title: Control KTC 0-12h 12h 1

tag: scan date


title: Control KTC 0-12h 12h 2

status: Public on Aug 01 2015

type: RNA

city: Cincinnati

first: Rong-Lin

last: Wang

address: 26 W MLK Dr

country: USA

institute: US EPA

hyb_protocol: The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 µm resolution

data_processing: Microarray image processing was performed using the latest Agilent's Feature Extraction software available at the time following the manufacturer’s protocol and recommendations.  Data processing was conducted using R package Limma.

molecule: total RNA

organism: Pimephales promelas

source_name: ovary tissue,fish in water control

label_protocol: cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling Kit; Agilent, Palo Alto, CA)

growth_protocol: Sexually mature adult fathead minnows (5-6 month old) were obtained from an on-site aquatic culture facility at the US EPA Mid-Continent Ecology Division, Duluth, MN, USA. Fish were held under a 16:8 light:dark photoperiod fed frozen adult brine shrimp (San Francisco Bay Brand, Newark, CA, USA). Fish survival, water temperature (mean ± SD; 25.0±0.3), and dissolved oxygen (mean ± SD; 7.0±0.2) were monitored daily over the duration of the exposure and did not vary significantly between treatment groups.

extract_protocol: Total RNA was isolated from ovary tissue of both fathead minnow using RNeasy kits (Qiagen, Valencia, CA, USA). RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and RNA was quantified spectrophotometrically (Nanodrop). Total RNA samples were stored at -80oC until used for microarray analyses.

treatment_protocol:
To initiate a typical experiment, four males and four females were placed together in a glass test tank holding 10 L of Lake Superior water (4 µM filtered, UV sterilized) or test chemical dissolved in Lake Superior water, which was continuously renewed at a rate of about 45 mL/min. There were two such tanks for each treatment condition. The animals were held at 25 +/- 0.5 °C under a 16:8 L:D photoperiod, and were fed brine shrimp to satiation twice per day.
chemical abbreviations: BPA, bisphenol-A; EE2, 17a-ethynyl estradiol; FAD, fadrozole; FLU, flutamide; GEM, Gemfibrozil; KTC, ketoconazole; PRO,prochloraz; RDX, hexahydro-1,3,5-trinitro-1,3,5-triazine; TB, 17 -trenbolone; TNT, 2,4,6-trinitrotoluene; TRI,trilostane; VIN, vinclozolin; WLSSD, effluent from Western Lake Superior Sanitary District

tag: tissue

value: ovary

tag: age (month)

tag: treatment

value: in water control

tag: treatment duration

tag: experiment

tag: sampling date

tag: rna date

tag: rna person

value: rnaL

tag: chip id


title: EW8 [miRNA]

city: Bethesda

first: Eric

middle: C

last: Polley

state: MD

address: 9609 Medical Center Drive, Rm 5W118

department: Biometric Research Branch

institute: National Cancer Institute

hyb_protocol: Samples were hybridized for 16 hrs to NanoString human miRNA probeset, which contains probe pairs specific for each miRNA with different fluorescent barcode labels. The probe pair consists of a Reporter Probe, which carries the fluorescent signal on its 5' end, and a Capture Probe which carries a biotin on its 3' end.  After hybridization, excess probes are washed away using a two step magnetic bead-based purification on the nCounter™ Prep Station and are immobilized in the cartridge for data collection.

scan_protocol: Data Collection is carried out in the nCounter Digital Analyzer. Digital images are processed and the barcode counts are tabulated in a RCC format.

data_processing: Data were analyzed using custom R scripts

label: fluorescence

organism: Homo sapiens

source_name: Ewing Sarcoma

label_protocol: Total RNA (100 ng) was ligated to unique oligonuceotide tag to increase the length of the short miRNA for subsequent detection in a single reaction without amplification using NanoString kit following manufacturer’s suggested protocol.

growth_protocol: Immortalized human cell lines derived from sarcoma's were purchased from ATCC or provided by Memorial Sloan Kettering Cancer Center , Children's Oncology Group, and Pediatric Preclinical Testing Program, and grown in their recommended media supplemented with  10-20% fetal bovine serum. Flasks of cells in media were maintained in incubators with 95% air and 5% CO2 at 37 degrees C, and passaged as the cells reached 70-90% confluency.

extract_protocol: Cells were grown in flasks to approximately 70% confluency, detatched with trypsin, and then total  RNA (including miRNA) extracted  using Qiagen miRNeasy  mini-kit according to manufacturers instructions. Quality of RNA was assessed using an Agilent 2100 Bioanalyzer and all samples were of good quality with RIN# > 8.

tag: cell line

tag: cell type

value: human Ewing Sarcoma cell line


title: Hs 913.T [miRNA]

source_name: Fibrosarcoma

value: human Fibrosarcoma cell line


title: SNs_NFIA_OE_2

city: Shinjuku-ku

first: Jun

last: Tsuyama

address: 35 Shinanomachi

country: Japan

institute: Keio University School of Medicine

description: gene expression after 12day culture since EBs

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 10x Agilent blocking agent according to the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hours at 65°C in a rotating hybridization oven.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505C) at the resolution of 3um.

data_processing: The scanned images were quantified with Feature Extraction Software 10.7.3.1 (Agilent).

organism: Mus musculus

source_name: NSPCs derived from WT/NFIA mixed sphere (Passeage 1, WT)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the Low Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA containing the small fraction was isolated from each sample using the RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions. Quality was confirmed using the Agilent 2100 Bioanalyzer.

value: NSPCs

tag: culture type

value: neurosphere (paseage 1)


title: Control KTC 0-12h 10h 4


title: ES-8 [miRNA]


title: PNs_NFIA_OE_2

description: gene expression after 6day culture since EBs

source_name: NSPCs derived from WT/NFIA mixed sphere (Passeage 0, NFIA OE line)

value: neurosphere (paseage 0)


title: SNs_CT_2

source_name: NSPCs derived from WT/NFIA mixed sphere (Passeage 1, NFIA OE line)


title: Control KTC 0-12h 10h 3


title: SNs_CT_1


title: SNs_NFIA_OE_1


title: PNs_CT_2


title: Control KTC 0-12h 10h 2


title: Control KTC 24h 6h 4

value: 6 h

value: rnaYYY


title: PNs_NFIA_OE_1

source_name: NSPCs derived from WT/NFIA mixed sphere (Passeage 0, WT)


title: WT SVZ Replicate 4

city: Montreal

first: Karl

middle: JL

last: Fernandes

state: Quebec

address: 900 Rue St-Denis, R09-474

department: Neurosciences

country: Canada

institute: Université de Montréal

description: raw data file: Pair-H-Samples15+16.gpr

hyb_protocol: 4 μg of labeled material was dried by Speedvac and resuspended in a total of 3.3 μl of tracking control solution. Hybridizations were carried out using the SurePrint G3 Mouse GE 8x60K Microarray (Agilent Technologies) containing probes targeting 39,430 Entre Gene RNAs and 16,251 lincRNAs.

scan_protocol: Arrays were scanned at 5μm resolution using a GenePix4000B scanner (Molecular Devices).

data_processing:
Data from scanned images were extracted using GenePix 6.1 (Axon). Chip annotations file was updated to a more recent version (20130207).   Expression data was analyzed using Bioconductor packages (http://www.bioconductor.org/) and R statistical language (www.r-project.org).    Bioconductor limma26 package was used to background correct, log2-transform, aggregate and quantile-normalize the median probe intensities.  Probe intensities were averaged when more than one probe was associated with a given probe identifier. The resulting matrix showing 55,681 probes as rows and 8 samples as columns was filtered to exclude lincRNA entries and probes in intensities below background in more than half of the samples.  32,684 probes were used as input for linear modeling using the method available in limma which uses a moderated t-statistic to assess significance.
Bioconductor limma26 package was used to background correct, log2-transform, aggregate and quantile-normalize the median probe intensities.  Probe intensities were averaged when more than one probe was associated with a given probe identifier.

source_name: WT SVZ

label_protocol: 1 μg of purified cDNA (in a total volume of 40 μl) was mixed with 40 μl of 5' Cy3 labeled random nonamers (Trilink Biotechnology) and heated at 95°C for 10 minutes and snap cooled in ice/water slurry for 10 minutes. The samples were then mixed with 10 μl of 10mM dNTP mix, 8 μl of water and 2 μl of Klenow fragment (3'to 5' exo-) (NEB) and incubated at 37ºC for 2 hours. The labeling reaction was stopped by adding 10 μl 0.5M EDTA and then isopropanol precipitated with the addition of 11 μl 5M NaCl. The labeled DNA was resuspended in 40 μL water and quantified using a Nanodrop.

extract_protocol: RNA was isolated from snap-frozen SVZ microdissections using the RNeasy mini microarray kit as per manufacturer’s instructions (Qiagen). For each sample, 5μg of RNA was reverse transcribed using Superscript II reverse transcriptase. The cDNA was purified using Qiagen PCR purification column as per the manufacturer’s protocol.

treatment_protocol: The lateral ventricle subventricular zone was microdissected from thick sections through through the forebrain of 7 month old female 3xTg and strain control (WT) mice.

tag: strain background

value: C57BL/6J females (B6) X 129S1/SvImJ males (129S)

tag: genotype/variation

value: wild type (control strain)

tag: age

value: 7 months

tag: gender

value: female

value: Subventricular zone


title: WT SVZ Replicate 3

description: raw data file: Pair-G-Samples13+14.gpr


title: ES-4 [miRNA]


title: 3xTg SVZ Replicate 4

description: raw data file: Pair-H-Samples15+16.gpr

source_name: 3xTg SVZ


title: WT SVZ Replicate 2

description: raw data file: Pair-F-Samples11+12.gpr


title: WT SVZ Replicate 1

description: raw data file: Pair-E-Samples9+10.gpr


title: PNs_CT_1


title: ES-3 [miRNA]


title: ES-7 [miRNA]


title: ES-1 [miRNA]


title: Control KTC 0-12h 10h 1

tag: scan date


title: 3xTg SVZ Replicate 3

description: raw data file: Pair-G-Samples13+14.gpr

tag: tissue


title: COG-E-352 [miRNA]


title: CHLA-9 [miRNA]


title: Control KTC 24h 6h 3

tag: age (month)


title: 3xTg SVZ Replicate 1

description: raw data file: Pair-E-Samples9+10.gpr


title: ASPS-1 [miRNA]

source_name: Alveolar Soft Part (Vistica)

value: human Alveolar Soft Part (Vistica) cell line


title: CHLA-10 [miRNA]


title: Control KTC 24h 6h 2

tag: treatment


title: Control KTC 24h 24h 3

tag: treatment duration


title: Control KTC 24h 24h 4

tag: experiment


title: MIN6m9, Fv2E PERK, AP 6h, rep1

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Division of Molecular Biology

institute: Institute for Genome Research

description: Gene expression of MIN6 Fv2E-PERK AP6h

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent Fragmentation buffer and 1x Agilent Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17.5 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air-dried immediately.

scan_protocol: Slides were scanned immediately after washing and drying on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%, NoXDR setting).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MIN6m9, Fv2E PERK, AP 6h, rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the Low Input Quick Amp Labeling Kit (One-Color) (Agilent) according to the manufacturer's instructions, followed by RNeasy mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: All the mouse protocols were approved by the Animal Experimentation Committee of the University of Tokushima. The mice were maintained under SPF conditions.

extract_protocol: Total RNA was extracted using the conventional acid guanidinium thiocyanate phenol-chloroform (AGPC) procedure and cleaned up using the RNeasy MinElute Cleanup Kit according to manufacturer's instructions (QIAGEN Valencia, CA).

treatment_protocol: Wild type MIN6m9 cells were treated with 400 uM Palmitate(Pal), 400 uM Oleate(Ole) or negative control condition(UT). In MIN6-Fv2E-PERK, AP20187 (1 nM) or vehicle (ethanol) were added and cells were harvested after 6, 12, 24, 48 h.

tag: genotype

value: 1nM AP 6h


title: MIN6m9, Fv2E PERK, AP 48h, rep1

description: Gene expression of MIN6 Fv2E-PERK AP48h

source_name: MIN6m9, Fv2E PERK, AP 48h, rep1

value: 1nM AP 48h


title: MIN6m9, Fv2E PERK, AP 24h, rep2

description: Gene expression of MIN6 Fv2E-PERK AP24h

source_name: MIN6m9, Fv2E PERK, AP 24h, rep2

value: 1nM AP 24h


title: 3xTg SVZ Replicate 2

description: raw data file: Pair-F-Samples11+12.gpr


title: S_I_Segment_Control

city: Fukuoka

first: Satoru

last: Koyanagi

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmaceutics

institute: Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (Agilent-028005 SurePrint G3 Mouse Gene Expression Microarray 8×60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were normalized by the quantile algorithm with the Bioconductor.

source_name: Vehicle-treated wild-type intestinal epithelial cells

label_protocol: cRNA was amplified and labelled using a Low Input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the intestinal epithelial cells after treatment with CA or vehicle. Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega).

treatment_protocol: Intestinal segments prepared from mice were incubated with 0.5 microM cholic acid (CA) or vehicle (0.05% DMSO and 0.25% ethanol) for 2hr.

value: wild type

value: male

value: Intestinal epithelial cells

value: vehicle


title: S_I_Segment_CA

source_name: CA-treated wild-type intestinal epithelial cells

value: cholic acid (CA)


title: Control KTC 24h 24h 2

value: ovary

value: in water control

tag: sampling date

tag: rna date


title: MIN6m9, Fv2E PERK, AP 12h, rep1

description: Gene expression of MIN6 Fv2E-PERK AP12h

source_name: MIN6m9, Fv2E PERK, AP 12h, rep1

value: 1nM AP 12h


title: Control KTC 24h 24h 1

tag: rna person

value: rnaYYY

tag: chip id


title: A-673 [miRNA]

tag: cell line

tag: cell type

value: human Ewing Sarcoma cell line


title: MIN6m9, Fv2E PERK, AP 48h, rep2

description: Gene expression of MIN6 Fv2E-PERK AP48h

source_name: MIN6m9, Fv2E PERK, AP 48h, rep2


title: MIN6m9, Fv2E PERK, AP 12h, rep2

description: Gene expression of MIN6 Fv2E-PERK AP12h

source_name: MIN6m9, Fv2E PERK, AP 12h, rep2


title: MIN6m9, Fv2E PERK, Mock, rep2

description: Gene expression of MIN6 Fv2E-PERK Mock

source_name: MIN6m9, Fv2E PERK, Mock, rep2

value: Mock


title: MIN6m9, Fv2E PERK, AP 24h, rep1

description: Gene expression of MIN6 Fv2E-PERK AP24h

source_name: MIN6m9, Fv2E PERK, AP 24h, rep1


title: MIN6m9, Fv2E PERK, AP 6h, rep2

description: Gene expression of MIN6 Fv2E-PERK AP6h

source_name: MIN6m9, Fv2E PERK, AP 6h, rep2


title: A-204 [miRNA]

source_name: Rhabdoid Tumor

value: human Rhabdoid Tumor cell line


title: MIN6m9, Fv2E PERK, Mock, rep1

description: Gene expression of MIN6 Fv2E-PERK Mock

source_name: MIN6m9, Fv2E PERK, Mock, rep1


title: Control KTC 24h 6h 1

source_name: ovary tissue,fish in water control

value: 6 h


title: MIN6m9, WT, Mock, rep2

description: Gene expression of MIN6 WT Mock

source_name: MIN6m9, WT, Mock, rep1

value: WT


title: MIN6m9, WT, Pal, rep3

description: Gene expression of MIN6 cells, Pal

source_name: MIN6m9, WT, Pal, rep3

value: 400 uM Palmitate 48h


title: Control KTC 24h 12h 3


title: MIN6m9, WT, Pal, rep1

description: Gene expression of MIN6 cells, Pal

source_name: MIN6m9, WT, Pal, rep1


title: Control KTC 24h 12h 2


title: MIN6m9, WT, Ole, rep1

description: Gene expression of MIN6 cells, Ole

source_name: MIN6m9, WT, Ole, rep1

value: 400 uM Oleate 48h


title: MIN6m9, WT, Mock, rep1

description: Gene expression of MIN6 WT Mock


title: MIN6m9, WT, Ole, rep3

description: Gene expression of MIN6 cells, Ole

source_name: MIN6m9, WT, Ole, rep3


title: MIN6m9, WT, Ole, rep2

description: Gene expression of MIN6 cells, Ole

source_name: MIN6m9, WT, Ole, rep2


title: Control, ID 115 [mRNA]

city: ottawa

first: hongyan

last: dong

address: 50 colombine Dr.

institute: health canada

hyb_protocol: Cy5-sample cRNA and Cy3-reference cRNA were hybridized to Agilent G4853A SurePrint G3 Rat GE 8 X 60K microarrays (Agilent Technologies Inc.) at 65°C overnight with Agilent hybridization solution.

scan_protocol: Slides were washed and scanned on an Agilent G2505B microarray scanner at 5 μM resolution and the data were acquired with Agilent Feature Extraction software version 10.7.3.1.

data_processing:
Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.
Microarray data were normalized using the transform.madata function in the MAANOVA library in R using global lowess with a span of 0.1. Differentially expressed genes were identified using the MAANOVA library in R. The Fs statistic (Cui et al., 2005) was used for the gene-specific variance components, and the associated p-values (unadjusted p) for all the statistical tests were estimated using the permutation method (30,000 permutations with residual shuffling). P-values were adjusted for multiple comparisons using the false discovery rate (FDR) approach (Benjamini et al., 2001). The least squares mean (Goodnight and Harvey, 1997; Searle et al., 1980), a function of the model parameters, was used to estimate the fold-change. Differentially expressed genes were identified if they had a FDR adjusted p-value < 0.05 and a fold change > 1.5.

organism: Rattus norvegicus

source_name: liver, control diet

label_protocol: Sample RNAs  were labelled with Cyanine 5-CTP using Low Input Quick Amp Labelling kits (Agilent Technologies Inc.) following the manufacturer’s instruction. Universal rat reference total RNA (Agilent Technologies Inc.) was labelled with Cyanine 3-CTP.

extract_protocol: Total RNA was extracted from frozen liver tissue of 4 rats from control and treatment group with mirVana miRNA isolation kits (Ambion, Inc., Foster city, CA, USA) according to the manufacturer’s instructions. RNA integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Mississauga, ON, Canada) and only high quality RNAs (RNA Integrity Number ≥ 8.0) were used for microarray analysis of miRNA expression

treatment_protocol: Male Sprague-Dawley adult rats were purchased from Charles River Laboratories (St. Constant, QC, Canada) and acclimatized for 1 week before studies began. Animals were exposed to control or PFOS-containing diet ad libitum for 28 consecutive days. Animal handling and treatment procedures were conducted according to the Guidelines of the Canadian Council of Animal Care and were approved by the Health Canada Animal Care Committee. At the end of the study, rats were killed by exsanguination under isoflurane anesthesia. Liver samples were collected and stored at -80°C.

tag: strain

value: Sprague-Dawley

tag: gener

value: adult

value: liver

source_name: Universal rat reference total RNA

tag: reference

value: Universal rat reference total RNA


title: MIN6m9, WT, Pal, rep2

description: Gene expression of MIN6 cells, Pal

source_name: MIN6m9, WT, Pal, rep2


title: Control GEM 8d-2

value: 8 d

value: Gemfibrozil

value: rnaL


title: Control KTC 24h 12h 4

value: ovary

value: in water control


title: Control GEM 8d-3


title: MIN6m9, WT, UT, rep3

description: Gene expression of MIN6 cells, UT

source_name: MIN6m9, WT, UT, rep3

value: Untreated


title: 50 mg/kg diet, ID 401 [mRNA]

source_name: liver, PFOS-containing diet

value: male

tag: age


title: Control GEM 8d-5

tag: scan date


title: 50 mg/kg diet, ID 408 [mRNA]

tag: tissue


title: Control KTC 24h 12h 1

tag: age (month)

value: rnaYYY


title: MIN6m9, WT, UT, rep1

description: Gene expression of MIN6 cells, UT

source_name: MIN6m9, WT, UT, rep1

tag: treatment


title: Control GEM 8d-4

tag: treatment duration


title: Control GEM 8d-1

tag: experiment


title: Control, ID 106 [mRNA]


title: Control FLU PHASE3 96hp E

value: post-96 h

value: rnaB


title: Control FLU PHASE3 96hp C


title: CD4+PD1-, biological rep3

city: London

first: Nathan

last: Johnston

state: Ontario

address: 339 Windermere Road

department: Pathology

institute: Western University

description: miRNA expression data from PD1- CD4 T cells

hyb_protocol: Biotinylated RNA were hybridized for 16 hrs at 48C on an Affymetrix GeneChip 3.0 miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 and Affymetrix GeneChip Command Console software

data_processing: The data were analyzed with Partek Genomics Suite

label: Biotin

source_name: CD4 T cell lacking expression of PD1

label_protocol: total RNA (500 ng) were biotin-labeled with the FlashTag Biotin HSR RNA Labeling Kit according to the manufacturer's instructions.

growth_protocol: B16F10 cells were injected subcutaneously into the backs of C57BL/6 mice and 16 days later lymph nodes and spleens were excised.

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

treatment_protocol: Lymph nodes and spleens were pressed through a 40 um strainer, washed with PBS, and stained with antibodies for FACS. Sorted cells were placed in Qiazol solution for total RNA extraction.

value: CD4 T cell lacking expression of PD1

value: lymph node/spleen


title: 50 mg/kg diet, ID 402 [mRNA]


title: AE104(delta 7) with 10 µM ZnCl2 replicate 2

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

country: Germany

hyb_protocol: Hybridisation was done by the service provider IMGM Laboratories GmbH (Martinsried)

scan_protocol: Agilent DNA microarray Scanner were used by the service provider IMGM Laboratories GmbH (Martinsried)

data_processing: First, dark and light control spots, and foreign DNA control spots were deleted. Secondly, if genes were represented by more than one spot, the mean value coming from these two, three or more spots was used and assigned to the gene number. The mean intensity of the pixels of the surrounding area was subtracted from the mean density of the pixels of the spots to give the signal strength

organism: Cupriavidus metallidurans CH34

source_name: cells of C. metallidurans

label_protocol: Labeling was done by the service provider IMGM Laboratories GmbH (Martinsried)

growth_protocol: C. metallidurans strains were grown in Mineral salts medium + 0.2 % Na-gluconate with ZnCl2 or EDTA to a cell turbidity of 100 Klett, then  cells were harvest by centrifugation for 1' at 4°C in 2.0 ml Tubes.

extract_protocol: RNeasy Mini Kit (Qiagen) was used according to the manufacturers manual including on-column DNase digestion. PCR were done to check for DNA contaminations, only RNA was used that did not generate products in the PCR reaction. RNA quality was checked on formamide gels and measured as RIN on Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

tag: genotype

value: AE104(delta 7)

value: 10 uM ZnCl2


title: 50 mg/kg diet, ID 404 [mRNA]

value: Sprague-Dawley

value: adult


title: Control, ID 110 [mRNA]

value: liver

value: Universal rat reference total RNA


title: Control FLU PHASE3 96hp D

tag: sampling date


title: AE104(delta 7) with 10 µM ZnCl2 replicate 3


title: CD4+PD1-, biological rep1


title: CD4+PD1+, biological rep3

description: miRNA expression data from PD1+ CD4 T cells

source_name: CD4 T cell expressing PD1

value: CD4 T cell expressing PD1


title: CD4+PD1-, biological rep2


title: AE104(delta 7) with 50 µM EDTA replicate 3

value: 50 uM EDTA


title: CD4+PD1+, biological rep1


title: AE104(delta 7) with 10 µM ZnCl2 replicate 1


title: MIN6m9, WT, UT, rep2

description: Gene expression of MIN6 cells, UT

source_name: MIN6m9, WT, UT, rep2

value: WT


title: CD4+PD1+, biological rep2


title: Control, ID 105 [mRNA]


title: 318a

city: Odense C

first: Martin

middle: Jakob

last: Larsen

address: Sdr. Boulevard 29

department: Dept. of Clinical Genetics

country: Denmark

institute: Odense University Hospital

hyb_protocol: Hybridization and washing were performed according to manufacture’s recommendations in a low ozone environment.

scan_protocol: Scanned using a Agilent G2565CA Microarray scanner

data_processing: Scanned images were quantified using Agilent Feature Extraction Software (version 10.7.3.1). Bad quality features flagged during feature extraction were removed and the remaining data were pre-processed. Data were background corrected (normexp, offset=50), then within-array normalized by loess normalization method and between-array normalizatized by the quantile method. The normalized values were used to calculate log2 transformed Cy5/Cy3 ratios. Replicate probes were collapsed by calculating the median. Probes without gene symbol annotation were filtered out. In cases of multiple probes per gene symbol only the probe with the maximum mean (Cy5) intensity was kept. Missing expression values were imputed by k-nearest neighbors averaging (k = 10).

source_name: Breast tumor tissue

label_protocol: RNA was amplified and labeled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted from freshly frozen tumor tissue using Trizol Reagent (Invitrogen) and RNeasy Micro Kit (Qiagen).

value: Premenopausal

tag: who

value: Invasive ductal carcinoma

tag: grade

tag: group

value: LumB

tag: er

tag: pr

value: FALSE

source_name: Universal Human Reference RNA (Stratagene)


title: AE104(delta 7) with 50 µM EDTA replicate 2


title: Control FLU PHASE3 96hp B

source_name: ovary tissue,fish in water control

value: ovary

value: in water control

value: post-96 h

tag: rna date

tag: rna person

tag: chip id


title: 319a

tag: age

value: Invasive lobular carcinoma

value: LumA

tag: reference

value: Universal Human Reference RNA (Stratagene)


title: 321a


title: AE104(delta 7) with 50 µM EDTA replicate 1

value: AE104(delta 7)


title: 312a

value: Metaplastic carcinoma

value: Basal

value: Sporadic-like


title: 317a

value: Normal


title: Control FLU PHASE3 96hp A

tag: tissue

tag: scan date

value: rnaB


title: Control FLU PHASE3 96h E

tag: age (month)

tag: treatment


title: Control FLU PHASE3 96h D

tag: treatment duration

tag: experiment


title: 174a


title: Control FLU PHASE3 96h C

tag: sampling date


title: 280a

value: Postmenopausal

tag: who


title: 301a

value: Premenopausal

tag: grade

value: TRUE


title: Control FLU PHASE3 96h A


title: Control FLU PHASE3 48hp C

value: post-48 h


title: Control FLU PHASE3 48hp E


title: Control FLU PHASE3 48hp B


title: 294a

value: Other

tag: group

value: FALSE


title: Control FLU PHASE3 48hp A

value: ovary

value: in water control


title: 282a

value: Invasive ductal carcinoma

value: LumB

tag: er


title: Control FLU PHASE3 48hp D


title: Control FLU PHASE3 48h A


title: 303a

tag: pr

value: Universal Human Reference RNA (Stratagene)


title: 271a


title: Control FLU PHASE3 96h B

tag: rna date


title: Control FLU PHASE3 48h D

tag: rna person


title: 299a

value: LumA


title: 207a


title: Control FLU PHASE3 24hp D

value: post-24 h

tag: chip id


title: 261a

tag: age


title: Control FLU PHASE3 48h C


title: Control FLU PHASE3 24hp C


title: 277a

tag: reference


title: 288a


title: 250a

value: Perimenopausal

value: Invasive lobular carcinoma


title: 253a


title: Control FLU PHASE3 48h B

tag: tissue


title: 270a

value: Sporadic-like


title: nub-MiT wing 3

city: Syracuse

first: Francesca

last: Pignoni

state: NY

address: 766 Irving Ave, 5322 Weiskotten Hall

department: Department of Ophthalmology

institute: SUNY Upstate Medical University

hyb_protocol: Arrays were hybridized in a Hybridization Oven 640

scan_protocol: scanned in GeneChip Scanner 7G Plus

data_processing: The gene expression levels were summarized using GCRMA method. P-values were corrected for multiple comparisons using Benjamini-Hochberg’s False Discovery Rate (FDR) method.

organism: Drosophila melanogaster

source_name: MiT overexpressed wing discs

label_protocol: 500 ng of total RNA were processed at the SUNY upstate Microarray Core Facility using the Affymetrix 3' IVT Express Kit.

growth_protocol: Drosophila larvae grow at 25oC in normal food

extract_protocol: homogenize the tissues and extract total RNA extraction from TRIzol following the protocol

treatment_protocol: L3 larval tissues were dissected and collected in TRIzol Reagent on ice

value: L3 larvae tissues


title: nub-MiT wing 2


title: Control FLU PHASE3 24hp B

tag: scan date

value: rnaB


title: 249a

value: Postmenopausal


title: Control FLU PHASE3 24hp A

tag: age (month)


title: Control FLU PHASE3 24h D

tag: treatment


title: wt wing 1

source_name: wt wing discs


title: wt wing 3


title: 236a

value: Premenopausal


title: wt wing 2


title: EMSTZ2 HD-MT 3

source_name: MiT mutant hindgut-malpighian tubules


title: Control FLU PHASE3 24h E

tag: treatment duration


title: Control FLU PHASE3 24h B

tag: experiment


title: Control FLU PHASE3 24h C

tag: sampling date


title: nub-MiT wing 1


title: 226a

tag: who


title: 227a

tag: grade


title: Control FLU PHASE3 192hp D

value: post-192 h


title: 245a

tag: group

value: Normal

value: TRUE


title: 333a

tag: er

value: FALSE


title: EMSTZ2 HD-MT 1


title: EMSTZ2 HD-MT 2


title: 336a

tag: pr


title: 331a


title: Control FLU PHASE3 24h A

value: ovary

value: in water control

tag: rna date


title: wt HD-MT 1

source_name: wt hindgut-malpighian tubules


title: Control FLU PHASE3 192hp B

tag: rna person


title: Skeletal Muscle Sample 24 (experiment, low-force)

city: Iowa City

first: Richard

last: Shields

address: 1-252 Medical Education Building

institute: The University of Iowa

description: RMA expression value derived from Partek Genomic Suites

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer and placed onto Affymetrix Human Exon 1.0 ST arrays. Hybridizations were performed by the DNA Core Facility at the University of Iowa.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the GeneChip operating software (GCOS) v1.4.

data_processing: Arrays were normalized using a Robust Multi-array Average (RMA) and transformed into a log2 hybridization signal using Partek Genomic Suites (v6.6 Copyright © 2013 Partek Inc., St. Louis, MO, USA).

source_name: skeletal muscle, experiment, low-force

label_protocol: 5μg of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

extract_protocol: Following harvest, muscle biopsy samples were immediately placed In RNALater (Ambion) and stored at -80 C until further use. Total RNA was extracted using TRIzol solution (Invitrogen) according to the manufacturer’s instructions. 50 ng of RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN MinElute Reaction Cleanup column (QIAGEN Cat #28204) according to modifications from NuGEN. Four μg of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.

treatment_protocol: Subjects completed a single unilateral session of low or high force exercise 3 hours before a muscle biopsy or subjects unilaterally trained one limb with exercise.

value: skeletal muscle

tag: gender

value: male

value: experiment, low-force


title: 328a

tag: age

value: Invasive ductal carcinoma

value: LumB

value: Universal Human Reference RNA (Stratagene)


title: Skeletal Muscle Sample 23 (control, high-force)

source_name: skeletal muscle, control, high-force

value: control, high-force


title: wt HD-MT 3

value: L3 larvae tissues


title: Control FLU PHASE3 192hp A

value: rnaB

tag: chip id


title: 214a

value: Basal

tag: reference


title: Control FLU PHASE3 192hp C

tag: tissue

tag: scan date


title: Control FLU PHASE3 192h F

tag: age (month)

tag: treatment


title: Skeletal Muscle Sample 22 (control, low-force)

source_name: skeletal muscle, control, low-force

value: control, low-force


title: wt HD-MT 2


title: 211a

value: Postmenopausal

value: LumA


title: 222a


title: Skeletal Muscle Sample 21 (experiment, high-force)

source_name: skeletal muscle, experiment, high-force

value: experiment, high-force


title: 204a

value: Premenopausal

value: Normal

value: FALSE


title: Control FLU PHASE3 192h D

value: ovary

value: in water control

tag: treatment duration

tag: experiment


title: Control FLU PHASE3 192h E

tag: sampling date


title: 215a

tag: who

value: Invasive lobular carcinoma


title: 202a

value: Invasive ductal carcinoma

tag: grade

tag: group


title: Skeletal Muscle Sample 20 (experiment, low-force)

value: skeletal muscle

value: male

value: experiment, low-force


title: Control FLU PHASE3 192h C


title: Control FLU PHASE3 192h B


title: 209a

value: LumB

tag: er

tag: pr

value: Sporadic-like

value: Universal Human Reference RNA (Stratagene)


title: Skeletal Muscle Sample 19 (control, high-force)

value: control, high-force


title: Control FLU 1-12h 8h 4

value: 8 h

tag: rna date

tag: rna person

value: rnaDDD


title: Control FLU PHASE3 192h A

value: rnaB


title: Control FLU 1-12h 8h 3


title: 192a

value: Premenopausal

tag: age

value: LumA


title: Skeletal Muscle Sample 15 (control, high-force)

tag: gender


title: Skeletal Muscle Sample 16 (experiment, low-force)


title: Control FLU 1-12h 8h 2

tag: chip id


title: 190a

value: FALSE

tag: reference


title: Skeletal Muscle Sample 18 (control, low-force)

tag: tissue

value: control, low-force


title: Skeletal Muscle Sample 17 (experiment, high-force)

value: experiment, high-force


title: Skeletal Muscle Sample 12 (experiment, low-force)


title: Skeletal Muscle Sample 11 (control, high-force)


title: TNs_control_OE

description: gene expression after 18day culture since EBs

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hours at 65°C in a rotating hybridization oven.

source_name: NSPCs derived from mouse ES cells

tag: cell type

value: NSPCs

tag: culture type

value: neurosphere (passeage 2)


title: Control FLU 1-12h 4h 3

value: ovary

tag: age (month)

tag: treatment

value: in water control

tag: treatment duration

value: 4 h

tag: scan date


title: 161a

tag: who

value: Invasive ductal carcinoma

tag: grade


title: 151a

tag: group

value: Basal

tag: er


title: Control FLU 1-12h 4h 4

tag: experiment

tag: sampling date

tag: rna date


title: Skeletal Muscle Sample 13 (experiment, high-force)

value: skeletal muscle

tag: gender

value: male


title: 185a

tag: age

tag: pr

value: Universal Human Reference RNA (Stratagene)


title: 146a

value: Postmenopausal

tag: reference


title: Control FLU 1-12h 4h 2

tag: tissue

tag: rna person

value: rnaDDD

tag: chip id


title: 177a

value: Premenopausal


title: SNs_CT

description: miRNAs expression after 12day culture since EBs

hyb_protocol: miRNA was hybridized to Agilent 8x15K mouse miRNA Microarray Kit, Rel.12.0 (Agilent Technologies) by Agilent’s miRNA Complete Labeling and Hybridization Kit V2 (Protocol Version 2.1, Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Microarray Scanner (G2505B) using 5um scan resolution.

data_processing: Array data were normalized with Genespring GX (Agilent). Data Transformation: Set measurements less than 1 to 1.

source_name: NSPCs derived from WT/NFIA mixed sphere (Passeage 1, NFIA OE line)

label_protocol: Total RNA samples were labeled by Agilent’s miRNA Complete Labeling and Hybridization Kit V2 (Protocol Version 2.1, Agilent Technologies).

extract_protocol: Total RNA containing the small fraction was isolated from each sample using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. Quality was confirmed using the Agilent 2100 Bioanalyzer.

tag: cell type

tag: culture type

value: neurosphere (paseage 1)


title: TNs_miR-153_OE


title: 145a

value: LumA

value: FALSE


title: Control FLU 1-12h 8h 1

tag: age (month)

tag: treatment

tag: treatment duration

value: 8 h

tag: scan date


title: Skeletal Muscle Sample 10 (control, low-force)

value: control, low-force


title: Skeletal Muscle Sample 9 (experiment, high-force)

value: experiment, high-force


title: 178a

tag: who

tag: grade

tag: group

tag: er


title: SNs_NFIA_OE

source_name: NSPCs derived from WT/NFIA mixed sphere (Passeage 1, WT)

value: NSPCs


title: Control FLU 1-12h 2h 4

value: ovary

value: in water control

value: 2 h

tag: experiment

tag: sampling date

tag: rna date


title: Control FLU 1-12h 4h 1

value: 4 h


title: 166a

tag: age

value: Invasive ductal carcinoma

tag: pr

tag: reference


title: PNs_CT

description: miRNAs expression after 6day culture since EBs

source_name: NSPCs derived from WT/NFIA mixed sphere (Passeage 0, NFIA OE line)

value: neurosphere (paseage 0)


title: Skeletal Muscle Sample 8 (experiment, low-force)

tag: tissue

value: skeletal muscle

tag: gender

value: male

value: experiment, low-force


title: Control FLU 1-12h 2h 3

tag: rna person

value: rnaDDD

tag: chip id


title: Skeletal Muscle Sample 7 (control, high-force)

tag: treatment

value: control, high-force


title: Control FLU 1-12h 2h 2

tag: age (month)

tag: treatment duration


title: 141a

value: Postmenopausal

value: LumB

value: Universal Human Reference RNA (Stratagene)


title: PNs_NFIA_OE

source_name: NSPCs derived from WT/NFIA mixed sphere (Passeage 0, WT)

tag: cell type

tag: culture type


title: 135a

value: Premenopausal

tag: who

tag: grade

tag: group

value: Basal

value: FALSE


title: 134a

value: Perimenopausal

tag: er


title: Control FLU 1-12h 2h 1

value: ovary

value: in water control

tag: experiment

tag: sampling date

tag: scan date

tag: rna date


title: HT_44T_H036 rep2

city: Gueishan Township

first: Chun-Nan

last: Yeh

state: Taoyuan County

address: No.5, Fusing St.

department: General Surgery

country: Taiwan

institute: Chang Gung Medical Foundation

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50C, non-speciﬁc binding targets were washed away by three different washing steps (Wash I: 42C 5 mins; Wash II: 42C, 5 mins, 25C 5 mins; Wash III: rinse 20 times)

scan_protocol: The arrays were scanned by GenePix 4200A 01 Autoloader (635nm power 100 PMT 320 ; 532nm power 10, PMT 335) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method. Normalize intensities: Median scaling performed on data set without flagged and control data.  Merge technical replicate data: Average intensity values calculated on technical replicates ['avrg_data.txt' available on Series records].
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: 6 IU/g Vit. D supplemented_tumor

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: Animals were fed with different diet and then TAA was used to induce tumorgenesis.

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280>1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN>8).

treatment_protocol: Animals were sacrificed and then tissue were dissected and immersed in liquid nitrogen. The samples were kept at -80C before RNA extraction.

tag: strain background

value: Sprague Dawley

tag: diet

value: supplemented with 6 IU/g vitamin D3(+6D)

tag: animal model

value: TAA-induced rat intrahepatic cholangiocarcinoma model

tag: tissue

value: tumor part


title: Skeletal Muscle Sample 4 (experiment, low-force)

value: skeletal muscle

tag: gender

value: male

tag: treatment


title: Control FLU 1-12h 1h 4

tag: age (month)

tag: treatment duration

value: 1 h

tag: rna person

value: rnaDDD

tag: chip id


title: Skeletal Muscle Sample 5 (experiment, high-force)

value: experiment, high-force


title: HT_42T_H031 rep1


title: Control FLU 1-12h 1h 1


title: HT_42T_H032 rep2


title: 132a

source_name: Breast tumor tissue

value: Postmenopausal

tag: age

tag: who

value: Invasive lobular carcinoma

tag: grade

value: LumA

tag: pr

tag: reference


title: HT_41T_H028 rep2


title: Control FLU 1-12h 1h 3

tag: experiment

tag: sampling date

tag: scan date


title: Skeletal Muscle Sample 2 (control, low-force)

value: control, low-force


title: Skeletal Muscle Sample 3 (control, high-force)

value: control, high-force


title: 113a

value: Invasive ductal carcinoma

tag: group

value: LumB

tag: er

value: Sporadic-like

value: FALSE

source_name: Universal Human Reference RNA (Stratagene)


title: HT_41T_H027 rep1

tag: strain background

value: Sprague Dawley

tag: diet

value: supplemented with 6 IU/g vitamin D3(+6D)

tag: animal model

tag: tissue


title: 120a

value: Premenopausal

value: Universal Human Reference RNA (Stratagene)


title: Skeletal Muscle Sample 6 (control, low-force)

value: skeletal muscle

tag: gender

value: male

tag: treatment


title: Control FLU 1-12h 1h 2

source_name: ovary tissue,fish in water control

value: ovary

tag: age (month)

value: in water control

tag: treatment duration

value: 1 h

tag: rna date

tag: rna person

value: rnaDDD

tag: chip id


title: 121a

tag: age

tag: who

tag: grade

tag: pr

tag: reference


title: 126a

tag: group

tag: er


title: Control FLU 1-12h 12h 4

tag: experiment

tag: sampling date

tag: scan date


title: 110a

value: Basal


title: HT_44T_H035 rep1

tag: strain background

tag: gender

tag: diet

tag: animal model

value: TAA-induced rat intrahepatic cholangiocarcinoma model

tag: tissue

value: tumor part


title: Control FLU 1-12h 12h 3

tag: age (month)

tag: treatment

tag: treatment duration

tag: rna date

tag: rna person


title: HT_27T_H024 rep2

source_name: 2 IU/g Vit. D supplemented_tumor

value: supplemented with 2 IU/g vitamin D3(+2D)


title: 105a

value: Postmenopausal

tag: age

tag: who

value: Invasive ductal carcinoma

tag: grade

value: LumB

tag: pr


title: Control FLU 1-12h 12h 2

tag: experiment

tag: chip id


title: CT_27T_H023 rep1

value: Sprague Dawley


title: 107a

tag: group

tag: er

value: FALSE

tag: reference


title: Skeletal Muscle Sample 1 (experiment, high-force)

tag: gender

value: experiment, high-force


title: 104a

value: LumA

value: Universal Human Reference RNA (Stratagene)


title: CT_21T_H019 rep1

tag: strain background

value: male

tag: diet

tag: animal model


title: CT_18T_H016 rep2

tag: tissue


title: CT_21T_H020 rep2


title: Control FLU 1-12h 12h 1

value: ovary

tag: age (month)

tag: treatment

tag: treatment duration

tag: sampling date

tag: scan date


title: Control FAD Phase3 96hp 7

value: in water control

value: 96 h post

tag: rna date

tag: rna person

value: rnaR


title: Control FAD Phase3 96hp 8

tag: experiment


title: cAMP1_062211

first: Stephen

middle: J

last: Renaud

address: 1151 Richmond St, MSB428

institute: University of Western Ontario

description: Gene expression data from BeWo trophoblast cells exposed to 250 uM 8-Br-cAMP for 24h

hyb_protocol: RNA samples hybridized to Affymetrix U133 2.0 DNA microarray chip using GeneChIP Hybridization Oven 640 (Affymetrix). Washing was performed using Genechip fluidics station 450 (Affymetrix).

scan_protocol: Scanning was performed using Affymetrix Genechip Scanner 3000 with autoloader.

data_processing: Hybridization signals were normalized to internal controls using the MAS5 algorithm in the Expression Console (Affymetrix). Analysis was limited to probe sets changing at least 2-fold between groups, with signal strengths ≥ 300 for the maximal value. Significant differences were determined by t-tests.

label: biotin

source_name: BeWo cells, cAMP-differentiated

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

growth_protocol: Cells were grown in DMEM/F12 media supplemented with 10% FBS and pennicilin/streptomycin in standard culture conditions (5% CO2, 37 C)

extract_protocol: Trizol-based extraction of total RNA (according to the manufacturer's protocol)

treatment_protocol: 8-bromo-cyclic adenosine monophosphate, 250 uM, 24 h

tag: cells

value: Choriocarcinoma trophoblast cells

tag: cell state

value: cAMP-differentiated

value: 250 uM 8-Br-cAMP for 24h


title: 103a

tag: age

tag: who

tag: grade

tag: group

tag: er

tag: pr


title: Control FAD Phase3 96hp 5

tag: tissue

tag: chip id


title: Cont3_062211

description: Gene expression data from BeWo trophoblast cells maintained in undifferentiated conditions

source_name: BeWo cells, undifferentiated

value: undifferentiated

tag: treatment


title: CT_18T_H015 rep1

tag: strain background

tag: gender

tag: diet

value: supplemented with 2 IU/g vitamin D3(+2D)

tag: animal model

value: TAA-induced rat intrahepatic cholangiocarcinoma model

value: tumor part


title: 098a

value: Premenopausal

value: Invasive ductal carcinoma

value: Basal

value: Sporadic-like

tag: reference


title: 089a

value: LumA

value: FALSE

value: Universal Human Reference RNA (Stratagene)


title: 50 mg/kg diet, ID 404 [miRNA]

hyb_protocol: Labelled RNA was hybridized on 8 X 15K Agilent rat miRNA microarray slides. 55C 20 rpm overnight.

scan_protocol: Arrays were scanned using an Agilent G2505B scanner (5 μM resolution).

data_processing:
Feature extraction (version 10.7.3.1, Agilent Tech. Inc.) was used to acquire the fluorescence intensity of each probe
Data were normalized in R using cyclic-lowess (Bolstad et al., 2003). Ratio-intensity plots, boxplots and cluster analyses were used to identify potential outliers. Seven samples passed the quality control tests and were used for subsequent analyses

source_name: liver, PFOS-containing diet

label_protocol: samples were labelled with Cy3 using miRNA Complete Labelling and Hybridization kit (Agilent Technologies Inc.)

tag: strain

value: Sprague-Dawley

tag: gener

value: male

value: Adult


title: LT_8T_H012 rep2

value: Sprague Dawley

value: control


title: Control FAD Phase3 96hp 4

hyb_protocol: The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.

value: ovary

tag: age (month)

value: in water control

tag: treatment duration

value: 96 h post

tag: experiment

tag: sampling date

tag: scan date

tag: rna date

tag: rna person

value: rnaR


title: cAMP2_062211

tag: cells

value: Choriocarcinoma trophoblast cells

tag: cell state

value: cAMP-differentiated

value: 250 uM 8-Br-cAMP for 24h


title: Control FAD Phase3 96hp 6

tag: tissue

tag: treatment

tag: chip id


title: Cont2_062211

value: undifferentiated


title: Cont1_062211


title: 086a

value: Postmenopausal

tag: age

tag: who

value: Invasive ductal carcinoma

tag: group

tag: er

tag: pr


title: Control, ID 106 [miRNA]

source_name: liver, control diet

tag: strain

tag: gener


title: LT_3T_H008 rep2

tag: strain background

tag: gender

tag: diet

tag: animal model

value: TAA-induced rat intrahepatic cholangiocarcinoma model

value: tumor part


title: 097a

value: Premenopausal

tag: grade

value: LumB

value: Sporadic-like

tag: reference

value: Universal Human Reference RNA (Stratagene)


title: Control FAD Phase3 96hp 3

tag: age (month)

tag: treatment duration

tag: experiment

tag: sampling date

tag: scan date

tag: rna date

tag: rna person


title: Control, ID 115 [miRNA]

value: Sprague-Dawley

value: male

tag: age

value: Adult


title: 50 mg/kg diet, ID 401 [miRNA]


title: cAMP3_062211

tag: cells

tag: cell state

tag: treatment


title: WT Adult cortex reg VP1_4C

type: SRA

city: Madrid

first: Ana

last: Losada

state: Madrid

address: C/ Melchor Fernández Almagro, 3.

department: Molecular Oncology Programme

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

description:
6cutter 4C sequencing
processed data file: Brain_Ebrain_l3.txt.zip
raw data file is available on sample GSM1841823

library_source: genomic

data_processing:
Library strategy: 4C-seq
Read files were quality-checked with FastQC.
Convert BAM files to FASTQ using bedtools v2.20.1 where needed
Transform to Illumina FASTQ using NGSQCToolkit v2.3
Convert and process (map, calculate cis interactions) FASTQ files using 4cseqpipe
Genome_build: GRCm37/mm9
Supplementary_files_format_and_content: Processed data files are 4cseqpipe mapped files for each original FASTQ/BAM file. They allow to generate figures for interactions around the viewpoints with 4cseqpipe

molecule: genomic DNA

source_name: cortex

extract_protocol:
Preparation of 4C samples was performed as described (van de Werken, 2012) with some modifications. Freshly collected tissues were incubated with collagenase (0.0065% collagenase I in 10% FBS/PBS for cortex, and 1.33 mg/ml collagenase P in HBSS for pancreas) for 40 min at 37ºC in a shaker. The resulting cell suspension was filtered through a 40-μm cell strainer in order to get a single cell preparation. Cells were centrifuged at 1,100 rpm for 5 min at RT and the cell pellet was resuspended in 10 ml of fixing solution containing 2% formaldehyde in 10% FBS/PBS. After 10 min, 0.125 M glycine was added to stop fixation and the mixture was incubated for 5 min at RT. Cells were pelleted and nuclei isolated upon incubation in cold lysis buffer in the following conditions: For the brain, 10 min in 50 mM Tris pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100 + protease inhibitors cocktail; for the pancreas, 40 min in 50 mM Tris pH 7.5, 50 mM NaCl, 5 mM EDTA, 1% NP40, 2% TX-100 + protease inhibitors cocktail. Proper lysis was determined by methyl green-pyronin staining.
4C-seq libraries were amplified using long primers with 18-21 bp homology to the bait sequence and Illumina paired-end adapter flanks. HindIII and CvIQ (NEB) were used as as first and second cutters, respectively for preparation of the 6-cutter libraries. DpnII and CvIQ (NEB) were used as first and second cutters, respectively for preparation of the 4-cutter libraries.  Pairs of samples were sequenced together thus the raw and processed data files are shared among samples. The 4cseqpipe software identifies the viewpoints and the possible cut points out of the raw data files and flags them in the processed files.

tag: strain

value: 8-10 week old


title: 50 mg/kg diet, ID 408 [miRNA]

tag: gener


title: 076a

tag: who

tag: group

value: Basal

tag: er

tag: pr


title: Control FAD Phase3 96hp 1

data_processing: Microarray image processing was performed using the latest Agilent's Feature Extraction software available at the time following the manufacturer’s protocol and recommendations.  Data processing was conducted using R package Limma.

tag: tissue

value: ovary

tag: age (month)

value: in water control

value: 96 h post

value: rnaR

tag: chip id


title: LT_1T_H004 rep2

tag: strain background

value: Sprague Dawley

tag: gender

tag: diet

value: control

tag: animal model


title: Skeletal Muscle Sample 14 (control, low-force)

source_name: skeletal muscle, control, low-force

value: skeletal muscle

value: control, low-force


title: Control FAD Phase3 96hp 2

tag: treatment duration

tag: experiment

tag: sampling date

tag: scan date

tag: rna date

tag: rna person


title: 50 mg/kg diet, ID 402 [miRNA]

tag: strain

tag: gener

tag: age


title: Control, ID 110 [miRNA]


title: LT_8T_H011 rep1

value: TAA-induced rat intrahepatic cholangiocarcinoma model

value: tumor part


title: WT Adult pancreas reg VP1_4C

description:
6cutter 4C sequencing
processed data file: Pancreas_KOEBrain_l4.txt.zip
raw data file is available on sample GSM1841825

source_name: pancreas


title: Control FAD Phase3 96h 8

tag: treatment


title: oral cancer cell_foeced-expression of SDF-1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: These cells were transfected with SDF-1 expression vector.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: forced-expression of SDF-1 cell

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle Medium (DMEM;SIGMA,St. Louis, MO, USA) supplemented with 10% fetal calf serum, 100 μg/ml streptomycin, and 100U/ml penicillin in a humidified atmosphere of 95% air and 5% CO2 at 37℃.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

tag: cell

value: tougue cancer cell


title: KO SA1 KO E17.5 cortex Pcdhg-R1_4C

description:
6cutter 4C sequencing
processed data file: HPancreas_KOEbrain_l5.txt.zip
raw data file is available on sample GSM1841824

source_name: whole brain

value: E17.5 embryo


title: 073a

value: Postmenopausal

tag: who

value: Invasive ductal carcinoma

tag: grade

tag: group

value: LumA

tag: er

tag: pr

value: FALSE

tag: reference

value: Universal Human Reference RNA (Stratagene)


title: Control FAD Phase3 96h 6

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 µm resolution

label_protocol: cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling Kit; Agilent, Palo Alto, CA)

extract_protocol: Total RNA was isolated from ovary tissue of both fathead minnow using RNeasy kits (Qiagen, Valencia, CA, USA). RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and RNA was quantified spectrophotometrically (Nanodrop). Total RNA samples were stored at -80oC until used for microarray analyses.

tag: tissue

value: ovary

tag: age (month)

tag: treatment duration

tag: chip id


title: Control FAD Phase3 96h 7

value: in water control

tag: experiment

tag: sampling date

tag: scan date

tag: rna date


title: 078a

tag: age


title: 066a

value: Premenopausal

value: Medullary carcinoma

value: Basal

value: TRUE


title: oral cancer cell_mock

description: These cells were transfected with empty vector.

source_name: mock cell

treatment_protocol: Cells were maintained in Dulbecco's Modified Eagle Medium (DMEM;SIGMA,St. Louis, MO, USA) supplemented with 10% fetal calf serum, 100 μg/ml streptomycin, and 100U/ml penicillin in a humidified atmosphere of 95% air and 5% CO2 at 37℃.


title: LT_3T_H007 rep1

tag: strain background

value: Sprague Dawley

tag: gender

value: male

tag: diet

value: control

tag: animal model


title: Control FAD Phase3 96h 4

tag: treatment

tag: rna person

value: rnaR


title: 002a

tag: group

value: LumB

tag: er

tag: pr


title: KO SA1 KO E17.5 cortex Pcdhg-R2_4C

tag: strain

value: E17.5 embryo


title: 006a

tag: who

tag: grade

tag: reference


title: LT_1T_H003 rep1

value: TAA-induced rat intrahepatic cholangiocarcinoma model

tag: tissue

value: tumor part


title: Control FAD Phase3 96h 5

tag: age (month)

tag: treatment duration

tag: experiment

tag: sampling date

tag: scan date

tag: chip id


title: Adult pancreas Pcdhg-R2_4C

description:
6cutter 4C sequencing
processed data file: 2nd_Pancreas,txt.zip
raw data file is available on sample GSM1841821

tag: age

value: 8-10 week old


title: 003a

value: Invasive lobular carcinoma

value: LumA

value: FALSE


title: Wt E17.5 cortex Pcdhg-R1_4C

description:
6cutter 4C sequencing
processed data file: Hpancreas_Ebrain_l4.txt.zip
raw data file is available on sample GSM1841822


title: Wt E17.5 cortex Pcdhg-R2_4C


title: Adult pancreas Pcdhg-R1_4C

description:
6cutter 4C sequencing
processed data file: Pancreas.txt.zip
raw data file is available on sample GSM1841820


title: MCF7EV16_dox_20hE2_rep2

city: Suita

first: Jonas

middle: Nørskov

last: Søndergaard

state: Osaka

address: IFReC Research Building, Osaka University 3-1 Yamadaoka

department: Center for Infectious Disease Education and Research (CIDER)

institute: Osaka University

description: MCF7EV16 control clone replicate 2 were treated with doxycyline for a total of 68h. After the first 24h, cells were serum starved for 24h to synchronize the cells. Subsequently, cells were released with 10 nM estradiol during the last 20 hours of culturing.

hyb_protocol: Standard Illumina hybridization protocol for Whole-Genome Gene Expression DASL Assays

scan_protocol: Standard Illumina scanning protocol for Whole-Genome Gene Expression DASL Assays

data_processing: The data were exported from GenomeStudio and normalised using quantile normalisation with the lumi package available in R

source_name: Breast Cancer Cell line (MCF7)

label_protocol: Biotinylated cRNA was prepared with the Whole-Genome Gene Expression DASL Assay with UDG for Illumina arrays

extract_protocol: RNA was extracted with the Quick RNA miniprep kit (Zymoresearch) and quantitated by NanoDrop, RiboGreen and MultiNA

tag: treatment

value: 68h doxycyline and 20h estradiol

tag: vector

value: MCF7EV16 Empty control vector


title: ∆gprH_MM vs ∆gprH_8h no carbon_3

city: Ribeirao Preto

first: Neil

last: Brown

address: Av. do Cafe

country: Brazil

institute: USP

description: Biological rep 3 of 3

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent’s instruction

scan_protocol: Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. After data were processed using TIGR platform. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test).

organism: Aspergillus nidulans

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for SEB-treated samples) for 2 hours at 40 oC.

growth_protocol: All A. nidulans strains were grown in MM for 24h, washed twice with dH2O and then transferred to MM without carbon for 4 and 8 hours.

extract_protocol: Total RNA was extracted with RNeasy® Plant Mini Kit  (Qiagen) following manufacturer's instructions, followed by DNAse treatment and purification using RNeasy® Mini Kit  (Qiagen).

value: ∆gprH

tag: condition

value: MM 24h

source_name: ∆gprH_8h no carbon

value: 8h no carbon


title: Adult cortex Pcdhg-R2_4C

description:
6cutter 4C sequencing
processed data file: 2nd_Brain.txt.zip
raw data file is available on sample GSM1841819


title: Control FAD Phase3 96h 2

city: Cincinnati

first: Rong-Lin

last: Wang

address: 26 W MLK Dr

institute: US EPA

value: ovary

value: in water control

tag: rna date

tag: rna person


title: Adult cortex Pcdhg-R1_4C

description:
6cutter 4C sequencing
processed data file: Brain.txt.zip
raw data file is available on sample GSM1841818

tag: strain


title: Control FAD Phase3 96h 3


title: Control FAD Phase3 48hp 8

value: 48 h post


title: Control FAD Phase3 96h 1

value: rnaR


title: ∆gprH_MM vs ∆gprH_8h no carbon_1

description: Biological rep 1 of 3


title: MCF7EV16_dox_20hE2_rep1

description: MCF7EV16 control clone replicate 1 were treated with doxycyline for a total of 68h. After the first 24h, cells were serum starved for 24h to synchronize the cells. Subsequently, cells were released with 10 nM estradiol during the last 20 hours of culturing.


title: MCF7SC29_dox_20hE2_rep2

description: MCF7SC29 replicate 2 were treated with doxycyline for a total of 68h (to induce DC-SCRIPT expression). After the first 24h, cells were serum starved for 24h to synchronize the cells. Subsequently, cells were released with 10 nM estradiol during the last 20 hours of culturing.

value: MCF7SC29 DC-SCRIPT-inducible


title: ∆gprH_MM vs ∆gprH_4h no carbon_3

description: Biological rep 3 of 3

source_name: ∆gprH_4h no carbon

value: 4h no carbon


title: ∆gprH_MM vs ∆gprH_8h no carbon_2

description: Biological rep 2 of 3


title: MCF7SC36_dox_20hE2_rep1

description: MCF7SC36 replicate 1 were treated with doxycyline for a total of 68h (to induce DC-SCRIPT expression). After the first 24h, cells were serum starved for 24h to synchronize the cells. Subsequently, cells were released with 10 nM estradiol during the last 20 hours of culturing.

value: MCF7SC36 DC-SCRIPT-inducible


title: Control FAD Phase3 48hp 7


title: Control FAD Phase3 48hp 6


title: ∆gprH_MM vs ∆gprH_4h no carbon_2

description: Biological rep 2 of 3


title: MCF7SC29_dox_20hE2_rep1

description: MCF7SC29 replicate 1 were treated with doxycyline for a total of 68h (to induce DC-SCRIPT expression). After the first 24h, cells were serum starved for 24h to synchronize the cells. Subsequently, cells were released with 10 nM estradiol during the last 20 hours of culturing.


title: MCF7SC36_dox_20hE2_rep2

description: MCF7SC36 replicate 2 were treated with doxycyline for a total of 68h (to induce DC-SCRIPT expression). After the first 24h, cells were serum starved for 24h to synchronize the cells. Subsequently, cells were released with 10 nM estradiol during the last 20 hours of culturing.


title: Control FAD Phase3 48hp 4


title: Control FAD Phase3 48hp 3


title: ∆gprH_MM vs ∆gprH_4h no carbon_1

description: Biological rep 1 of 3


title: Control FAD Phase3 48hp 5


title: Control FAD Phase3 48hp 2


title: WT_MM vs WT_8h no carbon_2

description: Biological rep 2 of 3

source_name: WT_MM 24h

source_name: WT_8h no carbon


title: WT_MM vs WT_8h no carbon_1

description: Biological rep 1 of 3


title: WT_MM vs WT_4h no carbon_3

description: Biological rep 3 of 3

source_name: WT_4h no carbon


title: WT_MM vs WT_4h no carbon_2

description: Biological rep 2 of 3


title: WT_MM vs WT_8h no carbon_3

description: Biological rep 3 of 3


title: Control FAD Phase3 48hp 1

source_name: ovary tissue,fish in water control


title: Control FAD Phase3 48h 6


title: Control FAD Phase3 48h 7


title: Control FAD Phase3 48h 4


title: Control FAD Phase3 48h 5


title: Patient 9 MLS-10

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using 3D-Gene Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Primary myxoid liposarcoma

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA was extracted from frozen samples using the miRNeasy Mini Kit (Qiagen in Japan, Tokyo, Japan) according to the manufacturer’s instructions.

treatment_protocol: All of the sample were not received preoerative treatment.

tag: status

value: alive

tag: histology

value: pure myxoid

tag: Sex

value: F


title: Patient 7 MLS-6

value: M


title: WT_MM vs WT_4h no carbon_1

description: Biological rep 1 of 3


title: CONTROL [265-0]

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 1.1 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA)

data_processing: Subsequent data analyses were performed using the Affymetrix Expression Console version 1.1.  Method = med-polish (rma-bg,quant-norm, sketch=-1, bioc=true, lowprecision=false, usepm=true, target=0, doavg=false)) To allow comparisons of transcript levels between samples, all samples were subjected to an all-probe set scaling to target signal 100.

source_name: PBMCs

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

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Patients had been fasting over night. Blood was collected in CPT-tubes (Becton Dickinson, USA, #362782). Samples were centrifuged at room temperature for 20 minutes at 1800 g. The cell layer was collected, mixed with PBS (Invitrogen, #14190-094) and centrifuged at room temperature for 15 minutes at 300 g. The supernatant was removed and the pellet was mixed with RLT buffer (Qiagen, RNeasy Mini Kit, #74106, , Valencia, CA, USA) and β-mercaptoethanol (Sigma M-3148) and stored at -70°C until RNA extraction.

tag: diet

value: CONTROL

tag: tissue

value: PBMCs

tag: genotype

value: female

tag: time point


title: Control FAD Phase3 48h 8

tag: age (month)

tag: treatment duration

tag: experiment

tag: sampling date


title: CONTROL [265-8]

tag: age


title: MFGM [264-8]

value: MFGM


title: Control FAD Phase3 48h 3

tag: treatment

tag: scan date

tag: chip id


title: MFGM [264-0]


title: Patient 5 MLS-2

description: The same patient with Patient 2; F-2


title: Patient 8 MLS-9


title: Control FAD Phase3 48h 2

tag: rna date

tag: rna person


title: Patient 3 F-4

description: The sample was obtained from the case of myxofibrosarcoma.

source_name: Normal fat tissue

tag: status


title: Patient 6 MLS-3

tag: histology


title: Control FAD Phase3 48h 1


title: Patient 1 F-1

description: The sample was obtained from the case of leiomyosarcoma.

tag: Sex


title: Patient 2 F-2

description: The sample was obtained from the patient 5; MLS-2.


title: CONTROL [263-8]

tag: diet


title: CONTROL [263-0]

tag: tissue


title: MFGM [262-0]

tag: genotype


title: MFGM [260-8]

tag: time point


title: Control FAD Phase3 24hp 8

tag: age (month)

value: 24 h post


title: Control FAD Phase3 24hp 7

tag: treatment duration


title: MFGM [262-8]


title: MFGM [260-0]


title: #5 K/D

source_name: HeLa cells_SUV39H1 knock down

growth_protocol: Both cells were maintained in DMEM supplemented with 10% FCS

extract_protocol: 48 hours later, RNA were extracted from cells using pure link RNA mini kit (Ambion)

treatment_protocol: siRNA against SUV39H1 or negative control siRNA was transiently transfected into HeLa cells.

tag: cell line

value: HeLa

tag: cell type

value: cervical cancer


title: Control FAD Phase3 24hp 6

value: ovary

value: in water control

tag: experiment

tag: sampling date


title: #4 K/D


title: #5 Control

source_name: HeLa cells


title: CONTROL [258-8]

tag: age


title: Control FAD Phase3 24hp 5

tag: treatment

tag: scan date

value: rnaR

tag: chip id


title: CONTROL [259-8]


title: CONTROL [259-0]


title: Control FAD Phase3 24hp 4

tag: rna date

tag: rna person


title: #4 Control


title: #1 K/D


title: Control FAD Phase3 24hp 2


title: #1Control


title: CONTROL [258-0]


title: Control FAD Phase3 24h 4


title: Control FAD Phase3 24hp 1


title: CONTROL [257-8]


title: CONTROL [257-0]


title: cross2_hexaploid_generation1_rep3

city: Yokohama

first: Yeonju

last: Jung

address: Maioka-cho 641-12

department: Yokohama City University

institute: Kihara Institute for Biological Research

hyb_protocol: Hybridizations were performed at 60°C for 17 h in a hybridization chamber (Agilent Technologies).

scan_protocol: The hybridized microarrays were scanned using a DNA microarray scanner (Agilent Technologies) and signal intensities were detected from the obtained digital images using Feature Extraction software (Agilent Technologies)

data_processing: Raw fluorescence intensities (raw signal intensity > 1.0 threshold) were transformed to log scale (base 2) using GeneSpring GX software (v12.6; Agilent Technologies). For normalization, transformed signals were shifted to the 75th percentile for all arrays and to the median for all probes. Quality control was performed as follows: (1) weakly hybridized probe spots were removed using a cut-off value of the raw signal intensity in all microarray slides of <20%; (2) only probes flagged as ‘detected’ in at least one of the 10 samples were chosen; (3) repeatable probes were chosen using coefficient of variation >50%.

organism: Triticum turgidum subsp. durum x Aegilops tauschii subsp. strangulata

source_name: synthetic hexaploid

label_protocol: 500 ng of RNA were labelled using the Agilent Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies, Santa Clara, CA) with cyamine 3-cytidine 5C-triphosphate (CTP)

growth_protocol: All plants were grown in a growth chamber maintained at 22°C and 40% relative humidity, with a 16 h light (6000 lux; 64,560 fc) and 8 h dark cycle.

extract_protocol: RNA was prepared using Plant RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions

value: two-leaves seedling


title: cross2_hexaploid_generation5_rep3


title: Control FAD Phase3 24h 3


title: CONTROL [254-8]


title: MFGM [256-0]


title: cross2_hexaploid_generation5_rep2


title: Control FAD Phase3 24h 5


title: Control FAD Phase3 24hp 3


title: MFGM [256-8]


title: cross2_hexaploid_generation1_rep1


title: cross2_hexaploid_generation1_rep2


title: Control FAD Phase3 24h 2


title: cross2_triploid_rep2

source_name: hybridized triploid


title: Control FAD Phase3 192hp 7

value: 192 h post


title: cross2_triploid_rep1


title: Control FAD Phase3 192hp 8


title: Control FAD Phase3 24h 1


title: Control FAD Phase3 192hp 6


title: cross2_paternal_rep3

organism: Aegilops tauschii subsp. strangulata

source_name: Ae. tauschii ssp. strangulata


title: cross2_hexaploid_generation5_rep1


title: CONTROL [254-0]


title: MFGM [253-0]


title: CONTROL [248-8]


title: CONTROL [248-0]


title: cross2_paternal_rep1


title: cross2_maternal_rep2

organism: Triticum turgidum subsp. durum

source_name: Triticum turgidum ssp. durum


title: Control FAD Phase3 192hp 5


title: cross2_paternal_rep2


title: cross2_maternal_rep3


title: MFGM [243-0]


title: Control FAD Phase3 192hp 3


title: MFGM [253-8]


title: Control FAD Phase3 192hp 4


title: MFGM [243-8]


title: Control FAD Phase3 192hp 1


title: MFGM [246-8]


title: MFGM [246-0]


title: Control FAD Phase3 192hp 2


title: Control FAD Phase3 192h 7


title: cross2_maternal_rep1


title: MFGM [238-8]


title: cross1_hexaploid_generation14_rep1

organism: Triticum dicoccon x Aegilops tauschii subsp. strangulata


title: Control FAD Phase3 192h 6


title: Control FAD Phase3 192h 5


title: cross1_hexaploid_generation14_rep2


title: MFGM [238-0]


title: Control FAD Phase3 192h 4


title: cross1_hexaploid_generation1_rep3


title: MFGM [237-8]


title: MFGM [236-8]


title: cross1_hexaploid_generation1_rep2


title: Control FAD Phase3 192h 2


title: MFGM [237-0]


title: Control FAD Phase3 192h 1


title: cross1_hexaploid_generation1_rep1


title: cross1_triploid_rep2


title: cross1_hexaploid_generation14_rep3


title: Control FAD 0-6h 6h 3

value: 6 h

value: rnaX


title: Control FAD 0-6h 6h 4


title: cross1_paternal_rep3


title: cross1_triploid_rep1


title: Control FAD Phase3 192h 3


title: Control FAD 0-6h 6h 2


title: CONTROL [234-0]


title: CONTROL [232-8]


title: cross1_paternal_rep2


title: MFGM [236-0]


title: CONTROL [232-0]


title: CONTROL [234-8]


title: Patient 4 MLS-1

tag: status

value: alive

tag: histology

value: pure myxoid

tag: Sex


title: Control FAD 0-6h 6h 1

tag: tissue


title: cross1_maternal_rep3

organism: Triticum turgidum subsp. dicoccum

source_name: Triticum turgidum ssp. dicoccum


title: cross1_maternal_rep2


title: cross1_paternal_rep1


title: CONTROL [231-8]

tag: diet

tag: genotype

tag: time point


title: CONTROL [230-8]


title: Control FAD 0-6h 4h 3

tag: age (month)

tag: treatment duration

value: 4 h


title: cross1_maternal_rep1


title: Control FAD 0-6h 4h 2

tag: experiment


title: CONTROL [231-0]

value: CONTROL


title: Control FAD 0-6h 4h 4

tag: sampling date


title: Tri6_Mutant-Replicate-3

city: Ottawa

first: Rajagopal

last: Subramaniam

address: 960 Carling

institute: Agriculture and Agri-Food Canada

library_source: transcriptomic

data_processing:
ELAND was used for read alignment
DESeq was used for data normalization and relative comparison between strains
Genome_build: Fusarium graminearum strain PH-1
Supplementary_files_format_and_content: delimited text files were generated for TAG COUNT and GENE COUNT data

organism: Fusarium graminearum

source_name: Tri6_Mutant cells

extract_protocol:
Trizol (Invitrogen, USA) and InviTrap Spin Cell RNA mini kit (Invitek, Germany) were used for RNA isolation
Illumina DGE Tag Profiling NlaIII Sample Prep Kit

tag: strain

tag: genotype/variation


title: Control FAD 0-6h 30m 4

tag: treatment

value: 30 min

tag: scan date


title: Control FAD 0-6h 30m 3

tag: rna date

tag: chip id


title: CONTROL [226-8]

value: PBMCs

value: female

tag: age


title: Control FAD 0-6h 4h 1

tag: rna person


title: MFGM [220-8]

value: MFGM


title: CONTROL [226-0]


title: Tri6_Mutant-Replicate-2


title: Control FAD 0-6h 2h 4

value: 2 h


title: CONTROL [230-0]


title: Control FAD 0-6h 30m 2


title: CONTROL [221-0]


title: MFGM [220-0]


title: Control FAD 0-6h 30m 1


title: CONTROL [221-8]


title: MFGM [218-8]


title: Control FAD 0-6h 2h 2


title: Control FAD 0-6h 2h 3


title: Tri6_Mutant-Replicate-1


title: Wildtype-Replicate-3

source_name: Wildtype cells

value: Wildtype


title: MFGM [217-8]


title: MFGM [218-0]


title: MFGM [217-0]


title: Wildtype-Replicate-2


title: Wildtype-Replicate-1


title: Control FAD 0-6h 1h 4

value: ovary

value: 1 h


title: MFGM [215-8]


title: Control FAD 0-6h 1h 3

value: in water control


title: MFGM [211-0]


title: Control FAD 24h 6h 4


title: Control FAD 24h 24h 3


title: Control FAD 24h 24h 4


title: MFGM [215-0]


title: CONTROL [203-8]


title: Control FAD 24h 6h 2


title: CONTROL [201-0 (a)]


title: Control FAD 24h 6h 1


title: Control FAD 0-6h 2h 1


title: CONTROL [203-0]


title: Control FAD 24h 24h 2


title: Control FAD 24h 6h 3


title: CONTROL [201-0 (b)]


title: MFGM [211-8]


title: Control FAD 0-6h 1h 1


title: 254706910043_b3 - col0_2 vs vcs-8_2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Role of RNA degradation in seed dormancy.

hyb_protocol: vcs-8_2 Cy5 / col0_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seed - Media: Petri dishes (coton+filter paper) imbibition 24h. Temperature: 25°C; Light: Dark.

treatment_protocol: no treatment

value: vcs-8 mutant

tag: background strain

value: columbia

tag: developmental stage (boyes et al. plant cell 2001)

value: seed

value: wildtype


title: 254706910040_b4 - vcs-8_1 vs col0_1

hyb_protocol: col0_1 Cy5 / vcs-8_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: tissue


title: 254706910043_b4 - vcs-8_2 vs col0_2

hyb_protocol: col0_2 Cy5 / vcs-8_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype


title: Control FAD 24h 12h 2

value: rnaX


title: Control FAD 24h 12h 4


title: 254706910041_b4 - vcs-8_3 vs col0_3

hyb_protocol: col0_3 Cy5 / vcs-8_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Control FAD 24h 24h 1


title: 254706910041_b3 - col0_3 vs vcs-8_3

hyb_protocol: vcs-8_3 Cy5 / col0_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Control FAD 24h 12h 3


title: Control BPA NOTEL 96h D

value: rnaJ


title: Control BPA NOTEL 96h A


title: 254706910040_b1 - col0_3 vs xrn4-5_3

hyb_protocol: xrn4-5_3 Cy5 / col0_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: xrn4-5 mutant


title: 254706910040_b2 - xrn4-5_3 vs col0_3

hyb_protocol: col0_3 Cy5 / xrn4-5_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910039_b4 - xrn4-5_2 vs col0_2

hyb_protocol: col0_2 Cy5 / xrn4-5_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Control BPA NOTEL 96h F


title: Control FAD 24h 12h 1


title: 254706910039_b3 - col0_2 vs xrn4-5_2

hyb_protocol: xrn4-5_2 Cy5 / col0_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Control BPA NOTEL 96h E


title: 254706910040_b3 - col0_1 vs vcs-8_1

hyb_protocol: vcs-8_1 Cy5 / col0_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: L1 all cells, repeat 1

city: Nasvhille

first: Siwei

last: He

state: TN

address: 465 21st Ave South

department: Cell and Developmental Biology

institute: Vanderbilt University

description: L1 all cells repeat 1

hyb_protocol: Affymetrix

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

data_processing: Data were normalized using quantile normalization and Robust Multiarray Analysis (RMA) summarization available in RMAExpress.

organism: Caenorhabditis elegans

source_name: All cells in L1 larvae

label_protocol: 5-10 ng of total RNA was ampified using the NuGEN WT-Ovation Pico Amplification System. Amplified cDNA was fragmented and labeled according to manufacturer's instructions in NuGEN Biotin RNA Amplification and Labeling System.

growth_protocol: Nematodes were grown on bacterial strain NA22.

extract_protocol: Total RNA was extracted from Trizol and DNase-treated using Zymo’s RNA cleanup kit: the “DNA-Free RNA Kit” (R1013) as described by the manufacturers.

treatment_protocol: Embryos were prepared by standard bleach-prep protocol and allowed to hatch overnight in M9 buffer at 20 C to produce a population of growth-arrested L1 stage larvae.

value: All L1 larval cells

value: L1 larva

tag: label


title: 254706910039_b1 - col0_1 vs xrn4-5_1

hyb_protocol: xrn4-5_1 Cy5 / col0_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: L1 DD, repeat 4

description: L1 DD repeat 4

source_name: DD neurons from L1 larvae

value: DD motor neurons

value: CZ8332 [juIs223 (pttr-39::mcherry, pttx-3::GFP) IV]

value: GFP


title: L1 DD, repeat 3

description: L1 DD repeat 3


title: Control BPA NOTEL 96h C

hyb_protocol: The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.

tag: age (month)


title: Control BPA NOTEL 96h B

tag: treatment duration


title: L1 all cells, repeat 3

description: L1 all cells repeat 3


title: L1 all cells, repeat 2

description: L1 all cells repeat 2