title: FREUND'S3B

description: Gene expression at 3 days after injection with antigen and Freund´s

source_name: Antigen and Freund´s, 3 day, replicate B


title: ANTIG3B

description: Gene expression at 3 days after injection with antigen

source_name: Antigen, 3 day, replicate B


title: Control Daphnias_F12 generation_replica2


title: Proband417


title: PBS3B


title: Control Daphnias_F12 generation_replica1


title: MATRIX-Q3A

source_name: Antigen and Matrix-Q, 3 day, replicate A


title: Proband421


title: Proband408


title: Proband422


title: Daphnias exposed to Cbz_F0 generation_replica3


title: MICRO3A

source_name: Antigen and microspheres, 3 day, replicate A


title: Proband416


title: Daphnias exposed to Cbz_F0 generation_replica2


title: Proband407


title: Proband409


title: PBS3A2

source_name: PBS, 3 day, replicate A


title: Daphnias exposed to Cbz_F0 generation_replica1


title: Proband415


title: Proband412


title: Control Daphnias_F0 generation_replica3


title: Daphnias exposed to Cbz_F12 generation_replica1


title: ANTIG3A

source_name: Antigen, 3 day, replicate A


title: Proband414


title: ALUM3A

source_name: Antigen and aluminium  hydroxide gel  , 3 day, replicate A


title: PBS1B2

description: Gene expression at 1 day after injection with PBS

source_name: PBS, 1 day, replicate B


title: PBS3A


title: Control Daphnias_F0 generation_replica2


title: MICRO1B

description: Gene expression at 1 day after injection with antigen and microspheres

source_name: Antigen and microspheres, 1 day, replicate B


title: Proband413

source_name: Whole Blood


title: Control Daphnias_F0 generation_replica1


title: FREUND'S3A

source_name: Antigen and Freund´s, 3 day, replicate A


title: ALUM1B

description: Gene expression at 1 day after injection with antigen and Alhydrogel

source_name: Antigen and aluminium  hydroxide gel  , 1 day, replicate B


title: Proband405


title: MATRIX-Q1B

description: Gene expression at 1 day after injection with antigen and Matrix-Q

source_name: Antigen and Matrix-Q, 1 day, replicate B


title: FREUND'S1B

description: Gene expression at 1 day after injection with antigen and Freund´s

source_name: Antigen and Freund´s, 1 day, replicate B


title: Control Daphnias_F12 generation_replica3


title: Proband410


title: Proband404


title: Primary Sjogren's Syndrome-PSS-9

city: Bethesda

first: John

middle: A

last: Chiorini

state: Maryland

address: 10 Center Drive, Bldg 10, MSC1190

department: Molecular Physiology and Therapeutics Branch

institute: National Institute of Dental and Craniofacial Research, National Institutes of Health

description:
Viral Transcripts in Minor Salivary Gland Biopsy
Vertebrate infecting viruses present in minor salivary gland biopsy

hyb_protocol: As per manufacturers recommended protocol: http://www.agilent.com/cs/library/usermanuals/Public/G4140-90040_GeneExpression_OneColor_6.9.pdf

data_processing: Quantile Normalization Using Genespring V 12.0

organism: Viruses

source_name: Primary Sjogren's Syndrome-PSS-9

extract_protocol: RNEASY RNA isolation protocol

tag: disease

value: Primary Sjogren's Syndrome


title: ANTIG1B

description: Gene expression at 1 day after injection with antigen

source_name: Antigen, 1 day, replicate B


title: Proband358


title: Primary Sjogren's Syndrome-PSS-8

scan_protocol: As per manufacturers recommended protocol: http://www.agilent.com/cs/library/usermanuals/Public/G4140-90040_GeneExpression_OneColor_6.9.pdf

source_name: Primary Sjogren's Syndrome-PSS-8


title: Primary Sjogren's Syndrome-PSS-7

source_name: Primary Sjogren's Syndrome-PSS-7

label_protocol: As per manufacturers recommended protocol: http://www.agilent.com/cs/library/usermanuals/Public/G4140-90040_GeneExpression_OneColor_6.9.pdf


title: Proband406


title: PBS1B


title: MICRO1A

source_name: Antigen and microspheres, 1 day, replicate A


title: MATRIX-Q1A

source_name: Antigen and Matrix-Q, 1 day, replicate A


title: Proband487


title: Proband411


title: ALUM1A

source_name: Antigen and aluminium  hydroxide gel  , 1 day, replicate A


title: PBS1A2

source_name: PBS, 1 day, replicate A


title: cord-blood from 2164122-2RN

city: Campinas

first: Mariana

last: Maschietto

state: São Paulo

address: Rua Márcia Mendes, 619

department: Research Center

country: Brazil

institute: Boldrini Children's Hospital

description:
bisulfite converted DNA from 2164122-2RN
DNA extracted from cord blood

hyb_protocol: As per Illumina protocol

scan_protocol: iScan SQ scanner (Illumina) using  GenomeStudio software (v.2011.1)

data_processing:
Unreliable measurements were identified using Greedycut (p>0.05) that removed 1,478 probes. Probes located in SNPs (n=4,776) as well those located in specific contexts (n=5,926, non-CpG sites and additional SNPs) were also excluded. Samples were retained only if >99% of sites assayed had detection p>0.05. The background was corrected using noob method, which is based on a normal-exponential convolution using out-of-band probes. Signal intensities values from probes type I and II were normalized using SWAN method that adjusts the intensities based on a quantile approach.
Normalized data (SWAN and noob) were transformed into M-values for statistical analyses

label: Cy5 and Cy3

source_name: cord blood, 2164122-2RN

label_protocol: As per Illumina protocol

extract_protocol: QIAamp DNA BloodMidi Kit as per protocol

treatment_protocol: DNA treated with sodium bisulfite

tag: age of the mother

tag: smoking cigarettes during pregnancy

value: No

tag: gestational stress

value: Yes


title: Primary Sjogren's Syndrome-PSS-6

source_name: Primary Sjogren's Syndrome-PSS-6


title: Proband403

department: Genetics and Genomic Sciences


title: Proband482


title: Primary Sjogren's Syndrome-PSS-5

source_name: Primary Sjogren's Syndrome-PSS-5


title: Primary Sjogren's Syndrome-PSS-4

source_name: Primary Sjogren's Syndrome-PSS-4


title: Proband483

source_name: Whole Blood


title: Proband486


title: Primary Sjogren's Syndrome-PSS-20

source_name: Primary Sjogren's Syndrome-PSS-20


title: FREUND'S1A

description: Gene expression at 1 day after injection with antigen and Freund´s adjuvant

source_name: Antigen and Freund´s, 1 day, replicate A


title: cord-blood from 2069223-3RN

description:
bisulfite converted DNA from 2069223-3RN
DNA extracted from cord blood

source_name: cord blood, 2069223-3RN


title: cord-blood from 2020613-1RN

description:
bisulfite converted DNA from 2020613-1RN
DNA extracted from cord blood

source_name: cord blood, 2020613-1RN


title: cord-blood from 726425-1RN

description:
bisulfite converted DNA from 726425-1RN
DNA extracted from cord blood

source_name: cord blood, 726425-1RN


title: Primary Sjogren's Syndrome-PSS-3

source_name: Primary Sjogren's Syndrome-PSS-3


title: ANTIG1A

source_name: Antigen, 1 day, replicate A


title: PBS1A


title: Primary Sjogren's Syndrome-PSS-12

source_name: Primary Sjogren's Syndrome-PSS-12


title: cord-blood from 2163012-1RN

description:
bisulfite converted DNA from 2163012-1RN
DNA extracted from cord blood

source_name: cord blood, 2163012-1RN


title: Proband481


title: Primary Sjogren's Syndrome-PSS-15

source_name: Primary Sjogren's Syndrome-PSS-15


title: cord-blood from 2166167-2RN

description:
bisulfite converted DNA from 2166167-2RN
DNA extracted from cord blood

source_name: cord blood, 2166167-2RN


title: Primary Sjogren's Syndrome-PSS-11

source_name: Primary Sjogren's Syndrome-PSS-11


title: Primary Sjogren's Syndrome-PSS-1

source_name: Primary Sjogren's Syndrome-PSS-1


title: HEALTHY CONTROL-HV-14

source_name: HEALTHY CONTROL-HV-14

value: Healhty Control


title: cord-blood from 2163493-1RN

description:
bisulfite converted DNA from 2163493-1RN
DNA extracted from cord blood

source_name: cord blood, 2163493-1RN


title: cord-blood from 382179-1RN

description:
bisulfite converted DNA from 382179-1RN
DNA extracted from cord blood

source_name: cord blood, 382179-1RN


title: cord-blood from 088120-2RN

description:
bisulfite converted DNA from 088120-2RN
DNA extracted from cord blood

source_name: cord blood, 088120-2RN


title: HEALTHY CONTROL-HV-13

source_name: HEALTHY CONTROL-HV-13


title: Primary Sjogren's Syndrome-PSS-10

source_name: Primary Sjogren's Syndrome-PSS-10


title: HEALTHY CONTROL-HV-12

source_name: HEALTHY CONTROL-HV-12


title: cord-blood from 451831-2RN

description:
bisulfite converted DNA from 451831-2RN
DNA extracted from cord blood

source_name: cord blood, 451831-2RN


title: cord-blood from 2163132-2RN

description:
bisulfite converted DNA from 2163132-2RN
DNA extracted from cord blood

source_name: cord blood, 2163132-2RN


title: cord-blood from 2169689-2RN

description:
bisulfite converted DNA from 2169689-2RN
DNA extracted from cord blood

source_name: cord blood, 2169689-2RN


title: MNNG-HOS-VECTOR_2

city: Nanjing

first: Shujie

state: Jiangsu

address: 300 Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

description:
Gene expression after vector transfected
vector_MNNG-HOS_2

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: osteosarcoma cells, vector

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: SPARCL1 overexpressed cell lines (MNNG-HOS) stablly overexpressed SPARCL1 compared the vector cells.

value: MNNG-HOS osteosarcoma cell line


title: cord-blood from 431412-1RN

description:
bisulfite converted DNA from 431412-1RN
DNA extracted from cord blood

source_name: cord blood, 431412-1RN


title: MNNG-HOS-VECTOR_1

description:
Gene expression after vector transfected
vector_MNNG-HOS_1

value: control


title: HEALTHY CONTROL-HV-11

description:
Viral Transcripts in Minor Salivary Gland Biopsy
Vertebrate infecting viruses present in minor salivary gland biopsy

source_name: HEALTHY CONTROL-HV-11


title: MNNG-HOS-VECTOR_3

description:
Gene expression after vector transfected
vector_MNNG-HOS_3


title: MNNG-HOS-OVER_3

description:
Gene expression after SPARCL1 overexpressed
SPARCL1_MNNG-HOS_3

source_name: osteosarcoma cells, SPARCL1 overexpressed

value: SPARCL1 overexpressed


title: MNNG-HOS-OVER_2

description:
Gene expression after SPARCL1 overexpressed
SPARCL1_MNNG-HOS_2


title: cord-blood from 843970-2RN

description:
bisulfite converted DNA from 843970-2RN
DNA extracted from cord blood

source_name: cord blood, 843970-2RN


title: HEALTHY CONTROL-HV-10

source_name: HEALTHY CONTROL-HV-10


title: cord-blood from 112257-1RN

description:
bisulfite converted DNA from 112257-1RN
DNA extracted from cord blood

source_name: cord blood, 112257-1RN


title: HEALTHY CONTROL-HV-9

source_name: HEALTHY CONTROL-HV-9


title: Panc-1_mutant JMJD3

city: Hong Kong

first: zhangang

last: XIAO

address: the school of biomedical sciences

country: Hong Kong

institute: the Chinese University of Hong Kong

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: panc-1 cells expressing mutant JMJD3

growth_protocol: Three stable cell lines which espressed wild type JMJD3, mutant JMJD3 and the blank control vector were established.

treatment_protocol: No further treatment

value: tumor cell

value: Pancreatic Ductal Adenocarcinoma


title: cord-blood from 2165240-2RN

description:
bisulfite converted DNA from 2165240-2RN
DNA extracted from cord blood

source_name: cord blood, 2165240-2RN

value: Female


title: MNNG-HOS-OVER_1

description:
Gene expression after SPARCL1 overexpressed
SPARCL1_MNNG-HOS_1


title: Primary Sjogren's Syndrome-PSS-13

source_name: Primary Sjogren's Syndrome-PSS-13


title: Panc-1_control

source_name: panc-1 cells contain MSCV-bank vector


title: cord-blood from 2163080-2RN

description:
bisulfite converted DNA from 2163080-2RN
DNA extracted from cord blood

source_name: cord blood, 2163080-2RN


title: HEALTHY CONTROL-HV-7

source_name: HEALTHY CONTROL-HV-7


title: Panc-1_wt_JMJD3

source_name: panc-1 cells expressing wildtype JMJD3


title: cord-blood from 367760-2RN

description:
bisulfite converted DNA from 367760-2RN
DNA extracted from cord blood

source_name: cord blood, 367760-2RN

value: Male


title: cord-blood from 007454-3RN

description:
bisulfite converted DNA from 007454-3RN
DNA extracted from cord blood

source_name: cord blood, 007454-3RN


title: cord-blood from 875114-2RN

description:
bisulfite converted DNA from 875114-2RN
DNA extracted from cord blood

source_name: cord blood, 875114-2RN


title: cord-blood from 2169945-1RN

description:
bisulfite converted DNA from 2169945-1RN
DNA extracted from cord blood

source_name: cord blood, 2169945-1RN


title: HEALTHY CONTROL-HV-6

source_name: HEALTHY CONTROL-HV-6


title: Pt 3 vehicle treatment

city: Columbus

first: Lianbo

last: Yu

state: OH

address: 1800 Cannon Drive

department: Center for Biostatistics

institute: The Ohio State University

description: Gene Expression following treatment

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), BioArray Eukaryotic Hybridization Controls (Enzo Life Sciences) •Heat 65oC for 5 minutes, 99oC for 5 minutes, 45oC for 5 minutes centrifuge top speed for 5 minutes  •Hybridize 16 hours at 45° at 60rpm• Fluidics script EukGE-WS2v4_450

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using Command Console

data_processing: The data were normalized by RMA method with Affymetrix Expression Console software. Linear model and moderated t-test was used for testing differentially expressed genes by using SAS and R packages.

source_name: ex vivo treatment

label_protocol: Samples were enzymatically labeled using BioArray High Yield RNA Transcript Labeling Kit (Enzo)

growth_protocol: CLL cells were selected using RosetteSep Human B Cell Enrichment reagent (Stem Cell Technologies, Vancouver, BC, Canada) and isolated by Ficoll density gradient centrifugation (Ficoll-Paque Plus, Amershan Biosciences, Piscataway, NJ). CLL patient T cells were isolated in a similar manner using RosetteSep Human T cell Enrichment Cocktail. Normal T cells were isolated in the same manner from Red Cross leukopacs (Red Cross). Cells were suspended in RPMI 1640 medium (Gibco, Life Technologies, Grand Island, NY) with 10% fetal bovine serum (Gibco), 2 mmol/l L-glutamine (Invitrogen, Carlsbad, CA), and 100 U/ml penicillin/100 g/ml streptomycin (Sigma-Aldrich, St. Louis, MO) at 37C in an atmosphere of 5% CO2.

extract_protocol: RNA extracted from primary CLL cells treated with vehicle, lenalidomide, vehicle and IL-21, or lenalidomide and IL-21, was quality assessed by Agilent bioanalyzer

treatment_protocol: CLL cells treated for 48 hours with vehicle or 0.5 μM lenalidomide, followed by 72 hour treatment with vehicle or lenalidomide with or without 100 ng/ml IL-21.

tag: patient number

value: CLL

tag: treatment

value: Media


title: Pt 3 IL-21 treatment

description: Gene Expression following treatment


title: HEALTHY CONTROL-HV-5

source_name: HEALTHY CONTROL-HV-5


title: glioma_34_withpressure_withAF

city: San Francisco

first: David

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

hyb_protocol: 90 microliters of hybridization sample were incubated in the Affymetrix GeneTitan Hybridization Oven instrument for 16 hours at 48C

scan_protocol: Arrays were processed with the Affymetrix GeneTitan Fluidics Station instrument, using the HuGene-2_1-st-16 fluidics script and GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates. Arrays were scanned in the Affymetrix GeneTitan Multi-Channel (MC) instrument with the AGCC GeneTitan Instrument Control.

data_processing: Arrays were quantile normalized and log2 transformed

source_name: glioma, patient 34, withpressure, withAF

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

extract_protocol: Immediately upon completion of compression studies, HA gels were removed from the bioreactor assembly and the triplicates combined in a single Eppendorf tubes with either RNA (700 μL) or protein (300 μL) lysis buffers. Gels were then crushed mechanically, sonicated briefly, and RNA/proteins were allowed to diffuse out into the supernatant on ice for 2 hours. Subsequently, HA gel-RNA/protein solution was sonicated at maximum speed at 4 °C for 10 minutes; supernatant was then aliquoted into new tubes. RNA was isolated using RNAeasy mini kit (Qiagen) and further purified to remove any remaining glycosaminoglycans (Zymo Research); all samples were then flash-frozen on dry ice and stored in -80 °C. The concentration and quality of RNA was determined using Nanodrop followed by use of a RNA 6000 Nano Kit (Agilent) and bioanalyzer chips (Applied Biosystems) to determine RIN values. We then sent 300 ng total RNA (50 ng/ml) to the UCSF Institute for Human Genetics for further processing. In brief, 150 ng was used in the first and second strand cDNA synthesis and IVT cRNA synthesis.  We then performed cRNA purification and samples were normalized to 13.33 μg cRNA in 24 μl volume.  Samples then go through a second cycle of cDNA synthesis and RNase H hydrolysis. The cDNA was purified and normalized to 5.5 μg cDNA in 31.2 μl volume.

treatment_protocol: Human GBM tumorspheres (GBM5, GBM14, GBM34, and GBM43) embedded in HA-gels were subjected to no compression or compression (48h, 30%, 50 mmHg) using a compression force bioreactor with/without incubation with 1 ng/ml AF peptide.

value: TRUE

value: patient 34

value: patient-derived GBM tumorsphere


title: Pt 3 lenalidomide + IL21 therapy

description: Gene Expression following treatment

value: Lenalidomide + IL-21


title: cord-blood from 2129133-2RN

description:
bisulfite converted DNA from 2129133-2RN
DNA extracted from cord blood

source_name: cord blood, 2129133-2RN


title: cord-blood from 94877-2RN

description:
bisulfite converted DNA from 94877-2RN
DNA extracted from cord blood

source_name: cord blood, 94877-2RN

value: missing


title: HEALTHY CONTROL-HV-4

source_name: HEALTHY CONTROL-HV-4


title: glioma_14_withpressure_withAF

source_name: glioma, patient 14, withpressure, withAF

value: patient 14


title: glioma_43_withpressure_noAF

source_name: glioma, patient 43, withpressure, noAF

value: FALSE

value: patient 43


title: glioma_43_withpressure_withAF

source_name: glioma, patient 43, withpressure, withAF


title: cord-blood from 2169699-2RN

description:
bisulfite converted DNA from 2169699-2RN
DNA extracted from cord blood

source_name: cord blood, 2169699-2RN

value: No


title: Pt 3 lenalidomide

description: Gene Expression following treatment

value: Lenalidomide


title: Pt 2 IL-21 treatment

description: Gene Expression following treatment


title: glioma_5_withpressure_withAF

source_name: glioma, patient 5, withpressure, withAF

value: patient 5


title: HEALTHY CONTROL-HV-3

source_name: HEALTHY CONTROL-HV-3

value: Healhty Control


title: HEALTHY CONTROL-HV-2

source_name: HEALTHY CONTROL-HV-2


title: HEALTHY CONTROL-HV-1

source_name: HEALTHY CONTROL-HV-1


title: glioma_34_withpressure_noAF

source_name: glioma, patient 34, withpressure, noAF


title: cord-blood from 2106181-3RN

description:
bisulfite converted DNA from 2106181-3RN
DNA extracted from cord blood

source_name: cord blood, 2106181-3RN

value: Yes


title: glioma_14_withpressure_noAF

source_name: glioma, patient 14, withpressure, noAF


title: Pt 2 lenalidomide + IL21 therapy

description: Gene Expression following treatment

source_name: ex vivo treatment


title: glioma_5_withpressure_noAF

source_name: glioma, patient 5, withpressure, noAF


title: cord-blood from 2164127-3RN

description:
bisulfite converted DNA from 2164127-3RN
DNA extracted from cord blood

source_name: cord blood, 2164127-3RN

value: Female


title: Pt 2 lenalidomide

description: Gene Expression following treatment


title: Pt 2 vehicle treatment

description: Gene Expression following treatment


title: glioma_43_nopressure_withAF

source_name: glioma, patient 43, nopressure, withAF


title: Primary Sjogren's Syndrome-PSS-2

description:
Viral Transcripts in Minor Salivary Gland Biopsy
Vertebrate infecting viruses present in minor salivary gland biopsy

source_name: Primary Sjogren's Syndrome-PSS-2

value: Primary Sjogren's Syndrome


title: cord-blood from 2164247-3RN

description:
bisulfite converted DNA from 2164247-3RN
DNA extracted from cord blood

source_name: cord blood, 2164247-3RN


title: cord-blood from 9891-3RN

description:
bisulfite converted DNA from 9891-3RN
DNA extracted from cord blood

source_name: cord blood, 9891-3RN


title: Pt 1 vehicle treatment

description: Gene Expression following treatment

value: CLL


title: cord-blood from 2085088-1RN

description:
bisulfite converted DNA from 2085088-1RN
DNA extracted from cord blood

source_name: cord blood, 2085088-1RN

value: Male


title: glioma_14_nopressure_withAF

source_name: glioma, patient 14, nopressure, withAF

value: TRUE


title: cord-blood from 2062988-2RN

description:
bisulfite converted DNA from 2062988-2RN
DNA extracted from cord blood

source_name: cord blood, 2062988-2RN


title: Pt 1 IL-21 treatment

description: Gene Expression following treatment


title: Pt 1 lenalidomide + IL21 therapy

description: Gene Expression following treatment


title: glioma_34_nopressure_withAF

source_name: glioma, patient 34, nopressure, withAF

value: patient 34


title: glioma_5_nopressure_withAF

source_name: glioma, patient 5, nopressure, withAF

value: patient-derived GBM tumorsphere


title: Pt 1 lenalidomide

description: Gene Expression following treatment


title: CB ctrl, rep3

city: Bonn

first: Joachim

last: Schultze

address: Carl-Troll-Strasse 31

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were normalised using quantile normalisation in Partek Genomic Suite. Expression values from different chip types (AB from HG-U133A, CB from HG-U133_Plus_2) were combined, keeping only probes with information from both chip types, resulting in 22277 probes. Further, only one probe per gene symbol was left by selecting the probes with the highest variance among all samples, resulting in 13515 unique transcripts.

source_name: Cord blood monocytes, Ctrl

label_protocol: cRNA were prepared and SAGE-labeled according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA) from 5 ug total RNA.

extract_protocol: Total RNA was isolated from monocytes using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: After o/n culture in teflon bags in McCoys modified medium supplemented with 1% glutamine, 1% penicillin-streptomycin and 15% FBS, monocytes were incubated for 4h with 10 ng/ml LPS.

value: Monocytes

tag: tissue source

value: Cord blood

value: Control

tag: array


title: CB ctrl, rep1


title: glioma_43_nopressure_noAF

source_name: glioma, patient 43, nopressure, noAF

value: FALSE


title: cord-blood from 2124616-1RN

description:
bisulfite converted DNA from 2124616-1RN
DNA extracted from cord blood

source_name: cord blood, 2124616-1RN


title: glioma_34_nopressure_noAF

source_name: glioma, patient 34, nopressure, noAF


title: cord-blood from 2166034-1RN

description:
bisulfite converted DNA from 2166034-1RN
DNA extracted from cord blood

source_name: cord blood, 2166034-1RN


title: cord-blood from 2164925-3RN

description:
bisulfite converted DNA from 2164925-3RN
DNA extracted from cord blood

source_name: cord blood, 2164925-3RN


title: HEALTHY CONTROL-HV-8

source_name: HEALTHY CONTROL-HV-8


title: CB LPS, rep3

source_name: Cord blood monocytes, LPS

value: Lipopolysaccharide (LPS)


title: CB ctrl, rep2


title: CB LPS, rep2