title: KB 1h PD98059 0.5h IL1a / KB 0.5h IL1a _rep2

hyb_protocol: cRNA synthesis, cRNA fragmentation, hybridization and washing was carried out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol’ V5.0.1(Agilent Technologies), except that 5µg of labeled cRNA were used for hybridization.

scan_protocol: Slides were scanned on an Agilent Microarray Scanner G2505B in extended dynamic range mode at two PMT settings (100 % and 5 %) to increase the dynamic range of the measurements.

data_processing: Data extraction was performed with the ‘Feature Extraction Software’ V9.5.3.1 by using the default extraction protocol files ‘GE2-v5_95_Feb07.xml’.

source_name: Human epithelial KB cells

label_protocol: cRNA synthesis was performed with the ‘Low RNA Input Linear Amplification Kit PLUS Two-Color’ (#5188-5340, Agilent Technologies).

treatment_protocol: An individual set of samples was treated identically with IL1a but after an initial preincubation for 1h with PD98059 (50 micromol/l). Each dual-color microarray represents a direct comparison of samples preincubated or not with PD98059.

value: KB

value: KB 0.5h IL1a _rep2


title: 3Gy_177Lu_4.5months_medulla_#1

status: Public on Dec 17 2014

type: RNA

city: Göteborg

first: Emil

last: Schüler

address: Gula stråket 2B

country: Sweden

institute: University of Gothenburg

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with BASE

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: 3Gy, 177Lu, 4.5months, medulla

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

tag: strain

value: Balb/c

tag: tissue

value: kidney medulla

tag: absorbed dose

value: 3 Gy

tag: nuclide


title: SM25

city: Urbana

first: Juan

middle: J.

last: Loor

state: IL

address: 1207 West Gregory Drive

department: Animal Sciences

country: USA

institute: University of Illinois

description: Sample RNA was cohybridized with the reference RNA to obtain ratios of expression

hyb_protocol: Labelled cDNA hybridised using 80 μL of the hybridization buffer #1 (Ambion).  Slides placed in humidified slide chambers (Corning) in water bath for 40 h at 42 °C. Prior scanning the microarray were washed for 5 min by agitation 3 times with wash buffers in the following order: 1×SSC and 0.2% SDS solution preheated at 42°C, 0.1×SSC and 0.2% SDS solution, and 0.1×SSC solution. Lastly, slides were inserted into a 50 mL tube, spin-dried and gassed with Argon to preserve dye from bleaching.

scan_protocol: Arrays were scanned with a ScanArray 4000 (GSI-Lumonics) dual-laser confocal scanner and images were processed and edited using GenePix 6.0 (Axon Instruments).

data_processing: Array quality was assessed using an in-house parser written in Perl language. Spots that received a -100 flag by GenePix 6.0 were removed from further analysis and background intensity was subtracted from the foreground intensity. Spots on the slide were considered “good” if the median intensity was ≥3 standard deviation above median background for each channel (i.e., dye). Spots were flagged “present” when both dyes passed the criteria, “marginal” if only one dye passed the criteria, or “absent” when both dyes failed to pass the criteria. Statistical analysis was conducted on oligos that were flagged as “present” and “marginal”. Data from a total of 109 microarrays were normalized for dye and array effects (i.e., Loess normalization and array centering and scaling) before statistical analysis.

organism: Bos taurus

source_name: Liver, control, Cow_7973

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) as manufacturers instructions.

growth_protocol: Lactating Holstein cows fed a common lactation diet

extract_protocol: A sample of mammary gland tissue was disected and snap-frozen in liquid nitrogen. Tissue was weighted (~0.5 g) and RNA extracted using ice-cold TRIZol. Genomic DNA was removed from RNA with DNAse (Qiagen) using RNeasy Mini Kit columns (Qiagen)

treatment_protocol: Lactating cows received an intrammmary LPS challenge or were not challenged

value: Liver

source_name: Reference

value: Mixture of tissues


title: 3Gy_177Lu_3months_medulla_#3

source_name: 3Gy, 177Lu, 3months, medulla


title: SM28

source_name: Liver, control, Cow_7821


title: SM27


title: SM26


title: SM30

source_name: Liver, control, Cow_7979


title: stem cell line BG01C

type: genomic

city: BALTIMORE

first: William

last: Freed

state: MD

address: 333 CASSELL DRIVE

institute: NIDA NIH

description: Hybridized to Genome-Wide Human SNP Array 6.0

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 4.0). Copy number values for individual SNPs were determined by Affymetrix Genotyping Console Software v.4.0.
chromosome, chromosome region start, chromosome region end, region=copy number region, signal=signal intensity, call=copy number state, confidence

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: stem cell line BG01C

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cells were grown on MEF feeders in standard conditions and separated using collagenase.

extract_protocol: Genomic DNA was extracted from embryonic stem cells using Qiagen Dneasy Tissue kit. DNA quality and quantity was assessed using a Tecan plate reader, PicoGreen and agarose gel electrophoresis.

tag: cell type

value: embryonic stem cell

tag: cell line


title: KB 1h PD98059 3h IL1a / KB 3h IL1a _rep2

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

extract_protocol: Total RNA utilized for microarray experiments was prepared with NucleoSpin RNA Kit (#740955.50, Macherey-Nagel, Düren, Germany) according to the manufacturer’s recommendations.

tag: treatment

value: KB 3h IL1a _rep2


title: 3Gy_177Lu_3months_medulla_#1


title: 3Gy_177Lu_3months_medulla_#2


title: KB 1h PD98059 1h IL1a / KB 1h IL1a _rep2

value: KB 1h IL1a _rep2


title: stem cell line BG01V2_EARLYA

source_name: stem cell line BG01V2_EARLYA


title: KB 1h PD98059 24h IL1a / KB 24h IL1a _rep2

value: KB 24h IL1a _rep2


title: SM22

source_name: Liver, LPS, Cow_7995


title: 3Gy_177Lu_1.5months_medulla_#3

source_name: 3Gy, 177Lu, 1.5months, medulla


title: KB 1h PD98059 / KB_rep2


title: SM23

source_name: Liver, control, Cow_7977


title: SM24


title: 10Gy_177Lu_4.5months_cortex_#3

source_name: 10Gy, 177Lu, 4.5months, cortex

value: kidney cortex

value: 10 Gy


title: KB 1h PD98059 3h IL1a / KB 3h IL1a _rep1

value: KB 3h IL1a _rep1


title: 3Gy_177Lu_1.5months_medulla_#1


title: KB 1h PD98059 0.5h IL1a / KB 0.5h IL1a _rep1

value: KB 0.5h IL1a _rep1


title: KB 1h PD98059 1h IL1a / KB 1h IL1a _rep1

value: KB 1h IL1a _rep1


title: 10Gy_177Lu_4.5months_cortex_#2


title: SM21


title: SM20

source_name: Liver, LPS, Cow_7920


title: SM19


title: KB 1h PD98059 24h IL1a / KB 24h IL1a _rep1

value: KB 24h IL1a _rep1


title: SM18

source_name: Liver, LPS, Cow_7828


title: SM14

source_name: Mammary, LPS, Cow_7920

value: Mammary gland


title: SM17


title: 3Gy_177Lu_1.5months_medulla_#2


title: 10Gy_177Lu_4.5months_cortex_#1


title: SM15

source_name: Mammary, control, Cow_7973


title: SM16


title: KB 1h PD98059 / KB_rep1

source_name: Human epithelial KB cells

value: KB


title: SM13


title: 10Gy_177Lu_3months_cortex_#1

source_name: 10Gy, 177Lu, 3months, cortex

value: Balb/c


title: 10Gy_177Lu_1.5months_cortex_#2

source_name: 10Gy, 177Lu, 1.5months, cortex


title: SM31

source_name: Liver, LPS, Cow_7939

source_name: Reference


title: 10Gy_177Lu_3months_cortex_#3


title: 0.3Gy_177Lu_4.5months_cortex_#2

source_name: 0.3Gy, 177Lu, 4.5months, cortex


title: 10Gy_177Lu_1.5months_cortex_#3


title: 10Gy_177Lu_1.5months_cortex_#1


title: SM12

source_name: Mammary, control, Cow_7979


title: 0.3Gy_177Lu_4.5months_cortex_#3


title: 0.3Gy_177Lu_3months_cortex_#3

source_name: 0.3Gy, 177Lu, 3months, cortex


title: 0.3Gy_177Lu_4.5months_cortex_#1


title: SM11


title: SM9

source_name: Mammary, LPS, Cow_7995


title: 0.3Gy_177Lu_3months_cortex_#1


title: SM7

source_name: Mammary, control, Cow_7821


title: SM5

source_name: Mammary, LPS, Cow_7939


title: SM10


title: SM4

source_name: Mammary, control, Cow_7977


title: 0.3Gy_177Lu_1.5months_cortex_#1

source_name: 0.3Gy, 177Lu, 1.5months, cortex


title: control_4.5months_cortex_#3

source_name: control, 4.5months, cortex


title: 0.3Gy_177Lu_3months_cortex_#2


title: 0.3Gy_177Lu_1.5months_cortex_#3


title: 0.3Gy_177Lu_1.5months_cortex_#2


title: SM3


title: SM6


title: control_3months_cortex_#3

source_name: control, 3months, cortex


title: SM1

source_name: Mammary, LPS, Cow_7828


title: control_3months_cortex_#2


title: control_4.5months_cortex_#1


title: A793 21b BON Cells TNFa

city: München

first: Carsten

last: Jäckel

address: Schillerstr 42

department: Klinische Biochemie

institute: Klinikum der Universität München, Klinische Biochemie

description: BON cells treated with TNFalpha

hyb_protocol: As per Manufacturer's instructions

scan_protocol: As per Manufacturer's instructions

data_processing:
Quality control using the MADMAX Platform (http://www.ncbi.nlm.nih.gov/pubmed/21778530) and normalized by RMA (Expression Console)
probe group file: HuGene-1_1-st-v1.r4.pgf
meta-probeset file: HuGene-1_1-st-v1.na34.1.hg19.probeset.csv

source_name: BON cells

label_protocol: As per Manufacturer's instructions

growth_protocol: Cells were seeded in 96 well plates and cultured overnight followed by 24 hours treatment

extract_protocol: RNA extraction (SV Total RNA Isolation system, Promega) and reverse transcription (RevertAid™ H Minus First Strand cDNA Synthesis Kit, Fermentas) performed as per Manufacturer's instructions

treatment_protocol: 1µg/ml TNFalpha over 24 hours

value: BON

value: treated with TNFalpha


title: control_3months_cortex_#1


title: SM2


title: control_1.5months_cortex_#2

source_name: control, 1.5months, cortex


title: control_4.5months_cortex_#2


title: control_1.5months_cortex_#3


title: A793 21 BON Cells TNFa

description: BON cells treated with TNFalpha


title: A793 19 BON Cells Control

description: BON cells untreated

value: untreated


title: 10Gy_177Lu_3months_cortex_#2

source_name: 10Gy, 177Lu, 3months, cortex


title: Foxo3 KO SLAM

city: Cincinnati

first: Xiaoli

last: Li

state: OH

address: 3333 Burnet Ave

institute: CCHMC

description: Foxo3a KO

hyb_protocol: Following fragmentation and labeling, cDNA was hybridized for 16 h at 45 C on on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.2.0.20
Data was further analyzed by Genespring GX11 software.

source_name: SLAM cells from Foxo3a KO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Mogene ST 2.0 protocol.

growth_protocol: Bone marrow cells from 2-month old WT, Fancd2KO, Foxo3aKO and DKO mice were collected

extract_protocol: Total RNA from sorted SLAM cells was performed by using RNeasy kit (Qiagen) following the manufacturer’s procedure

treatment_protocol: The HSCs (Lin-ckit+Sca-1+CD34-) were acquired by using the FACSAria II sorter. Immediatedly after sorting, SLAM cells were lysed by the lysis buffer and were stored at -80 C until total community RNA could be extracted

tag: age

tag: genotype/variation

value: Foxo3a Knockout

value: Bone marrow cells

value: SLAM (Lin-ckit+Sca-1+CD34-) cells


title: 3Gy_177Lu_4.5months_cortex_#3

source_name: 3Gy, 177Lu, 4.5months, cortex

value: 3 Gy


title: A793 20 NCI Cells TNFa

description: NCI-H295R cells treated with TNFalpha

source_name: NCI-H295R cells


title: WT SLAM

description: WT

source_name: SLAM Cells from WT mice

value: WT


title: DKO SLAM

description: DKO

source_name: SLAM cells from Fancd2 and Foxo3a DKO

value: Fancd2 and Foxo3a double knockout


title: A793 20b NCI Cells TNFa

description: NCI-H295R cells treated with TNFalpha


title: A793 19b BON Cells Control

description: BON cells untreated


title: D2KO SLAM

source_name: SLAM cells from Fancd2 KO

value: Fancd2 knockout


title: 3Gy_177Lu_4.5months_cortex_#1

value: kidney cortex


title: 3Gy_177Lu_3months_cortex_#2

source_name: 3Gy, 177Lu, 3months, cortex


title: 3Gy_177Lu_1.5months_cortex_#3

source_name: 3Gy, 177Lu, 1.5months, cortex


title: 3Gy_177Lu_3months_cortex_#3


title: control_1.5months_cortex_#1


title: 3Gy_177Lu_3months_cortex_#1


title: 3Gy_177Lu_4.5months_cortex_#2


title: 3Gy_177Lu_1.5months_cortex_#1


title: A793 18 NCI Cells Control

description: NCI-H295R cells untreated


title: PQ 50 mg/kg BW 2 day PQ high 2d_185

status: Public on Dec 16 2014

city: Bilthoven

first: Alexa

last: Vitins

address: P.O. Box 1

country: Netherlands

institute: RIVM

hyb_protocol: According to the Affymetrix Hybridization, Wash and Stain Kit (#901530)

scan_protocol: According to Affymetrix protocols

data_processing: Cell Intensity Files generated for each GeneChip using the Affymetrix GeneChip Command Console (v3.0) software were normalized using the Robust Multichip Average (RMA) algorithm from http://arrayanalysis.org (BiGCaT Maastricht University).  RMA normalized data were transformed to Log2 by arrayanalysis.org for further analysis.  Additionally, the quality of microarray images was inspected visually (http://arrayanalysis.org, BiGCaT Maastricht University). One sample, PQ med 1d, did not meet the quality criteria and was removed leaving 69 samples.

source_name: Mouse liver 2 days after PQ treatment

label_protocol: According to the protocol provided with the Affymetrix 3'IVT Express Labeling Kit (#901229)

extract_protocol: Upon sacrifice, liver was immediately dissected. Central half of the left lateral lobe was collected in RNA later and kept for a maximum of one week at 4 oC and frozen at -80 oC until use for RNA isolation. RNA was isolated using the RNeasy Mini Kit.

treatment_protocol: Mice were given a single treatment of vehicle or compound by oral gavage

value: PQ 50 mg/kg BW

tag: time

value: 2 day

tag: gender

value: male

value: 10 weeks

tag: weight

value: liver


title: INZ 88 mg/kg BW 2 day INZ high 2d_178

source_name: Mouse liver 2 days after INZ treatment

value: INZ 88 mg/kg BW


title: 3Gy_177Lu_1.5months_cortex_#2

value: Balb/c


title: INZ 88 mg/kg BW 2 day INZ high 2d_177


title: INZ 44 mg/kg BW 1 day INZ med 1d_190

source_name: Mouse liver 1 day after INZ treatment

value: INZ 44 mg/kg BW

value: 1 day


title: APAP 168.75 mg/kg BW 1 day APAP low 1d_189

source_name: Mouse liver 1 day after APAP treatment

value: APAP 168.75 mg/kg BW


title: PQ 50 mg/kg BW 1 day PQ high 1d_179

source_name: Mouse liver 1 day after PQ treatment


title: PQ 25 mg/kg BW 1 day PQ med 1d_173

value: PQ 25 mg/kg BW


title: PQ 12.5 mg/kg BW 1 day PQ low 1d_169

value: PQ 12.5 mg/kg BW


title: PQ 12.5 mg/kg BW 1 day PQ low 1d_168


title: INZ 88 mg/kg BW 2 day INZ high 2d_174


title: APAP 168.75 mg/kg BW 1 day APAP low 1d_163


title: INZ 88 mg/kg BW 1 day INZ high 1d_175


title: APAP vehicle 1 day APAP v 1d_181

source_name: Mouse liver 1 day after vehicle treatment

value: APAP vehicle


title: APAP 168.75 mg/kg BW 1 day APAP low 1d_164


title: INZ 88 mg/kg BW 1 day INZ high 1d_182


title: APAP 168.75 mg/kg BW 1 day APAP low 1d_165


title: INZ 44 mg/kg BW 1 day INZ med 1d_172


title: INZ 88 mg/kg BW 1 day INZ high 1d_158


title: APAP vehicle 1 day APAP v 1d_160


title: APAP vehicle 1 day APAP v 1d_167


title: INZ 22 mg/kg BW 1 day INZ low 1d_153

value: INZ 22 mg/kg BW


title: APAP vehicle 1 day APAP v 1d_161


title: INZ 44 mg/kg BW 1 day INZ med 1d_146


title: PQ 25 mg/kg BW 1 day PQ med 1d_154


title: APAP 168.75 mg/kg BW 1 day APAP low 1d_144


title: PQ 50 mg/kg BW 1 day PQ high 1d_151


title: APAP vehicle2 day APAP v 2d_150

source_name: Mouse liver 2 days after vehicle treatment


title: PQ 25 mg/kg BW 1 day PQ med 1d_139


title: PQ 50 mg/kg BW 1 day PQ high 1d_135


title: INZ 88 mg/kg BW 2 day INZ high 2d_138


title: APAP 300 mg/kg BW 2 day APAP high 2d_134

source_name: Mouse liver 2 days after APAP treatment

value: APAP 300 mg/kg BW


title: INZ 22 mg/kg BW 1 day INZ low 1d_143


title: INZ 44 mg/kg BW 1 day INZ med 1d_142


title: PQ 50 mg/kg BW 2 day PQ high 2d_137


title: PQ 12.5 mg/kg BW 1 day PQ low 1d_136


title: APAP 300 mg/kg BW 1 day APAP high 1d_121


title: SM8

source_name: Mammary, control, Cow_7821

value: Mammary gland

source_name: Reference

value: Mixture of tissues


title: APAP vehicle2 day APAP v 2d_119


title: INZ 22 mg/kg BW 1 day INZ low 1d_109


title: INZ 22 mg/kg BW 1 day INZ low 1d_112


title: APAP 225 mg/kg BW 1 day APAP med 1d_130

value: APAP 225 mg/kg BW


title: APAP 300 mg/kg BW 1 day APAP high 1d_111


title: APAP 300 mg/kg BW 2 day APAP high 2d_122

value: 2 day


title: APAP vehicle2 day APAP v 2d_115

value: male


title: APAP vehicle 1 day APAP v 1d_126

value: 10 weeks


title: PQ 25 mg/kg BW 1 day PQ med 1d_118

value: liver


title: PQ 50 mg/kg BW 2 day PQ high 2d_131

value: PQ 50 mg/kg BW


title: APAP 225 mg/kg BW 1 day APAP med 1d_116


title: APAP vehicle2 day APAP v 2d_113


title: APAP vehicle2 day APAP v 2d_117


title: INZ 88 mg/kg BW 2 day INZ high 2d_104

value: INZ 88 mg/kg BW


title: APAP 300 mg/kg BW 1 day APAP high 1d_103


title: PQ 12.5 mg/kg BW 1 day PQ low 1d_107


title: APAP 300 mg/kg BW 1 day APAP high 1d_105


title: PQ 50 mg/kg BW 1 day PQ high 1d_102


title: APAP 300 mg/kg BW 1 day APAP high 1d_205


title: APAP 225 mg/kg BW 1 day APAP med 1d_099


title: PQ 50 mg/kg BW 2 day PQ high 2d_108


title: APAP 300 mg/kg BW 2 day APAP high 2d_097


title: INZ 22 mg/kg BW 1 day INZ low 1d_204


title: PQ 50 mg/kg BW 2 day PQ high 2d_208


title: APAP 300 mg/kg BW 2 day APAP high 2d_196


title: APAP 225 mg/kg BW 1 day APAP med 1d_207


title: INZ 44 mg/kg BW 1 day INZ med 1d_195

value: INZ 44 mg/kg BW


title: APAP 300 mg/kg BW 2 day APAP high 2d_191


title: INZ 88 mg/kg BW 1 day INZ high 1d_100

value: 1 day


title: APAP 225 mg/kg BW 1 day APAP med 1d_202


title: PQ 12.5 mg/kg BW 1 day PQ low 1d_199


title: 1-naphtylisothiocyanate, 50 µM. sample 188

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

hyb_protocol: A total amount of 2.9 µg (25 ng/µl) fragmented ss cDNA was finally utilized for the hybridization on the Affymetrix Zebrafish ST Array. The Ambion WT Wash and Stain Kit for GeneTitan Hybridization (#901622) was used for the hybridization, washing, staining and scanning of the chips.

scan_protocol: The array plates were scanned via the Affymetrix GeneTitan scanner. Data quality was checked by Affymetrix Expression Console software.

data_processing: Data was normalized using the Robust Multichip Average (RMA) algorithm, using an MBNI custom CDF version (http://brainarray.mbni.med.umich.edu) version 15

organism: Danio rerio

source_name: zebrafish embryo

label_protocol: Samples were randomized, blinded and further processed for array analysis at ServiceXS (Leiden, The Netherlands) using Affymetrix Genechip Zebrafish ST Genome Array 1.1 array plates. Array analysis methods were according to manufacturer’s protocols. For each individual sample 100 ng RNA was  used for the labelling reaction. The Ambion WT Expression kit (#4411974) was used to synthesize labeled sense stranded cDNA starting from 100 ng total RNA. The Affymetrix Terminal Labeling Kit (#901524) was used to perform the fragmentation and terminal labeling step using 5.5 µg of the ss cDNA.

growth_protocol: For generation of zebrafish embryos, two male and two female adults were set together 1 day before spawning, after a period of 4-day separation to improve egg production. The breeding tank was constructed to prevent egg predation, and after spawning, a glass siphon was used to collect the eggs. All eggs were checked for fertility and thereafter pooled in a single petri dish containing Dutch Standard Water (DSW, demineralized water supplemented with NaHCO3 (100 mg/l), KHCO3 (20 mg/l), CaCl2 2H2O (200 mg/l), and MgSO4 7H2O (180 mg/l) aerated for 24 h at 27  C) until the start of the exposure.

extract_protocol: Total RNA was extracted from whole embryos using the MinElute Clean up. The concentration of the RNA was measured by Nanodrop (Thermo Scientific). The quality of the RNA was checked using the 2100 Bio-Analyzer (Agilent) and Shimadzu MultiNA. Samples with a RNA Integrity Number (RIN) ≥ 8 were used for microarray analysis.

treatment_protocol: All embryo exposures started at 3 days post fertilization (3dpf) with embryos which were randomly derived from at least 2 spawning units. Exposures were performed in 48-well plates (BD Biosciences) containing 1 ml of test medium per well. Exposures were performed in an incubator at 26.5 ± 1  C in a static way and lasted for 48 h. The exposures in this study were conducted with three concentrations (see sample information). Compounds used were: 17alpha-ethynylestradiol, 1-naphtylisothiocyanate, Acetaminophen, Adefovir, Amioderone, Chorpromazin, Cyclosporin A, D-Mannitol, Isoniazid, Lithium carbonate, Paraquat, Tetracycline, Thioacetamide, and Valproic Acid. Vehicle controls were DSW and 0.2 % DMSO.

tag: developmental stage

value: embryo

tag: compound

tag: concentration


title: Acetaminophen, 220 µM. sample 190

value: Acetaminophen


title: Thioacetamide, 3.3 mM. sample 191

value: Thioacetamide


title: Amioderone, 3.3 µM. sample 187

value: Amioderone


title: Amioderone, 3.3 µM. sample 186


title: Acetaminophen, 73.3 µM. sample 184


title: 1-naphtylisothiocyanate, 50 µM. sample 181


title: INZ 88 mg/kg BW 1 day INZ high 1d_198


title: Thioacetamide, 1.1 mM. sample 180


title: Isoniazid, 1.67 mM. sample 176

value: Isoniazid


title: Isoniazid, 0.5 mM. sample 174


title: DSW, vehicle. sample 173

value: DSW


title: Amioderone, 1.1 µM. sample 169


title: Lithium carbonate, 1.1 mM. sample 183

value: Lithium carbonate


title: Thioacetamide, 10 mM. sample 182


title: Amioderone, 1.1 µM. sample 189


title: Acetaminophen, 660 µM. sample 170


title: Tetracycline, 22.22 µM. sample 177

value: Tetracycline


title: PQ 50 mg/kg BW 1 day PQ high 1d_203


title: 1-naphtylisothiocyanate, 5.5 µM. sample 175


title: Paraquat, 10 mM. sample 179

value: Paraquat


title: Cyclosporin A, 6 µM. sample 178

value: Cyclosporin A

value: 6 µM.


title: D-Mannitol, 3 mM. sample 171

value: D-Mannitol

value: 3 mM.


title: Thioacetamide, 10 mM. sample 168


title: DMSO, 0.2 %. sample 166

value: DMSO


title: Paraquat, 1.1 mM. sample 167


title: Isoniazid, 5 mM. sample 172

value: 5 mM.


title: Acetaminophen, 73.3 µM. sample 163


title: Valproic Acid, 200 µM. sample 160

value: Valproic Acid


title: Adefovir, 100 µM. sample 162

value: Adefovir


title: Thioacetamide, 1.1 mM. sample 161

value: embryo


title: Amioderone, 1.1 µM. sample 157


title: 17alpha-ethynylestradiol, 0.38 µM. sample 159


title: Isoniazid, 0.5 mM. sample 192


title: Paraquat, 3.3 mM. sample 158


title: Tetracycline, 66.7 µM. sample 156


title: 17alpha-ethynylestradiol, 0.38 µM. sample 165


title: Acetaminophen, 73.3 µM. sample 155

value: Acetaminophen


title: D-Mannitol, 3 mM. sample 164


title: Cyclosporin A, 2 µM. sample 151

value: 2 µM.


title: DSW, vehicle. sample 148


title: Cyclosporin A, 0.67 µM. sample 150


title: Acetaminophen, 660 µM. sample 185


title: Chorpromazin, 1 µM. sample 154

value: Chorpromazin

value: 1 µM.


title: 17alpha-ethynylestradiol, 1.16 µM. sample 145


title: DSW, vehicle. sample 147

value: DSW


title: 17alpha-ethynylestradiol, 1.16 µM. sample 146


title: 1-naphtylisothiocyanate, 16.7 µM. sample 149


title: Cyclosporin A, 2 µM. sample 152


title: Cyclosporin A, 6 µM. sample 142


title: Cyclosporin A, 0.67 µM. sample 144


title: Cyclosporin A, 2 µM. sample 141


title: Acetaminophen, 220 µM. sample 140


title: Adefovir, 100 µM. sample 139


title: Isoniazid, 1.67 mM. sample 143

value: Isoniazid


title: Isoniazid, 0.5 mM. sample 137


title: DMSO, 0.2 %. sample 134


title: 1-naphtylisothiocyanate, 50 µM. sample 136


title: Valproic Acid, 600 µM. sample 131


title: Tetracycline, 22.22 µM. sample 130

value: Tetracycline


title: Paraquat, 3.3 mM. sample 129

value: Paraquat


title: 1-naphtylisothiocyanate, 16.7 µM. sample 126


title: Thioacetamide, 1.1 mM. sample 132

value: Thioacetamide


title: Tetracycline, 200 µM. sample 133


title: Valproic Acid, 600 µM. sample 138


title: DSW, vehicle. sample 128


title: 1-naphtylisothiocyanate, 16.7 µM. sample 135


title: Acetaminophen, 220 µM. sample 127


title: Chorpromazin, 0.33 µM. sample 124


title: Chorpromazin, 1 µM. sample 123


title: Paraquat, 10 mM. sample 119


title: 17alpha-ethynylestradiol, 3.5 µM. sample 121


title: Thioacetamide, 3.3 mM. sample 117


title: Isoniazid, 1.67 mM. sample 120


title: Cyclosporin A, 0.67 µM. sample 116

value: Cyclosporin A


title: Thioacetamide, 10 mM. sample 125


title: 1-naphtylisothiocyanate, 50 µM. sample 122


title: Amioderone, 10 µM. sample 118

value: Amioderone


title: Cyclosporin A, 6 µM. sample 115

value: 6 µM.


title: DSW, vehicle. sample 112


title: Paraquat, 10 mM. sample 110


title: Thioacetamide, 3.3 mM. sample 114


title: Valproic Acid, 200 µM. sample 107


title: DMSO, 0.2 %. sample 109

value: DMSO


title: Chorpromazin, 1 µM. sample 106


title: Chorpromazin, 0.33 µM. sample 108


title: Isoniazid, 5 mM. sample 111

value: 5 mM.


title: 1-naphtylisothiocyanate, 50 µM. sample 100


title: Tetracycline, 200 µM. sample 104


title: Amioderone, 1.1 µM. sample 113


title: Lithium carbonate, 1.1 mM. sample 102

value: Lithium carbonate


title: Lithium carbonate, 1.1 mM. sample 105


title: 17alpha-ethynylestradiol, 0.38 µM. sample 096


title: DMSO, 0.2 %. sample 099


title: Acetaminophen, 660 µM. sample 101


title: Amioderone, 3.3 µM. sample 103


title: Tetracycline, 66.7 µM. sample 094


title: Tetracycline, 22.22 µM. sample 092


title: Thioacetamide, 3.3 mM. sample 098


title: Paraquat, 3.3 mM. sample 090


title: Cyclosporin A, 2 µM. sample 093


title: DMSO, 0.2 %. sample 088


title: Valproic Acid, 600 µM. sample 091

value: Valproic Acid


title: Thioacetamide, 10 mM. sample 082

value: embryo


title: 1-naphtylisothiocyanate, 16.7 µM. sample 095


title: Adefovir, 100 µM. sample 097

value: Adefovir


title: Isoniazid, 5 mM. sample 087


title: Acetaminophen, 73.3 µM. sample 085

value: Acetaminophen


title: Paraquat, 1.1 mM. sample 083


title: Valproic Acid, 600 µM. sample 084


title: Isoniazid, 5 mM. sample 086


title: Tetracycline, 200 µM. sample 078


title: Acetaminophen, 660 µM. sample 071


title: Chorpromazin, 0.33 µM. sample 153

value: Chorpromazin


title: 17alpha-ethynylestradiol, 1.16 µM. sample 080


title: Valproic Acid, 66.7 µM. sample 079


title: Thioacetamide, 1.1 mM. sample 076


title: Valproic Acid, 200 µM. sample 077


title: 17alpha-ethynylestradiol, 3.5 µM. sample 068


title: Valproic Acid, 66.7 µM. sample 069


title: Isoniazid, 1.67 mM. sample 074


title: Paraquat, 3.3 mM. sample 075


title: Cyclosporin A, 6 µM. sample 066


title: Valproic Acid, 200 µM. sample 073


title: Adefovir, 100 µM. sample 072


title: Valproic Acid, 66.7 µM. sample 058


title: Tetracycline, 22.22 µM. sample 057


title: Thioacetamide, 10 mM. sample 056


title: Amioderone, 3.3 µM. sample 060


title: DSW, vehicle. sample 053


title: Lithium carbonate, 1.1 mM. sample 064


title: Isoniazid, 0.5 mM. sample 052


title: Valproic Acid, 200 µM. sample 055


title: DSW, vehicle. sample 059


title: 17alpha-ethynylestradiol, 1.16 µM. sample 063


title: Chorpromazin, 3 µM. sample 070

value: 3 µM.


title: Acetaminophen, 73.3 µM. sample 062


title: Amioderone, 10 µM. sample 067


title: 1-naphtylisothiocyanate, 5.5 µM. sample 054


title: Amioderone, 3.3 µM. sample 061


title: Tetracycline, 66.7 µM. sample 047


title: Chorpromazin, 1 µM. sample 048

value: 1 µM.


title: Amioderone, 10 µM. sample 049


title: Paraquat, 3.3 mM. sample 046


title: DMSO, 0.2 %. sample 045


title: Adefovir, 100 µM. sample 041


title: Thioacetamide, 1.1 mM. sample 044


title: DMSO, 0.2 %. sample 042


title: 1-naphtylisothiocyanate, 5.5 µM. sample 050


title: DMSO, 0.2 %. sample 040


title: Tetracycline, 66.7 µM. sample 038


title: Paraquat, 10 mM. sample 043


title: Chorpromazin, 3 µM. sample 051


title: Acetaminophen, 660 µM. sample 037


title: 17alpha-ethynylestradiol, 3.5 µM. sample 034


title: Cyclosporin A, 2 µM. sample 033

value: 2 µM.


title: 17alpha-ethynylestradiol, 1.16 µM. sample 032


title: Chorpromazin, 3 µM. sample 029


title: Cyclosporin A, 0.67 µM. sample 028


title: 17alpha-ethynylestradiol, 3.5 µM. sample 036


title: Paraquat, 1.1 mM. sample 039


title: 1-naphtylisothiocyanate, 5.5 µM. sample 027


title: Amioderone, 10 µM. sample 035


title: D-Mannitol, 3 mM. sample 022

value: D-Mannitol

value: 3 mM.


title: Amioderone, 1.1 µM. sample 024


title: 17alpha-ethynylestradiol, 0.38 µM. sample 023


title: Paraquat, 1.1 mM. sample 025

value: Paraquat


title: Tetracycline, 66.7 µM. sample 030

value: Tetracycline


title: Amioderone, 10 µM. sample 031

value: Amioderone


title: Thioacetamide, 3.3 mM. sample 017

value: Thioacetamide


title: Cyclosporin A, 0.67 µM. sample 026

value: Cyclosporin A


title: Tetracycline, 22.22 µM. sample 019


title: Chorpromazin, 1 µM. sample 018


title: 17alpha-ethynylestradiol, 0.38 µM. sample 021


title: Tetracycline, 200 µM. sample 015


title: 1-naphtylisothiocyanate, 16.7 µM. sample 016


title: Cyclosporin A, 6 µM. sample 012

value: 6 µM.


title: D-Mannitol, 3 mM. sample 011


title: Chorpromazin, 3 µM. sample 010


title: DSW, vehicle. sample 007

value: DSW


title: Chorpromazin, 0.33 µM. sample 004


title: DMSO, 0.2 %. sample 003

value: DMSO


title: Valproic Acid, 66.7 µM. sample 005

value: embryo

value: Valproic Acid


title: Acetaminophen, 220 µM. sample 014

value: Acetaminophen


title: Valproic Acid, 600 µM. sample 006


title: Acetaminophen, 220 µM. sample 009


title: Isoniazid, 0.5 mM. sample 020

value: Isoniazid


title: Isoniazid, 1.67 mM. sample 002


title: Isoniazid, 5 mM. sample 001

value: 5 mM.


title: 17alpha-ethynylestradiol, 3.5 µM. sample 013


title: MG132_2 / Control_2 biol. Rep. 2; techn. Rep. 2

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

hyb_protocol: Samples were combined and hybridize on a custom oligoarray with 4 x 44k elements produced by Agilent Technologies, the hybridization and washing steps were perfomed according to agilent instructions

scan_protocol: The washed slides were scanned using the equipament GenePix4000B (molecular devices)

data_processing: Data was extracted using Feature Extraction software (Agilent Technologies), the intensities were LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Schistosoma mansoni

label_protocol: All samples were linearly amplified and labeled using Agilent protocol with Low input RNA amplification kit

growth_protocol: Adult worms were obtained by portal perfusion in 56-days infected hamsters

extract_protocol: RNA from all samples was extract using Trizol reagent (invitrogen)  followed by DNAse treatment using RNeasy kit (QIAGEN) according to manufacturer´s instructions.

treatment_protocol: Adult worms were kept in culture 24 h with MG132 (50uM) or the veicule solution (DMSO)

value: Non-treated

value: Adult worms (DMSO) kept in culture during 24 h

tag: biological replicate

value: 2 (sample2)

value: MG132 Treated

value: Adult worms kept in culture during 24 h

value: 2 (sample 2)


title: MG132_4 / Control_4 biol. Rep. 4; techn. Rep. 2

value: 4 (sample4)

value: 4 (sample 4)


title: MG132_3 / Control_3 biol. Rep. 3; techn. Rep. 2

value: 3 (sample3)

value: 3 (sample 3)


title: MG132_2 / Control_2 biol. Rep. 2; techn. Rep. 1

value: Non-treated (DMSO)


title: MG132_4 / Control_4 biol. Rep. 4; techn. Rep. 1


title: MG132_1 / Control_1 biol. Rep. 1; techn. Rep. 1

value: 1 (sample 1)

value: 1 (sample1)


title: 15L_3

city: Shizuoka

first: Hiroshi

last: Fujii

state: Shizuoka

address: 485-6 Okitsunakacho, Shimizu

department: Division of Citrus Research

country: Japan

institute: Institute of Fruit Tree Science, NARO

hyb_protocol: Glass slides were hybridized overnight at 65 °C in a hybridization buffer containing a portion of Cy3 -labeled cRNA. After hybridization, slides were washed in Agilent Gene Expression Wash Buffer 1 (Agilent) with 0.005% Triton X-102 for 1 min at room temperature and Agilent Gene Expression Wash Buffer 2 (Agilent) with 0.005% Triton X-102 for 1 min at 37 °C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565A) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Vitis labrusca x Vitis vinifera

source_name: 15 berries incubated for 10 days under 15ºC/Light condition

label_protocol: Total RNA (250 ng) was labelled with Cy3 according to the instructions for the Quick Amp Labeling Kit (Agilent, Palo Alto, CA). Labeled cRNA was purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany).

extract_protocol: Total RNA was extracted from frozen samples by the hot borate method (Wan and Wilkins, 1994).

treatment_protocol: Grape berries just beginning to show color were collected from mature vines of 'Pione'; The berries were incubated for 10 days under one of four conditiond; 15ºC/Light, 15ºC/Dark, 35ºC/Light, 35ºC/Dark.

tag: cultivar

value: Pione

value: grape berry just beginning to show color


title: MG132_3 / Control_3 biol. Rep. 3; techn. Rep. 1


title: 35D_2

source_name: 15 berries incubated for 10 days under 35ºC/Dark condition


title: 15D_2

source_name: 15 berries incubated for 10 days under 15ºC/Darkt condition


title: 35L_1

source_name: 15 berries incubated for 10 days under 35ºC/Light condition


title: 15D_3


title: 35D_3


title: 7_A/Sn_naive

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: Cy3- labeled cRNA was hybridized to Agilent´s mouse 4x44k GE microarrays  for 16 h at 68 ºC and scanned using the Agilent DNA Microarray Scanner.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) according to manufacture´s recommendation

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_Dec08, GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.
Logbase: 2, Normalization: Scale mean to mean of all samples

source_name: TB-resistant host_naive

label_protocol: 200 ng of total RNA were applied for Cy3-labelling reaction using the MessageAmp II-Bacteria Kit according to supplier´s recommendation (Ambion). As a result of IVT (in vitro transcription) reaction using aminoallyl-dUTP antisense aRNA were generated and subsequently coupled with fluorescent dye Cy3.

extract_protocol: Total RNA was isolated using miRNeasy Mini Kit (QIAGEN; Hilden, Germany)

treatment_protocol: Male mice aged 10-12 weeks were infected intravenously with 5x10^6 CFU of mid-log phase M. tuberculosis strain H37Rv. Two weeks after infection, mice were sacrificed using CO2 asphyxiation, lungs harvested aseptically, and the low lobes of the right lungs from individualmice were used for RNA isolation. Lungs from non-infected animals were used as the control.

tag: strain

value: A/Sn

value: 10-12 weeks

value: male

tag: phenotype

value: TB-resistant

tag: infected with

value: none (uninfected control)

value: lung


title: 35L_3

tag: tissue


title: 15D_1


title: 35D_1


title: 35L_2


title: 10_A/Sn_infected

source_name: TB-resistant host_infected

value: M. tuberculosis strain H37Rv


title: 12_A/Sn_infected


title: 6_I/St_infected

source_name: TB-susceptible host_infected

value: I/St

value: TB-susceptible


title: 9_A/Sn_naive


title: 11_A/Sn_infected


title: MG132_1 / Control_1 biol. Rep. 1; techn. Rep. 2

value: Non-treated

value: Adult worms (DMSO) kept in culture during 24 h

value: MG132 Treated

value: Adult worms kept in culture during 24 h


title: 15L_2


title: 8_A/Sn_naive


title: LA

city: Münster

first: Boris

last: Greber

address: Von-Esmarch-Str. 54

institute: Max Planck Institute for Molecular Biomedicine

description: SAMPLE 10

hyb_protocol: 18 hours according to manufacturer's instructions (Illumina)

scan_protocol: default settings on a HiScan SQ (Illumina)

data_processing: cubic spline normalization with background subtration in GenomeStudio (Illumina)

source_name: human left atrium

label_protocol: Illumina TotalPrep RNA Amplification Kit (Life Technologies); 14h of in-vitro transcription

growth_protocol: undifferentiated hPSCs were in chemically defined FTDA medium; differentiated cardiomyocytes were maintained in 2% FCS / Knockout-DMEM under adherent conditions

extract_protocol: Qiagen RNeasy columns with on-column DNA-digestion

tag: time-point

value: adult

value: human heart, left atrium


title: RA

description: SAMPLE 9

source_name: human right atrium

value: human heart, right atrium


title: RV

description: SAMPLE 11

source_name: human right ventricle

value: human heart, right ventricle


title: 15L_1

value: Pione

value: grape berry just beginning to show color


title: LV

description: SAMPLE 12

source_name: human left ventricle

value: human heart, left ventricle


title: 5_I/St_infected

value: 10-12 weeks

value: male


title: 6wk

description: SAMPLE 7

source_name: differentiated cell line

value: 6 weeks

value: 6 week-old hPSC-CMs


title: 8wk

description: SAMPLE 8

value: 8 weeks

value: 8 week-old hPSC-CMs


title: 3_I/St_naive

source_name: TB-susceptible host_naive

value: I/St

value: TB-susceptible

value: none (uninfected control)

value: lung


title: 4_I/St_infected

value: M. tuberculosis strain H37Rv


title: 5wk

description: SAMPLE 6

value: 5 weeks

value: 5 week-old hPSC-CMs


title: 3wk

description: SAMPLE 4

value: 3 weeks

value: 3 week-old hPSC-CMs


title: 1_I/St_naive


title: 1wk

description: SAMPLE 2

value: 1 week

value: 1 week-old hPSC-CMs


title: 4wk

description: SAMPLE 5

value: 4 weeks

value: 4 week-old hPSC-CMs


title: 2wk

description: SAMPLE 3

value: 2 weeks

value: 2 week-old hPSC-CMs


title: Line 165d 28 weeks

city: Houston

last: Krencik

state: TX

address: 6670 Bertner Ave.

department: Neurosurgery

institute: Houston Methodist

hyb_protocol: Performed at UCSF genomics core facility with standard procedures

source_name: Human iPSC line 165d differentiated towards astrocytes for 28 weeks

growth_protocol: Maintained as a cell culture at 37C in 5% CO2 in neural media (DMEM/F12+glutamine, NEAA, N2, Heparin.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by Rneasy and on-column DNAse digestion (Qiagen).

treatment_protocol: Cells were dissociated with accutased and attached as a monolayer.  Growth factors EGF and FGF2 were removed and replaced with CNTF.

value: in vitro cell culture

tag: developmental lineage

value: Astrocyte

tag: differentiation age

value: 28 weeks of differentiation

tag: hras status

value: wildtype


title: Line 162d 28 weeks

scan_protocol: Performed at UCSF genomics core facility with standard procedures

source_name: Human iPSC line 162d differentiated towards astrocytes for 28 weeks


title: 2_I/St_naive

value: I/St

tag: age

value: 10-12 weeks

value: male

value: TB-susceptible

value: none (uninfected control)


title: Mouse_17_+/+

city: Berlin

first: Valerie

last: Begay

address: Robert-Rössle-Str. 10

institute: Max Delbrück Center

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Raw data was background corrected and normalized using quantile normalization (R/Bioconductor (1.8)).

label: Cyanine-3 (Cy3)

source_name: C/EBPb LIP wild type (+/+)_lymphoma

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared using TriPure reagent and RNA cleaning step. Quality samples was checked using Agilent's Bioanalyzer.

treatment_protocol: C/EBPb LIP heterozygous (+/L)  and wild type (+/+) mice were kept in a pathogen-free animal facility at least 25 months. Mice were checked twice a week for spontaneous lymphoma development. After dissection, one piece of the lymphoma was kept for histopathological analysis and the rest was snap-frozen and stored at - 80°C.

tag: genotype/variation

value: C/EBPb LIP wild type (+/+)

tag: age (in month)

value: female

value: lymphoma


title: 0wk

description: SAMPLE 1

source_name: cultured cell line

value: 0 weeks

value: undifferentiated hPSCs


title: Mouse_11_+/+

tag: gender


title: Mouse_517_+/L

source_name: C/EBPb LIP heterozygous (+/L)_lymphoma

value: C/EBPb LIP heterozygous (+/L)


title: Mouse_19_+/+


title: Line 16 8 weeks

data_processing: Performed at UCSF genomics core facility with standard procedures

source_name: Human iPSC line 16 differentiated towards astrocytes for 8 weeks

value: Astroglial progenitor

value: 8 weeks of differentiation

value: HRAS-G12S mutant


title: Line 13 28 weeks

source_name: Human iPSC line 13 differentiated towards astrocytes for 28 weeks

label_protocol: Performed at UCSF genomics core facility with standard procedures

value: in vitro cell culture

value: Astrocyte


title: Line 8 8 weeks

source_name: Human iPSC line 8 differentiated towards astrocytes for 8 weeks


title: DamID pro-B replicate 417

city: Baltimore

first: Karen

last: Reddy

address: 855 North Wolfe Street

department: Center for Epigenetics/Biological Chemistry

institute: Johns Hopkins University

description:
proB_DamID_log2ratio_chr11_chr12.bedgraph
DamID-chip pro-B cells (LmnB1/Dam)

hyb_protocol: Labeled samples were hybed on 2007-08-17_MM8_Economy_03 arrays using standard protocol found in Chapter 4, NimbleGen Arrays User's Guide, Version 1.0

scan_protocol: Arrays were scanned on an MS200_2 scanner using standard manafacturer protocol.

data_processing:
Data was processed using Nimblegen standard procedures for DEVA 1.0.2 to create .pair and Dam-LmnB1/Dam-only Log2 ratio files
DEVA 1.0.2 processed files, Dam-LmnB1/Dam-only Log2 ratio files were lifted over to mm9. Duplicates were quantile normalized and averaged together. Processed files are in UCSC compatible bedgraph format

source_name: Dam-LmnB1 data from RAG2-/- pro-B cells

label_protocol: 1 ug of sample DNA was labeled with Cy3 or Cy5 dye as described by Chapter 3, NimbleGen Arrays User's Guide, Version 1.0

growth_protocol: Cells were cultured on stromal layer of OP9s in the presence of 3ng/mL IL-7 in Opti-MEM

extract_protocol: gDNA was extracted using the QIAamp DNA Mini Kit. DamID was performed as described in Vogel et al, Nature Protocols, 2007 and previously described in Zullo et al, Cell, 2013  QIAamp DNA Mini Kit

treatment_protocol: Cells were infected with Dam-LmnB1 retroviral vectors in the presence of polybrene via spinfection. RAG2-/- pro-B cells are ex-vivo expanded primary cells.

tag: cell type

value: RAG2-/- pro-B cells

tag: damid construct

source_name: Dam-only data from RAG2-/- pro-B cells

treatment_protocol: Cells were infected with Dam-only retroviral vectors in the presence of polybrene via spinfection. RAG2-/- pro-B cells are ex-vivo expanded primary cells.

value: Dam-only


title: Mouse_101_+/+


title: Mouse_23_+/L


title: MM1S-BRD9876_1

city: Cambridge

first: Shrikanta

last: Chattopadhyay

state: MA

address: 415 Main Street

department: Center for the Science of Therapeutics

institute: Broad Institute

hyb_protocol: Following fragmentation, 30 µg of cRNA were hybridized with the GeneChip Human Genome U133 Plus 2.0 Array for 16 hr at 45C in a hybridization oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner G3000.

data_processing: CEL files were generated using the Affymetrix GeneChip® Command Console® Software (AGCC). These CEL files were analyzed with the Genepattern software (www.broadinstitute.org/genepattern) using the ExpressionFileCreator choosing the RMA method, quantile normalization and background correction.

source_name: MM1S cells treated with 10 µM BRD9876 for 6h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip® 3’ IVT Express Kit Manual, 2008, Affymetrix).

growth_protocol: MM1S cells were grown in 10% RPMI.

extract_protocol: Cell pellets were lyzed with the TRIzol reagent and total RNA extracted.

treatment_protocol: Cells were treated in duplicate either with DMSO or 10 µM BRD9876 for 6h then harvested with a cell scraper and centrifuged.

tag: treatment

value: Test compound

tag: cell line


title: Line 7 8 weeks

source_name: Human iPSC line 7 differentiated towards astrocytes for 8 weeks


title: DamID pro-B replicate 880


title: Line 165d 8 weeks

source_name: Human iPSC line 165d differentiated towards astrocytes for 8 weeks

value: wildtype


title: Mouse_866_+/L


title: MM1S-BRD9876_2


title: MM1S-DMSO_1

source_name: MM1S cells treated with DMSO for 6h

value: Control


title: Line 13 8 weeks

source_name: Human iPSC line 13 differentiated towards astrocytes for 8 weeks


title: Line 162d 8 weeks

source_name: Human iPSC line 162d differentiated towards astrocytes for 8 weeks


title: Mouse_20_+/L

value: male


title: Mouse_688_+/L


title: MM1S-DMSO_2


title: lung_WT_D39_High_48hrs_5

status: Public on Dec 15 2014

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

hyb_protocol: Illumina standard protocol

scan_protocol: Illumina standard protocol

data_processing:
NEQC normalized
R statistical environment packages beadarray and limma

source_name: WT lung, D39 high dose infected, 48 hours

label_protocol: Illumina standard protocol

growth_protocol: S. pneumoniae serotype 2 D39 strain and serotype 3 ATCC6303 strain were grown to mid-logarithmic phase at 37°C using Todd–Hewitt broth (Difco, Detroit, MI) supplemented with yeast extract (0.5%), harvested by centrifugation at 4000rpm for 15 min, and washed twice in isotonic saline. Suspensions of 2x107 (high dose) and 5x104 (low dose) colony forming units (CFU) in 50µL isotonic saline were used as the inocula.

extract_protocol: Nucleospin protocol

treatment_protocol: Lungs homogenated in PBS prior to RNA isolation

value: lung


title: lung_WT_D39_High_48hrs_4

value: female


title: lung_WT_D39_High_6hrs_1

source_name: WT lung, D39 high dose infected, 6 hours


title: lung_WT_D39_Low_6hrs_3

source_name: WT lung, D39 low dose infected, 6 hours


title: Mouse_40_+/+

source_name: C/EBPb LIP wild type (+/+)_lymphoma

value: C/EBPb LIP wild type (+/+)

value: lymphoma


title: lung_WT_D39_High_6hrs_3


title: lung_WT_3

source_name: WT lung, uninfected


title: lung_WT_D39_High_48hrs_male_2

source_name: WT lung, D39 high dose infected, male, 48 hours


title: lung_WT_D39_Low_6hrs_1


title: lung_WT_1


title: lung_WT_D39_High_48hrs_male_1


title: lung_WT_D39_High_48hrs_male_3


title: lung_WT_D39_High_6hrs_2


title: lung_WT_6303_Low_6hrs_2-3

source_name: WT lung, ATCC6303 low dose infected, Nlrp3 experimental day, 6 hours


title: lung_WT_D39_High_6hrs_4


title: lung_WT_D39_Low_6hrs_2


title: lung_WT_D39_Low_6hrs_4


title: lung_WT_2


title: lung_WT_6303_Low_6hrs_2-1


title: lung_WT_D39_High_48hrs_1


title: lung_WT_6303_Low_6hrs_2-2


title: lung_WT_D39_High_48hrs_3


title: lung_WT_D39_High_48hrs_2


title: lung_WT_6303_High_6hrs_2-2

source_name: WT lung, ATCC6303 high dose infected, Nlrp3 experimental day, 6 hours


title: lung_Nlrp3KO_1

source_name: Nlrp3 KO lung, uninfected


title: lung_Nlrp3KO_3


title: lung_Nlrp3KO_D39_Low_6hrs_3

source_name: Nlrp3 KO lung, D39 low dose infected, 6 hours


title: lung_Nlrp3KO_2


title: lung_Nlrp3KO_D39_High_6hrs_3

source_name: Nlrp3 KO lung, D39 high dose infected, 6 hours


title: lung_Nlrp3KO_D39_Low_6hrs_4


title: lung_Nlrp3KO_6303_Low_6hrs_1

source_name: Nlrp3 KO lung, ATCC6303 low dose dose infected, 6 hours


title: lung_Nlrp3KO_6303_Low_6hrs_3


title: lung_Nlrp3KO_6303_High_6hrs_2

source_name: Nlrp3 KO lung, ATCC6303 high dose infected, 6 hours


title: lung_Nlrp3KO_6303_High_6hrs_1


title: lung_Nlrp3KO_D39_High_6hrs_1


title: lung_Nlrp3KO_D39_Low_6hrs_1


title: lung_WT_6303_High_6hrs_1-1

source_name: WT lung, ATCC6303 high dose infected, Asc experimental day, 6 hours


title: lung_AscKO_3

source_name: Asc KO lung, uninfected


title: lung_WT_D39_Low_6hrs_1rep


title: lung_WT_6303_Low_6hrs_1-1

source_name: WT lung, ATCC6303 low dose infected, Asc experimental day, 6 hours


title: lung_Nlrp3KO_D39_High_6hrs_2


title: lung_Nlrp3KO_D39_Low_6hrs_2


title: lung_WT_6303_High_6hrs_2-1


title: lung_WT_6303_Low_6hrs_1-2


title: lung_WT_1rep


title: lung_Nlrp3KO_6303_Low_6hrs_2


title: lung_AscKO_D39_High_6hrs_4

source_name: Asc KO lung, D39 high dose infected, 6 hours


title: lung_AscKO_2


title: lung_AscKO_D39_Low_6hrs_3

source_name: Asc KO lung, D39 low dose infected, 6 hours


title: lung_WT_D39_High_48hrs_1rep

source_name: WT lung, D39 high dose infected, 48 hours


title: lung_WT_6303_Low_6hrs_1-3


title: lung_WT_6303_High_6hrs_1-3


title: lung_AscKO_1


title: lung_AscKO_D39_Low_6hrs_1


title: lung_AscKO_D39_Low_6hrs_2


title: 2032_B

city: Denmark

first: Qihua

last: Tan

address: J. B. Winsløws Vej 9B

country: Denmark

institute: University of Southern Denmark

description:
MZ twin
SAMPLE 312

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

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

data_processing: minfi; Data were normalized by SWAN. Average Beta values for each sample are included in the "Processed.csv" file available on the series record.

label: Cy3, Cy5

source_name: genomic DNA extracted and purified

label_protocol: Standard Illumina Protocol

extract_protocol: The blood was centrifuged at 1000 g for 10 min, and buffy-coat was frozen in aliquots at −80 °C. DNA was isolated from the buffy-coats using the salt precipitation method applying either a manual protocol or a semi-automated protocol based on the Autopure System (Qiagen, Hilden, Germany). Bisulphite treatment of 500 ng template genomic DNA was carried out with the EZ-96 DNA methylation kit (Zymo Research, Orange County, USA) following the manufacturer’s protocol.

value: whole blood

tag: birth-weight

tag: pair id


title: lung_AscKO_D39_High_6hrs_1

tag: strain


title: 2041_B

description:
MZ twin
SAMPLE 311


title: 2081

description:
MZ twin
SAMPLE 309


title: 3043

description:
MZ twin
SAMPLE 310


title: 2033_B

description:
MZ twin
SAMPLE 306


title: 2078

description:
MZ twin
SAMPLE 307


title: 2072

description:
MZ twin
SAMPLE 308


title: 2042_B

description:
MZ twin
SAMPLE 305


title: 3044

description:
MZ twin
SAMPLE 304


title: lung_AscKO_D39_High_6hrs_3


title: 2082

description:
MZ twin
SAMPLE 303


title: 2073

description:
MZ twin
SAMPLE 302


title: leaf

city: Çankırı

first: tugba

last: gurkok

address: Uluyazı

department: biology

country: Turkey

institute: Çankırı Karatekin University

hyb_protocol: hybridization was performed overnight on a µParaFlo microfluidic chip using a microcirculation pump (Atactic Technologies, USA).

scan_protocol: the images were captured using laser scanner (GenePix 4000B, Molecular Device, USA)

data_processing:
Array-Pro image analysis software (Media Cybernetics, USA).
The data was analyzed by subtracting of background and normalized by obtained signals with LOWESS method to eliminate system related variations.

label: Cy3 and Cy5

organism: Papaver somniferum

source_name: Papaver somniferum

label_protocol: The labeling was achieved with Cy3 and Cy5 fluorescent dyes

growth_protocol: The opium poppy (Papaver somniferum cv ofis 95, TMO, Turkey) plants were grown in growth cabin with 16 h/light 23 °C and 8 h/dark 20 °C with 70% humidity.

extract_protocol: Total RNAs were isolated using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions. sRNAs were isolated by miRVana (Ambion, CA, USA) kit according to the manufacturer’s instructions.

treatment_protocol: no treatment

tag: cultivar

value: Ofis 95

value: leaf


title: capsule

tag: tissue

value: capsule


title: stem

value: stem


title: root

value: root


title: 2066

description:
MZ twin
SAMPLE 300


title: lung_AscKO_6303_Low_6hrs_3

source_name: Asc KO lung, ATCC6303 low dose infected, 6 hours


title: lung_AscKO_6303_High_6hrs_2

source_name: Asc KO lung, ATCC6303 high dose infected, 6 hours


title: lung_AscKO_6303_Low_6hrs_2


title: lung_WT_6303_High_6hrs_1-2


title: 3057

description:
MZ twin
SAMPLE 299


title: 2100

description:
MZ twin
SAMPLE 297


title: 2096

description:
MZ twin
SAMPLE 298


title: 2084

description:
MZ twin
SAMPLE 295


title: lung_AscKO_6303_High_6hrs_3


title: lung_AscKO_6303_Low_6hrs_1


title: lung_AscKO_6303_High_6hrs_1


title: 3056

description:
MZ twin
SAMPLE 293


title: 2077

description:
MZ twin
SAMPLE 301


title: 2097

description:
MZ twin
SAMPLE 292


title: 2065

description:
MZ twin
SAMPLE 294


title: lung_AscKO_D39_High_6hrs_2


title: 2101

description:
MZ twin
SAMPLE 291


title: 2087

description:
MZ twin
SAMPLE 290


title: 2083

description:
MZ twin
SAMPLE 289


title: 2124

description:
MZ twin
SAMPLE 288


title: 2095

description:
MZ twin
SAMPLE 286


title: 2085_D

description:
MZ twin
SAMPLE 285


title: 2088

description:
MZ twin
SAMPLE 296


title: 2098

description:
MZ twin
SAMPLE 284


title: CMT3L

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: 100ng of each total RNA was lanelled and hybrized using Human MicroRNA Microarray Kit version 2 (Agilent technologies) according to the manufacture's protocol (Protocol for use with Agilent MicroRNA microarray version 2),

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

extract_protocol: Total RNA was extracted with TRIzol solution (Invitrogen, Carlsbad, CA, USA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Palo Alto, CA).

treatment_protocol: Fresh tissues were frozen in nitrogen and stored at –80°C

value: thyroid

tag: sample id

tag: tissue type

value: Tumor tissue

tag: ret mutation

value: positive


title: 3077

description:
MZ twin
SAMPLE 283


title: CMT2L

label_protocol: 100ng of each total RNA was lanelled and hybrized using Human MicroRNA Microarray Kit version 2 (Agilent technologies) according to the manufacture's protocol (Protocol for use with Agilent MicroRNA microarray version 2),


title: CMT2S

value: Normal tissue


title: CMT1L


title: CMT1S


title: ElkS

source_name: ElkS

value: Elk

value: negative


title: CavS

source_name: CavS

value: Cav


title: CavL

source_name: CavL


title: ReyS

source_name: ReyS

value: male

value: Rey


title: CMT3S

value: female


title: 3083

description:
MZ twin
SAMPLE 281


title: 2094

description:
MZ twin
SAMPLE 280


title: 2086

description:
MZ twin
SAMPLE 279


title: 2099

description:
MZ twin
SAMPLE 278


title: 3078

description:
MZ twin
SAMPLE 277


title: 0636319S


title: FayS

source_name: FayS

value: Fay


title: CMT4S


title: CMT5S


title: GO5124S


title: 2018

description:
MZ twin
SAMPLE 276

value: whole blood


title: 0630328S


title: FraS

source_name: FraS

value: Fra


title: AbeS

source_name: AbeS

value: Abe


title: MEES

source_name: MEES

value: MEE


title: 2125

description:
MZ twin
SAMPLE 282


title: 2116

description:
MZ twin
SAMPLE 272


title: 2019

description:
MZ twin
SAMPLE 270


title: 2103

description:
MZ twin
SAMPLE 273


title: AGUS

source_name: AGUS

value: AGU


title: 0630328L


title: ElkL

source_name: ElkL


title: 2006

description:
MZ twin
SAMPLE 274


title: FraL

source_name: FraL


title: 2005

description:
MZ twin
SAMPLE 268


title: 2118

description:
MZ twin
SAMPLE 269


title: 0636319L


title: CMT5L


title: GO5124L


title: 2115

description:
MZ twin
SAMPLE 266


title: 2001

description:
MZ twin
SAMPLE 265


title: CMT4L


title: 3101

description:
MZ twin
SAMPLE 264


title: 1045

description:
MZ twin
SAMPLE 263


title: 2117

description:
MZ twin
SAMPLE 275


title: 2002

description:
MZ twin
SAMPLE 271


title: MEEL

source_name: MEEL


title: FayL

source_name: FayL


title: AGUL

source_name: AGUL


title: ReyL

source_name: ReyL


title: AbeL

source_name: AbeL


title: 3113

description:
MZ twin
SAMPLE 260

source_name: genomic DNA extracted and purified


title: 3096

description:
MZ twin
SAMPLE 262


title: 3048

description:
MZ twin
SAMPLE 261


title: 3085

description:
MZ twin
SAMPLE 259


title: 1046

description:
MZ twin
SAMPLE 257


title: 2102

description:
MZ twin
SAMPLE 267


title: 3095

description:
MZ twin
SAMPLE 256


title: 3100

description:
MZ twin
SAMPLE 258


title: REIMS CHOS

source_name: REIMS CHOS

value: REIMS CHO


title: REIMS LESL

source_name: REIMS LESL

value: thyroid

value: REIMS LES


title: 3112

description:
MZ twin
SAMPLE 254


title: REIMS LESS

source_name: REIMS LESS

value: positive


title: 2030

description:
MZ twin
SAMPLE 255


title: 3091

description:
MZ twin
SAMPLE 253


title: REIMS CAPS

source_name: REIMS CAPS

value: REIMS CAP

value: Normal tissue


title: REIMS CAPL

source_name: REIMS CAPL

value: Tumor tissue

value: negative


title: CAL09-250L


title: CAL09-254S


title: CAL09-254L


title: 3099

description:
MZ twin
SAMPLE 252


title: CAL09-184L


title: CAL09-250S


title: REIMS CHOL

source_name: REIMS CHOL


title: 2128

description:
MZ twin
SAMPLE 251


title: 2112

description:
MZ twin
SAMPLE 249


title: 3115

description:
MZ twin
SAMPLE 250


title: CAL09-184S


title: 3071

description:
MZ twin
SAMPLE 247


title: 3098

description:
MZ twin
SAMPLE 246


title: CAL08-59L


title: 2132

description:
MZ twin
SAMPLE 245


title: CAL08-59S


title: 3116

description:
MZ twin
SAMPLE 244


title: 2091

description:
MZ twin
SAMPLE 243


title: CAL07-2S


title: 3106

description:
MZ twin
SAMPLE 240


title: 2119

description:
MZ twin
SAMPLE 242


title: 3072

description:
MZ twin
SAMPLE 241


title: 2138

description:
MZ twin
SAMPLE 239


title: 3084

description:
MZ twin
SAMPLE 287


title: CAL05-14L


title: CAL06-61S


title: CAL06-61L


title: CAL05-14S


title: 3093

description:
MZ twin
SAMPLE 238


title: 2109

description:
MZ twin
SAMPLE 248


title: LB08-501L


title: LB08-501S


title: LB04-130L

value: unknown


title: CAL07-2L


title: LB07-758S


title: LB07-758L


title: LB07-686S


title: LB07-686L


title: 3107

description:
MZ twin
SAMPLE 234


title: 2137

description:
MZ twin
SAMPLE 233


title: 3092

description:
MZ twin
SAMPLE 232


title: LB06-494S

value: male


title: LB06-143S


title: LB04-130S

value: female


title: 1067

description:
MZ twin
SAMPLE 231


title: 1068

description:
MZ twin
SAMPLE 237


title: 1061

description:
MZ twin
SAMPLE 236


title: 2092

description:
MZ twin
SAMPLE 228


title: 1060

description:
MZ twin
SAMPLE 230


title: 3081

description:
MZ twin
SAMPLE 229


title: 1017

description:
MZ twin
SAMPLE 226


title: 3082

description:
MZ twin
SAMPLE 235


title: 3031

description:
MZ twin
SAMPLE 227


title: 2085_C

description:
MZ twin
SAMPLE 225


title: LB05-581L


title: LB05-581S


title: 2063

description:
MZ twin
SAMPLE 223


title: 2093

description:
MZ twin
SAMPLE 222


title: 3052

description:
MZ twin
SAMPLE 224


title: LB05-267L


title: LB06-494L


title: LB05-344L


title: LB05-344S


title: LB05-267S


title: 3030

description:
MZ twin
SAMPLE 221


title: 1016

description:
MZ twin
SAMPLE 220


title: LB05-235L


title: LB05-104L


title: LB05-104S


title: LB06-143L


title: LB05-235S


title: 2086_C

description:
MZ twin
SAMPLE 219


title: 3051

description:
MZ twin
SAMPLE 218


title: 2061

description:
MZ twin
SAMPLE 217


title: LB05-54L


title: LB05-54S


title: LB04-114S


title: LB04-114L


title: LB04-78S


title: 2004

description:
MZ twin
SAMPLE 213


title: 1015

description:
MZ twin
SAMPLE 214


title: 3035

description:
MZ twin
SAMPLE 215


title: 2014

description:
MZ twin
SAMPLE 212


title: LB04-78L


title: 1028

description:
MZ twin
SAMPLE 210


title: 1002

description:
MZ twin
SAMPLE 211


title: 1014

description:
MZ twin
SAMPLE 208


title: 2003

description:
MZ twin
SAMPLE 207


title: 2020

description:
MZ twin
SAMPLE 206


title: 1030

description:
MZ twin
SAMPLE 216


title: 1003

description:
MZ twin
SAMPLE 205


title: 2045

description:
MZ twin
SAMPLE 204


title: 3034

description:
MZ twin
SAMPLE 209


title: 3032

description:
MZ twin
SAMPLE 202


title: 3005

description:
MZ twin
SAMPLE 203


title: 3079

description:
MZ twin
SAMPLE 201


title: Infarct Mouse + Telomerase Biological Replicate 3

city: Madrid

first: Christian

last: Baer

state: Madrid

address: Calle Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

description:
Gene Expression after Infarct + telomerase injection
SAMPLE 7

hyb_protocol: Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 600 ng. Volume: 50 µL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction was performed.

data_processing: Microarray background subtraction was carried out using normexp method. Normalization was performed using quantiles. Differentially expressed genes were obtained by applying linear models with R limma package {Smyth, 2005 #1166} (Bioconductor project, http://www.bioconductor.org). To account for multiple hypotheses testing, the estimated significance level (p value) was adjusted using Benjamini & Hochberg False Discovery Rate (FDR) correction.

source_name: Infarct Mouse_with telomerase

label_protocol: Amount of nucleic acid labeled: 100ng. Commercial One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90040 of May 2010. Amplification: by RNA polymerases.   Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of Cy3-CTP fluorophore.   Labeled samples are purified with silica-based spin columns.

growth_protocol: FVB/N mice were housed four or five per cage and fed ad libitum of a non-purified diet (nº 2018, Harlan).

extract_protocol: Total RNA fraction. RNA Integrity Numbers were in the range 7,4 to 8,3 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.

treatment_protocol: At one year of age mice were injected with AAV9 vectors with either  telomerase or an empty expression cassette. 2-3 weeks later myocardial infarction was induced via permanent LAD ligation. Six weeks later hearts were collected for RNA isolation. Control mice (Sample 9 -11) received neither virus nor LAD ligation treatment.

value: FVB/N

value: 1 year


title: 3025

description:
MZ twin
SAMPLE 199

value: whole blood


title: Control Mouse Biological Replicate 3

description:
Gene Expression in healthy mouse
SAMPLE 11

source_name: control Mouse


title: 3006

description:
MZ twin
SAMPLE 197


title: Infarct Mouse + Telomerase Biological Replicate 1

description:
Gene Expression after Infarct + telomerase injection
SAMPLE 5


title: Control Mouse Biological Replicate 1

description:
Gene Expression in healthy mouse
SAMPLE 9


title: 3033

description:
MZ twin
SAMPLE 196


title: 3080

description:
MZ twin
SAMPLE 195


title: Control Mouse Biological Replicate 2

description:
Gene Expression in healthy mouse
SAMPLE 10


title: Infarct Mouse - Biological Replicate 3

description:
Gene Expression after Infarct
SAMPLE 3

source_name: Infarct Mouse


title: Infarct Mouse + Telomerase Biological Replicate 4

description:
Gene Expression after Infarct + telomerase injection
SAMPLE 8


title: Infarct Mouse - Biological Replicate 1

description:
Gene Expression after Infarct
SAMPLE 1


title: Infarct Mouse + Telomerase Biological Replicate 2

description:
Gene Expression after Infarct + telomerase injection
SAMPLE 6


title: 2123

description:
MZ twin
SAMPLE 200


title: Infarct Mouse - Biological Replicate 4

description:
Gene Expression after Infarct
SAMPLE 4


title: 2044

description:
MZ twin
SAMPLE 198


title: 2122

description:
MZ twin
SAMPLE 194


title: 3026

description:
MZ twin
SAMPLE 193


title: 2136

description:
MZ twin
SAMPLE 191


title: 2067

description:
MZ twin
SAMPLE 190


title: 2108

description:
MZ twin
SAMPLE 189


title: Infarct Mouse - Biological Replicate 2

description:
Gene Expression after Infarct
SAMPLE 2


title: 1066

description:
MZ twin
SAMPLE 188


title: 2080

description:
MZ twin
SAMPLE 187


title: 2135

description:
MZ twin
SAMPLE 185


title: 2021

description:
MZ twin
SAMPLE 192


title: 2022

description:
MZ twin
SAMPLE 186


title: 2068

description:
MZ twin
SAMPLE 184


title: 2107

description:
MZ twin
SAMPLE 183


title: 1059

description:
MZ twin
SAMPLE 182


title: 2079

description:
MZ twin
SAMPLE 181


title: 2074

description:
MZ twin
SAMPLE 180


title: 3019

description:
MZ twin
SAMPLE 179


title: 2007

description:
MZ twin
SAMPLE 178


title: 1010

description:
MZ twin
SAMPLE 177


title: AML_CK_31

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

institute: Charité Universitätsmedizin Berlin

description: genome-wide analysis of alternative splicing in acute myeloid leukemia

hyb_protocol: The processed RNA was hybridized on GeneChip Human Exon 1.0 ST microarrays for 17 hours at 45oC and 60 rpm.

scan_protocol: The arrays were scanned using Affymetrix GeneChip® Scanner 3000.

data_processing:
Probe set summarization, background correction and normalization was performed by applying the robust multiarray average (RMA) algorithm. The exon array data were analysed in (1) R, oneChannelGUI 1.10.7 (Sanges R. et al., 2010), (2) easyExon 1.0.4 (Chang T-Y et al., 2008), (3) Xray 3.9 (Biotique Systems, Reno, NV) and (4) GeneSpring 11.0 (Agilent Technologies, Palo Alto, CA).
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: bone marrow

label_protocol: 0.2 microgram of total RNA was used for target preparation according to the manufacturer's protocol (GeneChip Whole Transcript Sense Target Labelling Assay manual, Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was isolated from the samples using the Trizol reagent (Invitrogen, Carlsbad, CA).

tag: patient sample type

value: Acute myeloid leukemia diagnostic sample

value: mononuclear cells

tag: disease state

value: AML with complex karyotype


title: AML_CK_40


title: AML_CK_39


title: AML_CK_37


title: hippocampus_freshfrozen_128

city: Bonn

first: Albert

last: Becker

address: Sigmund-Freud Str. 25

department: Neuropathology

institute: University of Bonn Medical Center

description: human brain tissue from pharmacoresistant TLE patients

hyb_protocol: Illumina Direct Hybridization Assay Kit according standard protocol

scan_protocol: Standard Illumina scanning protocol uisng Illumina BeadArray Reader

data_processing: Gene expression data were normalized using Illumina BeadStudio software suite by means of quantile normalization with background subtraction

source_name: hippocampal formation

label_protocol: Biotinylated cRNA were prepared with Illumina TotalPrep-96 RNA Amplification Kit (Life Technologies Corporation, Darmstadt).

extract_protocol: Total RNA was isolated from hippocampal tissue samples using ALLPrep DNA/RNA Mini Kit (Qiagen, Hilden) according manufacturer's protocoll. Tissue lysate was passed trough an AllPrep Rneasy spin collum to selectively isolate RNA.

value: hippocampal formation

tag: phenotype

value: epilepsy


title: 2133

description:
MZ twin
SAMPLE 176

tag: age


title: AML_CK_33


title: AML_CK_35

source_name: peripheral blood


title: hippocampus_freshfrozen_125


title: AML_CK_27


title: hippocampus_freshfrozen_129


title: AML_CK_29


title: AML_CK_36


title: hippocampus_freshfrozen_126


title: 1038

description:
MZ twin
SAMPLE 175


title: hippocampus_freshfrozen_127


title: AML_CK_38


title: 3018

description:
MZ twin
SAMPLE 173


title: 2075

description:
MZ twin
SAMPLE 174


title: AML_CK_25


title: AML_CK_34


title: 2011

description:
MZ twin
SAMPLE 172


title: AML_CK_23


title: 1008

description:
MZ twin
SAMPLE 171


title: AML_CK_24


title: AML_CK_22


title: 2134

description:
MZ twin
SAMPLE 170


title: AML_CK_30


title: 1037

description:
MZ twin
SAMPLE 169


title: 3104

description:
MZ twin
SAMPLE 168


title: AML_CK_20


title: AML_CK_21


title: 2126

description:
MZ twin
SAMPLE 166


title: AML_CK_28


title: 3108

description:
MZ twin
SAMPLE 167


title: 3076

description:
MZ twin
SAMPLE 164


title: hippocampus_freshfrozen_122


title: 1053

description:
MZ twin
SAMPLE 165


title: 3109

description:
MZ twin
SAMPLE 161


title: 2085_B

description:
MZ twin
SAMPLE 163


title: AML_CK_19


title: hippocampus_freshfrozen_120


title: 2127

description:
MZ twin
SAMPLE 160


title: hippocampus_freshfrozen_121


title: 3114

description:
MZ twin
SAMPLE 158


title: 1054

description:
MZ twin
SAMPLE 159


title: 3105

description:
MZ twin
SAMPLE 162


title: hippocampus_freshfrozen_119


title: AML_CK_15


title: hippocampus_freshfrozen_118


title: AML_CK_18


title: AML_CK_16


title: AML_CK_17


title: 2086_B

description:
MZ twin
SAMPLE 157


title: 3094

description:
MZ twin
SAMPLE 156


title: hippocampus_freshfrozen_117


title: 3065

description:
MZ twin
SAMPLE 155


title: 1041

description:
MZ twin
SAMPLE 154


title: AML_CK_14


title: AML_CK_13


title: 3063

description:
MZ twin
SAMPLE 153


title: AML_CK_26


title: hippocampus_freshfrozen_116


title: 2069

description:
MZ twin
SAMPLE 152


title: hippocampus_freshfrozen_115


title: 3059

description:
MZ twin
SAMPLE 151


title: hippocampus_freshfrozen_124


title: 3097

description:
MZ twin
SAMPLE 150


title: hippocampus_freshfrozen_114


title: AML_CK_12


title: AML_CK_11


title: 3062

description:
MZ twin
SAMPLE 147


title: 2070

description:
MZ twin
SAMPLE 146


title: 3064

description:
MZ twin
SAMPLE 149


title: AML_CK_32


title: 3058

description:
MZ twin
SAMPLE 145


title: 3070

description:
MZ twin
SAMPLE 144


title: 1043

description:
MZ twin
SAMPLE 148


title: 3054

description:
MZ twin
SAMPLE 143


title: AML_CK_10


title: hippocampus_freshfrozen_112


title: 1063

description:
MZ twin
SAMPLE 141


title: hippocampus_freshfrozen_111


title: AML_CK_9


title: AML_CK_8


title: 3066

description:
MZ twin
SAMPLE 140


title: hippocampus_freshfrozen_109


title: 2036

description:
MZ twin
SAMPLE 139


title: AML_CK_7


title: hippocampus_freshfrozen_113


title: hippocampus_freshfrozen_110


title: 3053

description:
MZ twin
SAMPLE 137


title: 1070

description:
MZ twin
SAMPLE 138


title: 3103

description:
MZ twin
SAMPLE 142


title: AML_CK_6


title: hippocampus_freshfrozen_107


title: hippocampus_freshfrozen_108


title: hippocampus_freshfrozen_106


title: 3102

description:
MZ twin
SAMPLE 136


title: 1062

description:
MZ twin
SAMPLE 135


title: 2039

description:
MZ twin
SAMPLE 133


title: AML_CK_5


title: AML_CK_4


title: 2048

description:
MZ twin
SAMPLE 132


title: AML_CK_3


title: 2057

description:
MZ twin
SAMPLE 130


title: 3050

description:
MZ twin
SAMPLE 129


title: hippocampus_freshfrozen_105


title: 3068

description:
MZ twin
SAMPLE 131


title: 3067

description:
MZ twin
SAMPLE 134


title: 1035

description:
MZ twin
SAMPLE 128


title: hippocampus_freshfrozen_123


title: hippocampus_freshfrozen_104


title: AML_CK_2


title: 2071

description:
MZ twin
SAMPLE 126


title: 3046

description:
MZ twin
SAMPLE 127


title: 3069

description:
MZ twin
SAMPLE 125


title: AML_CK_1


title: 2056

description:
MZ twin
SAMPLE 124


title: AML_CBF_24

value: Core binding factor AML, inv(16)


title: hippocampus_freshfrozen_101


title: hippocampus_freshfrozen_103


title: 3049

description:
MZ twin
SAMPLE 123


title: hippocampus_freshfrozen_100


title: 3047

description:
MZ twin
SAMPLE 121


title: 1036

description:
MZ twin
SAMPLE 122


title: AML_CBF_23


title: hippocampus_freshfrozen_102


title: 2050

description:
MZ twin
SAMPLE 120


title: hippocampus_freshfrozen_99


title: 2060

description:
MZ twin
SAMPLE 119


title: AML_CBF_22


title: 3041

description:
MZ twin
SAMPLE 118


title: AML_CBF_20


title: 2053

description:
MZ twin
SAMPLE 117


title: AML_CBF_19


title: AML_CBF_21


title: 1056

description:
MZ twin
SAMPLE 116


title: RSP_2888+pIND5-RSP_2888_Rep3

city: Madison

first: Timothy

middle: J

last: Donohue

state: WI

address: 1552 University Avenue

department: Bacteriology

institute: University of Wisconsin - Madison

description: Gene expression data from ΔRSP_2888 cells overexpressing RSP_2888 from an IPTG inducible plasmid obtained under photosynthetic conditions on SIS

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Microarray datasets were normalized by Robust Multichip Average (RMA) to log2 scale with background adjustment and quantile normalization.  Statistical analysis of normalized data to identify differentially expressed genes was done using the limma package.  Correction for multiple testing was done using Benjamini-Hochberg correction. All analyses were conducted in the R statistical programming environment.

organism: Cereibacter sphaeroides

source_name: ΔRSP_2888 cells overexpressing ΔRSP_2888 from an IPTG inducible plasmid (pIND5) grown photosynthetically on SIS

label_protocol: Synthesized cDNA was labeled with BioArray™ Terminal labeling kit with biotin-ddUTP

growth_protocol: R. sphaeroides strains that were grown in 500 ml cultures in roux bottles photosynthetically (bubbling with 95% N2, 5% CO2) on Sistrom's minimal media (SIS) (or SIS media with succinate replaced with acetate) and harvested at exponential phase. Some cells were grown in the dark under anaerobic respiratory conditions (bubbling with 95% N2, 5% CO2) with pyruvate provided as the main carbon source and DMSO as electron acceptor.

extract_protocol: RNA was extracted from R. sphaeroides cells by hot acid phenol extraction.


title: RSP_2888+pIND5-RSP_2888_Rep2


title: RSP_2888_Rep3

description: Gene expression data from ΔRSP_2888 cells obtained under photosynthetic conditions.

source_name: ΔRSP_2888 deletion cells grown photosynthetically on SIS


title: RSP_2888+pIND5-RSP_2888_Rep1


title: hippocampus_freshfrozen_98


title: hippocampus_freshfrozen_97


title: AML_CBF_17

value: Core binding factor AML, t(8,21)


title: 1065

description:
MZ twin
SAMPLE 115


title: hippocampus_freshfrozen_96


title: RSP_2888_Rep2


title: AML_CBF_18


title: 2049

description:
MZ twin
SAMPLE 114


title: hippocampus_freshfrozen_95


title: AML_CBF_16


title: 2059

description:
MZ twin
SAMPLE 113


title: RSP_2888_Rep1


title: JZ1691+pIND5-RSP_2572_Rep3

description: Gene expression data from JZ1691 (ΔFnrL) cells overexpressing RSP_2572 (CrpK) from an IPTG inducible plasmid obtained under photosynthetic conditions using a growth medium containing acetate as the sole carbon source.

source_name: JZ1691 (ΔFnrL) cells overexpressing RSP_2572 (CrpK) from an IPTG inducible plasmid (pIND5) grown photosynthetically on acetate

value: JZ1691 (ΔFnrL) + pIND5-RSP_2572 (CrpK)


title: hippocampus_freshfrozen_92


title: hippocampus_freshfrozen_94


title: hippocampus_freshfrozen_93


title: AML_CBF_15


title: 3040

description:
MZ twin
SAMPLE 112


title: 1055

description:
MZ twin
SAMPLE 110


title: JZ1691+pIND5-RSP_2572_Rep2


title: AML_CBF_13


title: AML_CBF_14


title: hippocampus_freshfrozen_90


title: 2076

description:
MZ twin
SAMPLE 111


title: hippocampus_freshfrozen_89


title: 1064

description:
MZ twin
SAMPLE 109


title: AML_CBF_10


title: JZ1691+pIND5-RSP_2572_Rep1


title: AML_CBF_11


title: hippocampus_freshfrozen_91


title: 2052

description:
MZ twin
SAMPLE 108


title: AML_CBF_12


title: AML_CBF_8


title: hippocampus_freshfrozen_88


title: JZ1691_Photosynthetic_Acetate_Rep2

description: Gene expression data from JZ1691 (ΔFnrL) cells obtained under photosynthetic conditions using a growth medium containing acetate as the sole carbon source.

source_name: JZ1691 (ΔFnrL) cells grown photosynthetically on acetate

value: JZ1691 (ΔFnrL)


title: AML_CBF_9


title: JZ1691_Photosynthetic_Acetate_Rep1


title: WT_Photosynthetic_Acetate_Rep2

description: Gene expression data from WT cells obtained under photosynthetic conditions using a growth medium containing acetate as the sole carbon source.

source_name: WT cells grown photosynthetically on acetate


title: hippocampus_freshfrozen_85


title: 2104

description:
MZ twin
SAMPLE 107

source_name: genomic DNA extracted and purified


title: 2015

description:
MZ twin
SAMPLE 106


title: AML_CBF_6


title: 1069

description:
MZ twin
SAMPLE 105


title: hippocampus_freshfrozen_87


title: AML_CBF_7


title: AML_CBF_5


title: 2027

description:
MZ twin
SAMPLE 103


title: 3014

description:
MZ twin
SAMPLE 104


title: 2105

description:
MZ twin
SAMPLE 101


title: 2051

description:
MZ twin
SAMPLE 102


title: 2024

description:
MZ twin
SAMPLE 100


title: WT_Photosynthetic_Rep1

description: Gene expression data from WT cells obtained under photosynthetic conditions.

source_name: WT cells grown photosynthetically on SIS


title: WT_DMSO_Rep2

description: Gene expression data from WT cells grown under anaerobic respiratory conditions with DMSO as the terminal electron acceptor and using pyruvate as the main carbon source


title: PrrA3_DMSO_Rep2

description: Gene expression data from PrrA3 cells grown under anaerobic respiratory conditions with DMSO as the terminal electron acceptor and using pyruvate as the main carbon source

source_name: ΔPrrA (PrrA3) cells grown under anaerobic respiratory conditions with DMSO as the terminal electron acceptor


title: PrrA3_DMSO_Rep1


title: WT_DMSO_Rep1

source_name: WT cells grown under anaerobic respiratory conditions with DMSO as the terminal electron acceptor


title: WT_Photosynthetic_Rep3


title: AML_CBF_4


title: hippocampus_freshfrozen_83


title: 2034

description:
MZ twin
SAMPLE 99


title: WT_Photosynthetic_Rep2


title: hippocampus_freshfrozen_81


title: hippocampus_freshfrozen_84


title: hippocampus_freshfrozen_82


title: Placenta_HighDose(biolrepl2)_LowDose(biolrepl2)

city: Rome

first: Sabrina

last: Tait

state: Italy

address: Viale Regina Elena 299

department: Dpt. Infectious Diseases

country: Italy

institute: Istituto Superiore di Sanità

hyb_protocol: Cy3 and Cy5 labelled samples, to be hybridized on same slides, were mixed and added with Agilent Fragmentation Buffer following manufaturer's instructions. Following 30 min incubation at 60 °C, Agilent GEx Hybridization Buffer was added, volumes loaded on gasket slides into the Agilent SureHyb chamber, array slides placed over and chamber closed. Arrays were incubated for 17h at 65°C with a 10rpm rotation in an Agilent hybridization oven. Arrays were then washed with Agilent Gene Expression Buffers 1 and 2.

scan_protocol: Scanned on an Agilent G2505B Microarray Scanner System. Data extraction and array quality control were performed through the Agilent Feature Extraction Software v9.5.

data_processing: The limma package, part of Bioconductor within the R environment, was used for background subtraction, Global Loess normalization, Aquantile between-arrays normalization, dye-effects and array quality weights evaluation.

source_name: Placenta, BPA 50 mg/kg treat, biolrepl2

label_protocol: cDNA and cRNA synthesis, amplification and labelling was performed using the Quick Amp Labelling Kit, Two Colors (Agilent), with spike-in internal controls (Agilent) following manufacturer’s instructions, with 1 µg of total RNA as input

growth_protocol: CD1 female mice were kept under standard laboratory conditions (22 ± 0.5 °C, 50–60% relative humidity, 12 h dark–light alternation with 12–14 air changes/h) with water and food available ad libitum. After 1 week of acclimatization, females were bred with CD sires of proven fertility. A sperm-positive vaginal smear served to define the Gestational day (GD) 0.

extract_protocol: Placenta samples were mechanically disrupted with an homogenizer in Lysis Buffer from RNAeasy Mini Kit (QIAGEN) then total RNA was extracted according to manufacturer's protocol

treatment_protocol: Pregnant mice were treated daily p.o. by gavage with 0 (vehicle only = olive oil), 0.5 or 50 mg/kg bw pro die of BPA dissolved in olive oil, from GD1 to GD11

tag: gender

value: placenta

tag: gestation day

source_name: Placenta, BPA 0.5 mg/kg treat, biolrepl2


title: hippocampus_freshfrozen_75


title: hippocampus_freshfrozen_76


title: hippocampus_freshfrozen_86


title: Placenta_LowDose(biolrepl2)_HighDose(biolrepl4)

source_name: Placenta, BPA 50 mg/kg treat, biolrepl4


title: Placenta_HighDose(biolrepl3)_LowDose(biolrepl3)

source_name: Placenta, BPA 50 mg/kg treat, biolrepl3

source_name: Placenta, BPA 0.5 mg/kg treat, biolrepl3


title: AML_CBF_2

source_name: bone marrow

tag: cell type


title: hippocampus_freshfrozen_77

source_name: hippocampal formation


title: Placenta_LowDose(biolrepl4)_HighDose(biolrepl3)

source_name: Placenta, BPA 0.5 mg/kg treat, biolrepl4


title: Placenta_LowDose(biolrepl3)_Ctrl(biolrepl3)

source_name: Placenta, vehicle treatment, biolrepl3


title: 3015

description:
MZ twin
SAMPLE 98


title: 1044

description:
MZ twin
SAMPLE 97


title: AML_CBF_3

source_name: peripheral blood


title: Placenta_HighDose(biolrepl4)_LowDose(biolrepl4)


title: WT_Photosynthetic_Acetate_Rep1


title: Placenta_Ctrl(biolrepl3)_HighDose(biolrepl2)


title: XP 3

city: Newcastle upon Tyne

first: Maya

last: Sieber-Blum

address: Centre for Life

department: Institute of Genetic Medicine

country: United Kingdom

institute: Newcastle University

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Scanning was performed on Illumina iScan

data_processing: Data was normalised using quantile normalisation in Illumina GenomeStudio software. Data was expressed as the logarithm of the average signal intensity of the three replicates of each sample. Corrected p values were obtained with Bonferroni correction. XP group was used as the reference group throughout the experiment.

source_name: ex vivo expanded hEPI-NCSC

label_protocol: RNA labelling was performed using the Ambion Total Prep-TM 96 kit and according to the manufacturer specifications.

growth_protocol: hEPI-NCSC (XP sample): see Clewes O et al, 2011. Schwann cells, unpublished data

extract_protocol: 1.8 million cells (“XP” sample) and 3 million cells (“Schwann” sample) were homogenised using Precellys 24 tissue homogenizer in 600μl Buffer RLT Plus (Qiagen) containing 0.5% (v/v) Reagent DX (Qiagen). RNA was extraction was performed using an AllPrep DNA/RNA/miRNA Universal Kit on a QIAcube platform (Qiagen) and eluted in 30μl RNase free water. RNA purity was determined using an Agilent 2100 Bioanalyser(RIN values: “XP” sample sample 9.9; “Schwann” sample 10.0).

treatment_protocol: Clewes o et a, 2011; and unpublished data

value: hEPI-NCSC


title: 3039

description:
MZ twin
SAMPLE 94


title: 2016

description:
MZ twin
SAMPLE 96


title: hippocampus_freshfrozen_78


title: hippocampus_freshfrozen_80


title: 3011

description:
MZ twin
SAMPLE 95


title: XP 2


title: hippocampus_freshfrozen_73


title: Placenta_Ctrl(biolrepl2)_HighDose(biolrepl1)

source_name: Placenta, vehicle treatment, biolrepl2

source_name: Placenta, BPA 50 mg/kg treat, biolrepl1


title: 2047

description:
MZ twin
SAMPLE 93

source_name: genomic DNA extracted and purified


title: hippocampus_freshfrozen_79


title: XP 1


title: hippocampus_freshfrozen_71


title: 2058

description:
MZ twin
SAMPLE 92


title: 2090

description:
MZ twin
SAMPLE 91


title: hippocampus_freshfrozen_72


title: hippocampus_freshfrozen_70


title: Placenta_LowDose(biolrepl1)_Ctrl(biolrepl1)

source_name: Placenta, BPA 0.5 mg/kg treat, biolrepl1

source_name: Placenta, vehicle treatment, biolrepl1


title: hippocampus_freshfrozen_74


title: Placenta_HighDose(biolrepl1)_Ctrl(biolrepl2)


title: 2017

description:
MZ twin
SAMPLE 90


title: Placenta_Ctrl(biolrepl1)_LowDose(biolrepl1)


title: 1012

description:
MZ twin
SAMPLE 89


title: 3038

description:
MZ twin
SAMPLE 88


title: Schwann 2

source_name: Schwann cells that were differentiated from hEPI-NCSC

value: Schwann cells


title: Schwann 1


title: 2046

description:
MZ twin
SAMPLE 87


title: Schwann 3


title: 2064

description:
MZ twin
SAMPLE 86


title: 2089

description:
MZ twin
SAMPLE 85


title: MCF7_MT1_3DCol_48h

city: Liège

first: Erik

last: Maquoi

address: Tour de Pathologie, B23 Sart-Tilman

country: Belgium

institute: University of Liège

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was preprocessed by Bioconductor lumi package. It was VST transformed and quantile normalized (log2 values are shown)

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPre-96 RNA Amplification Kit for Illumina arrays

growth_protocol: Cells were passaged in DMEM medium (Invitrogen) supplemented with heat-inactivated fetal bovine serum (Invitrogen), 2mM L-glutamine (Invitrogen) and penicillin-streptomycin (Invitrogen). Cells were routinely cultured in 37°C with 5% CO2. For the monolayer cultures, cells were seeded in 12-well plates, 20000 cells/well, in 1 ml of medium supplemented with 5.5% serum. For the 3D environment, cells were suspended in neutralized native rat tail type I collagen gels, 200000 cells/800 µl gel in 12-well plates and incubated 30 min at 37°C to allow polymerization of the collagen fibers. After polymerization, 1 ml of medium supplemented with 10% serum was added to each well, resulting in a final serum concentration of 5.5%. The culture medium was refreshed after 48 hours and cells were allowed to grow for 24, 48 and 72 hours. Four independent replicates were prepared for each treatment-time combination.

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

treatment_protocol: MCF-7 cells were stably transfected with either an empty pcDNA3.1/Zeo expression vector (Invitrogen) or human MMP-14 cDNA subcloned in pcDNA3.1/Zeo.

value: MCF-7 human breast adenocarcinoma cell line

tag: transfection

tag: culture condition

value: 3D type I collagen gel

tag: time (culture duration)

value: 48 hours


title: hippocampus_freshfrozen_68


title: 3075

description:
MZ twin
SAMPLE 84

tag: birth-weight

tag: pair id


title: MCF7_MT1_3DCol_72h

description: replicate 1

tag: cell line

value: 72 hours


title: MCF7_MT1_3DCol_24h

description: replicate 1

value: 24 hours


title: hippocampus_freshfrozen_69

tag: tissue


title: AML_CBF_1

value: Acute myeloid leukemia diagnostic sample


title: hippocampus_freshfrozen_67


title: 2130

description:
MZ twin
SAMPLE 83

value: whole blood


title: HGFs HEMA 96h (H) vs HGFs control 96h (G) technical replicate

city: Chieti

first: Valentina

last: Gatta

state: Abruzzo

address: Via Colle Dell'Ara

department: Department of Psychological SciencesDepartment of Psychological Sciences

institute: University G.d'Annunzio

description: Experiment 5 technical replicate

hyb_protocol: 2 µg of respectively Cy3-Cy5 labeled aRNA, from each treated cell culture and control culture, were fragmented and then hybridized on a Phalanx Human OneArray™  using 1.5X OneArray hybridization Buffer at 42°C in oven for 14-16 hrs.

scan_protocol: After hybridization, Cy3-Cy5 fluorescent signals were captured by a Confocal Laser Scanner ScanArray Express (Perkin Elmer, Waltham, MA, USA) and analysed using the software ScanArray Express - MicroArray Analysis System version 3.0 (Perkin Elmer, Waltham, MA, USA). The values of the median signal intensity from each spot were subtracted from the local median background intensity. For each slide after local background subtraction, a LOWESS algorithm was used for row data normalization to evaluate signal to noise ratio and generate log ratios of sample vs. reference signal.

data_processing: A gene was considered to be significantly expressed when showing an absolute value of log-ratio higher or equal to 0.5, an index that translates to a fold-change > 0.7 or < 1.4 in transcript quantity, a present call in at least the 75% of experiments and a p-Value <0.05. Probes from the platform GPL13693 were manually matched to probes from the platform GPL6254. In the analysis were excluded probes spotted only in GPL13693. The resulting gene lists underwent a clustering analysis (Cluster 3.0 and TreeView, Stanford University Labs) to unravel Genes Differentially Expressed (DEGs). Identified DEGs were, then, analysed by Ingenuity Pathways Analysis (IPA) software (Ingenuity Systems, Redwood City, CA, USA) to disclose the biological functions and the functional networks they are involved in.

source_name: cultured HGFs treated with 3mM HEMA for 96h (H)

label_protocol: Extracted RNA was linearly amplified using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Austin, TX, USA), following the 2 rounds amplification protocol. 10 to 20 µg of amplified aRNA were fluorescently labeled with Cy3 or Cy5 cyanins.

extract_protocol: After HEMA incubation, cells were trypsinized. Pellets (about 7∙106 cells/pellet) were washed with 1 ml of PBS and centrifuged at1,200 rpm for 5 min at 4°C three times.

value: HGFs obtained from fragments of healthy marginal gingival tissue from the retromolar area taken during surgical extraction of impacted third molars

value: male

source_name: cultured HGFs without HEMA harvested at 96 h (G)


title: 2121

description:
MZ twin
SAMPLE 82


title: hippocampus_freshfrozen_66

value: hippocampal formation

value: epilepsy


title: hippocampus_freshfrozen_65


title: 3111

description:
MZ twin
SAMPLE 81


title: hippocampus_freshfrozen_61


title: hippocampus_freshfrozen_63


title: MCF7_MT1_plastic_24h

description: replicate 1

value: monolayer on plastic


title: MCF7_CTRL_plastic_72h

description: replicate 1

value: pcDNA3.1/Zeo (control)


title: hippocampus_freshfrozen_62


title: MCF7_MT1_plastic_72h

description: replicate 1


title: 2031

description:
MZ twin
SAMPLE 80


title: HGFs HEMA 24h (B) vs HGFs control 24h (A) technical replicate

description: Experiment 1 technical replicate

source_name: cultured HGFs treated with 3mM HEMA for 24h (B)

source_name: cultured HGFs without HEMA harvested at 24 h (A)


title: hippocampus_freshfrozen_64


title: MCF7_CTRL_3DCol_24h

description: replicate 1


title: MCF7_CTRL_plastic_48h

description: replicate 1


title: MCF7_CTRL_plastic_24h

description: replicate 1


title: MCF7_MT1_plastic_48h

description: replicate 1


title: hippocampus_freshfrozen_58


title: MCF7_CTRL_3DCol_48h

description: replicate 1


title: hippocampus_freshfrozen_60


title: hippocampus_freshfrozen_59


title: 1033

description:
MZ twin
SAMPLE 79


title: hippocampus_freshfrozen_57


title: 3074

description:
MZ twin
SAMPLE 78


title: 2120

description:
MZ twin
SAMPLE 76


title: 2131

description:
MZ twin
SAMPLE 77


title: 3073

description:
MZ twin
SAMPLE 75


title: INF Tat2

city: Pune

first: Debashis

last: Mitra

state: Maharashtra

address: Ganeshkhind

country: India

institute: National Centre for Cell Science

description: INF Tat2_IP3 (Cy5) vs.WCE (Cy3)

hyb_protocol: 5 μg of each Cy-labeled samples were hybridized onto the human promoter 244K ChIP-on-chip Array. Hybridization was performed in the hybridization oven at 65°C for 40 hours, followed by washes with ChIP-on-chip Wash buffer 1 and 2 (Agilent, USA).

scan_protocol: The washed slides were scanned at 5 μm scan resolution using Agilent DNA microarray scanner as per Agilent Protocol.

data_processing: Data extraction done using Agilent Feature extraction software and normalized Using Agilent DNA Analytics software.

source_name: Input DNA from HIV-1 NL4-3 infected CEM-GFP cells

label_protocol: The DNA samples were blunted at 12°C for 20 minutes using T4 DNA polymerase as per the Mammalian Chip on Chip Protocol of Agilent Technologies.The blunted DNA was cleaned, precipitated and resuspended in water. Each sample was labeled using Agilent Genomic DNA Labeling Kit PLUS (5188-5309) with Cy3 or Cy5 dUTP. DNA yield and incorporation of label (specific activity) was measured using NanoDrop spectrophotometer.

growth_protocol: Infected CEM-GFP cells were maintained in RPMI with 10% fetal calf serum

extract_protocol: HIV-1 NL4.3-infected Day7 CEM-GFP cells (10E7) were cross-linked using 1% formaldehyde for 10 min at room temperature followed by quenching with 125 mM glycine for 5 min. The fixed cells were then sequentially washed twice with ice-cold PBS, once with wash buffer 1 {0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM HEPES pH 7.5, 1 mM PMSF, 10 mM sodium butyrate and 2X protease inhibitor cocktail (Roche)} and then using wash buffer 2 (0.2 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM HEPES pH 7.5, 1 mM PMSF, 10 mM sodium butyrate and 2X protease inhibitor cocktail). The washed pellet was then lysed in 500 μl of lysis buffer (150 mM NaCl, 25 mM Tris-HCl pH 7.5, 5 mM EDTA pH 8.0, 1% Triton X- 100, 0.1% SDS, 0.5% sodium deoxycholate, 1 mM PMSF, 10 mM sodium butyrate, 2X protease inhibitor cocktail), followed by sonication to shear the chromatin using Bioruptor (Diagenode, Europe). The lysates were centrifuged at 13,000 rpm for 10 min at 4°C to remove cell debris. Chromatin was estimated using NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific, USA). 100 μg of chromatin was taken and diluted in dilution buffer {0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl (pH 8.1), 167 mM NaCl) which was then pre-cleared by incubation with Protein A/G beads (Pierce, USA), salmon sperm DNA (Sigma, USA) and BSA (New England Biolabs, USA) followed by centrifugation. 10% of the precleared lysate was used as input. Rest 90% of the supernatant was used for immunoprecipitation with purified anti-Tat antibody or isotype-matched irrelevant antibody (GST antibody) as negative control. The chromatin antibody complex was immobilized on Protein A/G beads for 2 hours at 4°C followed by three washes each with RIPA wash buffer (0.1% SDS, 1% sodium deoxycholate, 150 mM NaCl, 10 mM sodium phosphate, pH 7.2, 2 mM EDTA, 1% IGEPAL) and TE (10 mM Tris HCl; pH 8.0, 1 mM EDTA). Immune complexes were then eluted in 100 μl of 2% SDS, 0.1 M NaHCO3 and 10 mM DTT. DNA was extracted after reverse crosslinking, proteinase K treatment and phenol chloroform extraction.

treatment_protocol: CEM-GFP cells were infected with HIV-1 NL4-3 at an MOI of 0.1 and harvested at day 7 post infection

value: CEM-GFP

value: T cell line

tag: hiv-1 infection stage

value: Day 7 post infection

tag: antibody

source_name: Tat ChIP DNA from HIV-1 NL4-3 Infected CEM-GFP cells

value: IgG purified from HIV-1_BH10 Tat antiserum raised in rabbit

tag: catalog number

tag: manufacturer

value: AIDS Research and Reference Reagent program (NIH)

tag: lot/ batch no.


title: 1034

description:
MZ twin
SAMPLE 73


title: 3045

description:
MZ twin
SAMPLE 74


title: 3037

description:
MZ twin
SAMPLE 71