title: L. monocytogenes EGDe, 24°C vs. 37°C, biological rep. 6, technical rep. right

city: Freising

first: Stefanie

last: Müller-Herbst

address: Weihenstephaner Berg 3

department: ZIEL and Chair for Microbial Ecology

institute: Technical University Munich

description: Sample 6b

hyb_protocol: Differently labeled samples derived from one RNA set were combined. The volume was reduced to approximately 30 µl using the Speed Vac Concentrator 5301 (Eppendorf). 6 µl 20 x SSC and 4 µl 1 % SDS were added, the tubes were incubated for 1 min at 94°C and subsequently put on ice. The cDNA sample was pipetted on the slides and hybridization was carried out for 16 - 18 h at 64°C. After hybridization, slides were washed in washing solution 1 (2 x SSC and 0.2 % SDS, 60°C, 10 min), washing solution 2 (2 x SSC, RT 10 min) and subsequently twice in washing solution 3 (0.2 x SSC, RT 10 min). Slides were briefly dipped into isopropanol (4°C) before they were dried via centrifugation (1 600 g, RT 3 min).

scan_protocol: Slides were scanned using the GenePix 4000B scanner (MDS Analytical Technologies) and analyzed via the GenePix Pro software version 6.0 (MDS Analytical Technologies).

data_processing: For normalization, the arithmetic mean of the ratios was set to one (GenePix Pro 6.0 software).   In general, only spots with a fluorescence signal higher than the local background plus one standard deviation were included in the final analysis. Spots with irregular morphology were in general excluded from the interpretation when the ratio of medians, the ratio of means and the regression ratio differed by more than 30 %. To minimize the possibility of incorrect exclusion of spots due to automated interpretation, raw data of spots with a log2 ratio of median ≥ 1.0 or ≤ -1.0 were further analyzed. If either the Cy5 or the Cy3 fluorescence intensity reached at least 50 % of the average intensity of all spots of the respective array, the spot was included in the final analysis. Genes were treated as significantly up or down regulated if (i) at least for nine valid spots the log2 ratio of medians (24°C/37°C) was ≥ 1.0 or ≤ -1.0 and (ii) the arithmetic mean of the log2 ratio of medians of valid spots was ≥ 1.0 or ≤ -1.0. log2 RTL (relative transcription level) indicates the arithmetic mean of the log2 ratio of medians of all valid spots.

organism: Listeria monocytogenes EGD-e

source_name: cells grown at 24°C

label_protocol: In cDNA synthesis reaction for three RNA sets, cDNA derived from cells incubated in minimal medium at 24°C was labeled with Cy3-dCTP (GE Healthcare) and cDNA of cells incubated in minimal medium at 37°C was labelled with Cy5-dCTP (GE Healthcare). Dye swap was performed for the three other RNA sets to exclude different labeling efficiencies. 30 µg of RNA were used for each labeling reaction during a first-strand reverse transcription reaction with Superscript III Reverse Transcriptase (200 U/µl; Invitrogen) and 3 µl random no-name oligonucleotides (GE Healthcare). cDNA synthesis was performed at 42°C for 2 hours. Afterwards, 2 µl DNase-free RNase (> 30 U/mg; Roche Diagnostics) were added and the sample was incubated for 45 min at 37°C. cDNA was purified with the QIAquick® PCR Purification Kit (Qiagen) according to the manufacturer´s protocol and eluted in 40 µl elution buffer.

growth_protocol: 30 ml of an in BHI incubated L. monocytogenes EGDe overnight culure was washed in minimal medium, resuspended in 20 ml minimal medium and 2.5 ml of the suspension were transferred into 28 ml minimal medium containing glucose (10 g/l) as carbon source. The cultures were grown at  24°C or 37°C to an OD 600 of 0.82-0.87.

extract_protocol: For RNA isolation, L. monocytogenes cell pellets were thawed on ice and re-suspended in 1 ml TRI® Reagent (Sigma). The suspension was transferred into a 2 ml shredder tube (Sarstedt), filled with silica beads (Ø 0.1 mm; Roth) and incubated for 5 min at room temperature. Cell destruction was carried out using the FastPrep®-24 (MP Biomedicals) (45 s, four times, speed 6.5 m/s, one min on ice between shaking). After centrifugation (16000 g, 3 min, RT) the supernatants were transferred into 2 ml Eppendorf tubes. 200 µl of chloroform were added, the suspension was mixed by inversion and incubated for 3 min at room temperature. After centrifugation (12000 g, 15 min, 4°C), the upper phase was transferred into a fresh 1.5 ml Eppendorf tube and 500 µl isopropanol were added. Samples were incubated for 10 min at room temperature before they were centrifuged (12000 g, 10 min, 4°C). RNA pellets were washed with 1 ml 70 % (v/v) EtOH, air dried and finally resuspended in 80 µl DEPC (diethylpyrocarbonate)-dH2O (0.1 % DEPC v/v). DNA was removed by addition of 10 µl DNaseI (1 U/µl) and 10 µl DNaseI Buffer (Promega) (45 min, 37°C). 500 µl of chloroform were added and the tubes were centrifuged (15000 g, 15 min, 4°C). The upper phase was purified via the RNeasy® Mini Kit (Qiagen) according to the manufacturer´s protocol “RNA cleanup” and an additional on column DNaseI digest was performed. RNA was eluted in RNase free water.

treatment_protocol: After reaching the final OD, cells were collected by centrifuging and the cell pellet was shock frozen immediately in liquid nitrogen. The cell pellet was stored at - 80°C untill further processing.

tag: growth temperature

tag: od600 at harvest

source_name: cells grown at 37°C


title: L. monocytogenes EGDe, 24°C vs. 37°C, biological rep. 6, technical rep. left

status: Public on May 23 2014

type: RNA

country: Germany

description: Sample 6a

molecule: total RNA


title: BI-1

city: Hangzhou

first: Yun

last: Xiao

address: Yuhangtang Road

country: China

institute: Zhejiang University

description: HepG2 cells

hyb_protocol: Labeled cDNA was hybridized to Affymetrix：GeneChip® PrimeView™ Human Gene Expression Array. Array hybridization and wash were performed using GeneChip Hybridization, Wash and Stain Kit (Affymetrix) in Hybridization Oven 645 (Affymetrix) and Fluidics Station (Affymetrix) by following the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000.

data_processing: Slides were scanned by GeneChip® Scanner 3000 and Command Console Software 3.1 with default settings. Spike-in control transcripts were monitored to verify hybridization integrity.

label: biotin

organism: Homo sapiens

source_name: hepatoma

label_protocol: Total RNA were amplified, labeled, and purified using GeneChip® 3’IVT Express Kit (Affymetrix) according to the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: R-HepG2 cells were cultured on tissue culture dishes in DMEM supplemented with 10% FCS, 50 mg/mL penicillin and 50 mg/mL streptomycin at 37 °C with 5% CO2.

extract_protocol: Total RNA was extracted using TRIZol Reagent (Life technologies) and purified using RNeasy Mini kit (QIAGEN), following manufacturers’ protocols.

treatment_protocol: R-HepG2 cells were treated with 1 ml serum-free DMEM overnight, after which the cell culture medium was replaced with 1mL DMEM, 1 ml insulin or BI solution (total insulin concentration was identical, 40 ug/ml). The cells were incubated at 37 °C and 5% CO2 for 4 h and washed using phosphate-buffered saline (PBS, pH = 7.4) and 0.03% ethylene diamine tetraacetic acid (EDTA) to remove any residual complexes.

tag: cell type

value: hepatoma carcinoma cell

tag: cell line

tag: tissue

value: liver


title: Insulin-3

description: HepG2 cells


title: CD4+CD25+CD127low stimulated d2 pool2

city: München

first: Thomas

last: Magg

address: Lindwurmstr. 2a

institute: Dr. von Haunersches Kinderspital der LMU München

description: gene expression in 48h (2d) stimulated Treg

hyb_protocol: After cRNA clean-up and quantification (NanoDrop ND-1000), Cyanine-3-labeled cRNA of each sample was fragmented and prepared for one-color based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). cRNA samples were hybridized for 17hrs at 65°C on separate Human GE 4x44K v2  Microarrays (Agilent Technologies, AMADID 026652).

scan_protocol: Microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).

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

source_name: CD4+CD25+CD127low, stimulated (pool 2)

label_protocol: 90 ng total RNA per sample were introduced into an RT-IVT reaction. Prior to this, the total RNA samples were spiked with in-vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) which serve as an internal labeling control for linearity, sensitivity and accuracy.  The spiked total RNA was reverse transcribed into cDNA and then converted into labeled cRNA by in-vitro transcription (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP.

growth_protocol: T cells were maintained in a 96-well round-bottom microplate in RMPI 1640 medium supplemented with 2mM glutamine, 100U/ml penicillin, 100µg/ml streptomycin and 10% FCS at a density of 105 cells per well.

extract_protocol: Total RNA was isolated from T cells using the miRNeasy Mini kit (Qiagen, Hilden, Germany)

treatment_protocol: T cells were stimulated for 48 hours with CD3/CD28 beads (Dynal Biotech, Oslo, Norway) at a ratio of 8:1 (cells:beads)

value: regulatory T cells (Treg)

tag: activation status

value: 48h (2d) stimulated


title: genomic DNA from R-HepG2_3

type: genomic

description: HepG2 cells

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium HumanMethylation450 BeadArray using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Normalization method by Average Beta
Unmethylated and methylated signal intensities are provided in supplementary file on series level.

label: biotin,DNP

molecule: genomic DNA

source_name: hepatic carcinoma

label_protocol: Standard Illumina Protocol

growth_protocol: R-HepG2 cells were cultured on tissue culture dishes in DMEM supplemented with 10% FCS, 50 mg/mL penicillin and 50 mg/mL streptomycin

extract_protocol: genomic DNA was extracted and purified using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: R-HepG2 cells were treated with 1 ml serum-free DMEM overnight, after which the cell culture medium was replaced with 1mL DMEM or 1 ml BI solution (total insulin concentration was identical, 40 ug/ml). The cells were incubated at 37 °C and 5% CO2 for 4 h and washed using phosphate-buffered saline (PBS, pH = 7.4) and 0.03% ethylene diamine tetraacetic acid (EDTA) to remove any residual complexes.

value: hepatic carcinoma cell


title: 1st_42_hours

city: Heidelberg

first: Anton

last: Shostak

address: Im Neuenheimer Feld 328

department: Circadian Rhythms and Molecular Clocks

institute: Heidelberg University Biochemistry Center (BZH)

hyb_protocol: Hybridization, blocking, and washing was performed following the Agilent instructions

scan_protocol: Scanning of arrays was eprformed using Agilent DNA Microarray Scanner and Agilent Scan control software (v A.8.4.1.)

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) Protocol: GE2_107_Sep09 with modifications; Background Substraction Method - Local Background; Detrend on Replicates Only - False; Robust Neg Ctrl Stats? - True; Choose universal error, or the most conservative - Use Universal Error Model; Dye Normalization Probe Selection Method/Variable Rank Tolerance - True; Max Number Ranked Probes - -1; Normalization Correction Method - Lowess Only; Spikein Target Used - False

source_name: U2OS cells

label_protocol: Samples were labeled with the Two-Color Low Input Quick Labeling kit (Agilent) according to the provided protocol. Samples were labeled in two colors to allow a comparison of RNA amounts from each of the 16 time points (labeled individually with Cyanine-5 (Cy5)) to the average of all time points (labeled together with Cy3).

growth_protocol: U2OS cells were temperature entrained at alternating 12 h, 33°C and 12 h, 37°C cycles. Medium changes were carried out at the transition from 33°C to 37°C.

extract_protocol: Cell pellets were harvested every 3 hours.  RNA was isolated using the RNeasy kit (Qiagen) following the manufacturers instructions.

treatment_protocol: For the1st time course, cells were pre-incubated under temperature entrainment for 4 days. On day 5, 160,000 cells/well were seeded in 35 mm dishes and grown for 5 more days under temperature entrainment until they reached confluence. Growth medium was exchanged directly before the cells were released to constant 37°C. 24 h and 48 h after medium change cells were harvested at 3 h intervals for 24 h. The 2nd time course was carried out similarly, with the exception that cells were incubated in two incubators with opposite temperature rhythms and harvested for 12 h on two days.

value: epithelial

value: bone

source_name: pooled RNA of all time points of experiment 1


title: genomic DNA from R-HepG2_1

description: HepG2 cells


title: genomic DNA from BI treated HepG2_3

description: HepG2 cells


title: genomic DNA from BI treated HepG2_2

description: HepG2 cells


title: 1st_45_hours


title: CD4+CD25-stimulated d2 pool2

description: gene expression in 48h (2d) stimulated Tcon

source_name: CD4+CD25-, stimulated (pool 2)

value: conventional T cells (Tcon)


title: genomic DNA from BI treated HepG2_1

description: HepG2 cells


title: 1st_27_hours


title: CD4+CD25+CD127low resting pool2

description: gene expression in resting Treg

source_name: CD4+CD25+CD127low, resting (pool 2)

value: resting


title: genomic DNA from R-HepG2_2

description: HepG2 cells


title: 1st_30_hours


title: CD4+CD25-stimulated d2 pool1

source_name: CD4+CD25-, stimulated (pool 1)


title: 1st_39_hours


title: Insulin-2

description: HepG2 cells


title: BI-2

description: HepG2 cells


title: 1st_36_hours


title: CD4+CD25-resting pool2

description: gene expression in resting Tcon

source_name: CD4+CD25-, resting (pool 2)


title: 1st_24_hours


title: 1st_33_hours


title: L. monocytogenes EGDe, 24°C vs. 37°C, biological rep. 5, technical rep. right

description: Sample 5b


title: L. monocytogenes EGDe, 24°C vs. 37°C, biological rep. 5, technical rep. left

description: Sample 5a


title: L. monocytogenes EGDe, 24°C vs. 37°C, biological rep. 4, technical rep. right

description: Sample 4b


title: L. monocytogenes EGDe, 24°C vs. 37°C, biological rep. 3, technical rep. right

description: Sample 3b


title: Empty-vector transfected PC-3 cell - Assay1

city: Rio de Janeiro

first: Tatiana

middle: Martins

last: Tilli

address: Andre Cavalcanti, 37 - Centro

country: Brazil

institute: Instituto Nacional de Câncer

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e., OPNc overexpressing cell/Empty vector transfected cell) ratios.

label: SYBR Green

source_name: Empty-vector transfected cell

label_protocol: Total RNA quality control, cDNA synthesis and the quantitative real-time RT-PCR (qRT-PCR) array were performed as recommended by the manufacturer (Qiagen).

growth_protocol: PC-3 cell line was cultured in medium supplemented with 10% fetal bovine serum (FBS), 100 IU/mL penicillin and 100 mg/mL streptomycin in a humidified environment containing 5% CO2 at 37ºC.

treatment_protocol: Transfections were performed using LipofectamineTM 2000 (Invitrogen, CA). Our previous data demonstrated that PC-3 stably transfected cells contain higher levels of protein and the mRNA OPNc splicing isoform in relation to their endogenous levels in empty vector-transfected cells [Tilli et al., 2012]. PC-3 cells transfected with empty vector (EV) were used as a negative control in these assays.

value: Prostate tumoral cells

tag: transfected with

value: empty-vector


title: Insulin-1

description: HepG2 cells


title: R-HepG2-3

description: HepG2 cells


title: L. monocytogenes EGDe, 24°C vs. 37°C, biological rep. 3, technical rep. left

description: Sample 3a


title: PC-3 OPNc - Assay1

description: SAMPLE 1

source_name: PC-3 overexpressing OPNc

extract_protocol: Total RNA quality control, cDNA synthesis and the quantitative real-time RT-PCR (qRT-PCR) array were performed as recommended by the manufacturer (Qiagen).

value: OPNc plasmid


title: PC-3 OPNc - Assay2

description: SAMPLE 2


title: L. monocytogenes EGDe, 24°C vs. 37°C, biological rep. 2, technical rep. right

description: Sample 2b


title: CD4+CD25+CD127low resting pool1

description: gene expression in resting Treg

source_name: CD4+CD25+CD127low, resting (pool 1)


title: L. monocytogenes EGDe, 24°C vs. 37°C, biological rep. 4, technical rep. left

description: Sample 4a


title: Empty-vector transfected PC-3 cell - Assay2


title: Empty-vector transfected cell - Assay2

description: SAMPLE 4

source_name: empty-vector control

growth_protocol: OvCar-3 cell line was cultured in medium supplemented with 20% fetal bovine serum (FBS), 100 IU/mL penicillin and 100 mg/mL streptomycin in a humidified environment containing 5% CO2 at 37ºC.

treatment_protocol: Transfections were performed using LipofectamineTM 2000 (Invitrogen, CA). Our previous data demonstrated that OvCar-3 stably transfected cells contain higher levels of protein and the mRNA OPNc splicing isoform in relation to their endogenous levels in empty vector-transfected cells [Tilli et al., 2012]. OvCar-3 cells transfected with empty vector (EV) were used as a negative control in these assays.

value: Ovarian tumoral cells


title: Empty-vector transfected cell - Assay1

description: SAMPLE 3


title: L. monocytogenes EGDe, 24°C vs. 37°C, biological rep. 1, technical rep. left

description: Sample 1a


title: L. monocytogenes EGDe, 24°C vs. 37°C, biological rep. 2, technical rep. left

description: Sample 2a


title: OvCar-3 OPNc - Assay2

description: SAMPLE 2

source_name: OvCar-3 overexpressing OPNc


title: R-HepG2-2

description: HepG2 cells


title: CD4+CD25+CD127low stimulated d2 pool1

source_name: CD4+CD25+CD127low, stimulated (pool 1)


title: R-HepG2-1

description: HepG2 cells


title: Neg1

city: Berkeley

first: Justin

last: Choi

state: CA

address: 255 Life Sciecnces Addition

department: Functional Genomics lab

country: USA

institute: UC Berkeley

description: Soted Fox Negative cells

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip CINT06a520380F (C. intestinalis) Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the G7 GeneChip Scanner.

data_processing: The data were analyzed with Bioconducter/R GCRMA. The trimmed mean target intensity of each array was arbitrarily set to 6.

label: Biotin

organism: Ciona intestinalis

source_name: Negative rep1

label_protocol: Biotinylated cRNA were prepared according to the standard NuGen's protocol from >50ng of total RNA

growth_protocol: Adult Ciona intestinalis animals were obtained from M-REP (San Diego, CA, USA) and maintain in a standard condition.

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

treatment_protocol: Protocols for fertilization, dechorionation, and electroporation have been described previously. Plasmid concentration for electroporation varied between 40-80 ug per replicate; all experiments were performed at least twice. U0126 (Promega) was resuspended in DMSO and diluted to 10 M in filtered artificial seawater (FASW). Phalloidin (Molecular Probes) was diluted 1:500 in PBT (PBS + 0.1% tween-20) and incubated with embryos overnight. Hoechst 33342 (Life Technologies) staining was performed at 2 ug/ml in PBT for 2-4 hours. Imaging was performed on a Zeiss 700 laser scanning confocal microscope or Zeiss AxioImager.A2 upright microscope.

value: Soted Fox Negative cells


title: CD4+CD25-resting pool1

description: gene expression in resting Tcon

source_name: CD4+CD25-, resting (pool 1)


title: OvCar-3 OPNc - Assay1

description: SAMPLE 1


title: Neg2

description: Soted Fox Negative cells

source_name: Negative rep2


title: FC1

description: Soted Fox positive cells

source_name: Fox+ rep1

value: Soted Fox positive cells


title: L. monocytogenes EGDe, 24°C vs. 37°C, biological rep. 1, technical rep. right

description: Sample 1b

source_name: cells grown at 24°C

source_name: cells grown at 37°C


title: FC2

description: Soted Fox positive cells

source_name: Fox+ rep2


title: FC3

description: Soted Fox positive cells

source_name: Fox+ rep3


title: Neg3

description: Soted Fox Negative cells

source_name: Negative rep3


title: Late_CTL_Rep6

status: Public on May 22 2014

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
251542110930_1_4
Gene expression in the fetal rhesus monkey uterus from late gestation with no exposure to BPA.

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

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

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

organism: Macaca mulatta

source_name: Uterus, late, control

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

extract_protocol: Total RNA was isolated from individual tissues following the QIAGEN RNeasy Mini Kit instructions. Briefly, frozen tissue was pulverized and homogenized in buffer provided in the kit. Lysate was cleared with 70% EtOH and filtered through an RNeasy spin column. DNase was applied to the column membrane for 15 min, centrifuged and washed several times to remove all traces of alcohol. RNA was eluted with 30 uL of RNase-free water. RNA concentration was measured using a Nanodrop and RNA quality was checked on an Agilent Bioanalyzer.

treatment_protocol: The BPA-exposed monkeys received a deuterated BPA (dBPA, CDN Isotopes, Quebec, Canada) fruit treat on a daily basis, at a dose of 400ug/kg/day. The dosing was aimed at achieving serum levels of BPA detected in adult human biomonitoring studies. The control animals received a vehicle control (ethanol) on a daily basis.

tag: gender

value: female

tag: age

value: full term (gestational day 165-168)

value: fetal uterus

tag: treatment

value: vehicle control


title: Late_CTL_Rep5

description:
251542110915_1_1
Gene expression in the fetal rhesus monkey uterus from late gestation with no exposure to BPA.


title: Late_BPA_Rep4

description:
251542110929_1_4
Gene expression in the fetal rhesus monkey uterus from late gestation with exposure to BPA.

source_name: Uterus, late, BPA

value: bisphenol A (BPA)


title: Late_BPA_Rep3

description:
251542110929_1_3
Gene expression in the fetal rhesus monkey uterus from late gestation with exposure to BPA.


title: Late_CTL_Rep3

description:
251542110914_1_3
Gene expression in the fetal rhesus monkey uterus from late gestation with no exposure to BPA.


title: Early_CTL_Rep2

description:
251542110912_1_1
Gene expression in the fetal rhesus monkey uterus from early gestation with no exposure to BPA.

source_name: Uterus, early, control

value: gestational day 100


title: Early_CTL_Rep3

description:
251542110914_1_1
Gene expression in the fetal rhesus monkey uterus from early gestation with no exposure to BPA.


title: Early_CTL_Rep5

description:
251542110929_1_1
Gene expression in the fetal rhesus monkey uterus from early gestation with no exposure to BPA.


title: Early_CTL_Rep1

description:
251542110911_1_1
Gene expression in the fetal rhesus monkey uterus from early gestation with no exposure to BPA.


title: Late_BPA_Rep5

description:
251542110912_1_4
Gene expression in the fetal rhesus monkey uterus from late gestation with exposure to BPA.


title: Late_CTL_Rep1

description:
251542110929_1_2
Gene expression in the fetal rhesus monkey uterus from late gestation with no exposure to BPA.


title: Early_BPA_Rep5

description:
251542110912_1_2
Gene expression in the fetal rhesus monkey uterus from early gestation with exposure to BPA.

source_name: Uterus, early, BPA


title: GRHL1 48h rep2

first: Johannes

last: Fabian

address: Im Neuenheimer Feld 280

department: CCU Pediatric Oncology

institute: German Cancer Research Center

hyb_protocol: Illumina standard hybridization protocol

scan_protocol: Microarray scanning was done using an iScan array scanner and Illumina standard protocol.

data_processing:
Data extraction was done for all beads individually, and outliers are removed when > 2.5 MAD (median absolute deviation). All remaining data points are used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated.
The data were normalized using quantile normalization in R

source_name: BE(2)-C cell line

label_protocol: Biotin-labeled cRNA samples for hybridization on Illumina Human Sentrix-12 BeadChip arrays (Illumina, Inc.) were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol

growth_protocol: DMEM 10% fetal bovine serum; 1% non-essential amino acids

extract_protocol: Total RNA was isolated from cell lines with the RNeasy Mini Kit (Qiagen) acording to manufacture protocol.

treatment_protocol: transfection with 2µg plasmid using effectene (Qiagen)

tag: transfection

tag: time (h)


title: Early_CTL_Rep4

description:
251542110911_1_2
Gene expression in the fetal rhesus monkey uterus from early gestation with no exposure to BPA.


title: GRHL1 72h rep2


title: empty vector 72h rep1


title: empty vector 72h rep2


title: Early_BPA_Rep3

description:
251542110911_1_3
Gene expression in the fetal rhesus monkey uterus from early gestation with exposure to BPA.


title: GRHL1 72h rep1


title: GRHL1 48h rep1


title: Early_BPA_Rep4

description:
251542110930_1_2
Gene expression in the fetal rhesus monkey uterus from early gestation with exposure to BPA.


title: empty vector 24h rep2


title: empty vector 24h rep1


title: empty vector 48h rep1


title: GRHL1 24h rep1


title: Early_BPA_Rep2

description:
251542110930_1_1
Gene expression in the fetal rhesus monkey uterus from early gestation with exposure to BPA.


title: empty vector 48h rep2


title: GRHL1 24h rep2


title: Early_BPA_Rep1

description:
251542110914_1_2
Gene expression in the fetal rhesus monkey uterus from early gestation with exposure to BPA.


title: canine primary osteosarcoma cell lines (UWKOS8)

city: Madison

first: Timothy

last: Stein

state: WI

address: 2015 Linden Drive

department: Medical Sciences

institute: University of Wisconsin-Madison

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000.

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.

organism: Canis lupus familiaris

source_name: canine primary osteosarcoma cell line grown under standard cell culture conditions

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Canine primary OSA cell lines (UWKOS1, UWKOS2, UWKOS3, UWKOS6, UWKOS7, UWKOS8) were maintained in complete minimum essential medium (CMEM): minimum essential medium Eagle (MEM) supplemented with 10% cosmic calf serum, sodium pyruvate, l-glutamine, MEM vitamins, non-essential amino acids, and 1% Pen/Strep (all products from Fisher Scientific, Fair Lawn, NJ)

treatment_protocol: All cell lines were treated inidentical fashion and RNA was collected from cells at approximately 70-80% confluency.

value: primary osteosarcoma cell line UWKOS8

tag: tumorigenicity

value: non-tumorigenic


title: canine primary osteosarcoma cell lines (UWKOS7)

value: primary osteosarcoma cell line UWKOS7

value: tumorigenic


title: canine primary osteosarcoma cell lines (UWKOS3)

value: primary osteosarcoma cell line UWKOS3


title: breast-normal-161

city: San Francisco

first: David

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

hyb_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis, Protocol 5.5

scan_protocol: Scanning on Agilent scanner G2505B

data_processing: Expression data were background-corrected and quantile normalized using limma in R. A batch effect from Scan Date was corrected using ComBat

source_name: uninvolved mammary tissue

extract_protocol: Trizol, following manufacturer's protocol

treatment_protocol: fresh frozen in liquid nitrogen

tag: disease state

value: breast cancer

value: uninvolved mammary tissue


title: canine primary osteosarcoma cell lines (UWKOS6)

value: primary osteosarcoma cell line UWKOS6


title: canine primary osteosarcoma cell lines (UWKOS1)

value: primary osteosarcoma cell line UWKOS1


title: breast-normal-137

label_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis, Protocol 5.5


title: breast-normal-170


title: breast-normal-159


title: breast-normal-175


title: breast-normal-125


title: breast-normal-115


title: breast-normal-148


title: breast-normal-064


title: breast-normal-065


title: breast-normal-056


title: breast-normal-160


title: breast-normal-053


title: canine primary osteosarcoma cell lines (UWKOS2)

value: primary osteosarcoma cell line UWKOS2


title: breast-normal-040


title: breast-normal-054


title: breast-normal-047


title: Human Male with Syndromic Intellectual disability

city: Valencia

first: Francisco

last: Martinez

state: Valencia

address: Avenida Campanar 21

department: Unidad de Genetica

country: Spain

institute: Hospital Universitari i Politecnic La Fe

hyb_protocol: Hybridization protocol was the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol Version 4.0.

scan_protocol: Scanning was made with Agilent G2565BA. For feature extraction we used the Agilent Feature Extraction Software 9.5.31.  The extraction protocol and metrics were  the Agilent protocol CGH-v4_95_Feb07 and the QC Metric Set CGH_QCM_Feb07.

data_processing: The algorithm used is the Z-score setting the cutoff 0.5 and threshold 3

source_name: peripheral blood DNA from patient

label_protocol: test  and control samples were first fragmented by enzymatic digestion and then were each labeled with a different fluorochrome, Cy5 (red) and Cy3 (green). 2000ng of DNA from both sample and reference were labeled with the Agilent Genomic DNA Labeling Kit PLUS

extract_protocol: DNA extraction was performed with a commercial kit QIAamp ® DNA Mini Kit (QIAGEN). The extraction was performed automatically, using equipment QIAcube (QIAGEN) with the recommended protocol with minor modifications.

tag: condition

value: Syndromic Intellectual disability

value: male

value: peripheral blood

source_name: pooled peripheral blood DNA from 10 healthy males

value: control


title: breast-normal-046


title: breast-normal-041


title: breast-normal-031


title: breast-normal-038


title: breast-normal-035


title: breast-normal-018


title: breast-normal-128


title: breast-normal-024


title: breast-normal-026


title: spawing rep7

city: Saint John

first: Paulina

middle: Andrea

last: Bahamonde

state: New Brunswick

address: 100 Tucker Park Road

department: Biology Department

country: Canada

institute: University of New Brunswick

description:
SAMPLE 7
Biological replicate 1 of 7: spawning

hyb_protocol: Agilent one color protocol; Microarrays were washed the following day according to the supplemental Agilent protocol “Preventing Ozone-Related Problems”.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, acetonitrile wash at room temperature for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm at both 10 and 100 PMT (Agilent G2505 B Microarray Scanner).  Agilent Feature Extraction Software (v9.5) formed a composite of the two scans and calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided here is Quantile Normalization.

organism: Etheostoma caeruleum

label_protocol: Agilent one color protocol for Cy3

extract_protocol: Trizol manufacture protocol

treatment_protocol: Reproductively mature rainbow darter collected form the Grand River, ON, Canada from a clean area during different season of the annual reproductive cycle.

value: adult

value: gonad; testis

tag: collection time

value: May (spawning), 2011


title: spawing rep3

description:
SAMPLE 18
Biological replicate 4 of 7: spawning


title: breast-normal-019


title: spawing rep6

description:
SAMPLE 29
Biological replicate 7 of 7: spawning


title: breast-normal-015


title: breast-normal-044


title: spawing rep4

description:
SAMPLE 22
Biological replicate 5 of 7: spawning


title: spawing rep2

description:
SAMPLE 12
Biological replicate 3 of 7: spawning


title: spawing rep1

description:
SAMPLE 10
Biological replicate 2 of 7: spawning


title: recrudescence rep5

description:
SAMPLE 3
Biological replicate 2 of 5: recrudescence

value: October (recrudescence), 2011


title: breast-normal-081


title: spawing rep5

description:
SAMPLE 26
Biological replicate 6 of 7: spawning


title: breast-normal-023


title: breast-normal-013


title: recrudescence rep3

description:
SAMPLE 17
Biological replicate 4 of 5: recrudescence


title: recrudescence rep1

description:
SAMPLE 1
Biological replicate 1 of 5: recrudescence


title: recrudescence rep2

description:
SAMPLE 13
Biological replicate 3 of 5: recrudescence


title: recrudescence rep4

description:
SAMPLE 21
Biological replicate 5 of 5: recrudescence


title: breast-normal-011


title: prespawing rep7

description:
SAMPLE 9
Biological replicate 3 of 7: pre-spawning

value: March (pre-spawning), 2012


title: breast-normal-028


title: prespawing rep6

description:
SAMPLE 8
Biological replicate 2 of 7: pre-spawning


title: prespawing rep5

description:
SAMPLE 6
Biological replicate 1 of 7: pre-spawning


title: breast-normal-001


title: breast-normal-010


title: prespawing rep4

description:
SAMPLE 28
Biological replicate 7 of 7: pre-spawning


title: prespawing rep3

description:
SAMPLE 23
Biological replicate 6 of 7: pre-spawning


title: 4339

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Caco2 human colorectal adenocarcinoma cells were obtained from ATCC (HTB-37, Rockville, MD, USA). Cells were grown in a humidified incubator (20% O2, 5% CO2 at 37°C) in Williams Medium E (WEM, InVitrogen) supplemented with 10% fetal calf serum, 2 mM L-glutamine, 20 mU/ml insulin, 50 nM dexamethasone, 100 U/ml penicillin, 100 µg/ml streptomycin, 2.5 µg fungizone, 50 µg/ml gentamycin and 100 µg/ml vancomycin (=WEM-C).

hyb_protocol: For Cy3 14 pmol and for Cy5 10 pmol incorporated dye was fragmented and resuspended in 55ul 2x GE hybridization buffer HI-RPM.The arrays were hybridized in microarray hybridization chambers (Agilent) overnight at 65ºC, rpm=10 for 17 hours.

scan_protocol: After washing, the slides were scanned with a DNA microarray scanner (Agilent) and images were processed with the Feature Extraction Software version 9.5.1.1 (Agilent).

data_processing: The Agilent processed signal values (i.e., features rProcessedSignal/gProcessedSignal from Agilent Feature Extraction v9.5.1.1) were used for the data analysis. Base 2 log-ratios (Cy5/Cy3) were computed, and in case of multiple probes for the same Agilent ID, average log-ratios were reported.

label_protocol: From 1 μg of cellular RNA, poly-A RNA was reversed transcribed using a poly dT-T7 primer. The resulting cDNA was immediately used for one round of amplification by a T7 in vitro transcription reaction in the presence of Cyanine 5-CTP. The amplified and labeled RNA probes were purified separately with RNeasy purification columns (Qiagen, Belgium). Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm and Cy5 incorporation at 650 nm using a Nanodrop spectrophotometer.

extract_protocol: Cells were seeded at 3x10^6 in 75 cm² tissue culture flasks (n=4) at 20% O2 and were grown until 70% confluence (during five days, with medium refreshment every two days). After reaching near-confluence, cells were washed with buffer and medium was refreshed. 2 flasks were placed in a humidified incubator with hypoxic conditions (2% O2, 5% CO2 at 37° C), while the other flasks (n=2) remained in normoxic conditions (20% O2). Cells were cultured for 72hrs in these different oxygen conditions, and after three days, cells were harvested after trypsin treatment, mixed with Trizol (InVitrogen, Merelbeke, Belgium) and stored in -80° C for further analysis.  Samples in Trizol were homogenized in a Dounce homogenizer for RNA extraction. Thereafter, RNA was isolated with the RNeasy Kit (Qiagen, Chatsworth, CA) according to the manufacturer's instructions. The quality of all RNA samples was monitored by measuring the 260/280 and 260/230 nm ratios with a NanoDrop spectrophotometer (NanoDrop Technologies, Centreville, DE) and by means of the Agilent 2100 BioAnalyzer (Agilent, Palo Alto, CA). Only RNA showing no signs of degradation or impurities (260/280 and 260/230 nm ratios, >1.8) was considered suitable for microarray analysis and used for labeling.

value: Caco2 (ATCC:HTB-37)

value: human colorectal adenocarcinoma cells

tag: exposure time

value: 72 hr

value: hypoxia (2% O2)

label_protocol: From 1 μg of cellular RNA, poly-A RNA was reversed transcribed using a poly dT-T7 primer. The resulting cDNA was immediately used for one round of amplification by a T7 in vitro transcription reaction in the presence of Cyanine 3-CTP. The amplified and labeled RNA probes were purified separately with RNeasy purification columns (Qiagen, Belgium). Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm and Cy3 incorporation at 550 nm using a Nanodrop spectrophotometer.

value: normoxia (20% O2)


title: 4396

description: HPAC pancreatic adenocarcinoma cells were obtained from ATCC (CRL-2199, Rockville, MD, USA). Cells were grown in a humidified incubator (20% O2, 5% CO2 at 37°C) in Williams Medium E (WEM, InVitrogen) supplemented with 10% fetal calf serum, 2 mM L-glutamine, 20 mU/ml insulin, 50 nM dexamethasone, 100 U/ml penicillin, 100 µg/ml streptomycin, 2.5 µg fungizone, 50 µg/ml gentamycin and 100 µg/ml vancomycin (=WEM-C).

value: HPAC (ATCC:CRL-2119)

value: pancreatic adenocarcinoma cells

extract_protocol: Cells were seeded at 3x10^6 in 75 cm² tissue culture flasks (n=4) at 20% O2 and were grown until 70% confluence (during five days, with medium refreshment every two days). After reaching near-confluence, cells were washed with buffer and medium was refreshed. 2 flasks were placed in a humidified incubator with hypoxic conditions (2% O2, 5% CO2 at 37° C), while the other flasks (n=2) remained in normoxic conditions (20% O2). Cells were cultured for 72hrs in these different oxygen conditions, and after three days, cells were harvested after trypsin treatment, mixed with Trizol (InVitrogen, Merelbeke, Belgium) and stored in -80° C for further analysis.  Samples in Trizol were homogenized in a Dounce homogenizer for RNA extraction. Thereafter, RNA was isolated with the RNeasy Kit (Qiagen, Chatsworth, CA) according to the manufacturer's instructions.  The quality of all RNA samples was monitored by measuring the 260/280 and 260/230 nm ratios with a NanoDrop spectrophotometer (NanoDrop Technologies, Centreville, DE) and by means of the Agilent 2100 BioAnalyzer (Agilent, Palo Alto, CA). Only RNA showing no signs of degradation or impurities (260/280 and 260/230 nm ratios, >1.8) was considered suitable for microarray analysis and used for labeling.


title: postspawing rep4

description:
SAMPLE 27
Biological replicate 5 of 6: post-spawning

value: August (post-spawning), 2011


title: postspawing rep5

description:
SAMPLE 31
Biological replicate 6 of 6: post-spawning


title: postspawing rep3

description:
SAMPLE 25
Biological replicate 4 of 6: post-spawning


title: postspawing rep1

description:
SAMPLE 15
Biological replicate 2 of 6: post-spawning


title: postspawing rep6

description:
SAMPLE 4
Biological replicate 1 of 6: post-spawning


title: 4395


title: mature DCs (SB202190)

city: cleveland

first: Yong

last: Lu

address: 9500 euclid avenue, NB40

institute: Cleveland Clinic

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R.

organism: Mus musculus

source_name: mature DCs, SB202190

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

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

treatment_protocol: Bone marrow cells were cultured with mGM-CSF (20 ng/ml) in the presence of 1.5 mM of SB202190 or 0.1% DMSO. At day 7, semi-adherent cells were collected as immature DCs (iDCs). iDCs were matured by TNF-a (10 ng/ml) and IL-1b (10 ng/ml) for 48 hours.

tag: strain/background

value: bone marrow

value: mature dendritic cells


title: postspawing rep2

description:
SAMPLE 20
Biological replicate 3 of 6: post-spawning

value: male


title: prespawing rep2

description:
SAMPLE 16
Biological replicate 5 of 7: pre-spawning


title: prespawing rep1

description:
SAMPLE 11
Biological replicate 4 of 7: pre-spawning


title: 4338


title: 4337


title: developing rep6

description:
SAMPLE 5
Biological replicate 2 of 6: developing

value: January (developing), 2012


title: 4340


title: iDCs (SB202190)

source_name: immature DCs, SB202190

value: immature dendritic cells


title: 4397


title: iDCs (DMSO)

source_name: immature DCs, DMSO

value: DMSO


title: 2-day-cultured cells (DMSO)

source_name: pre-DCs, DMSO

value: pre-dendritic cells


title: 2-day-cultured cells (SB202190)

source_name: pre-DCs, SB202190


title: 4394


title: mature DCs (DMSO)

source_name: mature DCs, DMSO


title: developing rep5

description:
SAMPLE 30
Biological replicate 6 of 6: developing

value: adult

value: gonad; testis


title: developing rep3

description:
SAMPLE 2
Biological replicate 1 of 6: developing


title: developing rep4

description:
SAMPLE 24
Biological replicate 5 of 6: developing


title: developing rep2

description:
SAMPLE 19
Biological replicate 4 of 6: developing


title: developing rep1

description:
SAMPLE 14
Biological replicate 3 of 6: developing


title: KO15+LPS

city: Dallas

first: Joshua

last: Mendell

state: Texas

address: 6000 Harry Hines Blvd NA 6.200

department: Molecular Biology

institute: UT Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: mouse colon ISEMF

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

growth_protocol: HgDMEM supplemented with 10% FBS, 10 ug/ml insulin, 10 ug/ml transferrin, Anti-Anti, and murine EGF (2ng/ml)

extract_protocol: Total RNA extracted using QIAGEN miRNeasy kit with DNase digestion

treatment_protocol: 1 ug/mL LPS for 24 hours

tag: genotype

value: with LPS


title: KO4+LPS


title: WT7+LPS

value: miR-143/145 wildtype


title: Dexamethasone (Exp #2) - C4

city: Houston

first: Jichao

last: Chen

state: TX

address: 2121 W. Holcombe Blvd, RM716

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

description:
biological replicate2
C4

scan_protocol: Standard Illumina scan protocol

data_processing: Rank invariant normalization by Genome Studio

source_name: mouse lung

label_protocol: Illuminar TotalPrep RNA amplification kit (Invitrogen, AMIL1791)

growth_protocol: E14 lungs were cultured on Whatman polycarbonate membranes (09-300-53, Fisher Scientific) in DMEM/F12 media (11320032, Invitrogen) with 1% fetal bovine serum (16140063, Invitrogen) and penicillin and streptomycin (15140148, Invitrogen).

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

treatment_protocol: dexamethasone (100 nM, D2915, Sigma) dissolved in water was added to the media of the treatment group for 24 hours

tag: embryonic stage

value: Cultured lung explant


title: KO4

value: without LPS


title: KO10+LPS


title: KO15


title: KO10


title: Dexamethasone (Exp #1) - C2

description:
biological replicate1
C2


title: WT5


title: WT5+LPS


title: WT7


title: WT13+LPS


title: Control (Exp #2) - C3

description:
biological replicate2
C3


title: Control (Exp #1) -C1

description:
biological replicate1
C1


title: Isx rep6

description:
Sample 27
Biological replicate 6 of 6: severe intersex

data_processing: Quantile Normalization using the software JMP Genomics (v 6.0)

source_name: intersex_severe intersex_adults

treatment_protocol: Reproductively mature rainbow darter collected form the Grand River, ON, Canada from reference and exposed sites to sewage effluents.

value: intersex

value: adults

tag: location

value: polluted site

value: gonad;

tag: intersex index

value: severe


title: R-F rep5

description:
Sample 26
Biological replicate 5 of 5: reference ovary

source_name: female_reference ovary_adults

value: female

value: reference site

tag: tissue

value: gonad; ovary


title: Ex-F rep4

description:
Sample 28
Biological replicate 4 of 4: exposed ovary

source_name: female_exposed ovary_adults


title: Bone-Marrow_SMM_S1530

city: Salamanca

first: Norma C.

last: Gutiérrez

state: Salamanca

address: Campus Miguel de Unamuno

department: Hematologia

institute: Centro de Investigación del Cáncer de Salamanca

hyb_protocol: Labeled RNA was hybridized to Human Gene 1.0 ST Array

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing:
Normalization was carried out by using the expression console (Affymetrix) with RMA algorithm which includes background correction, normalization and calculation of expression values (log2). Since myeloid contamination signature can be detected even in samples with high purity, those probes identifying genes exclusive of myeloid lineage were subtracted from the analysis from the out set.
Unsupervised analysis: In order to classify the samples, multidimensional scaling method (MDS) implemented with SIMFIT statistical package (version 6.4.1, available at http://www.simfit.manchester.ac.uk) was performed using Euclidean distance. In addition, an unsupervised hierarchical clustering with Euclidean distance as the distance measure, and group average as clustering method was carried out.
Supervised analysis: Significant Analysis of Microarrays (SAM) algorithm (http://www-stat.standford.edu/-tibs/SAM) was used to identify genes with statistically significant changes in expression between different classes(25). All data were permutated over 1,000 cycles by using the two-class and multiclass response format, without considering equal variances. Significant genes were selected based on the lowest q-value (q-value < 10-5).
Gene function analysis: The probe sets were functionally annotated and grouped according to their biological function using Gene Ontology biological process descriptions. The functional analysis to identify the most relevant biological mechanisms, pathways and functional categories in the data sets of genes selected by statistical analysis, was generated through the use of IPA (Ingenuity Systems, www.ingenuity.com).
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

source_name: Bone Marrow SMM patient

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: In all the samples a CD138-positive PC isolation using the AutoMACs separation system (Miltenyi-Biotec) was carried out. Final purity was >95% in all MM and SMM cases, and >90% in MGUS patients and healthy donors. Total RNA was extracted from normal and tumor plasma cells using miRNEasy Mini Kit (Qiagen, Valencia, USA) following manufacturer's protocol. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: tissue type

value: Bone Marrow

tag: cell type

value: Smoldering Multiple Myeloma (SMM) plasma cells


title: Isx rep5

description:
Sample 24
Biological replicate 5 of 6: severe intersex

tag: gender

tag: age


title: Bone-Marrow_SMM_S1535


title: Ex-M rep5

description:
Sample 25
Biological replicate 5 of 5: exposed testis

source_name: male_exposed testies_adults

value: male


title: Bone-Marrow_SMM_S1485


title: WT13

tag: treatment


title: R-F rep4

description:
Sample 22
Biological replicate 4 of 5: reference ovary


title: R-M rep5

description:
Sample 21
Biological replicate 5 of 5: reference testis

source_name: male_reference testis_adults


title: Bone-Marrow_SMM_S1586


title: Bone-Marrow_SMM_S1449


title: Bone-Marrow_SMM_S1433


title: R-F rep3

description:
Sample 19
Biological replicate 3 of 5: reference ovary


title: Isx rep4

description:
Sample 20
Biological replicate 4 of 6: severe intersex


title: Bone-Marrow_SMM_S1412


title: Ex-M rep3

description:
Sample 18
Biological replicate 3 of 5: exposed testis


title: Bone-Marrow_SMM_S1410


title: Ex-F rep3

description:
Sample 15
Biological replicate 3 of 4: exposed ovary


title: Bone-Marrow_SMM_S1496


title: Bone-Marrow_SMM_S1495


title: Ex-M rep4

description:
Sample 23
Biological replicate 4 of 5: exposed testis


title: Bone-Marrow_SMM_S1415


title: R-M rep4

description:
Sample 17
Biological replicate 4 of 5: reference testis


title: Ex-M rep2

description:
Sample 16
Biological replicate 2 of 5: exposed testis


title: Bone-Marrow_SMM_S1519


title: Ex-M rep1

description:
Sample 14
Biological replicate 1 of 5: exposed testis


title: nobad-Isx rep3

description:
Sample 13
Biological replicate 3 of 3: low intersex

source_name: intersex_low intersex_2 months

value: 2 months

value: low


title: Bone-Marrow_SMM_S1420


title: Ex-F rep2

description:
Sample 12
Biological replicate 2 of 4: exposed ovary


title: R-F rep1

description:
Sample 10
Biological replicate 1 of 5: reference ovary


title: Bone-Marrow_SMM_S1384


title: R-M rep3

description:
Sample 9
Biological replicate 3 of 5: reference testis

value: gonad; testis


title: R-F rep2

description:
Sample 11
Biological replicate 2 of 5: reference ovary


title: Bone-Marrow_SMM_S1395


title: Bone-Marrow_SMM_S1403


title: Bone-Marrow_SMM_S1398


title: Bone-Marrow_SMM_S1377


title: Isx rep3

description:
Sample 7
Biological replicate 3 of 6: severe intersex


title: Bone-Marrow_SMM_S1365


title: nobad-Isx rep2

description:
Sample 8
Biological replicate 2 of 3: low intersex


title: Bone-Marrow_SMM_S1340


title: Bone-Marrow_SMM_S1360


title: Bone-Marrow_SMM_S1336


title: Bone-Marrow_SMM_S1331


title: Isx rep2

description:
Sample 6
Biological replicate 2 of 6: severe intersex


title: Bone-Marrow_SMM_S1313


title: Bone-Marrow_SMM_S1329


title: Bone-Marrow_SMM_S1306


title: R-M rep2

description:
Sample 5
Biological replicate 2 of 5: reference testis


title: Bone-Marrow_SMM_S1335


title: Ex-F rep1

description:
Sample 4
Biological replicate 1 of 4: exposed ovary


title: Bone-Marrow_NPC_N1610

source_name: Bone Marrow Healthy Donor

value: Normal Plama Cells (NPC)


title: Bone-Marrow_SMM_S1259


title: Bone-Marrow_SMM_S1258


title: nobad-Isx rep1

description:
Sample 3
Biological replicate 1 of 3: low intersex


title: Bone-Marrow_SMM_S1221


title: Bone-Marrow_NPC_N1588


title: Isx rep1

description:
Sample 2
Biological replicate 1 of 6: severe intersex


title: Bone-Marrow_SMM_S1215


title: Bone-Marrow_SMM_S1216


title: Bone-Marrow_SMM_S1220


title: Bone-Marrow_NPC_N1645


title: Bone-Marrow_NPC_N1362


title: R-M rep1

description:
Sample 1
Biological replicate 1 of 5: reference testis


title: Bone-Marrow_NPC_N1351


title: Bone-Marrow_MM_M1148

source_name: Bone Marrow MM patient

value: Multiple Myeloma (MM) plasma cells


title: Bone-Marrow_MM_M1155


title: Bone-Marrow_MM_M1137


title: control, rep5

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

description:
CTRL5B
Control gilthead seabream.

hyb_protocol: Hybridized according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Array was scanned according to the standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%).

data_processing: Data were processed with Agilent Feature Extraction v9.5 and normalized using a cyclic lowess approach using R2.6.1 statistical software.

organism: Sparus aurata

source_name: brain of control gilthead seabream

label_protocol: Amplified and labeled according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

extract_protocol: Total RNA was extracted according to the Qiagen RNeasy Mini Kit protocol for tissue samples.

value: brain

value: control


title: control, rep4

description:
CTRL4B
Control gilthead seabream.


title: Bone-Marrow_MM_M1134


title: Bone-Marrow_MM_M1111


title: Bone-Marrow_MM_M1105


title: Bone-Marrow_MM_M1142


title: Bone-Marrow_MM_M1094


title: Bone-Marrow_MM_M1093


title: control, rep2

description:
CTRL2B
Control gilthead seabream.


title: Bone-Marrow_MM_M1117


title: Bone-Marrow_MM_M1070


title: control, rep1

description:
CTRL1B
Control gilthead seabream.


title: Adipogenic differentiation Day6 Replicate 2

city: Beijing

first: Runsheng

state: Beijing

address: 15 Datun Road

department: Noncoding RNA

institute: Institute of Biophysics, Chinese Academy of Sciences

description: Biological replicate 1

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: The lncRNA+mRNA array data were analyzed for data summarization, quantile normalization and quality control by using the GeneSpring software V11.5 (Agilent).

source_name: human mesenchymal stem cell

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Human adipose tissue was obtained from patients undergoing liposuction according to procedures approved by the Ethics Committee at the Chinese Academy of Medical Sciences and Peking Union Medical College. Fresh liposuction tissue was collected, digested and isolated according to an established method37. The cells were then cultured with hADSC culture medium containing DMEM/F-12, MCDB-201, 2% fetal bovine serum, 1×insulin transferrin selenium, 10-8M dexamethasone, 10-4M ascorbic acid 2-phosphate, 10ng/ml EGF, 10ng/ml PDGF-BB and 1ng/ml Activin A.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: The culture-expanded cells of 3th passage at 100% confluence were induced in the following adipogenic medium for 8 days: H-DMEM supplemented with 10% FCS, 1μM dexamethasone, 0.5 mM isobutylmethylxanthine, and 1 mM ascorbic acid. Adipogenesis was determined by oil red O staining. All reagents used in osteogenic and adipogenic differentiation were from Sigma Aldrich.

value: human mesenchymal stem cell

value: adipose


title: Bone-Marrow_MM_M1054


title: Adipogenic differentiation Day6 Replicate 3

description: Biological replicate 1


title: Adipogenic differentiation Day3 Replicate 2

description: Biological replicate 1


title: Adipogenic differentiation Day3 Replicate 1

description: Biological replicate 1


title: Bone-Marrow_MM_M1062


title: Adipogenic differentiation Day3 Replicate 3

description: Biological replicate 1


title: Adipogenic differentiation Day6 Replicate 1

description: Biological replicate 1


title: Bone-Marrow_MM_M1089


title: gilthead seabream exposed to AT, rep5

description:
AT5B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 1g/L AT and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).

source_name: brain of gilthead seabream exposed for 28 days to environmentally relevant concentrations of AT

value: exposed to atenolol (AT)

tag: treatment duration

value: 28 days


title: Bone-Marrow_MM_M1051


title: control, rep3

description:
CTRL3B
Control gilthead seabream.


title: gilthead seabream exposed to AT, rep3

description:
AT3B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 1g/L AT and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).


title: Bone-Marrow_MM_M1049


title: gilthead seabream exposed to AT, rep4

description:
AT4B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 1g/L AT and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).


title: Bone-Marrow_MM_M1041


title: Control (A8C)

city: Shanghai

first: Zhaohui

last: Gu

state: Shanghai

address: 197 Rui Jin Road II

department: School of Medicine

institute: Shanghai Jiao Tong University

description:
A8C
Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Using the Genotyping Module of Illumina Genome Studio software version 2011.1. B_Allele_Freq and Log_R_Ratio information used to detect both CNVs and UPDs for each sample.

source_name: Skin tissue

label_protocol: standard Illumina protocol

extract_protocol: standard Illumina protocol  standard Illumina protocol

value: MDS

tag: individual

value: patient A8

value: Female

value: control (skin)


title: gilthead seabream exposed to AT, rep2

description:
AT2B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 1g/L AT and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).


title: Control (A5C)

description:
A5C
Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

tag: disease state

value: patient A5

value: Male


title: Control (A2C)

description:
A2C
Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

value: patient A2


title: HMSC Cell Replicate 3

description: Biological replicate 1


title: gilthead seabream exposed to AT, rep1

description:
AT1B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 1g/L AT and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).


title: HMSC Cell Replicate 4

description: Biological replicate 1


title: Bone-Marrow_MM_M1037

value: Bone Marrow


title: HMSC Cell Replicate 2

description: Biological replicate 1


title: HMSC Cell Replicate 1

description: Biological replicate 1


title: Bone-Marrow_MM_M1042


title: Donor2_Ctrl_rep3

city: Huddinge

first: hui

last: Gao

address: Novum

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from fully differentiated preadipocyte after transfected with siRNA control for 48 hours

hyb_protocol: Biotinylated  RNAs were hybridized to  Gene 1.1 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: Standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA)

data_processing: Data were analyzed with packages available from Bioconductor (www.bioconductor.org). Normalization and calculation of gene expression was performed with the Robust Multichip Average expression measure using oligo package. Prior to further analysis, a non-specific filter was applied to include genes with expression signal >30 in at least 20% of all samples. Limma package was used to identify the differentially expressed genes

source_name: Human adipocytes transfected with siRNA control for 48hours

label_protocol: Total RNA were amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

extract_protocol: Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany)  according to the manufacturers’ instructions.

tag: transfection

value: siRNA control

value: fully differentiated adipocytes


title: Control (A3C)

description:
A3C
Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

value: patient A3


title: Control (A6C)

description:
A6C
Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

value: patient A6


title: gilthead seabream exposed to DMSO, rep5

description:
DMSO5B
Brain of gilthead seabream exposed for 28 days of DMSO.

source_name: brain of gilthead seabream exposed for 28 days to DMSO

value: brain

value: exposed to DMSO


title: Donor2_Ctrl_rep2


title: Bone-Marrow_MM_M1081

value: Multiple Myeloma (MM) plasma cells


title: Bone-Marrow_MM_M1018


title: gilthead seabream exposed to DMSO, rep4

description:
DMSO4B
Brain of gilthead seabream exposed for 28 days of DMSO.


title: Donor2_Ctrl_rep1


title: Donor2_siEBF1_rep3

description: Gene expression data from fully differentiated preadipocyte after transfected with siRNA tageting EBF1 for 48 hours

source_name: Human adipocytes transfected with siRNA targeting EBF1 for 48hours

value: siRNA targeting EBF1


title: Control (A7C)

description:
A7C
Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

value: patient A7


title: gilthead seabream exposed to DMSO, rep2

description:
DMSO2B
Brain of gilthead seabream exposed for 28 days of DMSO.

value: 28 days


title: MDS (A5A)

description:
A5A
Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

source_name: CD34+ bone marrow cells

value: MDS

value: CD34+ bone marrow cells


title: Bone-Marrow_MM_M1017


title: Bone-Marrow_MM_M1028


title: gilthead seabream exposed to DMSO, rep3

description:
DMSO3B
Brain of gilthead seabream exposed for 28 days of DMSO.


title: MDS (A3A)

description:
A3A
Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

value: Female


title: Control (A1C)

description:
A1C
Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

value: patient A1

value: control (skin)


title: MDS (A6A)

description:
A6A
Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).


title: MDS (A1A)

description:
A1A
Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

value: Male


title: Bone-Marrow_MM_M956

value: Bone Marrow


title: MDS (A2A)

description:
A2A
Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

value: patient A2


title: MDS (A8A)

description:
A8A
Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

value: patient A8


title: gilthead seabream exposed to CBZ, rep5

description:
CA5B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 1g/L CBZ and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).

source_name: brain of gilthead seabream exposed for 28 days to environmentally relevant concentrations of CBZ

value: exposed to carbamazepine (CBZ)


title: Donor2_siEBF1_rep1

value: fully differentiated adipocytes


title: MDS (A7A)

description:
A7A
Genomic DNA was extracted and genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).


title: Bone-Marrow_MM_M988


title: Donor1_Ctrl_rep2

description: Gene expression data from fully differentiated preadipocyte after transfected with siRNA control for 48 hours

value: siRNA control


title: Donor2_siEBF1_rep2


title: Donor1_Ctrl_rep3


title: gilthead seabream exposed to CBZ, rep4

description:
CA4B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 1g/L CBZ and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).

value: brain


title: gilthead seabream exposed to DMSO, rep1

description:
DMSO1B
Brain of gilthead seabream exposed for 28 days of DMSO.

value: exposed to DMSO


title: Bone-Marrow_MM_M995

value: Multiple Myeloma (MM) plasma cells


title: gilthead seabream exposed to CBZ, rep2

description:
CA2B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 1g/L CBZ and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).


title: gilthead seabream exposed to CBZ, rep3

description:
CA3B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 1g/L CBZ and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).


title: MLL#45pn

city: Ulm

first: Michael

last: Kuehn

address: Albert-Einstein-Allee 23

institute: University Hospital of Ulm

description: DNA extracted from tumor cells obtained at diagnosis

hyb_protocol: 200-270 micrograms of amplified and biotinylated DNA were hybridized for 16-18 hr at 50C on a GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Genotyping Console/birdseed-v2

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis

label_protocol: 250 nanograms of genomic DNA were digested to completion with NspI or StyI, ligated to adapaters and amplified by PCR. 200-270 micrograms of pooled amplified DNA were fragmented and end-labeled with a biotinylated nucleotide according to the Genome-Wide Human SNP Nsp/Sty 6.0 User Guide 702504 Rev 3, 2008, Affymetrix)

growth_protocol: DNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from AML cases with t(9;11)

extract_protocol: AllPrep DNA/RNA Mini Kit (Qiagen)

tag: disease

value: leukemia

value: t-AML


title: Bone-Marrow_MM_M906


title: Bone-Marrow_MM_M896


title: Donor1_siEBF1_rep3

description: Gene expression data from fully differentiated preadipocyte after transfected with siRNA tageting EBF1 for 48 hours

value: siRNA targeting EBF1


title: Donor1_Ctrl_rep1


title: Donor1_siEBF1_rep2


title: Bone-Marrow_MM_M833


title: gilthead seabream exposed to CBZ, rep1

description:
CA1B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 1g/L CBZ and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).

value: 28 days


title: Donor1_siEBF1_rep1


title: gilthead seabream exposed to APAP, rep4

description:
AC4B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 10g/L APAP prepared in DMSO and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).

source_name: brain of gilthead seabream exposed for 28 days to environmentally relevant concentrations of APAP

value: exposed to acetaminophen (APAP)


title: Bone-Marrow_MM_M856


title: Bone-Marrow_MM_M832


title: MLL#40pn


title: gilthead seabream exposed to APAP, rep2

description:
AC2B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 10g/L APAP prepared in DMSO and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).


title: Bone-Marrow_MM_M880


title: gilthead seabream exposed to APAP, rep3

description:
AC3B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 10g/L APAP prepared in DMSO and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).


title: gilthead seabream exposed to APAP, rep5

description:
AC5B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 10g/L APAP prepared in DMSO and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).


title: MLL#44

value: unknown


title: MLL#45


title: Bone-Marrow_MM_M942


title: Bone-Marrow_MM_M828


title: MLL#43


title: MLL#41


title: Bone-Marrow_MM_M801


title: Bone-Marrow_MM_M786


title: Bone-Marrow_MM_M758


title: Bone-Marrow_MM_M797


title: Bone-Marrow_MM_M813


title: C

city: Baltimore

first: Hafiz

last: Ahmed

address: 701 East Pratt Street

institute: University of Maryland

description:
3 replicate samples were averaged.
The F532 channel data in each raw data file should be ignored. Only Cy5 dye was used for the experiment.

hyb_protocol: Fragmented aRNA was hybridized at 42°c overnight using the HybBag mixing system with 1X OneArray® Hybridization Buffer (Phalanx Biotech), 0.01 mg/ml sheared salmon sperm DNA (Promega, Madison, WI, USA), at a concentration of 0.025 mg/ml labeled target. After hybridization, the arrays were washed according to the OneArray® protocol.

scan_protocol: Raw intensity signals for each microarray were captured using a Molecular Dynamics™ Axon 4100A scanner, measured using GenePixPro™ Software, and stored in GPR format.

data_processing: The data from all microarrays in each experimental set was then passed to Rosetta resolver (v.7.2.2.0.0) for analysis. Testing was performed by combining technical replicates and performing statistical analyses using Rosetta Resolver’s proprietary modeling techniques. Normalization algorithm -> Median scaling

source_name: PC3_untreated control

label_protocol: RNA was converted to cDNA using amino-allyl UTP and was subsequently conjugated with with Cy5™ NHS ester .

growth_protocol: PC3 cells were subjected to DMEM:F12 (1:1) medium containg FBS and respective antibiotics.

extract_protocol: Total RNA was extracted using Trizol followed by Kit protocol

treatment_protocol: Tunicamycin (10ug/ml) was added in the PC3 culture to study the gene expression

value: male

tag: cell line

value: prostate cancer (adenocarcinoma)

tag: metastatic site

value: bone

tag: tumor stage

value: grade IV

tag: tumor nature

value: epithelial


title: 24h

tag: treated with

value: Tunicamycin (10ug/ml) for 24hr


title: MLL#40


title: Bone-Marrow_MM_M687

value: Bone Marrow


title: Bone-Marrow_MGUS_G1702

source_name: Bone Marrow MGUS patient

value: Monoclonal Gammopathy of Undetermined Significance (MGUS) plasma cells


title: Bone-Marrow_MGUS_G1720


title: MLL#33

value: de novo AML


title: 72h

value: Tunicamycin (10ug/ml) for 72hr


title: Bone-Marrow_MGUS_G1694


title: gilthead seabream exposed to APAP, rep1

description:
AC1B
Gilthead seabream exposed for 28 days to environmentally relevant concentrations of 10g/L APAP prepared in DMSO and working stock solutions supplied to the tanks obtained by dilution of the stock solutions in SW maintaining the DMSO concentration in the tanks at 0.0005% (v/v).

value: brain


title: MLL#38

value: leukemia


title: S. lividans strain deficient in Lsp versus Wild Type (TK21), rep3

city: Campus de Cantoblanco

first: Sonia

last: Gullón

state: Madrid

address: Darwin 3

institute: CNB-CSIC

description:
replica3-TK21MLsp_vs_TK21
Biological replicate 3 of 3. Gene expression of S. lividans deficient in Lsp versus Wild Type strain (TK21).

hyb_protocol: Slides were prehybridized in 6x SSC, 0.5% SDS (w/v), and 1% BSA (w/v) at 42ºC for 30 min, followed by five rinses with milliQ water. Excess water was drained with a 2000-rpm spin for 2 min. 300 pmol of dye of each cDNA labeled with either Cy3 or Cy5 were resuspended in 50% formamide, 3x SSC, 5x Denhardt's, 1% SDS and 5% Dextransulphate. This mix was boiled for 5 min at 95ºC and then added to the prehybridized slide. Hybridization took place overnight at 37ºC in a hybridization chamber. Arrays were then washed for 5 min at 37ºC in 0.5x SSPE, Tween20 0.1%, twice for 5 min at room temperature (21ºC) with 0.5x SSPE, Tween20 0.1%, three times with 0.5x SSPE at room temperature, and 5 min with 0.1x SSPE. The slides were drained with a 2000-rpm spin for 2 min and stored in darknesss until they were scanned.

scan_protocol: The slides were scanned with a GenePix 4000B scanner, and the images were quantified with GenePix Pro 5.1 software (Molecular Devices).

data_processing: Data processing was carried out using the LIMMA package (Smyth, 2003) of the Bioconductor project. Raw intensities were background-subtracted by the NORMEXP method with an offset of 50. Signals (in log2 scale) were then normalized by the LOWESS algorithm (intra-arrays normalization), followed by adjustment of their quantiles (inter-arrays normalization).

organism: Streptomyces lividans

source_name: Streptomyces lividans TK21, WT

label_protocol: RNA was labeled with Cy3 or Cy5 by using the SuperScript Indirect cDNA labeling system (Invitrogen) as described in the instruction manual.

growth_protocol: Transcriptomic analyses were done with cultures grown in liquid NMMP medium. Total RNA was extracted from cell cultures at the late exponential phase of growth.

extract_protocol: Total RNA was isolated from mycelia harvested and stored from liquid cultures using the RNeasy midi Kit from Qiagen largely according to manufacturer’s instructions, but with several modifications. Cells pellets were mixed with glass beads (3.5-4.5 mm diameter) previously freezed with 5 ml (SDS 1%, EDTA 160mM, DEPC-treated H2O). After adding  phenol-chloroform (1ml), samples were vortexed twice resting on ice for 2 minutes between vortex. After addition of RNeasy RLT buffer (4 ml), samples were vortexed again and extracted twice with phenol-chloroform  (8 ml). Extracts were then treated with ethanol (2.8 ml) and applied to the RNeasy midi columns for purification according to the manufacturer's protocol.

tag: strain

tag: genotype

value: wild type

source_name: Streptomyces lividans, LSP deficient

value: lsp mutant


title: S. lividans strain deficient in Lsp versus Wild Type (TK21), rep2

description:
replica2-TK21MLsp_vs_TK21
Biological replicate 2 of 3. Gene expression of S. lividans deficient in Lsp versus Wild Type strain (TK21).


title: Bone-Marrow_MGUS_G1559

tag: tissue type


title: MLL#32

tag: cell type


title: MLL#34


title: ML#L36


title: MLL#30


title: Bone-Marrow_MGUS_G1356


title: Bone-Marrow_MM_M724

value: Multiple Myeloma (MM) plasma cells


title: Bone-Marrow_MGUS_G991


title: S. lividans strain deficient in Lsp versus Wild Type (TK21), rep1

description:
replica1-TK21MLsp_vs_TK21
Biological replicate 1 of 3. Gene expression of S. lividans deficient in Lsp versus Wild Type strain (TK21).


title: SARSmus, UV-V+TLR, Virus, PM, 1dpi, 06

city: Shinnjuku-ku

first: Naoko

last: Iwata-Yoshikawa

state: Tokyo

address: 1-23-1 Toyama

department: Pathology

country: Japan

institute: National institute of infectious diseases

description: Gene expression of CD11b positive cells were isolated from lung of mouse immunized with UV-V and TLR ligands at 1 day after SARS-CoV challenge

hyb_protocol: After the purification of labeled cRNA, 1.65 mg labeled samples were fragmented by the incubation with Fragmentation Buffer (Agilent) at 60°C for 30 min.  These samples were hybridized onto the Whole Mouse Genome Microarray 60k probes × 8 arrays/ slide (Agilent) at 65°C for 16 h in a rotating hyb oven at a speed of 10 rounds per min (RPM).  Microarrays slides were washed in the order of Wash Solution 1 (Agilent), Wash Solution 2 (Agilent) and acetonitrile (Wako).

scan_protocol: Microarrays slides were scanned at 5 micrometer resolution on a microarray scanner (Agilent) with excitation of the fluorophores Cy3.

data_processing: The image files were analyzed by using of Feature Extraction software (Agilent) and automatically exported with flag information. GeneSpring GX 12.1(Agilent) was used for data analysis. The raw data were normalized per chip to the 75th percentile expression level and per gene to the median expression intensity of all samples.

source_name: SARSmus, UV-V+TLR, Virus, PM, 1dpi

label_protocol: Twenty five nanogram of total RNA and spike-in control was amplified and labeled using Low RNA Input Linear Amplification Kit (Agilent). RNA was denatured and reverse transcribed to cDNA. cDNA was transcribed from 25 ng of total RNA using a poly-T nucleotide primer containing a T7 RNA polymerase promoter.  cRNA was subsequently synthesized and labeled with cyanine-3 (Cy3) by T7 RNA polymerase.

extract_protocol: Total RNA was purified from the samples using RNeasy mini kit (Qiagen) according to the manufacturer’s protocol. The concentrations and qualities of total RNA were measured by Spectrophotometer ND-100 (Nanodrop Technologies) and Agilent 2100 bioanalyzer (Agilent), respectively.

treatment_protocol: CD11b positive cells were isolated from mouse lungs treated with lysis buffer of RNeasy mini kit (Qiagen) were stored at -80°C until use.

value: BALB/c

tag: gender

value: female

value: 21 weeks

value: lung

value: CD11b positive


title: SARSmus, UV-V+TLR, Virus, PM, 1dpi, 05

tag: age


title: Bone-Marrow_MGUS_G1386


title: MLL#31

value: t-AML


title: MLL#28


title: SARSmus, UV-V+TLR, Virus, PM, 1dpi, 04


title: MLL#29


title: MLL#26


title: MLL#27


title: MLL#25


title: Bone-Marrow_MGUS_G850


title: MLL#23


title: Bone-Marrow_MGUS_G736


title: Bone-Marrow_MGUS_G779


title: MLL#21


title: SARSmus, UV-V+TLR, Virus, PM, 1dpi, 01


title: SARSmus, UV-V+TLR, MEM, PM, 1dpi, 06

description: Gene expression of CD11b positive cells were isolated from lung of mouse immunized with UV-V and TLR ligands at 1 day after MEM challenge

source_name: SARSmus, UV-V+TLR, MEM, PM, 1dpi


title: SARSmus, UV-V+TLR, Virus, PM, 1dpi, 03


title: Bone-Marrow_MGUS_G800


title: SARSmus, UV-V+TLR, Virus, PM, 1dpi, 02


title: MLL#21pn

description: DNA extracted from tumor cells obtained at remission

source_name: Leukemic cells obtained from bone marrow or blood at remission

value: leukemia (remission)


title: SARSmus, UV-V+TLR, MEM, PM, 1dpi, 05


title: Bone-Marrow_MGUS_G727


title: SARSmus, UV-V+TLR, MEM, PM, 1dpi, 04


title: MLL#24


title: SARSmus, UV-V+TLR, MEM, PM, 1dpi, 03


title: MLL#20


title: SARSmus, UV-V+TLR, MEM, PM, 1dpi, 02


title: Bone-Marrow_MGUS_G683


title: Bone-Marrow_MGUS_G721


title: Bone-Marrow_MGUS_G626


title: SARSmus, UV-V, Virus, PM, 1dpi, 06

description: Gene expression of CD11b positive cells were isolated from lung of mouse immunized with UV-V at 1 day after SARS-CoV challenge

source_name: SARSmus, UV-V, Virus, PM, 1dpi


title: Bone-Marrow_MGUS_G693


title: MLL#18


title: MLL#17pn


title: Bone-Marrow_MGUS_G588


title: SARSmus, UV-V, Virus, PM, 1dpi, 04


title: SARSmus, UV-V+TLR, MEM, PM, 1dpi, 01


title: MLL#19


title: MLL#16


title: MLL#14


title: Bone-Marrow_MGUS_G417


title: AsxR_reps1-3

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

description:
Three replicates
control channel RNAs are pooled

hyb_protocol: The slides were incubated for 20 min in prewarmed Universal Pre-Soak solution at 42 °C and washed twice in 0.1_SSC, 0.1% SDS for 30 s at room temperature. Slides were immediately transferred into prewarmed prehybridization solution (5_ SSC, 0.1% SDS, and 0.1% bovine serum albumin) and incubated for 2-4 h at 42 °C. The microarray slides were finally washed at room temperature once in 0.1x SSC, 0.1% SDS for 1 min and twice in 0.1x SSC for 30 s, briefly dipped in water and then ethanol, and dried by centrifugation for 5 min at 800g. For each experiment, equal quantities Alexa fluor 555 and 647-labeled cDNA were added to hybridization solution containing 25% formamide, 10 micro grams of bovine serum albumin (fraction V) per ml, 5x SSC (1x SSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% SDS, 8 micro grams of poly(A), and 1x Denhardt's solution. The cDNA probes were denatured at 95 °C for 3 min and hybridized for 16 h at 42 °C. After hybridization was complete, the slides were washed in 2_SSC, 0.1% SDS at 42 °C for 2 min in 0.1x SSC, 0.1% SDS for 2 min at room temperature, and finally twice in 0.1x SSC for 2 min at room temperature. The microarray slides were dried by centrifugation for 5 min at 800g.

scan_protocol: Slide was scanned at 532 and 630 nm by using a Genepix 4000A scanner (Axon Instruments, Union City, CA).

data_processing: LOWESS was used to normalise data generated by GenePix using Genespring GX 7.3.1.  Flags: -50, -75, -100.

label: Alexa fluor 555

organism: Escherichia coli O157:H7

source_name: TUV93-0 pAsxR

label_protocol: Total RNA was labelled using the Superscript Plus indirect labelling system as per manufacters instructions

growth_protocol: Strains were cultured overnight in LB media at 37 degrees and diluted 1/100 into MEM-HEPES media supplemented with 0.1% glucose and 250nM FeCl3. Cell were harvested at OD600 0.8

extract_protocol: Total RNA was extracted using an Qiagen RNeasy mini Kit as per manufacter instructions.

treatment_protocol: 10ml of cells were incubated in an equal volume of RNAprotect and centrifuged.

tag: genotype/variation

value: pAsxR

tag: media

value: MEM-HEPES

label: Alexa fluor 647

source_name: TUV93-0 pBAD+1

value: empty vector (pBAD+1)


title: SARSmus, UV-V, Virus, PM, 1dpi, 05


title: Bone-Marrow_MGUS_G403

value: Bone Marrow

value: Monoclonal Gammopathy of Undetermined Significance (MGUS) plasma cells


title: SARSmus, UV-V, Virus, PM, 1dpi, 03


title: Bone-Marrow_MGUS_G492


title: KOT 81 bleomycin treated

city: Chicago

first: Rajasekaran

last: Subbiah

state: IL

address: 909, South Wolcott Ave, Room # 7160

department: Pediatrics

institute: University of Illinois at Chicago

hyb_protocol: Following fragmentation, 80 µl of hybridization cocktail containing 2.75 ug of fragmented cRNA placed on chip - Hybridized for overnight. The whole hybridization was performed according to Gene Chip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.

data_processing: Data extraction was processed by Affymetrix MoGene 1.0ST v1 Array. The raw probe signal intensities were quantile normalized over all samples, summarized with the robust multi-array average (RMA) algorithm and log2 transformed with a median polish, using the Affymetrix Power Tools. We considered a transcript cluster (gene-level) to be reliably expressed in a sample if the Affymetrix implemented DABG (detection above ground) p-value was less than 0.05. We used local-pooled-error (LPE) estimates and robust statistical tests for evaluating significance of each gene's differential expression in a comparison.

label_protocol: First strand cDNA synthesis, 2nd strand cDNA, IVT, 2nd cycle cDNA synthesis, hydrolysis of cRNA, clean up of the 2nd cycle cDNA, fragmentation of cDNA, and labeling of fragmented single strand cDNA.

extract_protocol: Total RNA extraction was performed using Qiagen Rneasy micro kit according to the manufacturer's protocol.

treatment_protocol: 30 µl of PBS or PBS containing bleomycin (0.075U/mouse) instilled intratracheally for 5 days

tag: strain background

value: Fra-1-/-:Fra-1 KO

value: 2 months

value: 30 µl of PBS containing bleomycin (0.075U/mouse) for 5 days

tag: tissue


title: MLL#13

description: DNA extracted from tumor cells obtained at diagnosis

value: leukemia

value: de novo AML


title: MLL#15


title: KOT 80 bleomycin treated


title: SARSmus, UV-V, Virus, PM, 1dpi, 01

value: BALB/c


title: KOT 72 bleomycin treated

value: female


title: SARSmus, UV-V, Virus, PM, 1dpi, 02

value: 21 weeks


title: KOC 67 PBS treated

value: 30 µl of PBS for 5 days

value: lung


title: SARSmus, UV-V, MEM, PM, 1dpi, 05

description: Gene expression of CD11b positive cells were isolated from lung of mouse immunized with UV-V at 1 day after MEM challenge

source_name: SARSmus, UV-V, MEM, PM, 1dpi

value: CD11b positive


title: SARSmus, UV-V, MEM, PM, 1dpi, 06


title: RPETetraploid_2.CEL

city: Boston

first: Neil

middle: J

last: Ganem

state: MA

address: 72 E. Concord St

department: Pharmacology and Medicine

institute: Boston University School of Medicine

description: Tissue Culture Cells

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing: Data was normalized with RMA using the affy package of Bioconductor

source_name: Evolved Tetraploid RPE Cells

label_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not routinely be carried forward in the analysis. Should this occur, investigators would be notified and asked how they would like to proceed.The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: Cells grown in DMEM:F12 at 37 degrees celsius

extract_protocol: Qiagen Total RNA isolation kit RNAEasy

value: retina

value: epithelial

tag: ploidy

value: tetraploid


title: KOC 55 PBS treated


title: RPETetraploid_1.CEL

description: Tissue Culture Cells

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.


title: MLL#10pn

tag: disease

value: leukemia (remission)


title: SARSmus, UV-V, MEM, PM, 1dpi, 04


title: MLL#12


title: RPEDiploid_3.CEL

description: Tissue Culture Cells

source_name: Diploid RPE Cells

value: diploid


title: MLL#15pn


title: SARSmus, UV-V, MEM, PM, 1dpi, 03


title: KOC 53 PBS treated


title: MLL#8pn

value: t-AML


title: MLL#22


title: RPEDiploid_2.CEL

description: Tissue Culture Cells


title: RPETetraploid_3.CEL

description: Tissue Culture Cells


title: MLL#12pn


title: SARSmus, UV-V, MEM, PM, 1dpi, 02


title: WTT 164 bleomycin treated

value: Fra-1+/+; wild type


title: MLL#10


title: MLL#17


title: RPEDiploid_1.CEL

description: Tissue Culture Cells


title: BJTetraploid_3.CEL

description: Tissue Culture Cells

source_name: Evolved Tetraploid BJ Cells

value: foreskin

value: fibroblast


title: BJTetraploid_2.CEL

description: Tissue Culture Cells


title: WTC 158 PBS treated

value: 2 months


title: MLL#9

value: leukemia

value: de novo AML


title: WTT 160 bleomycin treated.

value: female

value: 30 µl of PBS containing bleomycin (0.075U/mouse) for 5 days


title: Gene expression comparison of shRNA-mediated GALNT3 KD clone 2 vs control (mock-transfected) A2780s clone_dye-swap

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

institute: CHU-Q, Centre de recherche-HDQ

description:
shGALNT3 cl2 - C
Cy5 label sample being the reference

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
Sample data table contains normalized log10 ratio (Cy3/Cy5) representing test/reference for non-dye-swap samples; normalized log10 ratio (Cy5/Cy3) representing test/reference for dye-swap samples

source_name: shRNA-GALNT3 knockdown (KD) A2780s clone 2

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 µg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes.

growth_protocol: A2780s cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 (HyClone Europe Ltd, Cramlington, UK) supplemented with 10% heat-inactivated fetal calf serum, 2 mM l-glutamine, 1 mM sodium pyruvate, 100 units/ml penicillin and 100 μg/ml streptomycin (all reagents were from HyClone Europe). Cells were grown as adherent cells in a humidified atmosphere at 37°C in 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

treatment_protocol: The human ovarian adenocarcinoma A2780s cell line was stably transfected with GALNT3 shRNA cloned into the pSilencer 4.1 puro vector (Ambion). Viral supernatants were generated by transfecting 293T cells with the shRNA construct and the packaging vectors psPAX2 and pMD2.G (Addgene, Cambridge, MA). A2780s cells were stably transfected with the shRNA-GALNT3 plasmid using the ExGen 500 transfection reagent (Fermentas Canada Inc., Burlington ON), according to the manufacturer’s instructions. Cells were consecutively grown for 2 weeks in selection medium containing 5 μg/mL puromycin (Wisent, Canada) to isolate stable clones. Cells were also mock-transfected with the pSilencer 4.1 puro vector, and stably transfected clones were isolated as controls.

tag: cell line

value: ovarian adenocarcinoma cell line

value: shRNA-GALNT3 knockdown A2780s clone 2

source_name: control (mock-transfected) A2780s clone

value: control (mock-transfected) A2780s clone


title: Gene expression comparison of shRNA-mediated GALNT3 KD clone 1 vs control (mock-transfected) A2780s clone_dye-swap

description:
shGALNT3 cl1 - C
Cy5 label sample being the reference

source_name: shRNA-GALNT3 knockdown (KD) A2780s clone 1

value: shRNA-GALNT3 knockdown A2780s clone 1


title: BJLateTetraploid_1.CEL

description: Tissue Culture Cells


title: MLL#9pn


title: Gene expression comparison of shRNA-mediated GALNT3 KD clone 2 vs control (mock-transfected) A2780s clone

description:
shGALNT3 C - cl 2
Cy3 label sample being the reference

source_name: control (mock-transfected) A27803 clone

value: control (mock-transfected) A27803 clone


title: WTT 161 bleomycin treated

value: lung


title: Gene expression comparison of shRNA-mediated GALNT3 KD clone 1 vs control (mock-transfected) A2780s clone

description:
shGALNT3 C - cl1
Cy3 label sample being the reference


title: SARSmus, UV-V, MEM, PM, 1dpi, 01

value: BALB/c

value: 21 weeks

value: CD11b positive


title: MLL#7pn

value: leukemia (remission)


title: RPE1-BAZ1B-A6-3

status: Public on May 21 2014

city: Tallahassee

first: Brian

middle: P

last: Chadwick

state: FL

address: 319 Stadium Drive, King 3076

department: Biological Science

institute: Florida State University

description: RPE1 BAZ1B heterozygous mutant.

hyb_protocol: Hybridization was performed at a NimbleGen Systems certified core facility at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed at a NimbleGen Systems certified core facilty at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.

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

source_name: hTERT-RPE1 (retinal pigment epithelial cells), BAZ1B heterozygote

label_protocol: Labeling was performed at a NimbleGen Systems certified core facility at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Cells were grown in DMEM/F12, supplemented with 10% FBS, Pen/Strep, 2mM L-Glutamine, 0.348% NaBicarbonate. Cells were maintained at 37C in 5% CO2, humidified.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Spin Kit. RNA was treated with DNaseI, before cleaning on an RNeasy spin column. Confirmation of DNA absence was performed by PCR to the repeat element DXZ4, and RNA quality was determined by agarose gel electrophoresis.

treatment_protocol: The BAZ1B gene was knocked out by targeting both copies of exon-7 using zinc finger nucleases (D5, F3 and M1 - all independent clones). Clone A6 is targeted at one allele only and is a heterozygous mutant clone.

value: BAZ1B heterozygous knockout

tag: clone


title: WTC 76 PBS treated

value: Fra-1+/+; wild type

value: 30 µl of PBS for 5 days


title: RPE1-BAZ1B-M1-2

description: RPE1 BAZ1B homozygous mutant.

source_name: hTERT-RPE1 (retinal pigment epithelial cells), BAZ1B knockout

value: BAZ1B knockout


title: RPE1-BAZ1B-F3-1

description: RPE1 BAZ1B homozygous mutant.


title: RPE1-BAZ1B-M1-3

description: RPE1 BAZ1B homozygous mutant.


title: BJDiploid_1.CEL

description: Tissue Culture Cells

source_name: Diploid BJ cell

value: foreskin

value: fibroblast

value: diploid


title: RPE1-BAZ1B-A6-1

description: RPE1 BAZ1B heterozygous mutant.

value: female


title: RPE1-BAZ1B-F3-2

description: RPE1 BAZ1B homozygous mutant.


title: RPE1-BAZ1B-D5-3

description: RPE1 BAZ1B homozygous mutant.


title: RPE1-BAZ1B-A6-2

description: RPE1 BAZ1B heterozygous mutant.


title: MLL#6pn

value: t-AML


title: BJDiploid_2.CEL

description: Tissue Culture Cells


title: MLL#6

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis

value: leukemia