title: LSIL_patient #8

source_name: Low-grade intraepithelial lesion RNA from patient #8


title: LSIL_patient #5

status: Public on Aug 01 2010

type: RNA

city: Aveiro

first: Patrícia

middle: Matos

last: Pereira

address: Campus Universitário de Santiago

department: Biology

country: Portugal

institute: University of Aveiro

hyb_protocol: PREHYBRIDIZATION:  1. Make 100 ml prehybridization buffer (for a maximum of 4 slides) containing 1M Tris-HCL pH=9 pre-heated at 50ºC, 100mM ethanolamide and 0.1% SDS.   2. Heat the prehybridization solution to 50 ºC in a 100 ml Coplin Jar.   3. Place slides to be analyzed into the pre-heated pre-hybridization buffer. Incubate for 20 minutes at 50 ºC with constant agitation, if possible.   4. Wash thoroughly by inverting or gently shaking the container with nuclease-free water constantly for 1 minute. Decant the water and repeat this rising step with fresh nuclease-free water.  5. Allow the slides to dry by centrifuging 3 minute 800 rpm. Slides should be used immediately following prehybridization.     HYBRIDIZATION:   Pre-heat 3x hybridization solution (Ambion) to 65 ºC for at least 5 min to overcome SDS precipitation. Combine target (moDC 0h- and 16h-post LPS stimulation labelled RNA) with hybridization buffer (preheated to 65 ºC). Heat at 95 ºC for 3 minutes. Immediately put on ice for at least 1 min. Spin-down briefly. Add 4x blocking reagent (Kreatech). Incubate on dark for 1 minute at room temperature.     Using Agilent gasket slides (G2534-60003), Agilent SureHyb hybridization chambers (G2534A) and hybridization oven (G2545A), see Agilent User Manual for instructions:   1. For each array, put a gasket slide onto a SureHyb chamber and add a total of 250 ul target as 1 dot in the center of the chamber.   2. Put a microarray slide on the gasket slide by holding it in place with your fingertips, towards the top edge of the gasket chamber.   3. Gently (!) allow the microarray slide to drop onto the gasket chamber by lowering it with the aid of your other hand. Do not move the microarray slide after it is in place.   4. Place the SureHyb chamber into the hybridization oven at 42 ºC for 16 hours.

scan_protocol: Scanning of slides using the Agilent G2565AA DNA microarray scanner:  Resolution: 10 um   Red laser PMT= 100%, Green laser PMT= 100%

data_processing: Pre-processing of the data was performed using BRB-ArrayTools v3.4.0 software. Manually flagged bad spots were eliminated and the local background was subtracted, followed by the averaging of replicate features on the array. Data points were removed when intensities values for both dyes were below 200% of background.  Feature extraction was performed with QuantArray v3.0 software, using the adaptative circle method for measuring the Median signal intensity and Median background intensity.For background calculations were considered the 5-20 percentile of least intense pixels and for signal calculations the 80-95 percentile of most intense pixels. The feature extraction grid was adjusted manually and visually bad spots were flagged using the software flag tool.  A global median normalization of microarray data was applied and log2 intensity ratios (M values) were obtained.

molecule: total RNA

organism: Homo sapiens

source_name: Commercial normal cervix RNA pool

label_protocol: Total RNA was labelled using the miRacULS II miRNA labelling kit (Kreatech) according manufacture’s instructions. Briefly, 3 µg of total RNA from test and reference (pool of 4 First Choice Human Cervix RNAs, Ambion) samples were incubated with Cy5- and Cy3-ULS, respectively for 15 min at 85ºC. The labelled RNAs were purified to remove non-reacted Cy-ULS. Dye incorporation was monitored by UV-visible spectroscopy.

extract_protocol: Total RNA was extracted using the miRVanaTM miRNA isolation kit (Ambion). Briefly, tissues were disrupted in lysis solution using a homogeneizer and miRNA homogenate additive added. An acid phenol:chloroform extraction was then performed followed by a filter cartridge purification.RNA quantity and quality was assessed using the Nanodrop and Agilent 2100 bioanalyzer systems, respectively. Samples with a RIN number above 7 were used in the study.

tag: hpv status

value: no specified

tag: cin and tumour stage

value: Normal cervix

source_name: Low-grade intraepithelial lesion RNA from patient #5

value: positive

value: CINI


title: control drug-treated kidneys vs. HDACi-treated kidneys  Replicate 2

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: LA

address: 1430 Tulane Ave

department: Pediatrics

country: USA

institute: Tulane University School of Medicine

description: Biological replicate 2 of 3- swap. Control drug-treated  E13.5 kidneys(Nullscript 2.0 μg/ml x 6hrs) Vs. HDACi-treated E13.5 kidneys (Scriptaid 2.0 μg/ml x 6hrs)

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples (100µl per microarray slot) were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Agilent Technologies Scanner G2505B US22502611.

data_processing: Images were quantified by Agilent Feature Extraction Software (protocol GE1‐v5_95_Feb 97 and Grid: 014868_D_20060807).

organism: Mus musculus

source_name: Mouse embryonic kidneys (E13.5), treated with Scriptaid (2.0 μg/ml)  for 6 hours

label_protocol: Fluorescently labeled cRNA (Cy5) was generated from 1.0 μg of total RNA, and purified by the RNeasy Mini Kit (Qiagen, Valencia, CA).

growth_protocol: Embryonic kidneys were aseptically microdissected from timed-pregnant CD1 mice at E13.5 and were cultured on polycarbonate transwell filters (0.4µm pore size, Corning Costar, Acton, MA) over medium (DMEM/F12 medium + 10% FBS (Invitrogen)), at 37°C and 5% CO2.

extract_protocol: Total RNA was isolated from kidney rudiments using RNAqueous-96 Automated Kit (Ambion, Austin, TX)

treatment_protocol: Paired metanephroi were treated with the HDACi (Scriptaid 2.0 μg/ml) or control drug (Nullscript 2.0 μg/ml) for 6 hours.

tag: age

tag: tissue

value: kidneys

tag: strain

value: CD1 mice

source_name: Mouse embryonic kidneys (E13.5), treated with Nullscript (2.0 μg/ml)  for 6 hours

label_protocol: Fluorescently labeled cRNA (Cy3) was generated from 1.0 μg of total RNA, and purified by the RNeasy Mini Kit (Qiagen, Valencia, CA).


title: HDACi-treated kidneys vs. control drug-treated kidneys  Replicate 2

description: Biological replicate 2 of 3. HDACi-treated E13.5 kidneys (Scriptaid 2.0 μg/ml x 6hrs)  Vs. Control drug-treated  E13.5 kidneys(Nullscript 2.0 μg/ml x 6hrs)


title: HDACi-treated kidneys vs. control drug-treated kidneys  Replicate 3

description: Biological replicate 3 of 3. HDACi-treated E13.5 kidneys (Scriptaid 2.0 μg/ml x 6hrs)  Vs. Control drug-treated  E13.5 kidneys(Nullscript 2.0 μg/ml x 6hrs)


title: HDACi-treated kidneys vs. control drug-treated kidneys  Replicate 1

description: Biological replicate 1 of 3. HDACi-treated E13.5 kidneys (Scriptaid 2.0 μg/ml x 6hrs)  Vs. Control drug-treated  E13.5 kidneys(Nullscript 2.0 μg/ml x 6hrs)


title: LSIL_patient #1

source_name: Low-grade intraepithelial lesion RNA from patient #1


title: LSIL_patient #3

source_name: Low-grade intraepithelial lesion RNA from patient #3


title: control drug-treated kidneys vs. HDACi-treated kidneys  Replicate 3

description: Biological replicate 3 of 3- swap. Control drug-treated  E13.5 kidneys(Nullscript 2.0 μg/ml x 6hrs) Vs. HDACi-treated E13.5 kidneys (Scriptaid 2.0 μg/ml x 6hrs)


title: control drug-treated kidneys vs. HDACi-treated kidneys  Replicate 1

description: Biological replicate 1 of 3- swap. Control drug-treated  E13.5 kidneys(Nullscript 2.0 μg/ml x 6hrs) Vs. HDACi-treated E13.5 kidneys (Scriptaid 2.0 μg/ml x 6hrs)


title: SCC_patient #19

source_name: Squamous cervical carcinoma RNA from patient #19


title: SCC_patient #22

source_name: Squamous cervical carcinoma RNA from patient #22


title: Pool normal cervix_#2

source_name: Pool RNA of equal amounts of each adjacent normal cervix RNA extracted from all patients

value: negative


title: SCC_patient #25

source_name: Squamous cervical carcinoma RNA from patient #25

value: IIB


title: Pool normal cervix_#1


title: SCC_patient #13

source_name: Squamous cervical carcinoma RNA from patient #13


title: Pool normal cervix_#3


title: normal cervix_patient #24

source_name: Adjacent normal cervix RNA from patient #24


title: normal cervix_patient #23

source_name: Adjacent normal cervix RNA from patient #23


title: normal cervix_patient #3

source_name: Adjacent normal cervix RNA from patient #3


title: normal cervix_patient #21

source_name: Adjacent normal cervix RNA from patient #21


title: Pool normal cervix_#4


title: normal cervix_patient #17

source_name: Adjacent normal cervix RNA from patient #17


title: normal cervix_patient #10

source_name: Adjacent normal cervix RNA from patient #10


title: normal cervix_patient #20

source_name: Commercial normal cervix RNA pool

source_name: Adjacent normal cervix RNA from patient #20


title: normal cervix_patient #15

source_name: Adjacent normal cervix RNA from patient #15


title: normal cervix_patient #18

source_name: Adjacent normal cervix RNA from patient #18


title: 0mM t60g_t0r

status: Public on Nov 01 2010

city: Wageningen

first: Clint

last: van Melis

address: Bomenweg 2

department: Agro- & Food Science Group

country: Netherlands

institute: Wageningen University and Research centre

description: No extra description

hyb_protocol: The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 200ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, according to the Agilent protocol at 50% laser intensity, and 10 micron scan resolution.

data_processing: Lowess-normalization, performed in Feature Extract, Agilent. Subsequently normalized data was processed with the Vampire webbased microarray suite.

organism: Bacillus cereus ATCC 14579

label_protocol: Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.

extract_protocol: RNA was extracted as described by van Schaik et al., 2007

treatment_protocol: Dormant spores germinated under in buffered BHI (100mM, pH5.5) containing 0mM undissociated sorbic acid. Sample was taken after 60 minutes.

value: Bc ATCC 14579

treatment_protocol: Dormant spores were used as t0 samples


title: normal cervix_patient #19

source_name: Adjacent normal cervix RNA from patient #19


title: normal cervix_patient #2

source_name: Adjacent normal cervix RNA from patient #2


title: normal cervix_patient #1

source_name: Adjacent normal cervix RNA from patient #1


title: normal cervix_patient #9

source_name: Adjacent normal cervix RNA from patient #9


title: normal cervix_patient #6

source_name: Adjacent normal cervix RNA from patient #6


title: normal cervix_patient #5

source_name: Adjacent normal cervix RNA from patient #5


title: normal cervix_patient #8

source_name: Adjacent normal cervix RNA from patient #8


title: Pt4523 (Expression)

status: Public on Jul 31 2010

city: Bronx

last: Parekh

state: NY

address: 1300 Morris Park Ave

department: Cancer center

institute: Albert Einstein College of Medicine

hyb_protocol: Followed standard Affymetrix protocols

scan_protocol: Followed standard Affymetrix protocols

data_processing: The samples in the analysis were analyzed  on two different Affymetrix GeneChip  platforms, Human Genome U133A 2.0 (11 samples) and  Human Genome U133 Plus 2.0 (5 samples).  To facilitate cross-comparison, CEL files from each platform were imported into Partek Genomics Suite and a mixed model ANOVA was used to estimate the batch effect due to the different platforms and correct the normalized data for this effect.  The samples in the analysis were analyzed  on two different Affymetrix platforms, Platform 1 (12 samples) and Platform 2 (5 samples).  To facilitate cross-comparison, CEL files from each platform were imported into Partek Genomics Suite and a mixed model ANOVA was used to estimate the batch effect due to the different platforms and correct the normalized data for this effect.

label: biotin

source_name: magnetic bead purified CD19+ fractions from blood from Patient newly diagnosed with MCL.  Sample was collected  before treatment.

label_protocol: Followed standard Affymetrix protocols

extract_protocol: RNeasy Protect Kits (Qiagen) were used according to the manufacturer's instructions.

tag: cell line

tag: sample type


title: normal cervix_patient #11

source_name: Adjacent normal cervix RNA from patient #11


title: normal cervix_patient #12

source_name: Adjacent normal cervix RNA from patient #12


title: normal cervix_patient #13

source_name: Adjacent normal cervix RNA from patient #13


title: Pt4458 (Expression)

value: magnetic bead purified CD19+ fractions from blood from Patient newly diagnosed with MCL


title: Pt3073 (Expression)


title: Pt4530 (Expression)


title: MCL-13 (Methylation)

type: genomic

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ,Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details.

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as  “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background.PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding  windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.)

molecule: genomic DNA

source_name: Whole blood without selection from Patient with leukemic phase MCL, before treatment

label_protocol: Random 9-mers pre-labeled with either Cy5 or Cy3

extract_protocol: Genomic DNA from blood was isolated using Puregene Cell and Tissue Kit according to the manufacturer instructions (Qiagene). Genomic DNA from RNeasy (Qiagen) flow-through was first precipitated with Ethanol, then purified following proteinase K digestion and standard phenol/choloroform extraction protocol.  Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55).

tag: restriction enzyme

value: MspI representation of genomic DNA

source_name: Whole blood without selection from patient with leukemic phase MCL.  Sample was collected  before treatment.

value: HpaII representation of genomic DNA


title: MCL-9 (Methylation)

description: Genomic DNA from blood was isolated using Puregene Cell and Tissue Kit

value: Whole blood without selection from Patient with leukemic phase MCL, before treatment

value: Whole blood without selection from patient with leukemic phase MCL


title: Pt4040 (Expression)


title: MCL-10 (Methylation)


title: MCL-12 (Methylation)


title: MCL-15 (Methylation)


title: MCL-16 (Methylation)


title: MCL-11 (Methylation)


title: MCL-8 (Methylation)


title: testis-wildtype#2-rep2

status: Public on Sep 30 2010

city: Vancouver

first: Steven

last: McKinney

state: BC

address: 675 West 10th Ave

department: Molecular Oncology

country: Canada

institute: British Columbia Cancer Agency

description: RMA expression value derived from ArrayAssist version 5.0 software; core+extended gene level analysis

hyb_protocol: Labelled RNA was probed on GeneChip Mouse Exon Array 1.0 ST chips (Affymetrix, Santa Clara, California) for gene expression analysis and scanned at the CTAG Facility of the British Columbia Cancer Agency, Vancouver, BC, Canada.

scan_protocol: Array scanning was performed according to the manufacturer's instructions (Affymetrix).

data_processing:
CEL files were processed using ArrayAssist 5.0. Raw intensity calls were normalized using quantile normalization (Bolstad, 2003) and probeset summarization undertaken with gc-rma (Wu, 2004). In this analysis we considered only transcript level summarization for the core plus extended set of probes on the array (about 800,000 probesets). Outliers with greater than 2.0 fold change between genotypes and level of significance, p < 0.05 were selected for further analysis by quantitative PCR (Q-PCR).
ArrayAssist results (Gene and Exon) are available on the series record. Affynetrix Command Console normalized data are presented in the sample tables.

source_name: whole testes

label_protocol: Samples with a resulting total RNA of 1 µg or greater and with a RNA integrity number (RIN) of 7.0 or greater were used and the whole transcript sense target labeling procedure followed the Affymetrix protocol, including the RiboMinus™ rRNA removal step. Three biological replicates were compared for each of the genotypes (wild type and homozygous Mll5-/-) for a total of six experiments.

growth_protocol: Testes from freshly euthanized adult male mice (strain 129S6 (129SvEv)) were flash frozen and stored at -80 °C.

extract_protocol: Total RNA was isolated from three frozen wild type and age-matched homozygous Mll5-/- testes using QIAzol™ lysis reagent (Qiagen, Maryland, USA). The tissues were homogenized in 800 µL QIAzol and transferred to Phase Lock Gel tubes (2 mL, heavy) (Eppendorf AG, Hamburg, Germany) to which 200 µL chloroform was added. Samples were centrifuged and the aqueous phase was removed and transferred to a new tube with an equal volume of isopropanol. After centrifugation, the supernatant was removed from the precipitated RNA pellets, and the pellets were washed with 70% ethanol. The air-dried RNA was dissolved in RNase/DNase free water and stored frozen at -80 °C. Total RNA samples were analyzed on a NanoDrop (Thermo Fisher Scientific, Waltham, MA) spectrophotometer to determine RNA quality and concentration. One µL of the RNA (was adjusted within a range of 25-500 ng/µL) was analyzed on the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) using the RNA 6000 Nano kit.

tag: gender

value: Male

value: whole testes

tag: genome/variation

value: wildtype


title: testis-wildtype#3-rep3


title: MCL-6 (Methylation)


title: MCL-5 (Methylation)


title: testis-Mll5KO#1-rep1


title: testis-Mll5KO#2-rep2


title: MCL-4 (Methylation)


title: MCL-7 (Methylation)


title: testis-Mll5KO#3-rep3


title: MCL-1 (Methylation)


title: testis-wildtype#1-rep1


title: Pt4040 (Methylation)

description: Genomic DNA was pruified from RNeasy (Qiagen) flow-through by standard phenol/Chloroform extraction protocol

source_name: magnetic bead purified CD19+ fractions from blood from Patient diagnosed with MCL before treatment

source_name: magnetic bead purified CD19+ fractions from apheresis product from patient diagnosed with MCL. Sample was collected  before treatment.


title: Pt4458 (Methylation)

value: magnetic bead purified CD19+ fractions from blood from Patient diagnosed with MCL before treatment

value: magnetic bead purified CD19+ fractions from apheresis product from patient diagnosed with MCL


title: MCL-2 (Methylation)


title: Pt4523 (Methylation)


title: Pt2788 (Methylation)

source_name: magnetic bead purified CD19+ fractions from apheresis product from Patient diagnosed with MCL before treatment


title: Pt3073 (Methylation)


title: Pt4530 (Methylation)


title: Pt2909 (Methylation)


title: Z138 (Methylation)

source_name: MCL cell line

value: MCL cell line


title: SP-53 (Methylation)


title: SP49 (Methylation)


title: Mino (Methylation)

value: MINO


title: Cardiac Muscle_Cmah KO_mdx_rep3

city: Columbus

first: Paul

middle: T

last: Martin

state: OH

address: 700 Children's Drive

institute: Columbus Children's Research Institute

description:
Gene expression data from cardiac muscle of two-month-old mouse deficient in Neu5Gc sialic acid and dystrophin.
7 Cmah KO mdx Heart

hyb_protocol: For each array, 2.2 µg of fragmented and labeled cDNA was hybridized onto 430 2.0 GeneChips® (Affymetrix Inc., USA), for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA).

data_processing: CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA) and probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene). Differential gene expression was determined by pair-wise comparisons.

label: Biotin

source_name: Heart, Cmah KO, mdx, 2 months old

label_protocol: The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from 25 ng of total RNA following manufacturer’s instructions.

growth_protocol: All mice were maintained in the institute animal facility following the IACUC guidelines.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by further purification on a silica-gel-based membrane (RNeasy-Mini; Qiagen, Valencia, CA).

tag: genotype

value: Cmah KO, mdx

value: male

value: 2 months

value: cardiac muscle


title: Pt2677 (Methylation)

value: magnetic bead purified CD19+ fractions from apheresis product from Patient diagnosed with MCL before treatment


title: UPN1 (Methylation)


title: Cardiac Muscle_Cmah KO_mdx_rep1

description:
Gene expression data from cardiac muscle of two-month-old mouse deficient in Neu5Gc sialic acid and dystrophin.
6 Cmah KO mdx Heart


title: JVM-2 (Methylation)


title: Cardiac Muscle_mdx_rep2

description:
Gene expression data from cardiac muscle of two-month-old mouse deficient in dystrophin.
82 mdx Heart

source_name: Heart, mdx, 2 months old

value: mdx


title: Cardiac Muscle_mdx_rep3

description:
Gene expression data from cardiac muscle of two-month-old mouse deficient in dystrophin.
336 mdx Heart


title: JEKOBR (Methylation)

source_name: Adapted Bortezomide resistent MCL cell line

value: MspI representation of genomic DNA

value: JEKOBR


title: Cardiac Muscle_Cmah KO_mdx_rep2

description:
Gene expression data from cardiac muscle of two-month-old mouse deficient in Neu5Gc sialic acid and dystrophin.
8 Cmah KO mdx Heart


title: JEKOPT (Methylation)

value: JEKOPT

value: HpaII representation of genomic DNA


title: HBL2BR (Methylation)

value: Adapted Bortezomide resistent MCL cell line


title: Cardiac Muscle_Cmah KO_rep3

description:
Gene expression data from cardiac muscle of two-month-old mouse deficient in Neu5Gc sialic acid.
10 Cmah KO Heart

source_name: Heart, Cmah KO, 2 months old

value: Cmah KO


title: Cardiac Muscle_WT_rep3

description:
Gene expression data from cardiac muscle of two-month-old WT mouse.
66 WT Heart

source_name: Heart, WT, 2 months old

value: wild type


title: HBL2PT (Methylation)


title: NBC10 (Methylation)

source_name: magnetic bead purified IgD+ naïve B cell from healthy donors undergoing routine tonsillectomy


title: Jeko (Methylation)

value: JEKO


title: Granta519 (Methylation)


title: HBL2 (Methylation)


title: NBC6 (Methylation)

value: magnetic bead purified IgD+ naïve B cell from healthy donors undergoing routine tonsillectomy


title: NBC7 (Methylation)


title: NBC8 (Methylation)


title: Cardiac Muscle_Cmah KO_rep2

description:
Gene expression data from cardiac muscle of two-month-old mouse deficient in Neu5Gc sialic acid.
7 Cmah KO Heart


title: NBC9 (Methylation)


title: Cardiac Muscle_Cmah KO_rep1

description:
Gene expression data from cardiac muscle of two-month-old mouse deficient in Neu5Gc sialic acid.
5 Cmah KO Heart


title: Cardiac Muscle_WT_rep2

description:
Gene expression data from cardiac muscle of two-month-old WT mouse.
61 WT Heart


title: Gastrocnemius Muscle_Cmah KO_mdx_rep3

description:
Gene expression data from skeletal muscle of two-month-old mouse deficient in Neu5Gc sialic acid and dystrophin.
8Cmah KO mdx Skeletal Muscle

source_name: Gastrocnemius, Cmah KO, mdx, 2 months old

value: Gastrocnemius muscle


title: Cardiac Muscle_WT_rep1

description:
Gene expression data from cardiac muscle of two-month-old WT mouse.
65 WT Heart


title: Cardiac Muscle_mdx_rep1

description:
Gene expression data from cardiac muscle of two-month-old mouse deficient in dystrophin.
340 mdx Heart


title: Gastrocnemius Muscle_mdx_rep2

description:
Gene expression data from skeletal muscle of two-month-old mouse deficient in dystrophin.
336mdx Skeletal Muscle

source_name: Gastrocnemius, mdx, 2 months old


title: Gastrocnemius Muscle_Cmah KO_mdx_rep2

description:
Gene expression data from skeletal muscle of two-month-old mouse deficient in Neu5Gc sialic acid and dystrophin.
7Cmah KO mdx Skeletal Muscle


title: Gastrocnemius Muscle_Cmah KO_mdx_rep1

description:
Gene expression data from skeletal muscle of two-month-old mouse deficient in Neu5Gc sialic acid and dystrophin.
6Cmah KO mdx Skeletal Muscle


title: Gastrocnemius Muscle_mdx_rep3

description:
Gene expression data from skeletal muscle of two-month-old mouse deficient in dystrophin.
340mdx Skeletal Muscle


title: NBC4 (Methylation)

description: Genomic DNA from blood was isolated using Puregene Cell and Tissue Kit


title: NBC5 (Methylation)


title: Gastrocnemius Muscle_Cmah KO_rep3

description:
Gene expression data from skeletal muscle of two-month-old mouse deficient in Neu5Gc sialic acid.
10 Cmah KO Skeletal Muscle

source_name: Gastrocnemius, Cmah KO, 2 months old


title: NBC2 (Methylation)


title: Gastrocnemius Muscle_mdx_rep1

description:
Gene expression data from skeletal muscle of two-month-old mouse deficient in dystrophin.
82mdx Skeletal Muscle


title: NBC3 (Methylation)


title: Pt2909 (Expression)

source_name: magnetic bead purified CD19+ fractions from blood from Patient newly diagnosed with MCL.  Sample was collected  before treatment.


title: Pt2797 (Expression)

value: magnetic bead purified CD19+ fractions from blood from Patient newly diagnosed with MCL


title: Pt2681 (Expression)


title: SP-53 (Expression)

value: MCL cell line


title: NBC1 (Methylation)


title: Gastrocnemius Muscle_WT_rep1

description:
Gene expression data from skeletal muscle of two-month-old WT mouse.
66WT Skeletal Muscle

source_name: Gastrocnemius, WT, 2 months old

value: male


title: Gastrocnemius Muscle_WT_rep2

description:
Gene expression data from skeletal muscle of two-month-old WT mouse.
65WT Skeletal Muscle

value: 2 months


title: Gastrocnemius Muscle_WT_rep3

description:
Gene expression data from skeletal muscle of two-month-old WT mouse.
61WT Skeletal Muscle


title: JVM2 (Expression)


title: Gastrocnemius Muscle_Cmah KO_rep2

description:
Gene expression data from skeletal muscle of two-month-old mouse deficient in Neu5Gc sialic acid.
7Cmah KO Skeletal Muscle


title: Gastrocnemius Muscle_Cmah KO_rep1

description:
Gene expression data from skeletal muscle of two-month-old mouse deficient in Neu5Gc sialic acid.
5Cmah KO Skeletal Muscle


title: Mino (Expression)

value: Mino


title: HBL2 (Expression)


title: Jeko1 (Expression)


title: Granta519 (Expression)


title: UPN1 (Expression)


title: S. aureus-DMSO-rep3

status: Public on Jul 02 2010

city: Memphis

first: Matthew

middle: Wilmer

last: Frank

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St Jude Children's Research Hospital

description: Gene expression data for S. aureus treated with DMSO only

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on a GeneChip S. aureus Genome  array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Staphylococcus aureus

source_name: S. aureus (RN4220) treated with DMSO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: S. aureus strain RN4220 was grown to an OD at 600nm = 0.4 in 1% tryptone broth

extract_protocol: Total RNA was isolated using Ambion RNAqueous purification kit according to the manufacturer's instructions and the purified RNA sample was treated with Turbo Dnase (Ambion).

treatment_protocol: S. aureus cells were treated with AFN-1252 (50 ng/mL) or and equal volume in DMSO from 15 minutes

value: RN4220 (derivative of  NCTC8325)


title: S. aureus-AFN-1252-rep1

description: Gene expression data for S. aureus treated with AFN-1252

source_name: S. aureus (RN4220) treated with AFN-1252


title: PPARGC1-1-Cy5-2

city: St. Louis

first: David

middle: Michael

last: Alvarado

state: MO

address: 4565 Scott Ave

department: Genetics

institute: Washington University in St. Louis

description: PPARGC1 siRNA versus GFP siRNA, biological replicate number 1

hyb_protocol: cDNA populations were resuspended in 40ul hybridization buffer (0.25M NaPO4, 0.5% SDS, 1 mM EDTA, 1x SSC and 2X Denhardt's Solution). Microarray slides were hybridized at 42 degrees C for 16 hrs, washed and rehybridized with Cy3 and Cy5 dyes per manufactures recommendations

scan_protocol: Microarray chips were scanned using a GMS 418 Scanner (Affymetrix, Santa Clara, CA)

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed PPARGC1 siRNA signal/processed GFP siRNA signal

molecule: polyA RNA

organism: Gallus gallus

source_name: Utricle sensory epithelia

label_protocol: Purified run-off RNAs from each sample were used for indirect labeling using Genisphere 3DNA Array 50 Kit following manufacturers protocols

extract_protocol: Isolation of RNA, cDNA synthesis and amplification were carried out as described in Hawkins et al, 2003 (PMID: 12761041). Following the second round of amplification, cDNA was added to an in vitro transcription kit (Ambion) as per the manufacturers instructions

value: utricle sensory epithelia

tag: treatment

value: GFP control siRNA

value: PPARGC1 siRNA


title: S. aureus-DMSO-rep1


title: S. aureus-AFN-1252-rep3


title: S. aureus-AFN-1252-rep2


title: Z138 (Expression)


title: PPARGC1-1-Cy3-2


title: KIPp27-1-Cy5_1

description: KIPp27 siRNA versus GFP siRNA, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed KIPp27 siRNA signal/processed GFP siRNA signal

value: KIPp27 siRNA


title: KIPp27-1-Cy5_2


title: KIPp27-1-Cy3_1


title: PPARGC1-1-Cy3_1


title: ID1-1-Cy5_2

description: ID1 siRNA versus GFP siRNA, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed ID1 siRNA signal/processed GFP siRNA signal

value: ID1 siRNA


title: ID1-1-Cy3_1


title: KIPp27-1-Cy3_2


title: ID1-1-Cy3_2


title: ID1-1-Cy5_1


title: EZH2-1-Cy5_1

description: EZH2 siRNA versus GFP siRNA, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed EZH2 siRNA signal/processed GFP siRNA signal

value: EZH2 siRNA


title: HES1-1-Cy3-1

description: HES1 siRNA versus GFP siRNA, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed HES1 siRNA signal/processed GFP siRNA signal

value: HES1 siRNA


title: EZH2-1-Cy5_2


title: HES1-1-Cy5-1


title: HES1-1-Cy5_2


title: EZH2-1-Cy3_1


title: HES1-1-Cy3_2


title: JNK-2-Cy5_2

description: JNK inhibitor versus DMSO control, biological replicate number 2

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed JNK inhibitor signal/processed DMSO control signal

value: 0.1% DMSO control treatment

value: JNK inhibitor in 0.1% DMSO treatment


title: JNK-1-Cy5_1

description: JNK inhibitor versus DMSO control, biological replicate number 1


title: JNK-2-Cy5_1


title: EZH2-1-Cy3_2


title: JNK-2-Cy3_1


title: JNK-1-Cy3_2


title: JNK-2-Cy3_2


title: PAX3-1-Cy3_1

description: PAX3 siRNA versus GFP siRNA, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed PAX3 siRNA signal/processed GFP siRNA signal

value: PAX3 siRNA


title: PPARGC1-1-Cy5_1


title: JNK-1-Cy3_1


title: PAX3-1-Cy5_2


title: TRIP15-1-Cy5_1

description: TRIP15 siRNA versus GFP siRNA, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed TRIP15 siRNA signal/processed GFP siRNA signal

value: TRIP15 siRNA


title: JNK-1-Cy5_2


title: PAX3-1-Cy3_2


title: TIME-1-Cy5_1

description: TIME siRNA versus GFP siRNA, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed TIME siRNA signal/processed GFP siRNA signal

value: TIME siRNA


title: S. aureus-DMSO-rep2


title: RARA-1-Cy5_2

description: RARA siRNA versus GFP siRNA, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed RARA siRNA signal/processed GFP siRNA signal

value: RARA siRNA


title: TRIP15-1-Cy3_1


title: RARA-1-Cy3_2


title: RARA-1-Cy3_1


title: RARA-1-Cy5_1


title: TIME-1-Cy3_2


title: TIME-1-Cy3_1


title: CUTL1-1-Cy5_1

description: CUTL1 siRNA versus GFP siRNA, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed CUTL1 siRNA signal/processed GFP siRNA signal

value: CUTL1 siRNA


title: MYT1L-1-Cy5_1

description: MYT1L siRNA versus GFP siRNA, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed MYT1L siRNA signal/processed GFP siRNA signal

value: MYT1L siRNA


title: CUTL1-1-Cy5_2


title: PAX3-1-Cy5_1


title: MYT1L-1-Cy3_1


title: MYT1L-1-Cy3_2


title: CTNNB1-1-Cy5_2

description: CTNNB1 siRNA versus GFP siRNA, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed CTNNB1 siRNA signal/processed GFP siRNA signal

value: CTNNB1 siRNA


title: CUTL1-1-Cy3_1


title: CTNNB1-1-Cy3_2


title: CBX4-1-Cy3_2

description: CBX4 siRNA versus GFP siRNA, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed CBX4 siRNA signal/processed GFP siRNA signal

value: CBX4 siRNA


title: CBX4-1-Cy3-1

value: utricle sensory epithelia


title: CBX3-1-Cy5_1

description: CBX3 siRNA versus GFP siRNA, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed CBX3 siRNA signal/processed GFP siRNA signal

value: GFP control siRNA

value: CBX3 siRNA


title: BCL11A-2-Cy5_1

description: BCL11A siRNA versus GFP siRNA, biological replicate number 2

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed BCL11A siRNA signal/processed GFP siRNA signal

value: BCL11A siRNA


title: BCL11A-2-Cy3_2


title: BCL11A-2-Cy3_1


title: CBX4-1-Cy5-1


title: BCL11A-1-Cy3_1

description: BCL11A siRNA versus GFP siRNA, biological replicate number 1


title: BCL11A-2-Cy5_2


title: CTNNB1-1-Cy3_1


title: BCL11A-1-Cy5_1


title: CBX3-1-Cy3_1


title: CTNNB1-1-Cy5_1


title: WNT4-2-Cy3_2

description: WNT4 siRNA versus GFP siRNA, biological replicate number 2

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed WNT4 siRNA signal/processed GFP siRNA signal

value: WNT4 siRNA


title: WNT4-2-Cy5_2


title: WNT4-2-Cy5_1


title: BCL11A-1-Cy5_2


title: WNT4-1-Cy3_1

description: WNT4 siRNA versus GFP siRNA, biological replicate number 1


title: WNT4-1-Cy5_2


title: WNT4-1-Cy3_2


title: WNT4-2-Cy3_1


title: WNT4-1-Cy5_1


title: SHH-1-Cy3_1

description: SHH inhibitor versus DMSO control, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed SHH inhibitor signal/processed DMSO control signal

value: SHH inhibitor in 0.1% DMSO treatment


title: SHH-1-Cy3_2


title: SHH-1-Cy5_1


title: BCL11A-1-Cy3_2


title: SHH-1-Cy5_2


title: MAPK-1-Cy5_2

description: MAPK inhibitor versus DMSO control, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed MAPK inhibitor signal/processed DMSO control signal

value: MAPK inhibitor in 0.1% DMSO treatment


title: MAPK-1-Cy5_1

value: 0.1% DMSO control treatment


title: MAPK-1-Cy3_2


title: IGF-1-Cy3_2

description: IGF inhibitor versus DMSO control, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed IGF inhibitor signal/processed DMSO control signal

value: IGF inhibitor in 0.1% DMSO treatment


title: IGF-1-Cy3_1


title: IGF-1-Cy5_2


title: PAX7-2-Cy5_2

description: PAX7 siRNA versus GFP siRNA, biological replicate number 2

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed PAX7 siRNA signal/processed GFP siRNA signal

value: PAX7 siRNA


title: PAX7-2-Cy5_1


title: MAPK-1-Cy3_1


title: PAX7-2-Cy3_1


title: PAX5-2-Cy3_2

description: PAX5 siRNA versus GFP siRNA, biological replicate number 2

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed PAX5 siRNA signal/processed GFP siRNA signal

value: PAX5 siRNA


title: PAX5-2-Cy5_1


title: PAX7-1-Cy5_1

description: PAX7 siRNA versus GFP siRNA, biological replicate number 1


title: PAX5-2-Cy5_2


title: PAX7-1-Cy5_2


title: PAX5-1-Cy5_1

description: PAX5 siRNA versus GFP siRNA, biological replicate number 1


title: PAX5-1-Cy3_1


title: PAX2-2-Cy5_2

description: PAX2 siRNA versus GFP siRNA, biological replicate number 2

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed PAX2 siRNA signal/processed GFP siRNA signal

value: PAX2 siRNA


title: PAX5-1-Cy5_2


title: PAX2-2-Cy3_2


title: PAX2-2-Cy5_1


title: PAX7-1-Cy3_2


title: PAX7-1-Cy3_1


title: PAX7-2-Cy3_2


title: IGF-1-Cy5_1


title: PAX5-2-Cy3_1


title: PAX5-1-Cy3_2


title: CUTL1-1-Cy3_2

description: CUTL1 siRNA versus GFP siRNA, biological replicate number 1


title: PAX2-1-Cy5_2

description: PAX2 siRNA versus GFP siRNA, biological replicate number 1


title: PAX2-2-Cy3_1


title: PAX2-1-Cy3_1


title: BTAF1-2-Cy5_1

description: BTAF1 siRNA versus GFP siRNA, biological replicate number 2

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed BTAF1 siRNA signal/processed GFP siRNA signal

value: BTAF1 siRNA


title: PAX2-1-Cy3_2


title: LRP5-1-Cy5_2

description: LRP5 siRNA versus GFP siRNA, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed LRP5 siRNA signal/processed GFP siRNA signal

value: LRP5 siRNA


title: PAX2-1-Cy5_1


title: LRP5-1-Cy5_1


title: LRP5-1-Cy3_1


title: LRP5-1-Cy3_2


title: BTAF1-2-Cy3_2


title: LRP5-2-Cy3_2

description: LRP5 siRNA versus GFP siRNA, biological replicate number 2


title: LRP5-2-Cy5_1


title: JUND-2-Cy5_1

description: JUND siRNA versus GFP siRNA, biological replicate number 2

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed JUND siRNA signal/processed GFP siRNA signal

value: JUND siRNA


title: BTAF1-2-Cy5_2


title: JUND-2-Cy3_2


title: LRP5-2-Cy5_2


title: BTAF1-1-Cy5_2

description: BTAF1 siRNA versus GFP siRNA, biological replicate number 1


title: BTAF1-2-Cy3_1


title: JUND-2-Cy3_1


title: JUND-1-Cy5_2

description: JUND siRNA versus GFP siRNA, biological replicate number 1


title: BTAF1-1-Cy3_2


title: BTAF1-1-Cy5_1


title: LRP5-2-Cy3_1


title: BTAF1-1-Cy3_1


title: JUND-1-Cy5_1


title: JUND-1-Cy3_2


title: JUND-2-Cy5_2


title: JUND-1-Cy3_1


title: CEBPG-2-Cy5_1

description: CEBPG siRNA versus GFP siRNA, biological replicate number 2

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed CEBPG siRNA signal/processed GFP siRNA signal

value: CEBPG siRNA


title: CEBPG-2-Cy5_2


title: CEBPG-1-Cy5_2

description: CEBPG siRNA versus GFP siRNA, biological replicate number 1


title: CEBPG-1-Cy3_1


title: CEBPG-1-Cy3_2


title: CEBPG-2-Cy3_1


title: CEBPG-1-Cy5_1


title: CEBPG-2-Cy3_2


title: MLD AML sample #45

status: Public on Jul 01 2010

city: New York

first: Hans-Ulrich

last: Klein

department: Neurology

institute: Columbia University Medical Center

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.22.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)

source_name: mononuclear cells after Ficoll purification

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

growth_protocol: not applicable

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.

treatment_protocol: Samples are from untreated AML patients

tag: npm1 mutation

tag: disease state

value: without MLD

tag: flt3-itd mutation

tag: cell type

value: mononuclear cell


title: MLD AML sample #42

value: FLT3-wild type


title: MLD AML sample #48

value: NPM1-wild type

value: with MLD


title: MLD AML sample #47


title: MLD AML sample #46


title: MLD AML sample #41


title: MLD AML sample #44


title: MLD AML sample #40


title: MLD AML sample #34


title: MLD AML sample #43


title: MLD AML sample #39


title: MLD AML sample #35


title: MLD AML sample #36


title: MLD AML sample #37


title: MLD AML sample #38


title: MLD AML sample #29


title: MLD AML sample #31


title: CD34(+) hematopoietic progenitor cells for comparison

city: Berlin

first: Matthias

last: Futschik

address: Invalidenstrasse 41

country: Germany

institute: Charite

description: Gene expression data from CD34(+) hematopoietic progenitor cells

hyb_protocol: Arrays were hybridized at 45°C, washed and stained using GeneChip Fluidics.

scan_protocol: Each slide was scanned on the Affymetrix scanner with a resolution of 10µm/slide.

data_processing: Signal intensities of scanned output files were extracted using the Affymetrix software after exclusion of hybridisation artefacts. Intensities for probe sets  were computated using the Bioconductor implementation of MAS5.

source_name: Human umbilical cord

label_protocol: Total RNA was then used to develop targets for microarray analysis. Biotinylated cRNA was produced by in vitro transcription and fragmented.

growth_protocol: Cord blood specimens were collected in heparin-coated syringes and blue caps from full-term deliveries, after informed consent was obtained from the mothers. Thereafter, the mononuclear cell fraction was isolated by Ficol (Biochrom, Berlin, Germany) followed by two wash steps. The number of viable cells was determined by a hemocytometer after trypan blue exclusion. Human umbilical cord EC were harvested by flushing umbilical veins with 0.1% collagenase (Sigma-Aldrich, Steinheim, Germany). These cells were cultured in endothelial cell conditioning medium consisting of M199 (Biochrom, Berlin, Germany) supplemented with 16% fetal bovine serum (FBS, Hyclone, South Logan, UT), 4% human serum from healthy volunteers, 2 mM L-glutamine, 0.15 mg/ml endothelial growth factor supplement (Intracel; Rockville, MD), 0.015 mg/ml heparin, and 1% fungicide.  Cell pellets were dissolved in RNA lysis buffer (Qiagen, Hilden, Germany) supplemented with beta-mercaptoethanol (10µg/ml) and stored at –80°C until further processing.

extract_protocol: Lysed cells were mixed with 0.2 ml of chloroform for 3 minutes at room temperature and then centrifuged at 11.500 rpm for 15 minutes at 4°C. The upper aqueous phase was collected in RNAse-free eppendorf tubes and mixed with 0.5 ml isopropanol for 10 minutes. Supernatants were aspirated after recentrifugation, and pellets were resuspended in 75% ethanol in DEPC-H20 by vortexing. After airdrying, the RNA quantity was measured by spectrophotometry. Following RNA isolation, samples were run through an RNeasy column (Qiagen, Hilden, Germany) to eliminate DNA and protein contamination. Samples were precipitated with ethanol followed by TBE ethidium bromide gel electrophoresis to confirm the presence of highly pure RNA.

treatment_protocol: Confluent endothelial cells passage 2-4 were stimulated with IL-1beta for 4, 8 and 16 hours, and cells were harvested by collagenase (0.1% in PBS). CD34(+) hematopoietic progenitor cells were used directly post isolation.

value: CD34+ hematopoietic progenitor cells


title: MLD AML sample #33


title: MLD AML sample #30


title: MLD AML sample #32


title: MLD AML sample #28


title: MLD AML sample #26


title: MLD AML sample #25


title: MLD AML sample #27


title: MLD AML sample #24


title: MLD AML sample #23


title: MLD AML sample #22


title: MLD AML sample #20


title: MLD AML sample #17


title: MLD AML sample #12


title: MLD AML sample #21


title: MLD AML sample #16


title: MLD AML sample #13


title: MLD AML sample #10


title: MLD AML sample #6


title: MLD AML sample #9


title: MLD AML sample #14


title: MLD AML sample #11


title: MLD AML sample #19


title: MLD AML sample #8


title: MLD AML sample #2


title: MLD AML sample #4


title: MLD AML sample #18


title: MLD AML sample #15


title: MLD AML sample #5


title: MLD AML sample #7


title: MLD AML sample #3


title: MLD AML sample #1


title: MA5_OD=0.5_rep2

city: Rehovot

first: Amnon

last: Horovitz

address: P.O.Box 26

department: Structural Biology

country: Israel

institute: Weizmann Institue of Science

description: Gene expression data from MA5 strain grown to OD(600)=0.5

hyb_protocol: Biotinylated cRNA was hybridized to the GeneChip Yeast Genome 2.0 array for 16 hrs at 45 °C with shaking.

scan_protocol: The chips were scanned using a GeneChip 3000 scanner.

data_processing: analysis was carried out using Partek Genome Suite software (Partek Inc., St. Louis, Missouri 63141, http://www.partek.com), using RMA.

organism: Saccharomyces cerevisiae

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

growth_protocol: Overnight cultures of the wild-type and each of the MA strains were diluted appropriately and then grown until an O.D. of 0.5 was reached.

extract_protocol: Total RNA was purified using the MasterPure Yeast RNA purification kit (Epicentre Biotechnologies).

treatment_protocol: The cells were then pelletted by centrifugation for 1 min at 600 g, flash-frozen at -80 °C in liquid N2 and stored at -80 °C until use

tag: genotpye


title: MA5_OD=0.5_rep1


title: MA6_OD=0.5_rep2

description: Gene expression data from MA6 strain grown to OD(600)=0.5


title: MA3_OD=0.5_rep1

description: Gene expression data from MA3 strain grown to OD(600)=0.5


title: MA3_OD=0.5_rep2


title: Mhyo_RNA_slide6.1_lower_array

status: Public on Jun 30 2010

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

description: cDNA was generated from M. hyopneumoniae RNA using random hexamers (IDT; Integrated DNA Technologies, Inc. Coralville, IA) and a set of 129 hexamer oligonucleotide primers designed for M. hyopneumoniae mRNA. A single total RNA sample was split into eight 5 μg samples, and cDNA synthesis was conducted on four of these samples using the random hexamers (IDT); for the other four samples, cDNA was generated using primers designed for M. hyopneumoniae as described by Madsen. In each set of four, two samples were fluorescently labeled with Cy3 and the other two were labeled with Cy5 using an indirect labeling protocol. After labeling and cleanup, all 8 samples were quantified on a Nanodrop ND-1000 spectrophotometer. For each array on the slide, 1 μg of labeled cDNA from each type of primer generation (Cy3 or Cy5, random or specific primer set) was combined and hybridized to a PCR featured array and an oligonucleotide featured array. This resulted in 2 arrays of PCR probes hybridized with dye swaps and 2 arrays of oligonucleotide probes with dye swaps.

hyb_protocol: After the purification of the cDNA targets, they were hybridized to the array using the previously described protocol [Madsen, M. L., D. Nettleton, E. L. Thacker, R. Edwards, and F. C. Minion. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infect. Immun. 74:160-166.]. Slides were washed using the Corning UltraGAPS slide wash protocol and dried by centrifugation at 1500 x g for two minutes.

scan_protocol: After hybridization and washing, the arrays were scanned using a ScanArray Express laser scanner (Applied Biosystems) three times with varying photomultiplier tube gain settings to encompass the dynamic range of the signal intensities [Dudley, A. M., J. Aach, M. A. Steffen, and G. M. Church. 2002. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. USA 99:7554-7559.].

data_processing: Slide images were analyzed using the SoftWorx Tracker package (Applied Precision, Inc.), acquiring mean spot intensity and median background intensity for each spot. Spot signals were corrected for background by subtracting the median background intensity from the mean spot intensity. The natural logarithms of these background-corrected signals were adjusted by an additive constant to give a common median to each scan of the same array-dye combination. The data from both dye channels on a given array were normalized by locally weighted scatterplot smoother (LOWESS) normalization. These normalized data sets were then adjusted by an additive constant to make each median the same across all arrays. The triplicate spots were averaged together to produce one normalized measurement for each probe on the array. Value is calculated as the difference in Rnd signal - MhRnd signal.

organism: Mesomycoplasma hyopneumoniae

source_name: Mhyo 232 normal in vitro conditions, MhRnd primers

label_protocol: Fluorescently labeled cDNA targets were generated and purified using a modified protocol as described in [Boyce, J. D., I. Wilkie, M. Harper, M. L. Paustian, V. Kapur, and B. Adler. 2004. Genomic-scale analysis of Pasteurella multocida gene expression during growth within liver tissue of chickens with fowl cholera. Microbes Infect. 6:290-298.] with a 129 hexamer primer set specific for M. hyopneumoniae open reading frames used in previous studies [Madsen, M. L., D. Nettleton, E. L. Thacker, R. Edwards, and F. C. Minion. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infect. Immun. 74:160-166.].

growth_protocol: Cultures were passed fewer than 15 times in vitro in Friis media. 250 ml flasks containing 125 ml cultures were grown at 37ºC to early exponential phase as determined by medium color change and optical density.

extract_protocol:
Cells were pelleted by centrifugation at 24,000 x g, and 500 μl RNAlater (Ambion, Austin, TX) was added to the pellet. Pellets were stored at -70ºC until the total RNA was isolated.
RNA was isolated from frozen cell pellets using Ambion’s RiboPure Kit (Ambion) according to the manufacturer’s protocol. Each sample was treated with 4 U of DNase (Ambion) at 37°C for 30 min followed by purification using an Ultracell YM-30 Microcon Centrifugal Filter Unit (Millipore Corp., Bedford, MA). Quantification and purity checks of each sample were done using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Inc., Wilmington, DE). RNA samples were confirmed DNA free via PCR and gel electrophoresis.

value: 232, a derivative of strain 11

source_name: Mhyo 232 normal in vitro conditions, Rnd primers


title: MA8_OD=0.5_rep2

description: Gene expression data from MA8 strain grown to OD(600)=0.5


title: MA7_OD=0.5_rep1

description: Gene expression data from MA7 strain grown to OD(600)=0.5


title: Mhyo_RNA_slide3.3_lower_array_oligo

hyb_protocol: Oligonucleotides were resuspended to 100 pmol/μl in nuclease free water, and then 9 μl were vacuum dried and diluted to 30 μM in IDT Epoxide spotting buffer. These oligonucleotides were spotted to Corning Epoxide substrates in triplicate. After the purification of the cDNA targets, they were hybridized to the array using the previously described protocol [Madsen, M. L., D. Nettleton, E. L. Thacker, R. Edwards, and F. C. Minion. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infect. Immun. 74:160-166.].

label_protocol: Fluorescently labeled cDNA targets were generated and purified using a modified protocol as described in [Boyce, J. D., I. Wilkie, M. Harper, M. L. Paustian, V. Kapur, and B. Adler. 2004. Genomic-scale analysis of Pasteurella multocida gene expression during growth within liver tissue of chickens with fowl cholera. Microbes Infect. 6:290-298.] using random hexamers (IDT; Integrated DNA Technologies, Inc. Coralville, IA)


title: Mhyo_RNA_slide3.1_upper_array_oligo


title: Mhyo_RNA_slide6.1_upper_array


title: Mhyo_RNA_slide3.1_lower_array_oligo


title: MA6_OD=0.5_rep1


title: MA8_OD=0.5_rep1


title: MA7_OD=0.5_rep2


title: Mhyo_RNA_slide3.3_upper_array_oligo


title: MA1_OD=0.5_rep2

description: Gene expression data from MA1 strain grown to OD(600)=0.5


title: MA1_OD=0.5_rep1


title: MA2_OD=0.5_rep1

description: Gene expression data from MA2 strain grown to OD(600)=0.5


title: MA2_OD=0.5_rep2


title: WT_OD=0.5_rep1

description: Gene expression data from WT strain grown to OD(600)=0.5

source_name: WT strain, OD(600)=0.5


title: WT_OD=0.5_rep2


title: 32D vs 32D/EDAG

city: Beijing

first: changyan

last: li

address: 27 Taiping Road

country: China

institute: Beijing Institute of Radiation Medicine

description: compare gene expression profiles of control 32D cells with EDAG-overexpression 32D cells

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean  of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated.

source_name: myeloid cell line 32D

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Cells were cultured in RPMI 1640 (Gibco Invitrogen, CA) supplemented with 10% WEHI-conditioned medium as a source of IL-3, 10% fetal calf serum at 37°C with 5% CO2.

extract_protocol: Stably transfected cells and control 32D cells were harvest, and total RNA was extracted with Trizol Reagent (BD Biosciences Clontech, Palo Alto, CA) and ethanol precipitation.

treatment_protocol: For stable transfection, cells were washed, resuspended in 0.5 ml of ice-cold PBS, mixed with linearized pcDNA3.1 (His/Myc)-EDAG or control plasmid DNA (15 μg) and subjected to electroporation (960 mF; 220 V) in a 0.4-cm-wide electroporation cuvette. Cells were then cultured in 10 ml of complete RPMI 1640 medium for 2 days and selected with 800 mg/ml G418.

value: myeloid 32D

tag: system

value: hematopoietic

value: control 32D cells


title: Af293_TSA_rep2

city: Wako

first: Takayuki

last: Motoyama

state: Saitama

address: 2-1 Hirosawa

country: Japan

institute: RIKEN

description: It is the second of two technical replicates used in this experiment, both from a TSA-treated culture.

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

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

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

organism: Aspergillus fumigatus Af293

source_name: A. fumigatus Af293, TSA-treated

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

growth_protocol: 2x10e8 conidia of Aspergillus fumigatus Af293 strain were inoculated into 20 ml PD medium (2.4% potato dextrose, Difco Co., Detroit, MI). Cells were grown for 24 h at 28°C on a rotary shaker at 160 rpm and then harvested by filtration.

extract_protocol: Total RNA was extracted using the RNeasy Plant Mini kit (Qiagen KK, Tokyo, Japan). RNA quality and concentration were determined by analysis with an Agilent 2100 bioanalyzer.

treatment_protocol: Cells were grown with TSA (1 μM) for 24 h at 28°C.

value: trichostatin A

tag: phenotype

value: growth inhibition


title: Af293_(-)_rep2

description: It is the second of two technical replicates used in this experiment, both from a non-treated culture.

source_name: A. fumigatus Af293, non-treated

treatment_protocol: Cells were grown without TSA for 24 h at 28°C.

value: normal


title: Af293_(-)_rep1

description: It is the first of two technical replicates used in this experiment, both from a non-treated culture.


title: Af293_TSA_rep1

description: It is the first of two technical replicates used in this experiment, both from a TSA-treated culture.


title: Case 6 - KIT exon 11 del (13058608)

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

description: Case 6. See Table 1 in Arne et al 2009.

hyb_protocol: Hybridization was performed in a Corning Hybridization Chamber during 17 hours in 42ºC water bath, followed by post-hybridization washes (Pronto! Plus Systems; Corning B.V, Schiphol, Netherlands).

scan_protocol: Microarrays were quantified in an Agilent microarray scanner (G2505B; Agilent Technologies, Palo Alto, CA) and image processing was carried out using Feature Extraction Software v7.5 (Agilent Technologies).

data_processing: The microarray data was normalized using lowess normalization. No background correction was done.

source_name: Universal human reference RNA (UHRR) from Stratagene

value: reference RNA pool

source_name: Fresh GIST tissue, with exon 11 deletion

label_protocol: Tumor RNA was labeled with Cy3-dCTP (Amersham BioSciences, Buckinghamshire, UK). Labeled cDNA probes were purified using Pronto! Plus Systems (Corning B.V, Schiphol, Netherlands).

extract_protocol: Total RNA was isolated from biopsies by homogenization with Trizol  Reagent (Invitrogen Life Technologies, CA) using a TissueLyzer (Qiagen, MD) followed by RNA purification (RNeasy mini kit; Qiagen, Valencia, CA). The RNA quality was verified by gel electrophoresis. Fluorescence-labeled cDNA was synthesized from extracted RNA by reverse transcription using ChipShot™ Direct Labeling System (Pronto! Plus Systems; Corning B.V, Schiphol, Netherlands).

treatment_protocol: Fresh tumors were frozen with liquid nitrogen and homogenizated with Tirzol Reagent (Invitrogen Life Technologies).

value: fresh GIST tumor sample

value: KIT exon 11 del


title: Case 5 - KIT exon 11 del (13058597)

description: Case 5. See Table 1 in Arne et al 2009.

label_protocol: Fluorescence-labeled cDNA was synthesized from extracted RNA by reverse transcription using ChipShot™ Direct Labeling System (Pronto! Plus Systems; Corning B.V, Schiphol, Netherlands).


title: Case 10 - wt (13058613)

description:
Case 10. See Table 1 in Arne et al 2009.
Technical replicate 1 of 2.

source_name: Fresh GIST tissue, without exon 11 deletion

value: wt


title: Filtered air exposure 2 -24 hours post-exposure

city: Durham

first: Yuh-Chin

middle: Tony

last: Huang

state: NC

address: Erwin Rd

department: Medicine

institute: Duke University Medical Center

description: Gene expression data from circulating mononuclear cells after filtered air exposure

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

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: The data were RMA-normalized and analyzed using Partek Genomics Suite 6.4

source_name: Circulating mononuclear cells after exposure

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression

extract_protocol: RNAs were extracted using TRIZOL®LS (Invitrogen Corp., Carlsbad, CA), amplified by the Affymetrix Two-Cycle cDNA synthesis kit

treatment_protocol: Subjects underwent a 2-hr mouthpiece exposure to either filtered air (FA) or UFP (50 ug/m3), with four 15-min exercise periods on a bicycle ergometer (target minute ventilation 20 L/min/m2 body surface area).  Peripheral blood samples were obtained before exposure (0 hour) and at 24 hours after exposure

value: mononuclear cells

tag: agent

value: FA

tag: time

value: 24 hours


title: Filtered air exposure 3 -baseline

description: Gene expression data from circulating mononuclear cells before exposure

source_name: Circulating mononuclear cells before exposure

value: 0 hour


title: Case 3 - KIT exon 11 del (13058595)

description:
Case 3. See Table 1 in Arne et al 2009.
Technical replicate 2 of 2.

tag: tissue


title: Case 3 - KIT exon 11 del (13058604)

description:
Case 3. See Table 1 in Arne et al 2009.
Technical replicate 1 of 2.


title: Ultrafine particle exposure 2 -baseline

value: UFP


title: Filtered air exposure 2 -baseline


title: Case 8 - KIT exon 11 del (13058262)

description: Case 8. See Table 1 in Arne et al 2009.


title: Case 9 - KIT exon 11 del (13058261)

description: Case 9. See Table 1 in Arne et al 2009.


title: Ultrafine particle exposure 3 -24 hours post-exposure

description: Gene expression data from circulating mononuclear cells after ultrafine carbon particle exposure


title: Ultrafine particle exposure 1 -24 hours post-exposure


title: Ultrafine particle exposure 2 -24 hours post-exposure


title: Case 1 - KIT exon 11 del (13058260)

description:
Case 1. See Table 1 in Arne et al 2009.
Technical replicate 1 of 2.


title: Ultrafine particle exposure 3 -baseline


title: Filtered air exposure 3 -24 hours post-exposure


title: Case 11 - wt (13058601)

description: Case 11. See Table 1 in Arne et al 2009.


title: Case 7 - KIT exon 11 del (13058611)

description: Case 7. See Table 1 in Arne et al 2009.


title: Case 12 - wt (13058599)

description: Case 12. See Table 1 in Arne et al 2009.


title: Case 1 - KIT exon 11 del (13058256)

description:
Case 1. See Table 1 in Arne et al 2009.
Technical replicate 2 of 2.


title: Case 4 - KIT exon 11 del (13058258)

description: Case 4. See Table 1 in Arne et al 2009.


title: Case 10 - wt (13058263)

description:
Case 10. See Table 1 in Arne et al 2009.
Technical replicate 2 of 2.


title: Case 2 - KIT exon 11 del (13058596)

description: Case 2. See Table 1 in Arne et al 2009.


title: Case 13A - PDGFR (13058259)

description:
Case 13A. See Table 1 in Arne et al 2009.
Technical replicate 1 of 2.

value: PDGFR mutation


title: Case 15 - PDGFR (13058610)

description: Case 15. See Table 1 in Arne et al 2009.


title: Case 16 - KIT exon 9 dupl (13058270)

description: Case 16. See Table 1 in Arne et al 2009.

value: KIT exon 9 dupl


title: LTLvramA rep6

status: Public on Jun 20 2010

city: college park

first: jie

last: zheng

state: MD

address: 5100 paint branch parkway

department: division of microbiology

institute: center for food safety and applied nutrition, FDA

hyb_protocol: hybridization of labeled DNA and cDNA v2.1 from TIGR PFGRC available at  ftp://ftp.jcvi.org/pub/data/PFGRC/pdf_files/protocols/M008.pdf

scan_protocol: Arrays scanned using a GSI Lumonics:ScanArray 4000 scanner and imaged using ScanArray acquisition software 3.1. Average signal intensity and local background measurements were obtained for each spot on the array using Spotfinder software to generate mev files from TIFF array images.

data_processing: Data analysis was carried out using bioinformatic package Limma in BioConductor. The mean values from each channel were log2 transformed and normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values. Between-array normalization was conducted with the quartile method. Normalized values were used to calculate the Cy3/Cy5 fluorescence ratios from experimental and biological repeats with all replicates combined. Data was compiled from six cultures each with a dye-swap replicate, thus providing six biological repeats within twelve technical repeats.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: log-phase cultured control strain

label_protocol: microbial RNA aminoallyl labeling for microarrays protocol v2.0 from TIGR PFGRC availble at    ftp://ftp.jcvi.org/pub/data/PFGRC/pdf_files/protocols/M007.pdf

growth_protocol: Overnight bacterial cultures were diluted 1:100 in fresh MH broth and grown to mid-logarithmic phase (A600 = 0.4-0.45) at 37°C.

extract_protocol: Bacterial cultures flushed directly into QIAGEN RNAprotect before total RNA isolation using TRIzol reagent. Total RNA was cleaned using QIAGEN RNEasy Midi kit with on column DNAse digestion. Ribosomal RNA was further removed using Ambion MicrobExpress bacterial mRNA purification kit.

treatment_protocol: A ramA deletion mutant of LTL (LTLvramA) was constructed using λ red site specific recombination, in which ramA gene was replaced with an aph cassette expressing kanamycin resistance.

tag: strain

value: LTL

source_name: log-phase cultured mutant strain

value: LTLvramA


title: LTLvramA rep5 (dye swap)


title: LTLvramA rep4


title: LTLvramA rep1 (dye swap)


title: LTLvramA rep2


title: LTLvramA rep4 (dye swap)


title: LTLvramA rep1


title: LTLvramA rep2 (dye swap)


title: Case 13B - PDGFR (13058598)

description: Case 13B. See Table 1 in Arne et al 2009.


title: LTLvramA rep6 (dye swap)


title: LTLvramA rep5


title: LTLvramA rep3


title: LTLvramA rep3 (dye swap)


title: Ultrafine particle exposure 1 -baseline


title: Filtered air exposure 1 -baseline


title: LLO

status: Public on Jun 29 2010

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: LLO

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: Mesenteric lymph nodes, LLO

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

growth_protocol: IMDM medium

extract_protocol: Qiagen RNAeasy

treatment_protocol: 3 hours with 0.25 ug/ml LLO

tag: genetic modification

value: wild type

value: mesenteric lymph nodes, spleen

value: CD4+ T cells

value: listeriolysin O (LLO)


title: Iono

description: Iono

source_name: Mesenteric lymph nodes, Iono

treatment_protocol: 3 hours with 1 uM Ionomycin

value: ionomycin (Iono)


title: Filtered air exposure 1 -24 hours post-exposure


title: Case 13A - PDGFR (13058269)

description:
Case 13A. See Table 1 in Arne et al 2009.
Technical replicate 2 of 2.

value: reference RNA pool

value: fresh GIST tumor sample


title: Case 14 - PDGFR (13058609)

description: Case 14. See Table 1 in Arne et al 2009.


title: E16_5_whole embryo_B

status: Public on Jun 16 2010

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

country: Italy

institute: CBM

hyb_protocol: CombiMatrix 12K ECD microarrays were prehybridized for 10 min at 45C and hybridized for 1 hr at 45C with sample in 2x hybridization buffer (CombiMatrix). Arrays were washed 1x with 3xSSPE with Tween 20, 2x with 2xPBS with Tween 20 and then blocked with 5x PBS/Casein (BioFX) for 5 min at RT. Arrays were labeled with Streptavidin-HRP (Sigma) for 30 min at RT and then washed 2x with 2x PBST, 2x with pH4 buffer (BioFX), and 1x with TMB substrate (BioFX). TMB was added to the array which was scanned with CombiMatrix ElectraSense scanner and data were analyzed with CombiMatrix analysis software.

scan_protocol: Arrays were scanned with CombiMatrix ElectraSense scanner.

data_processing: The raw probe signal intensity data was obtained from CombiMatrix ElectraSense Software. Quantile normalization was performed using functions within R.

source_name: whole embryo

label_protocol: Linear amplification kit Ambion #IL1791 following the manufacturer's instructions.

extract_protocol: Qiagen RNeasy kit with on-column DNA digestion following the manufacturer's instructions.

value: whole embryo

tag: developmental stage

value: embryo E16.5


title: E16_5_whole embryo_A


title: E16_5_whole embryo_C


title: Ctrl

description: Ctrl

source_name: Mesenteric lymph nodes, control

treatment_protocol: Untreated control


title: E14_5_whole embryo_C

value: embryo E14.5


title: E14_5_whole embryo_A


title: E12_5_whole embryo_C

value: embryo E12.5


title: E14_5_whole embryo_B


title: CP-Hcys01-cy5

status: Public on Jun 01 2010

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description: Biological replicate 1 of 4

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers.

scan_protocol: Scanned on an GenePix 4200L dual-channel laser scanner.

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

organism: Clostridium perfringens

source_name: strain 13 grown in the presence of homocysteine

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP, dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C. perfringens strain 13 was grown in minimal medium in the presence of 1 mM homocysteine or 0.5 mM cystine until late exponential growth phase.

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

tag: growth protocol

value: 1 mM homocysteine

source_name: strain 13 grown in the presence of cystine

value: 0.5 mM cystine


title: E12_5_whole embryo_A


title: CP-Hcys04-cy3

description: Biological replicate 4 of 4


title: ES_cells_A

source_name: cells

value: embryonic stem cells


title: E12_5_whole embryo_B


title: ES_cells_B


title: CP-Hcys02-cy5

description: Biological replicate 2 of 4


title: CP-Hcys03-cy3

description: Biological replicate 3 of 4


title: CP-Hcys02-cy3

description: Biological replicate 2 of 4


title: ES_cells_C


title: CP-Hcys01-cy3

description: Biological replicate 1 of 4


title: Testis_LindaneC2_Rep2

city: Madrid

first: Luis

middle: A.

last: Lopez-Fernandez

address: Dr. Esquerdo 46

department: Pharmacy

country: Spain

institute: Hospital General Universitario Gregorio Marañon

description:
Dye-Swap replicates were performed: one slide hybridized with experimental and control targets labeled with Cy3 and Cy5, respectively; and the second slide with the same type of targets but inversely labeled. Target refers to labeled aRNA while probe refers to the oligonucleotides spotted on the microarray platform.
Imaging and data generation were carried out using a GenePix 4000B (Axon Instruments) and associated software from Axon Instruments, Inc. The microarray slides were scanned with dual lasers with wavelength frequencies to excite Cy3 and Cy5. Images were captured in TIFF files. Information extraction for a given spot was based on the median value for the signal pixels minus the median value for the background pixels to produce a gene set data file for all the DNA spots. The Cy3 and Cy5 fluorescence signal intensities were normalized.

hyb_protocol: Prehybridization was performed at 42ºC for 30-45 minutes in 6X SSC, 0.5% SDS and 1% BSA. Slides were rinsed five times with destilled water. Cy5 and Cy3 amplified RNA (aRNA) probes were mixed (150 pmol of each label) with 10 µg of PolyA (Sigma) and 1 µg of Cot-DNA (Invitrogen) in a final volume of 40 µl of hybridization buffer (50% formamide, 6X SSC, 0.5% SDS, 5X Denhardt’s). The probe was denatured at 95ºC for 5 minutes and applied to the slide using a coverslip. Slides were then incubated at 42ºC for 16h in hybridization chambers (Array-It). After incubation, slides were washed twice with 0.1X SSC, 0.1% SDS for 5 minutes each, three times with 0.1X SSC for 5 minutes and finally in distilled water for 10 seconds. Slides were dried by centrifugation at 563g for 1 minute.

scan_protocol: Images from Cy3 and Cy5 channels were equilibrated and captured with an Axon 4000B scanner (Axon Instruments) and spots quantified using GenePix 5.1 software (Axon). GPR files were then included in almaZen database software (Bioalma). Signals were background subtracted, and normalized by total intensity and lowess_print_tip_group.

data_processing: GPR files with raw data were introduced in almaZen database software (http://www.Bioalma.com). Signals were background subtracted, and normalized by total intensity and Print_tip_group_Lowess.

label_protocol: Starting with total RNA from pools (Three animals), full length cDNAs were synthesized from oligo(dT) primers bearing a T7 promoter. These cDNAs were used as template for in vitro transcription by T7-RNA-Polymerase to amplify the mRNAs; following the Amino Allyl MessageAmp™ aRNA Kit (Ambion, Inc.) protocol. The amplified mRNAs (aRNA) were labeled either with Cy3 or Cy5 dyes, using Amersham CyDye Post-Labeling Reactive Dyes (Amersham Biosciences). The incorporated dye was spectrophotometrically quantified using NanoDrop (NanoDrop Technologies)

extract_protocol: Total RNA from testes of animals was extracted using TRIzol reagent (Invitrogen), according to the manufacturer’s standard protocol. RNA samples were spectrophotometrically quantified using NanoDrop (NanoDrop Technologies). To minimize the effect of inter-individual expression variability we made pools of RNA from at least 3 individual RNA samples from each experimental condition (same quantity of total RNA per sample). Pools of RNA were checked for quality performing Experion analysis (Bio-Rad Laboratories).

treatment_protocol: No treatment. Testis from four weeks mice were collected and RNA isolated.

tag: gender

value: Male

value: Testis

tag: age

value: four weeks

value: not exposed to chemical compounds.

label_protocol: Starting with total RNA from pools (three animals), full length cDNAs were synthesized from oligo(dT) primers bearing a T7 promoter. These cDNAs were used as template for in vitro transcription by T7-RNA-Polymerase to amplify the mRNAs; following the Amino Allyl MessageAmp™ aRNA Kit (Ambion, Inc.) protocol. The amplified mRNAs (aRNA) were labeled either with Cy3 or Cy5 dyes, using Amersham CyDye Post-Labeling Reactive Dyes (Amersham Biosciences). The incorporated dye was spectrophotometrically quantified using NanoDrop (NanoDrop Technologies).

treatment_protocol: Mothers were exposed to Lindane (in DMSO) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 100 mg/l.. Male offspring were sacrificed to obtain the testis four weeks after birth.

value: Mothers were exposed to Lindane (in DMSO) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth,100 mg/


title: CP-Hcys04-cy5

description: Biological replicate 4 of 4


title: Testis_Estradiol_treatmentA1_Rep2

treatment_protocol: Mothers were exposed to Estradiol for two weeks before mating, 0.02 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth.

value: Mothers were exposed to Estradiol (in ethanol) two weeks before mating, 0.02 mg/l.


title: Testis_LindaneC3_Rep1

treatment_protocol: Mothers were exposed to Lindane (in DMSO) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 200 mg/l.. Male offspring were sacrificed to obtain the testis four weeks after birth.

value: Mothers were exposed to Lindane (in DMSO) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth,200 mg

extract_protocol: Total RNA from testes of animals was extracted using TRIzol reagent (Invitrogen), according to the manufacturer’s standard protocol. RNA samples were spectrophotometrically quantified using NanoDrop (NanoDrop Technologies). To minimize the effect of inter-individual expression variability we made pools of RNA from at least 3 individual RNA samples from each experimental condition (same quantity of total RNA per sample). Pools of RNA were checked for quality performing Experion analysis (Bio-Rad Laboratories)


title: CP-Hcys03-cy5

description: Biological replicate 3 of 4


title: Testis_LindaneC2_Rep1

value: Mothers were exposed to Lindane (in DMSO) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth,100 mg


title: Testis_LindaneC3_Rep2

treatment_protocol: No treatment. Testis from four weeks mice were collected and RNA isolated


title: Testis_LindaneC1_Rep2

treatment_protocol: Mothers were exposed to Lindane (in DMSO) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 50 mg/l.. Male offspring were sacrificed to obtain the testis four weeks after birth.

value: Mothers were exposed to Lindane (in DMSO) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth,50 mg/


title: Testis_Estradiol_treatmentA1_Rep1


title: Testis_Estradiol_treatmentA3_Rep2

treatment_protocol: Mothers were exposed to estradiol for two weeks before mating, 0.04 mg/l. Then, administration was interrupted. Male offspring were sacrificed to obtain the testis four weeks after birth.

value: Mothers were exposed to estradiol (in ethanol) two weeks before mating, 0.16 mg/l.


title: Testis_LindaneC1_Rep1


title: Testis_Estradiol_treatmentA3_Rep1


title: Testis_LindaneB1_Rep2

treatment_protocol: Mothers were exposed to Lindane for two weeks before mating and maintained during pregnancy, 50 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth

value: Mothers were exposed to Lindane (in DMSO) two weeks before mating and maintained during pregnancy,50 mg/l.


title: Testis_Estradiol_treatmentC3_Rep2

treatment_protocol: Mothers were exposed to estradiol (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 0.16 mg/l. Male offspring were sacrificed to obtain the testis four weeks after birth.

value: Mothers were exposed to Estradiol (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 0.16 mg/l.


title: Testis_LindaneB2_Rep2

value: not exposed to chemical compounds

treatment_protocol: Mothers were exposed to Lindane for two weeks before mating,100 mg/l. Then, administration was interrupted. Male offspring were sacrificed to obtain the testis four weeks after birth

value: Mothers were exposed to Lindane (in DMSO) two weeks before mating, 100 mg/l.


title: Testis_LindaneB3_Rep1

treatment_protocol: Mothers were exposed to Lindane for two weeks before mating and maintained during pregnancy, 200 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth

value: Mothers were exposed to Lindane (in DMSO) two weeks before mating and maintained during pregnancy, 200 mg/l.

label_protocol: Starting with total RNA from pools (three animals), full length cDNAs were synthesized from oligo(dT) primers bearing a T7 promoter. These cDNAs were used as template for in vitro transcription by T7-RNA-Polymerase to amplify the mRNAs; following the Amino Allyl MessageAmp™ aRNA Kit (Ambion, Inc.) protocol. The amplified mRNAs (aRNA) were labeled either with Cy3 or Cy5 dyes, using Amersham CyDye Post-Labeling Reactive Dyes (Amersham Biosciences). The incorporated dye was spectrophotometrically quantified using NanoDrop (NanoDrop Technologies)


title: Testis_Estradiol_treatmentB3_Rep2

treatment_protocol: Mothers were exposed to Estradiol for two weeks before mating and maintained during pregnancy, 0.16 mg/l. Then, administration was interrupted. Male offspring were sacrificed to obtain the testis four weeks after birth.

value: Mothers were exposed to Estradiol (in ethanol) two weeks before mating and maintained during pregnancy, 0.16 mg/l.


title: Testis_Estradiol_treatmentA2_Rep2

value: Mothers were exposed to estradiol (in ethanol) two weeks before mating, 0.04 mg/l.


title: Testis_Estradiol_treatmentB3_Rep1

value: Male


title: Testis_Estradiol_treatmentB1_Rep2

value: Testis

treatment_protocol: Mothers were exposed to Estradiol for two weeks before mating and maintained during pregnancy, 0.02 mg/l. Then, administration was interrupted. Male offspring were sacrificed to obtain the testis four weeks after birth.

value: Mothers were exposed to Estradiol (in ethanol) two weeks before mating and maintained during pregnancy, 0.02 mg/l.


title: Testis_Estradiol_treatmentB2_Rep2

value: four weeks

value: not exposed to chemical compounds.

treatment_protocol: Mothers were exposed to Estradiol for two weeks before mating and maintained during pregnancy, 0.04 mg/l. Then, administration was interrupted. Male offspring were sacrificed to obtain the testis four weeks after birth.

value: Mothers were exposed to Estradiol (in ethanol) two weeks before mating and maintained during pregnancy, 0.04 mg/l.


title: Testis_LindaneA2_Rep2


title: Testis_Estradiol_treatmentA2_Rep1

tag: train


title: Testis_Estradiol_treatmentC3_Rep1


title: Testis_Estradiol_treatmentC1_Rep1

treatment_protocol: Mothers were exposed to estradiol (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 0.02 mg/l.. Male offspring were sacrificed to obtain the testis four weeks after birth

value: Mothers were exposed to Estradiol (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 0.02 mg/l.


title: Testis_Estradiol_treatmentB1_Rep1


title: Testis_Estradiol_treatmentB2_Rep1


title: Testis_Estradiol_treatmentC2_Rep2

treatment_protocol: Mothers were exposed to estradiol (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 0.04 mg/l. Male offspring were sacrificed to obtain the testis four weeks after birth.

value: Mothers were exposed to Estradiol (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 0.04 mg/l.


title: Testis_LindaneA1_Rep2

treatment_protocol: Mothers were exposed to Lindane for two weeks before mating, 50 mg/l. Then, administration was interrupted. Male offspring were sacrificed to obtain the testis four weeks after birth.

value: Mothers were exposed to Lindane (in DMSO) two weeks before mating, 50 mg/l.


title: Testis_Estradiol_treatmentC2_Rep1

treatment_protocol: No treatment. Testis from four weeks mice were collected and RNA isolated.


title: Testis_LindaneA1_Rep1

treatment_protocol: Mothers were exposed to Lindane for two weeks before mating,50 mg/l. Then, administration was interrupted. Male offspring were sacrificed to obtain the testis four weeks after birth.


title: Testis_LindaneB1_Rep1

value: Mothers were exposed to Lindane (in DMSO) two weeks before mating and maintained during pregnancy, 50 mg/l.


title: Testis_MEHP_treatmentC3_Rep2

treatment_protocol: Mothers were exposed to MEHP (in DMSO) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 139.17 mg/l.. Male offspring were sacrificed to obtain the testis four weeks after birth

value: Mothers were exposed to MEHP (in DMSOl) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth,278.34 mg/l


title: Testis_LindaneB3_Rep2


title: Testis_LindaneA3_Rep2

treatment_protocol: No treatment. Testis from four weeks mice were collected and RNA isolate

treatment_protocol: Mothers were exposed to Lindane for two weeks before mating,200 mg/l. Then, administration was interrupted. Male offspring were sacrificed to obtain the testis four weeks after birth

value: Mothers were exposed to Lindane (in DMSO) two weeks before mating, 200 mg/l


title: Testis_LindaneA3_Rep1

treatment_protocol: Mothers were exposed to Lindane for two weeks before mating,200 mg/l. Then, administration was interrupted. Male offspring were sacrificed to obtain the testis four weeks after birth.

value: Mothers were exposed to Lindane (in DMSO) two weeks before mating, 200 mg/l.

treatment_protocol: No treatment. Testis from four weeks mice were collected and RNA isolated

value: not exposed to chemical compounds


title: Testis_LindaneB2_Rep1

treatment_protocol: Mothers were exposed to Lindane for two weeks before mating and maintained during pregnancy, 100 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth

value: Mothers were exposed to Lindane (in DMSO) two weeks before mating and maintained during pregnancy, 100 mg/l.


title: Testis_LindaneA2_Rep1

treatment_protocol: Mothers were exposed to Lindane for two weeks before mating,100 mg/l. Then, administration was interrupted. Male offspring were sacrificed to obtain the testis four weeks after birth.

value: Mothers were exposed to Lindane (in DMSO) two weeks before mating, 100 mg/l.


title: Testis_Zearalenone_treatmentC3_Rep1

treatment_protocol: Mothers were exposed to Zearalenone (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 20 mg/l. Male offspring were sacrificed to obtain the testis four weeks after birth.


title: Testis_Zearalenone_treatmentC3_Rep2

value: Mothers were exposed to Zearalenone (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 20 mg/l.


title: Testis_MEHP_treatmentC3_Rep1

value: Male

treatment_protocol: Mothers were exposed to MEHP (in DMSOl) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth,278.34 mg/l.


title: Testis_Estradiol_treatmentC1_Rep2

value: Testis

treatment_protocol: Mothers were exposed to estradiol (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 0.02 mg/l. Male offspring were sacrificed to obtain the testis four weeks after birth.


title: Testis_Zearalenone_treatmentC2_Rep2

treatment_protocol: Mothers were exposed to Zearalenone (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 12 mg/l. Male offspring were sacrificed to obtain the testis four weeks after birth.


title: Testis_Zearalenone_treatmentB3_Rep1

treatment_protocol: Mothers were exposed to Zearalenone for two weeks before mating and maintained during pregnancy, 12 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth.

value: Mothers were exposed to Zearalenone (in ethanol) two weeks before mating and maintained during pregnancy, 20 mg/l.


title: Testis_MEHP_treatmentC1_Rep1

treatment_protocol: Mothers were exposed to MEHP (in DMSO) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 27.83 mg/l.. Male offspring were sacrificed to obtain the testis four weeks after birth

value: four weeks

value: Mothers were exposed to MEHP (in DMSOl) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth,27.83 mg/l .


title: Testis_MEHP_treatmentC1_Rep2

value: not exposed to chemical compounds.

value: Mothers were exposed to MEHP (in DMSOl) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth,27.83 mg/l


title: Testis_Zearalenone_treatmentC2_Rep1

value: Mothers were exposed to Zearalenone (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 12 mg/l.


title: Testis_Zearalenone_treatmentB2_Rep2

value: Mothers were exposed to Zearalenone (in ethanol) two weeks before mating and maintained during pregnancy, 12 mg/l.


title: Testis_Zearalenone_treatmentC1_Rep1

treatment_protocol: Mothers were exposed to Zearalenone (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 4 mg/l. Male offspring were sacrificed to obtain the testis four weeks after birth


title: Testis_Zearalenone_treatmentB1_Rep2

treatment_protocol: Mothers were exposed to Zearalenone for two weeks before mating and maintained during pregnancy, 4 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth.

value: Mothers were exposed to Zearalenone (in ethanol) two weeks before mating and maintained during pregnancy, 4 mg/l.


title: Testis_MEHP_treatmentB3_Rep2

treatment_protocol: Mothers were exposed to MEHP for two weeks before mating and maintained during pregnancy, 278.34 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth.

value: Mothers were exposed to MEHP (in DMSO) two weeks before mating and maintained during pregnancy,278.34 mg/l

treatment_protocol: No treatment. Testis from four weeks mice were collected and RNA isolated.

value: No treatment


title: Testis_Zearalenone_treatmentB2_Rep1


title: Testis_Zearalenone_treatmentA3_Rep1

treatment_protocol: Mothers were exposed to Zearalenone for two weeks before mating, 20 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth.

value: Mothers were exposed to Zearalenone (in ethanol) two weeks before mating, 20 mg/l.


title: Testis_MEHP_treatmentC2_Rep2

treatment_protocol: Mothers were exposed to MEHP (in DMSO) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 139.17 mg/l.. Male offspring were sacrificed to obtain the testis four weeks after birth

value: Mothers were exposed to MEHP (in DMSOl) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth,139.17 mg/l .


title: Testis_Zearalenone_treatmentB3_Rep2


title: Testis_Zearalenone_treatmentC1_Rep2

value: Mothers were exposed to Zearalenone (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 4 mg/l.


title: Testis_MEHP_treatmentB3_Rep1


title: Testis_Zearalenone_treatmentA3_Rep2


title: Testis_Zearalenone_treatmentA2_Rep2

treatment_protocol: Mothers were exposed to Zearalenone for two weeks before mating, 12 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth.

value: Mothers were exposed to Zearalenone (in ethanol) two weeks before mating, 12 mg/l.


title: Testis_Zearalenone_treatmentB1_Rep1


title: Testis_MEHP_treatmentB2_Rep1

treatment_protocol: Mothers were exposed to MEHP for two weeks before mating and maintained during pregnancy, 139.17 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth.

value: Mothers were exposed to MEHP (in DMSO) two weeks before mating and maintained during pregnancy,139.17 mg/l.


title: Testis_Zearalenone_treatmentA1_Rep2

value: Male

treatment_protocol: Mothers were exposed to Zearalenone for two weeks before mating, 4 mg/l. Then, administration was interrupted. Male offspring were sacrificed to obtain the testis four weeks after birth.

value: Mothers were exposed to Zearalenone (in ethanol) two weeks before mating, 4 mg/l.


title: Testis_Zearalenone_treatmentA1_Rep1

treatment_protocol: Mothers were exposed to Zearalenone for two weeks before mating, 4 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth.

value: Testis


title: Testis_MEHP_treatmentB2_Rep2

treatment_protocol: No treatment. Testis from four weeks mice were collected and RNA isolated

value: four weeks


title: Testis_MEHP_treatmentB1_Rep1

treatment_protocol: Mothers were exposed to MEHP for two weeks before mating and maintained during pregnancy, 27,83 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth.

value: Mothers were exposed to MEHP (in DMSO) two weeks before mating and maintained during pregnancy, 27,83 mg/l.


title: Testis_MEHP_treatmentB1_Rep2


title: Testis_Zearalenone_treatmentA2_Rep1

value: not exposed to chemical compounds.


title: Testis_MEHP_treatmentA2_Rep1

treatment_protocol: Mothers were exposed to MEHP for two weeks before mating,139.17mg/l. Then, administration was interrupted. Male offspring were sacrificed to obtain the testis four weeks after birth

value: Mothers were exposed to MEHP (in DMSO) two weeks before mating, 139.17 mg/l.

value: not exposed to chemical compounds


title: Testis_Bisphenol_treatmentC3_Rep1

treatment_protocol: Mothers were exposed to Bisphenol A (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 200 mg/l. Male offspring were sacrificed to obtain the testis four weeks after birth.