title: 1 week control rep1 and 2 week BaP rep1

city: Leioa

first: Unai

last: Vicario

state: Bizkaia

address: Barrio Sarriena SN

department: Zoology and Animal Cell Biology

country: Spain

institute: University of the Basque Country (UPV/EHU)

hyb_protocol: Samples from the different treatments were hybridized in two n+2 (n = 9) A-optimal loop design. Additionally, these two designs were linked by two extra hybridizations to enable comparison between time points. 825 ng of both Cy3 and Cy5 labelled cRNA was applied onto every microarray according to the hybridization design. Microarray slides were incubated at 65 °C for 17 h in a rotating Agilent hybridization chamber. Slides were subsequently washed with Agilent wash buffers and acetonitrile and finally submersed in stabilization and drying solution (Agilent Technologies) to prevent ozone-induced Cy5-degradation.

scan_protocol: Microarrays were scanned using a Genepix Personal 4100A confocal scanner (Axon Instruments, Union City, CA, USA) at a resolution of 5 μm. The photomultiplier tube voltages for separate wavelengths were adjusted to obtain an overall green/red ratio of one. Images were processed using GenePix Pro 4.1 software (Axon Instruments) for spot identification and quantification of the fluorescent signal intensities.

data_processing: Samples were hybridized in two n+2 (n=9) A-optimal loop design that were linked using two extra microarrays.  Data provided in matrix_log2FC_4contrasts.txt (linked as a supplementary file on Series record) correspond to the FC values of the final contrasts obtained for each of the exposure when compared to the controls (these data together with the average expression values are provided in the supplementary Log*txt. files). Statistical analysis was performed using the LIMMA R package after discarding two arrays (one in each time point) that did not reach quality standards (finally 22 arrays were used in the statistical analysis). Spots for which red or green FG<BG+2SD on all arrays were deleted before analysis (FG: median foreground intensity; BG: average local background intensity calculated over the full microarray; SD: standard deviation of local background intensities). Median intensity data were background corrected using a normal-exponential convolution model using the function background Correct with method “normexp”, offset=50. Data was loess-normalized using the function normalizeWithinArrays. Between-array normalization, like variance stabilization, was not necessary because of the low inter-array variability of the printed arrays. Linear models were fitted to intensity ratios, after which probes were ranked in order of evidence of differential expression using an empirical Bayes method. The averaged values of both treatments at both time points were contrasted against the averaged values of their respective controls. These contrasts were fitted to the linear models.

label_protocol: Fluorescently labelled cRNA was constructed starting from total RNA extracts, following Agilent's two-colour microarray-based gene expression analysis protocol (version 5.7, http://www.agilent.com) using the Quick Amp kit (Agilent Technologies, Diegem, Belgium).

growth_protocol: Adult zebrafish (Danio rerio; AB Tubingen) were raised and maintained at 27 ± 1 ºC with a 14-hour light / 10-hour dark cycle in 100 l tanks at a density of 1.5 fish/l. Tank water was prepared by conditioning osmotic water with marine basic salt (Sera Gmbh, Heinsberg, Germany) and KH/pH plus (Sera) up to 600 µS and pH 7.4, before mechanical filtering (1 µm) and sterilization by ultraviolet light. Water aeration and biological filtration was achieved by an airlift pump in each tank. Residual metabolites were measured using Sera GmbH ammonium, nitrite and nitrates kit, maintaining water at 0-0.5 mg/L; 0-0.5 mg/L and 5-10 mg/L respectively. When the highest concentration values were surpassed water was partially replaced. Fish were fed ad libitum with live Artemia nauplii (INVE, Dendermonde, Belgium) and commercial dry food, Microgran (Sera).

extract_protocol: Total RNA extraction was performed following the TRIzol® extraction method (Invitrogen Life-Technologies, Merelbeke, Belgium).

treatment_protocol: 3 months old fish were exposed to nominal concentrations of 0.3 mg/l B(a)P (Sigma-Aldrich, St. Louis, USA) or 0.3 mg/l DMBA (Sigma-Aldrich) for 2 weeks at a density of 1.375 fish/l in 50 l tanks using one tank per experimental group. During the experiment, 20% of the water in each tank was renewed and the corresponding amount of test solution was added twice a week. DMSO (Sigma-Aldrich) was used as a carrier for the exposure at a final concentration of 0.01%, being present in the control group as well as in the exposure groups. Samples from each treatment were collected after 1 and 2 weeks of exposure.From each treatment at each sampling time 3 biological pseudoreplicates consisting of pools of 5 livers each were prepared. Fish were sacrificed, after euthanasia by overdose of MS-222 (tricaine methane-sulfonate, Sigma-Aldrich), and livers were dissected, immersed in RNA Later ® (Sigma-Aldrich), immediately frozen in liquid nitrogen, and stored at -80ºC until RNA extraction.

tag: FISH strain

value: AB Tubingen

tag: age

value: 3 months

value: pooled livers 5 livers per pool

tag: exposure time

value: 1 week

value: BaP 0.3mg/l disolved in 0.01%DMSO

value: 2 week


title: 200nM_silver_5h_rep2

status: Public on Oct 01 2013

type: RNA

city: Duebendorf

first: Smitha

last: Pillai

address: Ueberlandstrasse 133

country: Switzerland

institute: Eawag

hyb_protocol: Labeling, purification and hybridization was done according the ‘One-Color Microarray-Based Gene Expression Analysis’ system (Agilent Technologies) following the manufacturer's protocol.

scan_protocol: Hybridized slides were scanned with the Agilent DNA Microarray scanner and quantified using the Agilent Feature Extraction software following the manufacturer's protocol.

data_processing: Data analyses were performed with the R/Bioconductor software provided by the Functional Genomics Center Zürich using the log2 values of the 50 percentile -normalized and background-processed median signals. Significant differences of average signal intensities between conditions was determined by one-way analysis of variance (ANOVA) followed by Tukey’s pairwise comparison. Induction was calculated as log2 of the ratio between the sample and the untreated wild-type condition using only genes with a threshold signal value of 10.

molecule: total RNA

organism: Chlamydomonas reinhardtii

source_name: treated with 200nM silver at 5h exposure

growth_protocol: Cultures were grown mixotrophically in Talaquil medium at 25°C and 100 μmol photons m-2 s-1 photosynthetically active radiation (PAR) on a rotary shaker (120 rpm).

extract_protocol: Samples were harvested by centrifugation (3000g, 5 min) and total RNA was isolated with the RNeasy Mini Kit (Qiagen) as described by the manufacturer’s protocol. DNA was digested on column using the RNase-Free DNase Set (Qiagen). After purification, RNA was quantified with a NanoDrop2000 (Thermo Fisher Scientific) and quality was assessed on a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Algal culture in logarithmic growth phase with a cell density of 2.5 x 10^5 cells/ml were exposed to varying concentrations of silver for varying durations

tag: strain

tag: genotype

value: wild type

tag: treatment

value: 200nM silver

tag: time


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML13

city: New Haven

first: Jijun

last: Cheng

state: CT

address: 10 Amistad St.., Rm 214K

department: Genetics

country: USA

institute: Yale University

description: Individual AML sample

hyb_protocol: Labeled biotinylated miRNAs were hybridized to colored beads with covalently bound detection probes in 1.5X TMAC buffer (1.5X TMAC Buffer: for each 50ml, add 45ml 5M TMAC (Sigma T3411-1L), 0.375ml 20% sarkosyl, 3.75ml 1M Tris-Cl pH8.0, 0.6ml 5M EDTA and 0.275ml water) on a PCR machine, with 95ºC for 5minutes and 50ºC on hold for more than 4 hours. The detection beads are created by covalently coupling 5’-animo-modified oligonucleotide-capture probes (complementary to miRNAs) to carboxylated 5-micron polystyrene beads, with one miRNA coupled to beads with a specific color combination. Bead color is made possible by variably mixing two fluorescent dyes at variable ratios (up to 500 combinations), and can be easily differentiated with flow cytometry. After the hybridization, the beads were washed once with 1X TMAC buffer (dilute 1.5X TMAC with water), followed by binding of the fluorescent streptavidin-phycoerythrin to biotin at 50ºC for 10 minutes.  The beads were washed twice with 1X TMAC buffer before detection by flow cytometry.

scan_protocol: Beads detection were performed with flow cytometry (Luminex FlexMap 3D machine) to identify the specific bead color (reflecting miRNA identity) and quantify phycoerythrin intensity on the bead (reflecting the level of hybridized miRNAs).

data_processing: Profiling data were first scaled according to the post-labelling-controls and then the pre-labelling-controls, in order to normalize readings from different probe/bead sets for the same sample, and to normalize for the labelling efficiency, respectively. Data were thresholded at 16 and log2-transformed.

label: Biotin

organism: Homo sapiens

source_name: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics

label_protocol: miRNAs were enriched from total RNA through hybridization-based miRNA capturing in a 96-well format. Subsequent biochemical reactions are performed in the same capture plate, involving ligating mature miRNAs with 3’ adaptor and 5’ adaptor consecutively and reverse transcribing from a primer complementary to the 3’adatpor. Lastly, PCR-based labeling is then performed with a common pair of primers matching 5’ and 3’ adaptors, with the 5’ adaptor-matching primer containing a biotin label.

growth_protocol: For human AML samples, mononuclear cells were separated from bone marrow samples by Ficoll Hypaque, frozen and banked, and subjected to genomic DNA and total RNA preparations.  For BaF3 and K562, cells were grown in RPMI and DMEM, respectively, supplemented with 10% heat-inactivated FBS, penicillin/ streptomycin/glutamine and 2 µg/ml puromycon, and cultured for 5 days.

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

treatment_protocol: For cell lines, they were infected with control virus, TET2 overexpression virus or shTET2 virus in biological triplicates.

tag: cell type

value: AML genotype TET2 mutant


title: Tumor UVA366 Xenograft Generation 5_rep2

city: Charlottesville

first: Edik

middle: Matthew

last: Blais

state: Virginia

address: 415 Lane Road

department: Biomedical Engineering

institute: University of Virginia

description: Gene expression of an orthotopically implanted tumor in mouse

hyb_protocol: Hybridized to arrays at 45°C for 16 hours

scan_protocol: Affymetrix GeneChip system performed by University of Virginia Biomolecular Research Facility. Laser GeneArray scanner was used for measuring amounts of bound probes

data_processing: Data were processed in the R/Bioconductor programming environment. Affymetrix CEL files were preprocessed with Robust Multi-array Average (RMA) and quantile normalized using the 'affy' package. For  analyses, probesets with 'AFFX' appendices or without mapped Entrez genes were excluded from analyses using featureFilter from the 'geneFilter' package.

label: biotin

source_name: Patient-derived tumor in mouse

label_protocol: Biotin labelled according to the standard Affymetrix protocol

growth_protocol: Tumor samples were grown in a novel orthotopic xenograft model of pancreatic cancer, retrieved directly from patients as described in the associated manuscript, or cultured as cell lines.

extract_protocol: Total RNA was extracted from samples using the RNAeasy kit (Qiagen).

treatment_protocol: Allprotect (Qiagen), RNAlater, cryopreservation, or freezing was necessary for the preservation of RNA in all tissue samples. A TissueLyzer LT (Qiagen) was used to homogenize tissue and RNA was extracted using the Allprep kit (Qiagen). Qiashredder was used to prepare RNA from cell lines.

tag: tissue

value: Patient-derived tumor in mouse

tag: malignancy

value: Cancer

tag: host organism

value: mus musculus

tag: patient/line

tag: generation in xenograft model

tag: tissue preserve method

value: frozen


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML12

description: Individual AML sample

value: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics


title: Sample 1146

type: genomic

city: London

first: Jun

last: Wang

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary, London

description: Hybridized to genome-wide human SNP Array 6.0

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

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

data_processing:
The raw CEL files were processed following the PennCNV-Affy workflow. First, the apt-probeset-genotype program in Affymetrix Power Tools (APT) was used to generate genotyping calls from the raw CEL files using the Birdseed v2 algorithm. The APT software apt-probeset-summarize program was then used to extract allele-specific signal values for each SNP, after applying quantile normalisation and median polish on the data. the Log R Ratio (LRR) values and the B Allele Frequency (BAF) values were subsequently calculated using PennCNA. The reference set we used to generate LRR and BAF values for each DNA samples was indeed the HapMap project DNA samples, which pennCNA provides as its default clustering file for the following calculation.
VALUE: Log R ratio against the reference set; VALUE2: B Allele Frequency

molecule: genomic DNA

source_name: transformed FL sample 1146

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from the GL, FL and tFL samples using DNeasy Tissue Kit (Qiagen)

tag: tissue source

value: transformed follicular lymphoma

tag: sample source

tag: patient source


title: Sample 1883

source_name: Follicular lymphoma sample 1883

value: follicular lymphoma


title: 10nM_silver_5h_rep3

source_name: treated with 10nM silver at 5h exposure

label_protocol: Labeling, purification and hybridization was done according the ‘One-Color Microarray-Based Gene Expression Analysis’ system (Agilent Technologies) following the manufacturer's protocol.

value: 10nM silver


title: Tumor UVA366 Xenograft Generation 5_rep1


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML11

description: Individual AML sample


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML10

description: Individual AML sample


title: Sample 625

source_name: Follicular lymphoma sample 625


title: 0nM_silver_5h_rep3

source_name: untreated at 5h exposure

value: 0nM silver


title: 1 week BaP rep1 and 2 week control rep1

organism: Danio rerio

tag: FISH strain

value: AB Tubingen

value: 3 months


title: 2 week DMBA rep3 and 2 week BaP rep3

tag: age

value: pooled livers 5 livers per pool

value: DMBA 0.3mg/l disolved in 0.01%DMSO


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML9

description: Individual AML sample


title: Sample AD1787

source_name: transformed FL sample AD1787


title: 2 week BaP rep2 and 2 week DMBA rep3

value: BaP 0.3mg/l disolved in 0.01%DMSO

tag: exposure time

value: 2 week


title: 10nM_silver_5h_rep2

tag: strain

value: wild type


title: Sample 1148

source_name: Germline sample 1148

value: germline


title: Sample AD1548

source_name: Follicular lymphoma sample AD1548


title: 2 week BaP rep3 and 2 week DMBA rep1


title: Tumor UVA232 Xenograft Generation 1_rep2

value: Patient-derived tumor in mouse


title: Tumor UVA215 Xenograft Generation 2

value: Cancer

value: Allprotect


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML8

description: Individual AML sample

tag: genotype

value: AML genotype TET2 mutant


title: Blood_Hyperplasia

city: shanghai

first: xiaoyan

last: jiang

state: shanghai

address: No.1239 siping road

country: China

institute: tongji university

hyb_protocol: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 6 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs/mRNAs between two groups were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 12.0). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: varicose vein tissue

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was  fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

growth_protocol: Varicose vein specimens were retrieved from patients of Human Primary Varicose GSVs (Great Saphenous Veins) who were undergone GSVs varicose vein excision in Shanghai East Hospital, Tongji University School of Medicine, China. Diagnosis of Primary Varicose GSVs was based on the clinical signs and duplex ultrasound scanning. All patients were characterized as having primary varicosities, and the patients of the secondary varicosities were excluded. All patients had no history of deep venous thrombosis, superficial thrombotic phlebitis, post-thrombotic syndrome, Klipple-Trenannay syndrome, May-Thurner syndrome or any other venous diseases. According to CEAP (the clinical, aetiological, anatomical and pathological elements) classification for CVD (chronic lower-extremity venous disease), all of the patients were in class 4-6 for clinical signs. Preoperative lower-extremity venous duplex ultrasound scanning assessment was performed on all patients, and both the superficial and the deep venous systems examination were conducted. All patients exhibited reflux in the GSVs.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: According to visual inspection and pathological examination, varicose veins (VVs) tissues was the obvious varicose vein of the varicose great saphenous vein patient, and normal segments of saphenous veins (NVs) was the adjacent normal vein apart from VV about 3-4cm as control vein. The tissues were snap-frozen into liquid nitrogen as soon as resection for later RNA extraction.

tag: gender

value: male

tag: ceap grade

value: varicose vein


title: Cell Line UVA366

description: Gene expression of cancer cell line derived from mouse xenograft

source_name: Patient-derived cancer cell line

tag: cell line

value: in vitro


title: Tumor UVA232 Xenograft Generation 1_rep1

tag: tissue

value: mus musculus

value: frozen


title: Blood_Control

value: normal adjacent vein


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML7

description: Individual AML sample

tag: cell type

value: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics


title: Sample 2666

source_name: transformed FL sample 2666

value: transformed follicular lymphoma


title: Normal Tissue UVA190

source_name: Patient pancreas tissue

value: Patient pancreas tissue

tag: malignancy

value: Non-cancer

tag: host organism

value: homo sapiens


title: Sample 2207

source_name: Follicular lymphoma sample 2207

value: follicular lymphoma


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML5

description: Individual AML sample


title: Sample AD1145

source_name: transformed FL sample AD1145


title: Sample 1209

source_name: Germline sample 1209

value: germline


title: Tumor UVA1049 Xenograft Generation 2

value: Patient-derived tumor in mouse

tag: patient/line

tag: generation in xenograft model


title: Sample BH saliva

source_name: Germline sample BH saliva

tag: tissue source

value: BH saliva


title: 2 week BaP rep2 and 2 week DMBA rep2

value: AB Tubingen

value: 3 months

value: pooled livers 5 livers per pool

tag: treatment

value: BaP 0.3mg/l disolved in 0.01%DMSO

value: 2 week

value: DMBA 0.3mg/l disolved in 0.01%DMSO


title: 5-Hyperplasia

value: male

value: varicose vein


title: 4-Hyperplasia

value: female


title: 2 week DMBA rep2 and 2 week control rep2


title: Sample 2043

source_name: Follicular lymphoma sample 2043

tag: sample source

tag: patient source


title: 5-Control

tag: age

value: normal adjacent vein


title: 2 week control rep1 and 2 week BaP rep2

tag: FISH strain

tag: exposure time


title: 10nM_silver_5h_rep1

tag: strain

tag: genotype

value: wild type

value: 10nM silver

tag: time


title: 2 week BaP rep1 and 2 week control rep1


title: PMA treated, no doxycycline; biological replicate 3

city: Kansas City

first: Joseph

last: Fontes

state: KS

address: 3901 Rainbow Blvd

department: Biochemistry and Molecular Biology

institute: Univ Kansas Medical Center

description:
Veh_PMA_3
Gene expression data from cell line differentiated with PMA in the absence of doxycycline-inducible knockdown of ZXDC1/2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array in a GeneChip hybridization oven 640. GeneChips were singly scanned using a Genechip scanner 3000 7G with autoloader. Fluidics and scan functions were controlled by Command Console software ver 1.1 (AGCC).

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

data_processing: The data were analyzed with AltAnalyze version 2.02 beta, using RMA for normalization.

source_name: U937-derived cell line harboring TRIPZ-shRNAmir TetOn cassette (clone ID: V3THS-381738)

label_protocol: Biotinylated cRNA were prepared according to the GeneChip 3' IVT Express kit  from 100 ng total RNA (Affymetrix catolog # 901228).

growth_protocol: U937 stably transduced with TRIPZ-shRNAmir (Thermo/OpenBiosystems) were cultured in RPMI + 10% FBS, 100 U/mL penicilli, 100 ug/mL streptomycin, and 0.5 ug/mL Puromycin

extract_protocol: Total RNA was extracted via Qiagen Rneasy Micro kit according to the manufacturer's instruction

treatment_protocol: Individual cell lines were treated with 0.5 ug/mL doxycycline every day for four days to achieve inducible knockdown of ZXDC1/2.  After the first two days of doxycycline treatment, cell lines were treated with either 100 nM PMA or vehicle (0.1% DMSO) and allowed to differentiate for 3 days.

tag: cell line

value: histiocytic lymphoma

tag: genotype/variation

value: control

tag: agent

value: PMA


title: PMA treated, doxycycline treated; biological replicate 3

description:
Dox_PMA_3
Gene expression data from cell line differentiated with PMA in the presence of doxycycline-inducible knockdown of ZXDC1/2

tag: cell type

value: ZXDC1 knockdown


title: Sample 1599

source_name: Follicular lymphoma sample 1599

value: follicular lymphoma


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML3

description: Individual AML sample

source_name: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics

value: AML genotype TET2 mutant


title: Sample AD1508

source_name: transformed FL sample AD1508

value: transformed follicular lymphoma


title: Vehicle treated,  doxycycline treated; biological replicate 3

description:
Dox_Veh_3
Gene expression data from cell line treated with vehicle in the presence of doxycycline-inducible knockdown of ZXDC1/2

value: vehicle


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML1

description: Individual AML sample

value: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML2

description: Individual AML sample


title: Sample 2756

source_name: Follicular lymphoma sample 2756


title: 1 week DMBA rep3 and 1 week BaP rep3

value: AB Tubingen

value: 3 months

tag: tissue

value: pooled livers 5 livers per pool

value: 1 week

value: BaP 0.3mg/l disolved in 0.01%DMSO


title: 2 week DMBA rep1 and 2 week BaP rep1

value: DMBA 0.3mg/l disolved in 0.01%DMSO

value: 2 week


title: Sample 790

source_name: Germline sample 790

value: germline


title: 2 week control rep2 and 2 week DMBA rep1


title: 1 week BaP rep3 and 1 week DMBA rep1


title: 3-Hyperplasia

tag: gender

value: female

tag: ceap grade

value: varicose vein


title: 1 week BaP rep2 and 1 week DMBA rep3


title: 4-Control

value: normal adjacent vein


title: Vehicle treated, no doxycycline; biological replicate 3

description:
Veh_Veh_3
Gene expression data from cell line treated with vehicle in the absence of doxycycline-inducible knockdown of ZXDC1/2

value: histiocytic lymphoma

value: control


title: 3-Control


title: PMA treated, doxycycline treated; biological replicate 2

description:
Dox_PMA_2
Gene expression data from cell line differentiated with PMA in the presence of doxycycline-inducible knockdown of ZXDC1/2

value: ZXDC1 knockdown

value: PMA


title: Sample 974

source_name: Follicular lymphoma sample 974

tag: tissue source

value: follicular lymphoma


title: PMA treated, no doxycycline; biological replicate 2

description:
Veh_PMA_2
Gene expression data from cell line differentiated with PMA in the absence of doxycycline-inducible knockdown of ZXDC1/2


title: 2-Hyperplasia


title: Vehicle treated,  doxycycline treated; biological replicate 2

description:
Dox_Veh_2
Gene expression data from cell line treated with vehicle in the presence of doxycycline-inducible knockdown of ZXDC1/2

value: vehicle


title: 2-Control


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML4

description: Individual AML sample

value: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics

value: AML genotype TET2 mutant


title: 1 week control rep3 and 1 week BaP rep2

value: AB Tubingen

value: 3 months

value: pooled livers 5 livers per pool

tag: treatment


title: 1 week DMBA rep1 and 1 week control rep3

value: DMBA 0.3mg/l disolved in 0.01%DMSO

value: 1 week


title: Sample 700

source_name: Follicular lymphoma sample 700

tag: sample source


title: 2 week control rep3 and 2 week BaP rep2

value: 2 week

value: BaP 0.3mg/l disolved in 0.01%DMSO


title: 1 week DMBA rep2 and 1 week control rep2


title: 1 week BaP rep2 and 1 week DMBA rep2


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML6

description: Individual AML sample


title: 1-Hyperplasia

source_name: varicose vein tissue

value: male

value: varicose vein


title: 1 week DMBA rep1 and 1 week BaP rep1


title: 1 week BaP rep1 and 1 week control rep1


title: Sample AD1557

source_name: Follicular lymphoma sample AD1557

tag: patient source


title: 1-Control

tag: age

value: normal adjacent vein


title: Vehicle treated, doxycycline treated; biological replicate 1

description:
Dox_Veh_1
Gene expression data from cell line treated with vehicle in the presence of doxycycline-inducible knockdown of ZXDC1/2

value: histiocytic lymphoma


title: 1 week control rep1 and 1 week BaP rep2

tag: FISH strain


title: PMA treated, doxycycline treated; biological replicate 1

description:
Dox_PMA_1
Gene expression data from cell line differentiated with PMA in the presence of doxycycline-inducible knockdown of ZXDC1/2

value: ZXDC1 knockdown


title: Vehicle treated, no doxycycline; biological replicate 2

description:
Veh_Veh_2
Gene expression data from cell line treated with vehicle in the absence of doxycycline-inducible knockdown of ZXDC1/2

value: control


title: PMA treated, no doxycycline; biological replicate 1

description:
Veh_PMA_1
Gene expression data from cell line differentiated with PMA in the absence of doxycycline-inducible knockdown of ZXDC1/2

value: PMA


title: 200GV A150 vs. 200GV A- GV2

city: Quebec

first: maella

last: gohin

state: Qc

address: 2440 Bl. Hochelaga

department: Animal science

country: Canada

institute: Laval University

hyb_protocol: Using the microarray Hybridization Station 400 Pro (Tecan Group Ltd., Männedorf, Switzerland), the slide was washed in agilent prehybridization buffer for 1 min at 65°C and hybridization were performed in 2X GEx hybridization buffer HI-RPM (Agilent Technologies) at 65°C for 20h. The slide was washed with gene expression wash buffer 1 for 2 min at room temperature, and then with the gene expression wash buffer 2 for 2 min at 37°C. Finally, the slide was dried for 2 min at room temperature

scan_protocol: the slide was scanned using the Tecan PowerScanner microarray scanner (Tecan Group Ltd., Männedorf, Switzerland). Microarray images were processed with the ArrayPro 6.4 Analyzer software (Media Cybernetics, Bethesda, MD).

data_processing: Loess and quantile normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Flexarray software was used.

organism: Bos taurus

label_protocol: The WT-Ovation™ One-Direct RNA Amplification System (Cat. # 3500-12, NuGen) was used to amplified 2 µl of the samples. 2,5 µg of amplified DNAs were labeled using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent.

growth_protocol: Immature oocytes were denuded from Cumulus-Oocyte Complex of cold Bos taurus Holstein cow ovaries obtained from a slaughterhouse and transported on ice in saline solution (0.9% NaCl) with an antibiotic–antimycotic agent.

extract_protocol: Total RNA was extracted using the PicoPure RNA Isolation Kit (life technologies) and depleted from ribosomal RNAs using the Ribominus kit (life technologies). 18S-28S depleted RNAs were purified according to their polyadenylation states using the dynabeads kit (life technologies). Recommended volumes were divided by 5. Deadenylated RNAs (A-) were recovered from concentrated flowthrough and washing volumes (ribominus concentration module, life technologies) and polyadenylated (A150) were recovered by thermal elution at 75°C with 10µl of water, after a first elution at 42°C .

tag: sample type

value: poly(A) tail length  A150 (A≥150)

value: oocyte

tag: developmental stage

value: germinal vesicle

tag: breed

value: Holstein

value: poly(A) tail length A- (A≤50)


title: 200GV A- vs. 200GV A150 GV3


title: Vehicle treated, no doxycycline; biological replicate 1

description:
Veh_Veh_1
Gene expression data from cell line treated with vehicle in the absence of doxycycline-inducible knockdown of ZXDC1/2

value: vehicle


title: 200GV A150 vs. 200GV A- GV1


title: N_H004

city: TAIPEI

first: chien yu

last: wang

country: Taiwan

institute: ndmc

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 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by GenePix 4200A 01 Autoloader (635nm power 100 PMT 325 ; 532nm power 10, PMT 325) 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.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

organism: Rattus norvegicus

source_name: NGF

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).

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).

value: NGF

value: rat-tail interverbral disc cells


title: RD, replicate 2

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

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

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

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

organism: Nicotiana tabacum

source_name: RLKox suspension cells sampled 6 days after culture with 10 µM of DPI

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

growth_protocol: Every BY-2 suspension cell culture was maintained in modified liquid MS media [4.4 g·L-1 MS vitamin and salts, 30 g·L-1 sucrose, 0.21 g·L-1 potassium phosphate monobasic, 0.2 mg·L-1 2,4-dichlorophenoxyacetic acid (2,4-D), pH 5.7] on a rotary shaker (130 rpm) at 25°C in the darkness and subcultured weekly.

extract_protocol: Total and polysomal RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen), and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

tag: cultivar

value: RLK1ox suspension cells

value: overexpression line of CaRLK1 gene

tag: phenotype

value: normal

value: DPI


title: C_H002

source_name: PBS

value: PBS


title: RD, replicate 1

tag: genotype/variation


title: N_H003


title: C_H001


title: 200GV A- vs. 200GV A150 GV4


title: RD, replicate 3


title: RA, replicate 3

source_name: RLKox suspension cells sampled 6 days after culture without applying auxin (2,4-D)

value: auxin-free


title: RA, replicate 1


title: RA, replicate 2


title: RLK, replicate 3

source_name: RLKox suspension cells sampled 6 days after culture


title: Untreated HPAM1 #3

city: Baltimore

first: chunbo

last: shao

state: MD

address: 1550 Orleans Street

department: Otolaryngology

institute: Johns Hopkins University

description:
CSha-SGT-HPAM3_Ctrl-1a-U133Plus2_2.CHP
CSha-SGT-HPAM3_Ctrl-1a-U133Plus2_2.CEL

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

source_name: ATCC normal salivary gland epithelial cell line, untreated

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual)

growth_protocol: The cell lines are propagated in serum-free medium comprised of keratinocyte basal medium supplemented with insulin (5 μg/ml), hydrocortisone (0.5 μg/ml), epidermal growth factor (EGF, 10 ng/ml), bovine pituitary extract (25 μg/ml), and antibiotics.

extract_protocol: RNeasy Kit (QIAGEN)

treatment_protocol: Cells were treated with 5 uM 5-Aza dC for 96 hours and 300 nmol/L TSA for the last 24 hours.

tag: cell line

value: HPAM1 epithelial acinar cell line

tag: agent

value: untreated

value: male

value: passage 50


title: Untreated HPAM1 #1

description:
CSha-SGT-HPAM1_Ctrl-1a-U133Plus2.CHP
CSha-SGT-HPAM1_Ctrl-1a-U133Plus2.CEL


title: 5-Aza dC/TSA treated HPAM1 #1

description:
CSha-SGT-HPAM1_5AC-1a-U133Plus2.CHP
CSha-SGT-HPAM1_5AC-1a-U133Plus2.CEL

source_name: ATCC normal salivary gland epithelial cell line, treated

value: 5-Aza dC, TSA


title: Untreated HPAM1 #2

description:
CSha-SGT-HPAM2_Ctrl-1a-U133Plus2.CHP
CSha-SGT-HPAM2_Ctrl-1a-U133Plus2.CEL


title: RLK, replicate 2

tag: cell type


title: BY, replicate 3

source_name: BY-2 suspension cells sampled 6 days after culture

value: BY-2 suspension cells

value: wild-type


title: RLK, replicate 1


title: Untreated HPAF1 #3

description:
CSha-SGT-HPAF3_Ctrl-1a-U133Plus2.CHP
CSha-SGT-HPAF3_Ctrl-1a-U133Plus2.CEL

value: HPAF1 epithelial acinar cell line

tag: gender

value: female

value: passage 40


title: BY, replicate 2


title: BY, replicate 1


title: Untreated HPAF1 #2

description:
CSha-SGT-HPAF2_Ctrl-1a-U133Plus2.CHP
CSha-SGT-HPAF2_Ctrl-1a-U133Plus2.CEL


title: rTGEV-delta7 infected cells, 12 hpi, rep1

status: Public on Sep 30 2013

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

description: A7 12h  rTGEV-delta7 infected cells, 12 hpi rep1

hyb_protocol: cRNA preparations (15 µg) were fragmented at 94ºC for 35 min into 35-200 bases in length and added to a hybridization solution (100 mM 4-morpholinopropanosulfonate acid, 1M Na+, 20 mM EDTA, 0.01% Tween-20). The cRNAs (10 µg) were hybridized to Genechip Porcine Genome Arrays (Affymetrix) at 45ºC for 16 hours. Independent microarrays were hybridized for each sample.

scan_protocol: The arrays were stained with streptavidin-phycoerythrin and read at 1.56 µm in a GeneChip Scanner 3000 7G System (Affymetrix).

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

organism: Sus scrofa

source_name: A7 12h 1  rTGEV-delta7 infected cells, 12 hpi

label_protocol: RNAs were biotin-labeled using the One Cycle Target-labeling kit (Affymetrix). Briefly, cDNA was synthesized from 5 µg total RNA using an oligo-dT primer with a T7 RNA polymerase promoter site added to the 3’ end. After a second strand synthesis, in vitro transcription was performed using T7 RNA polymerase to produce biotin-labeled cRNA.

growth_protocol: One day after confluence ST cells, grown on 35-mm-diameter plates, were mock infected or infected at a moi of 5 with rTGEV-wt or rTGEV-delta7. To decrease sample variability due to cell state, nine independent infections were performed in each case.

extract_protocol: Total RNA was extracted, at 6 and 12 hpi, using a RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions. RNAs were pooled three by three, obtaining three biological replicates for each experimental condition, and RNA integrity was measured in a bioanalyzer (Agilent Technologies).

value: swine testis (ST) cells

value: ST

tag: infection

tag: time


title: 5-Aza dC/TSA treated HPAF1 #1

description:
CSha-SGT-HPAF1_5AC-1a-U133Plus2.CHP
CSha-SGT-HPAF1_5AC-1a-U133Plus2.CEL


title: rTGEV-delta7 infected cells, 6 hpi, rep1

description: A7 6h  rTGEV-delta7 infected cells, 6 hpi rep1

source_name: A7 6h 1  rTGEV-delta7 infected cells, 6 hpi

value: 6 h


title: rTGEV-delta7 infected cells, 12 hpi, rep3

description: A7 12h  rTGEV-delta7 infected cells, 12 hpi rep3

source_name: A7 12h 3  rTGEV-delta7 infected cells, 12 hpi


title: 5-Aza dC/TSA treated HPAM1 #2

description:
CSha-SGT-HPAM2_5AC-1a-U133Plus2.CHP
CSha-SGT-HPAM2_5AC-1a-U133Plus2.CEL


title: rTGEV-delta7 infected cells, 6 hpi, rep2

description: A7 6h  rTGEV-delta7 infected cells, 6 hpi rep2

source_name: A7 6h 2  rTGEV-delta7 infected cells, 6 hpi


title: Untreated HPAF1 #1

description:
CSha-SGT-HPAF1_Ctrl-1a-U133Plus2.CHP
CSha-SGT-HPAF1_Ctrl-1a-U133Plus2.CEL


title: 5-Aza dC/TSA treated HPAF1 #2

description:
CSha-SGT-HPAF2_5AC-1a-U133Plus2.CHP
CSha-SGT-HPAF2_5AC-1a-U133Plus2.CEL


title: rTGEV-wt infected cells, 12 hpi, rep2

description: WT 12h  rTGEV-wt infected cells, 12 hpi rep2

source_name: WT 12h 2  rTGEV-wt infected cells, 12 hpi

value: rTGEV-wt


title: 5-Aza dC/TSA treated HPAM1 #3

description:
CSha-SGT-HPAM3_5AC-1a-U133Plus2.CHP
CSha-SGT-HPAM3_5AC-1a-U133Plus2.CEL


title: rTGEV-delta7 infected cells, 12 hpi, rep2

description: A7 12h  rTGEV-delta7 infected cells, 12 hpi rep2

source_name: A7 12h 2  rTGEV-delta7 infected cells, 12 hpi


title: rTGEV-wt infected cells, 12 hpi, rep3

description: WT 12h  rTGEV-wt infected cells, 12 hpi rep3

source_name: WT 12h 3  rTGEV-wt infected cells, 12 hpi


title: rTGEV-wt infected cells, 12 hpi, rep1

description: WT 12h  rTGEV-wt infected cells, 12 hpi rep1

source_name: WT 12h 1  rTGEV-wt infected cells, 12 hpi


title: rTGEV-delta7 infected cells, 6 hpi, rep3

description: A7 6h  rTGEV-delta7 infected cells, 6 hpi rep3

source_name: A7 6h 3  rTGEV-delta7 infected cells, 6 hpi


title: 5-Aza dC/TSA treated HPAF1 #3

description:
CSha-SGT-HPAF3_5AC-1a-U133Plus2.CHP
CSha-SGT-HPAF3_5AC-1a-U133Plus2.CEL


title: Hypothalamus_PVHvsARH_rep2

city: Houston

first: Ge

last: Li

state: TX

address: 1100 Bates St.

department: Pediatrics

institute: Baylor College of Medicine

description: Biological replicate 2 of 2.

hyb_protocol: Equal amount (~4µg) of Cy3 or Cy5 labeled MSAM products were combined for cohybridization. Hybridization of the arrays was carried out according to the Agilent Chip-on-chip mammalian protocol (version 9.1, 2006).

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction Software (9.1.3.1) was used for background subtraction and LOWESS normalization.Probe ratios within one SmaI interval were averaged and the median of the P value log10 ratios of the probes within one SmaI interval was calculated.

organism: Mus musculus

source_name: Hypothalamus PVH

label_protocol: 2µg MSAM products from each sample were labeled with either Cy3 or Cy5 according to the Agilent Chip-on-chip mammalian protocol (version 9.1, 2006).

extract_protocol: Genomic DNA was isolated with phenol/chloroform extraction followed by ethanol precipitation

tag: strain

value: mixed

value: postnatal day 10

tag: tissue

value: paraventricular (PVH)

source_name: Hypothalamus ARH

value: ventromedial (VMH) nuclei


title: Hypothalamus_PVHvsARH_rep1

description: Biological replicate 1 of 2.


title: rTGEV-wt infected cells, 6 hpi, rep3

description: WT 6h rTGEV-wt infected cells, 6 hpi rep3

source_name: WT 6h 3  rTGEV-wt infected cells, 6 hpi


title: rTGEV-wt infected cells, 6 hpi, rep1

description: WT 6h rTGEV-wt infected cells, 6 hpi rep1

source_name: WT 6h 1  rTGEV-wt infected cells, 6 hpi


title: FTE283_2D rep3

status: Public on Sep 27 2013

city: Los Angeles

first: Kate

last: Lawrenson

state: CA

address: 1450 Biggy Street

department: Preventive Medicine

institute: University of Southern California

hyb_protocol: Standard Illumina protocols

scan_protocol: Standard Illumina protocols

data_processing: Data were normalised in GenomeStudio (v.2011.1, quantile normalisation, missing values excluded)

label_protocol:
Samples were profiled using Illumina HumanHT-12 Expression BeadChip microarrays at the USC Epigenome Core facility.
The samples have a biotin moiety and the Illumina kit contains to streptavidin dye which is CY3

growth_protocol: Cells were grown in 2D, or in 3D using polyHEMA coated pleates

extract_protocol: QIAgen RNA extraction kit (RNeasy)

tag: patient id

value: Fallopian tube secretory epithelial cells (FTSECs)

tag: cell culture condition

value: 2D culture


title: Non infected cells, rep2

description: Mock Non infected cells rep2

source_name: Mock 2  Non infected cells

value: mock


title: FTE03_2D rep3


title: Non infected cells, rep3

description: Mock Non infected cells rep3

source_name: Mock 3  Non infected cells


title: Non infected cells, rep1

description: Mock Non infected cells rep1

source_name: Mock 1  Non infected cells


title: FTE02_2D rep2


title: rTGEV-wt infected cells, 6 hpi, rep2

description: WT 6h rTGEV-wt infected cells, 6 hpi rep2

source_name: WT 6h 2  rTGEV-wt infected cells, 6 hpi


title: FTE02_3D rep3

value: 3D culture


title: FTE283_3D rep2


title: FTE03_2D rep2


title: FTE03_3D rep2


title: FTE03_3D rep3


title: FTE283_2D rep1


title: FTE283_2D rep2


title: FTE02_3D rep1


title: FTE02_3D rep2


title: FTE03_2D rep1


title: EE2-Series5-30 pM

status: Public on Sep 10 2013

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Following fragmentation, biotinylated cRNA probe (25 ng/uL in 200 uL hybridizationconcktail) were hybridized for 17 hr at 45C on GeneChip Human U133 version 2 plu (GPL570) sarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (protocol FS450_0001).

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

data_processing: The data were analyzed with Affymetrix GeneChip Command Console (AGCC).  affymetrix-algorithm-name = rma-gene-default  affymetrix-algorithm-version = 1.0  program-name = Expression Console

label_protocol: Biotinylated cRNA probes were synthesized using the GeneChip Whole Transcript Sense Target Labeling Assay Kit (Affymetrix) following the manufacturer's instructions.

growth_protocol: MCF-7 cells were grown in DMEM supplemented with 5% FCS, 2 mM glutamine, and 1X Penicillin/Streptomycin.

extract_protocol: Total RNA was extracted directly from cell cultures grown on 10 cm dishes using QIAGEN RNeasy kit.

treatment_protocol: Subconfluent MCF-7 cells in 10 cm dishes were exposed to varying concentrations of xenoestrogen chemicals for exactly 48 hours and subjected to immediate isolation of total RNA. Xenoestrogen chemicals tested in this study were Bisphenol A, Diethylstilbestrol, 17alpha-ethynylestradiol, p-nonylphenol, genistein, and daidzein. Transcriptomal effects of physiological estrogen 17beta-estradiol was also examined.

tag: xenoestrogen

tag: series

tag: molar concentration


title: EE2-Series5-3 pM


title: FTE03_3D rep1


title: FTE283_3D rep1


title: FTE283_3D rep3


title: FTE02_2D rep1


title: Diploid, t=10d, rep1

status: Public on Sep 07 2013

city: rehovot

first: Noam

last: Vardi

address: herzel 235

department: molecular genetics

country: Israel

institute: Weizmann Institute of Science

description: chemostat, 7.3mM  Pi (cy5), block 7

hyb_protocol: Agilent yeast dual color expression microarrays (8x15K, G2509F)

scan_protocol: Agilent microarray scanner

data_processing:
The scanned images were analyzed using SpotReader software (Niles Scientific). Problematic probes (flagged by SpotReader, or highly variable, with no signal, or at regions of spatial bias) were declared 'missing values'. Dye-dependent (Cy3 vs. Cy5) and array-dependent (same color in different arrays) biases were corrected by converting the samples distributions to their reference distribution using percentile normalization
Normalized log-2-ratio of the sample signal (diploids cells at a chemostat, D=0.3[1/hr], averaged over 2 repeats for each time point. t=0 is averaged over 8 repeats), relative to the control signal (one repeat of diploid cells after 10 days in the chemostat).

organism: Saccharomyces cerevisiae

source_name: wild type, t=10d

label_protocol: The samples were amplified, labeled with Agilent's Low Input Quick Amp Labeling Kit.

extract_protocol: Total RNA was extracted using MasterPure™ yeast RNA purification Kit (Epicentre).  Total RNA was extracted using MasterPure™ yeast RNA purification Kit (Epicentre).  Total RNA was extracted using MasterPure™ yeast RNA purification Kit (Epicentre).

tag: treatment

value: Diploid, t=10, chemostat, Pfeed=7.3mM Pi, D=0.3[1/hr]


title: Diploid, t=10d, rep2

description: chemostat, 7.3mM  Pi (cy5), block 8


title: Diploid, t=5d, rep2

description: chemostat, 7.3mM Pi, block 6 (cy5)

source_name: wild type, t=5d

value: Diploid, t=5, chemostat, Pfeed=7.3mM Pi, D=0.3[1/hr]


title: EE2-Series5-1 pM


title: Control

status: Public on Sep 21 2013

city: BARCELONA

first: DOLORS

last: COLOMER

address: VILLARROEL 170

institute: IDIBAPS-HOSPITAL CLINIC

description: SAMPLE 1

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the Gene Titan instrument.

data_processing:
Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software (AGCC) (Affymetrix).
Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm of Expression Console Software (v1.1, Affymetrix).

source_name: Primary CLL_untreated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA

growth_protocol: CLL cells were incubated in complete RPMI medium plus 10%FBS at 37ºC 5%CO2

extract_protocol: Total RNA was extracted, using the Trizol  reagent

treatment_protocol: GSI and fludarabine for 48 hours

value: primary NOTCH1-mutated CLL cells

tag: treated with

value: none (untreated control)


title: Diploid, t=2d, rep2

description: chemostat, 7.3mM Pi, block 1 (cy5)

source_name: diploids, t=2d

value: Diploid, t=2, chemostat, Pfeed=7.3mM Pi, D=0.3[1/hr]


title: Fludarabine

description: SAMPLE 3

source_name: Primary CLL_fludarabine

value: fludarabine


title: Diploid, t=5d, rep1

description: chemostat, 7.3mM Pi, block 5 (cy5)


title: EE2-Series5-100 pM


title: Diploid, t=2d, rep1

description: chemostat, 7.3mM Pi, block 3 (cy5)


title: GSI

description: SAMPLE 2

source_name: Primary CLL_GSI

value: GSI (Gamma-secretase inhibitor)


title: EE2-Series4-3 pM


title: EE2-Series4-30 pM


title: EE2-Series4-100 pM


title: Diploid, t=0.35d, rep1

description: chemostat, 7.3mM Pi, block 1 (cy5)

source_name: diploids, t=0.35d

value: Diploid, t=0.35, chemostat, Pfeed=7.3mM Pi, D=0.3[1/hr]


title: Diploid, t=0.35d, rep2

description: chemostat, 7.3mM Pi, block 2 (cy5)


title: BPA-Series2-7.81 nM

value: Bisphenol A


title: Diploid, t=0, rep2

description: chemostat, 0.3mM Pi (cy3), block 8

source_name: Diploid, t=0, chemostat, Pfeed=0.3mM Pi, D=0.3[1/hr]


title: Diploid, t=0, rep1

description: chemostat, 0.3mM Pi (cy3) block 7

value: Diploid, t=0, chemostat, Pfeed=0.3mM Pi, D=0.3[1/hr]


title: sic-1, biological rep2

status: Public on Aug 18 2013

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

description:
whole genome expression data from sic-1 mutant
JZVC_ha27_2

hyb_protocol: Hybridization was performed in Affymetrix Hybridization Oven 645 and washed and stained in Fluidics Station 450 according to manufactuerer's instructions.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing:
TILING array probes were first re-mapped to the Arabidopsis genome (TAIR9) using SOAP2 (Li et al., 2009), and only probes that perfectly matched to a unique position in the genome were used for subsequent analyses. A custom Chip Definition File (CDF) was created using the mapping result and was used to quantile-normalize raw tiling array data with the aroma.affymetrix framework (http://www.aroma-project.org). For the purpose of this study, only probes that were uniquely mapped to gene region (including intronic regions), 200bp downstream regions, and non-coding RNA genes were considered. Only PM intensity values were used.
JZVC_ha27_2_QN.txt (in-house script to used extract quantile-normalized values of each probe from the normalized *.CEL files).

organism: Arabidopsis thaliana

source_name: sic-1 Arabidopsis seedlings

label_protocol: prepared by using the GeneChip® WT Double-Stranded cDNA Synthesis Kit and the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix) according to manufacturer's instructions.

growth_protocol: Arabidopsis seedling were grown for 2 weeks on MS agar plates supplemented with 3% sucrose and with daily cycles of 16 h of light at 22°C and 8 h of dark at 18°C.

extract_protocol: Total RNA was isolated from the seedlings by using the RNeasy plant mini kit. DNA contamination in RNA samples were eliminated by with DNAse digestion (Qiagen)

value: seedlings

value: sic-l mutant


title: BPA-Series2-31.25 pM


title: wildtype, biological rep2

description:
whole genome expression data from wildtype plants
JZVC_Col0_2

data_processing:
TILING array probes were first re-mapped to the Arabidopsis genome (TAIR9) using SOAP2 (Li et al., 2009), and only probes that perfectly matched to a unique position in the genome were used for subsequent analyses. A custom Chip Definition File (CDF) was created using the mapping result and was used to quantile-normalize raw tiling array data with the aroma.affymetrix framework (http://www.aroma-project.org). For the purpose of this study, only probes that were uniquely mapped to gene region (including intronic regions), 200bp downstream regions, and non-coding RNA genes were considered. Only PM intensity values were used.
JZVC_Col0_2_QN.txt (in-house script to used extract quantile-normalized values of each probe from the normalized *.CEL files).

source_name: Arabidopsis wildtype seedlings

value: wildtype


title: sic-1, biological rep1

description:
whole genome expression data from sic-1 mutant
JZVC_ha27_1

data_processing:
TILING array probes were first re-mapped to the Arabidopsis genome (TAIR9) using SOAP2 (Li et al., 2009), and only probes that perfectly matched to a unique position in the genome were used for subsequent analyses. A custom Chip Definition File (CDF) was created using the mapping result and was used to quantile-normalize raw tiling array data with the aroma.affymetrix framework (http://www.aroma-project.org). For the purpose of this study, only probes that were uniquely mapped to gene region (including intronic regions), 200bp downstream regions, and non-coding RNA genes were considered. Only PM intensity values were used.
JZVC_ha27_1_QN.txt (in-house script to used extract quantile-normalized values of each probe from the normalized *.CEL files).


title: wildtype, biological rep1

description:
whole genome expression data from wildtype plants
JZVC_Col0_1

data_processing:
TILING array probes were first re-mapped to the Arabidopsis genome (TAIR9) using SOAP2 (Li et al., 2009), and only probes that perfectly matched to a unique position in the genome were used for subsequent analyses. A custom Chip Definition File (CDF) was created using the mapping result and was used to quantile-normalize raw tiling array data with the aroma.affymetrix framework (http://www.aroma-project.org). For the purpose of this study, only probes that were uniquely mapped to gene region (including intronic regions), 200bp downstream regions, and non-coding RNA genes were considered. Only PM intensity values were used.
JZVC_Col0_1_QN.txt (in-house script to used extract quantile-normalized values of each probe from the normalized *.CEL files).


title: BPA-Series2-31.25 nM


title: EE2-Series4-1 pM


title: BPA-Series4-3.125 uM


title: BPA-Series2-3.125 uM


title: IFNa, w/o CHX, Replikate 1

status: Public on Jul 04 2013

city: Cambridge

first: Lars

last: Dölken

state: Cambridgeshire

address: Addenbrookes Hospital, Hills Road

department: Medicine

institute: University of Cambridge

description:
A2_IFNa_RepA
nascent RNA, 30-60 min
gene expression data

hyb_protocol: standard Affy

scan_protocol: AGCC

data_processing: Expression Console

source_name: IFNa, w/o CHX

label_protocol: standard Affy

extract_protocol: Total cellular RNA was isolated using Trizol reagent and nascent RNA was purified as described (Dölken et al. RNA 2008) .

treatment_protocol: NIH-3T3 cells were pretreated for 15 min with either DMSO (mock) or cycloheximide followed by addition of either mock, 100 U/ml IFNalpha or 100 U/ml IFNgamma for 1h. During the last 30 min, 500 µM 4-thiouridine was added to cell culture medium.

value: NIH-3T3 fibroblasts

tag: replicate


title: IFNg, w/o CHX, Replikate 2

description:
B3_IFNg_RepB
nascent RNA, 30-60 min
gene expression data

source_name: IFNg, w/o CHX


title: IFNa, w/o CHX, Replikate 2

description:
B2_IFNa_RepB
nascent RNA, 30-60 min
gene expression data


title: IFNa, + CHX, Replikate 1

description:
A5_CHX_IFNa_RepA
nascent RNA, 30-60 min
gene expression data

source_name: IFNa, + CHX


title: IFNg, + CHX, Replikate 2

description:
B6_CHX_IFNg_RepB
nascent RNA, 30-60 min
gene expression data

source_name: IFNg, + CHX


title: Mock, + CHX, Replicate 1

description:
A4_CHX_Mock_RepA
nascent RNA, 30-60 min
gene expression data

source_name: Mock, + CHX


title: OC-BAP- (negative) cells, sample Avo1 15.3, biological rep. 1

status: Public on May 17 2013

city: Padova

first: Nicol

last: Poncina

address: via Giustiniani, 2

department: Department of Medicine

country: Italy

institute: University of Padova

description:
Expression data from OC- and BAP- (negative) sorted cells from buffy coat of human blood
Avo1_-/- 15.3

hyb_protocol: 10ug of fragmented and biotin-labeled aRNA were hybridized for 16 hr at 45C on Affymetrix Human U133 Plus 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software

data_processing: Expression values were generated from fluorescence signals using the robust multiarray average (RMA).

source_name: sorted OC-BAP- (negative) cells, from buffy coat

label_protocol: 250ng total RNA was converted to cDNA using the Affymetrix® GeneChip® 3' IVT Express Kit, followed by in vitro transcription, biotin-labeling and fragmentation to make labeled aRNA according to manufacturer's intructions.

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

treatment_protocol: No treatment, PBMCs were isolated form the blood of healthy non-diabetic donors, and OC+BAP+ double positive or OC-BAP- negative were sorted (in total around 5-10million cells) by FACS for total RNA extraction

tag: donor

tag: donor phenotype

value: healthy, non diabetic

value: blood

value: OC-BAP- (negative) cells


title: Mock, w/o CHX, Replicate 1

description:
A1_Mock_RepA
nascent RNA, 30-60 min
gene expression data

source_name: Mock, w/o CHX

tag: cell line


title: Mock, + CHX, Replicate 2

description:
B4_CHX_Mock_RepB
nascent RNA, 30-60 min
gene expression data


title: Mock, + CHX, Replicate 3

description:
D4_CHX_Mock_RepD
nascent RNA, 30-60 min
gene expression data


title: OC+BAP+ (positive) cells, sample Avo4 20.3 biological rep. 2

description:
Expression data from OC+ and BAP+ (positive) sorted cells from buffy coat of human blood
Avo4_+/+ 20.3

source_name: sorted OC+BAP+ (positive) cells, from buffy coat

tag: cell type

value: OC+BAP+ (positive) cells


title: IFNg, w/o CHX, Replikate 1

description:
A3_IFNg_RepA
nascent RNA, 30-60 min
gene expression data


title: OC-BAP- (negative) cells, sample Avo6 06.03, biological rep. 3

description:
Expression data from OC- and BAP- (negative) sorted cells from buffy coat of human blood
Avo6_-/- 06.03


title: IFNa, w/o CHX, Replikate 3

description:
D2_IFNa_RepD
nascent RNA, 30-60 min
gene expression data


title: OC+BAP+ (positive) cells, sample Avo2 15.3, biological rep. 1

description:
Expression data from OC+ and BAP+ (positive) sorted cells from buffy coat of human blood
Avo2_+/+ 15.3


title: IFNg, + CHX, Replikate 3

description:
D6_CHX_IFNg_RepD
nascent RNA, 30-60 min
gene expression data


title: IFNa, + CHX, Replikate 3

description:
D5_CHX_IFNa_RepD
nascent RNA, 30-60 min
gene expression data


title: Mock, w/o CHX, Replicate 3

description:
D1_Mock_RepD
nascent RNA, 30-60 min
gene expression data


title: IFNg, + CHX, Replikate 1

description:
A6_CHX_IFNg_RepA
nascent RNA, 30-60 min
gene expression data


title: IFNa, + CHX, Replikate 2

description:
B5_CHX_IFNa_RepB
nascent RNA, 30-60 min
gene expression data


title: hw985

status: Public on May 15 2013

first: Guangxu

last: Jin

address: 6670 Bertner Ave

institute: The Methodist Hospital Research Institute

hyb_protocol: From each biopsy specimen, 15µg of labeled cRNA were hybridized onto the Human Genome U133 GeneChip using recommended procedures for prehybridization, hybridization, washing, and staining with streptavidin-phycoerythrin (SA-PE).

data_processing: Commercial software Partek

source_name: primary tumor of breast cancer patient

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

extract_protocol: Core biopsies from primary tumors of 52 breast cancer patients were obtained using an MC1410 MaxCore biopsy instrument. Two to three core biopsy specimens were immediately transferred for snap freezing at –80◦C for cDNA array analysis. The RNA (RNeasy kit, QIAGEN) was isolated and reverse transcription was done in accordance with protocols recommended by Affymetrix using commercially available buffers and proteins.

tag: brain metastasis

value: 1 (with brain metastasis)


title: hw960

value: 0 (without brain metastasis)

value: 1 (HER2-positive)


title: hw889


title: OC-BAP- (negative) cells, sample Avo3 20.3, biological rep. 2

description:
Expression data from OC- and BAP- (negative) sorted cells from buffy coat of human blood
Avo3_-/- 20.3


title: Combination

description: SAMPLE 4

source_name: Primary CLL_GSI and fludarabine

value: primary NOTCH1-mutated CLL cells

value: GSI + fludarabine


title: Mock, w/o CHX, Replicate 2

description:
B1_Mock_RepB
nascent RNA, 30-60 min
gene expression data


title: hw854


title: hw849


title: hw829


title: hw838


title: hw842


title: hw830


title: hw743


title: hw744


title: hw748


title: hw672


title: hw742


title: hw747


title: hw676


title: hw663


title: FTE02_2D rep3

value: Fallopian tube secretory epithelial cells (FTSECs)

value: 2D culture


title: hw735


title: hw650


title: hw608


title: hw624


title: hw637


title: hw551


title: hw602


title: hw535


title: hw625


title: hw51


title: hw604


title: hw654


title: hw626


title: hw635


title: hw432


title: hw492


title: hw419


title: hw440


title: hw1385


title: hw377


title: hw1388


title: hw413


title: hw1463


title: hw400


title: hw1269


title: hw1291


title: hw1089


title: hw1196


title: hw1109


title: ATF4-3

status: Public on May 01 2013

city: Boston

first: Katrina

last: Steiling

address: 72 East Concord Street, E-631

institute: Boston Univeristy School of Medicine

description:
AS_B7_ATF4.3B
gene expression data from BEAS2B cells
ATF4 overexpression

hyb_protocol: The labeled fragmented cDNA was hybridized to Affymetrix Human Gene ST v1.0 microarrays for 16-18 hours in the GeneChip Hybridization Oven 640 (45C, 60rpm rotation).  The hybridized samples were washed.  Using Affymetrix Fluidics Station 450 (Hybridization Washing and Staining Kit, Affymetrix), the samples were first stained with strepavidin (SAPE).  This was followed by signal amplification with a biotinylated goat anti-streptavidin antibody and a second SAPE stain.

scan_protocol: Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix)

data_processing: RMA normalization (R statistical environment using the affy package), EntrezGene v11.0.1 CDF

source_name: bronchial brushing, BEAS2B cells, ATF4

label_protocol: Total RNA was processed and hybridized to Affymetrix Human Gene Arrays ST v1.0 as described in the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).  Briefly, 200ng of RNA was reverse transcribed (Whole Transcript cDNA Sythesis Kit, Affymetrix).  The resulting cDNA was used as a template for in vitro transcription (IVT) (Whole Transcript cDNA Amplification Kit, Affymetrix).  The resulting antisense cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix) and then reverse transcribed with dUTP incorporation (Whole Transcript cDNA Synthesis Kit, Affymetrix, Santa Clara, CA).  The resulting single-stranded sense DNA was fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1).  The fragmented DNA was labeled using DNA Labeling Reagent which is covalently linked to biotin with terminal deoxynucleotidyl transferase (TdT) (Whole Transcript Terminal Labeling Kit, Affymetrix).

extract_protocol: Total RNA was isolated from BEAS2B cells.

value: BEAS2B bronchial epithelium cell line

tag: genotype/variation

value: ATF4 overexpression


title: hw374

tag: time


title: Control-2

description:
AS_A8_Ctrl.2B
gene expression data from BEAS2B cells
empty vector

source_name: bronchial brushing, BEAS2B cells, Control

value: control


title: hw1207


title: Control-1

description:
AS_A7_Ctrl.1B
gene expression data from BEAS2B cells
empty vector


title: ATF4-1

description:
AS_B5_ATF4.1B
gene expression data from BEAS2B cells
ATF4 overexpression


title: hw1138


title: ATF4-2

description:
AS_B6_ATF4.2B
gene expression data from BEAS2B cells
ATF4 overexpression


title: OC+BAP+ (positive) cells, sample Avo5 06.03, biological rep. 3

description:
Expression data from OC+ and BAP+ (positive) sorted cells from buffy coat of human blood
Avo5_+/+ 06.03


title: hw1489


title: hw1073


title: X33_normal epithelium_sample 3

status: Public on Apr 19 2013

city: Frederick

first: Ludmila

last: Szabova

address: 1050 Boyles Street

department: CAPR

institute: Frederick National Laboratory for Cancer Research

hyb_protocol: Labeled cDNA (4.4 ug) of each sample was hybridized to Affymetrix mouse 430 2.0 GeneChip array.at 45°C for 16 hrs. GeneChip arrays were washed on Affymetrix Fluidics Station 450 using manufacturer’s recommended scripts and scanned on Affymetrix GeneChip scanner 3000. Data were collected using Affymetrix AGCC software.

data_processing: The obtained .cel files were processed and normalized by RMA (robust multi-chip average). Principle component analysis (PCA) was plotted (Figure S7A) by using the first two principle components based on 45,048 probes with excluding affymetrix control probes on mouse 430 2.0 array. 9,070 probes out of the total 45,048 probes on the chip were obtained by filtering with coefficient of variation greater than 8%. After standardization (mean as 0 and standard deviation as 1), the data was subjected to two-dimensional unsupervised hierarchical clustering with agglomerative approach using Pearson correlation coefficient as similarity metric by avearge linkage (Figure S7B). Both clustering and PCA analysis were done within partek genomic suite (www.partek.com).

source_name: normal ovarian epithelium

label_protocol: RNA (10 ng) was amplified and labeled with Ovation Whole Blood Solution kit (Nugen) following manufacturer’s protocol.

extract_protocol: Total RNA was isolated from flash frozen tumor pieces using TRIZOL reagent (Invitrogen) according the manufacturer’s protocol with the modification of binding the precipitated RNA on RNAeasy column (Qiagen) for consequent washing and elution. For control RNA, frozen 10 μm ovary sections were stained with Methylgreen (Vector Laboratories) containing RNAProtect (Sigma) for 20 seconds, followed by dehydration in 100% ethanol and xylene. Ovarian surface epithelial cells were microdissected from frozen sections using PixCell IIe laser capture microdissection instrument (Arcturus). Targets of ovarian epithelium collected from 20 sections were combined for a single RNA extraction as lysates. RNA was isolated by AllPrep RNA/DNA extraction kit (Qiagen) with the protocol for simultaneous recovery of small and large RNAs. RNA quality was assayed with an Agilent Bioanalyzer. All samples used for microarray analysis had high quality score (RIN >9).

tag: strain background

value: FVB/NJ

value: wild type

value: normal ovarian epithelium


title: Control-3

description:
AS_B1_Ctrl.3B
gene expression data from BEAS2B cells
empty vector


title: X31_normal epithelium_sample 1

scan_protocol: scanned on Affymetrix GeneChip scanner 3000

tag: tissue


title: X22_SEOC_R5810

source_name: ovarian tumor

value: K18 tg, p53 fl/fl

value: ovarian tumor

tag: tumor stage

value: no data


title: X19_SEOC_238721

value: B1 fl/fl, K18 tg, p53 fl/fl

value: IV


title: X20_SEOC_238767


title: X06_SEOC_23185

value: B2 fl/fl, K18 tg, p53 m/fl


title: X25_SEOC_R5838

value: IB


title: X18_SEOC_236477


title: X17_SEOC_235746


title: X13_SEOC_195571


title: X16_SEOC_235744

value: IIIB


title: X03_SEOC_21981


title: X26_SEOC_R5843


title: X15_SEOC_235132


title: X23_SEOC_R5817


title: X28_SEOC_R5854


title: X24_SEOC_R5831


title: X04_SEOC_22864

value: B1 fl/fl, K18 tg, p53 m/fl


title: X29_SEOC_R5855


title: X02_SEOC_15825

value: IIB


title: X09_SEOC_25604


title: X01_SEOC_48


title: X08_SEOC_24661

value: IIA


title: IFNg, w/o CHX, Replikate 3

description:
D3_IFNg_RepD
nascent RNA, 30-60 min
gene expression data

value: NIH-3T3 fibroblasts


title: X32_normal epithelium_sample 2


title: X05_SEOC_23172


title: X14_SEOC_216648


title: X27_SEOC_R5848

value: IIIA


title: X07_SEOC_23615


title: X10_SEOC_30200


title: MCMV 5-6hpi 200µM 4sU newly synthesized RNA Rep.3

status: Public on Feb 01 2013

description: 1h newly transcribed RNA

hyb_protocol: Affymetrix standard

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner

data_processing: RMA

label: biotion

source_name: NIH-3T3 cells 5-6hpi 200µM 4sU + MCMV

label_protocol: Affymetrix one cycle target labeling protocol

growth_protocol: DMEM + 5%FCS, 37°C, 5% CO2

extract_protocol: Trizol extraction of total RNA was performed following the modified protocol described by Chomczynski et al.

treatment_protocol: NIH-3T3 cells (5th to 15th passage after thawing) were plated at 40% density 24 h before the begin of the experiment (=> 80% density at start of experiment)

value: NIH-3T3 cells

tag: infection

value: MCMV

value: 5-6 hpi

tag: sample type

value: newly synthesized RNA


title: MCMV 2hpi 200µM 4sU total RNA Rep.2

description: total cellular RNA

source_name: NIH-3T3 cells 1-2hpi 200µM 4sU + MCMV

value: 1-2 hpi

value: total RNA


title: 1h mock newly synthesized RNA Rep.2

description: 1h newly transcribed RNA

source_name: NIH-3T3 cells 1h 200µM 4sU

value: mock

value: control


title: 1h mock newly synthesized RNA Rep.1

description: 1h newly transcribed RNA


title: MCMV 6hpi 200µM 4sU total RNA Rep.3

description: total cellular RNA


title: MCMV 6hpi 200µM 4sU total RNA Rep.2

description: total cellular RNA


title: 1h mock newly synthesized RNA Rep.3

description: 1h newly transcribed RNA


title: MCMV 1-2hpi 200µM 4sU newly synthesized RNA Rep.2

description: 1h newly transcribed RNA


title: MCMV 3-4hpi 200µM 4sU newly synthesized RNA Rep.1

description: 1h newly transcribed RNA

source_name: NIH-3T3 cells 3-4hpi 200µM 4sU + MCMV

value: 3-4 hpi


title: MCMV 6hpi 200µM 4sU total RNA Rep.1

description: total cellular RNA


title: MCMV 1-2hpi 200µM 4sU newly synthesized RNA Rep.3

description: 1h newly transcribed RNA


title: MCMV 5-6hpi 200µM 4sU newly synthesized RNA Rep.1

description: 1h newly transcribed RNA


title: MCMV 3-4hpi 200µM 4sU newly synthesized RNA Rep.2

description: 1h newly transcribed RNA


title: MCMV 5-6hpi 200µM 4sU newly synthesized RNA Rep.2

description: 1h newly transcribed RNA


title: MCMV 1-2hpi 200µM 4sU newly synthesized RNA Rep.1

description: 1h newly transcribed RNA


title: MCMV 3-4hpi 200µM 4sU newly synthesized RNA Rep.3

description: 1h newly transcribed RNA


title: 1h mock total RNA Rep.3

description: total cellular RNA


title: MCMV 4hpi 200µM 4sU total RNA Rep.2

description: total cellular RNA


title: MCMV 2hpi 200µM 4sU total RNA Rep.3

description: total cellular RNA


title: 1h mock total RNA Rep.2

description: total cellular RNA


title: MCMV 4hpi 200µM 4sU total RNA Rep.1

description: total cellular RNA


title: MCMV 2hpi 200µM 4sU total RNA Rep.1

description: total cellular RNA


title: 1h mock total RNA Rep.1

description: total cellular RNA


title: MCMV 4hpi 200µM 4sU total RNA Rep.3

description: total cellular RNA


title: hw502

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

value: 0 (without brain metastasis)


title: SNU-886

status: Public on Mar 20 2012

first: Nicolas

last: Stransky

address: 7 Cambridge center

department: Cancer Program

institute: Broad Institute

description: SNP array data from the CCLE

hyb_protocol: After denaturation, 200ul of sample are injected into a Genome-Wide Human SNP 6.0 array. Arrays are loaded in the GeneChip® Hybridization Oven 640 @ 50 °C temp, rotating arrays @ 60 rpm. Samples are hybridized for 16 to 18 hours.

scan_protocol: Genome-Wide Human SNP Array 6.0 are stained using the GeneChip® Fluidics Station 450 and scanned using the GeneChip® Scanner 3000

data_processing: The raw CEL files were normalized to copy number estimates using a GenePattern pipeline, as described in Cancer Genome Atlas Research Network et al, Nature, 2008, and hg18 Affymetrix probe annotations. Normalized copy number estimates (log2 ratios) were segmented using the Circular Binary Segmentation (CBS) algorithm, followed by median centering of the segment values to a value of zero in each sample.

source_name: KCLB

label_protocol: PCR amplification fragments (200 and 1100 bp) are labeled using terminal deoxynucleotidyl transferase following the Affymetrix GenomeWideSNP_6 protocol

growth_protocol: Cells lines were cultured following growth recommendations from the cell line source vendors. Cells were incubated at 37 ºC at 5% CO2 until 70% confluency was reached.  Pellets were harvested 48 hours post media change, flash frozen, and stored at -80 ºC until nucleic acid extraction.

extract_protocol: DNA was extracted from frozen cell pellets, containing an average cell count of 4.5 million cells, using the Qiagen Gentra Puregene method following the manufacturers recommendations. Samples were quantified using picogreen on a ThermoScientific Varioskan Flash instrument.

tag: primary site

value: liver

tag: histology

value: carcinoma

tag: histology subtype1


title: Human_ThGARP_T100min

status: Public on Nov 23 2012

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

description: transcriptomic data to construct a dynamic functional network of human regulatory T cell genes

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

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

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

source_name: human peripheral blood of healthy donor

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

growth_protocol: taken from donors, sorted, expanded ex vivo and stimulated

extract_protocol: RNeasy

treatment_protocol: Human Tregs or Teffs were mixed with anti-CD3/anti-CD28-coated Dynabeads (Invitrogen) at a ratio of 1:1 and with 100 U/ml of IL2 (Proleukin, Novartis) and were distributed with 4x106 cells into 1.5 ml microtubes (Eppendorf) for each time point. Before the cells were cultured at 37°C, they were first stored at 4°C to allow cells and beads to settle properly. Samples were taken every 20 min during the first six hours following stimulation, except for TeffGARP and TeffGFP cells, which were measured at time points 0, 100 and 360 min. The cells were centrifuged, and the cell pellets were lysed in RLT buffer (Qiagen) and immediately stored at -70°C.

value: sorted human Teff GARP-overexpressed cells (CD4+CD25-) stimulated by anti-CD3/anti-CD28 Dynal beads/IL2


title: Human_ThGARP_T360min


title: Liver biopsy before immunosuppressive therapy W37P

status: Public on Jan 09 2012

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

description: Liver biopsy before immunosuppressive therapy (AFFY_W37P) with a TOL status

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'gcrma' function of the Bioconductor package (v2.4) 'gcrma' in R.2.9.1

label_protocol: Standard Affymetrix protocol

extract_protocol: For total RNA extraction cryopreserved liver tissue samples were homogenized in TRIzol reagent (Invitrogen, San Diego, CA, USA) using pestle and nuclease-free 1,5ml reaction tubes (Ambion). Total RNA was then extracted following the manufacturers guidelines and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

tag: immunotolerance group

value: TOL


title: Liver biopsy before immunosuppressive therapy W15P

description: Liver biopsy before immunosuppressive therapy (AFFY_W15P) with a Non TOL status

value: Non TOL


title: Liver biopsy before immunosuppressive therapy W83P

description: Liver biopsy before immunosuppressive therapy (AFFY_W83P) with a Non TOL status


title: Liver biopsy before immunosuppressive therapy W89P

description: Liver biopsy before immunosuppressive therapy (AFFY_W89P) with a Non TOL status


title: Liver biopsy before immunosuppressive therapy W20P

description: Liver biopsy before immunosuppressive therapy (AFFY_W20P) with a TOL status


title: Human_ThGARP_T0min


title: Jijoye total RNA; 2. Replicate

status: Public on Feb 04 2011

description: gene expression data

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

source_name: Jijoye total RNA (control)

label_protocol: Affymetrix protocol

growth_protocol: DG75-eGFP, DG75-10/12 and BCBL-1 were cultured in RPMI 1640 medium containing 100 IU/ml Penicillin, 100 µg/ml Streptomycin and 2 mM L-Glutamin. BL41, BL41 B95.8 and Jijoye were cultered in RPMI 1640 medium containing 10% fetal calf serum and Penicillin/Streptomycin as well as Bykomycine and Nystatin.

extract_protocol: 5x10e08 cells were lyzed in 10 ml of lysis buffer containing 25 mM Tris HCl pH 7.5, 150 mM KCl, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, and protease inhibitors (Roche); incubated for 30 min at 4°C and cleared by centrifugation at 20,000 g for 30 min.   Conditions for immunoprecipitation: 60 µl Protein-G sepharose beads were incubated with 5 m RPMI containing 6µg of either anti hAgo2 (11A9) or anti-BrdU (abcam) over night. Next morning columns were drained by gravity flow and washed once with lysis buffer. Next, 5 ml of lysates were added and incubated for 3 h at 4°C. In the meanwhile, total RNA was prepared from 100µl of cell lysates. This was analyzed for BL41, B41 B95.8 and Jijoye instead of the BrdU-IP.    Following the incubation, beads were washed 4x with IP wash buffer (300 mM NaCl, 50 mM Tris HCl pH 7.5, 5 mM Mg2Cl, 0.1% NP-40, 1 mM NaF) and once with PBS. RNA was recovered using miRNeasy (Qiagen).

tag: replicate


title: Liver biopsy before immunosuppressive therapy W40P

description: Liver biopsy before immunosuppressive therapy (AFFY_W40P) with a Non TOL status


title: Liver biopsy before immunosuppressive therapy W21P

description: Liver biopsy before immunosuppressive therapy (AFFY_W21P) with a Non TOL status


title: Liver biopsy before immunosuppressive therapy W81P

description: Liver biopsy before immunosuppressive therapy (AFFY_W81P) with a Non TOL status


title: Liver biopsy before immunosuppressive therapy W111P

description: Liver biopsy before immunosuppressive therapy (AFFY_W111P) with a immunotolerance TOL status


title: Liver biopsy before immunosuppressive therapy W12P

description: Liver biopsy before immunosuppressive therapy (AFFY_W12P) with a Non TOL status


title: Liver biopsy before immunosuppressive therapy W65P

description: Liver biopsy before immunosuppressive therapy (AFFY_W65P) with a Non TOL status


title: Human_ThGFP_T100min

value: sorted human Teff GFP-expressing cells (CD4+CD25-) stimulated by anti-CD3/anti-CD28 Dynal beads/IL2


title: Liver biopsy before immunosuppressive therapy W11P

description: Liver biopsy before immunosuppressive therapy (AFFY_W11P) with a Non TOL status


title: Liver biopsy before immunosuppressive therapy W8P

description: Liver biopsy before immunosuppressive therapy (AFFY_W8P) with a TOL status


title: Liver biopsy before immunosuppressive therapy W120P

description: Liver biopsy before immunosuppressive therapy (AFFY_W120P) with a TOL status


title: Liver biopsy before immunosuppressive therapy W113P

description: Liver biopsy before immunosuppressive therapy (AFFY_W113P) with a TOL status


title: Liver biopsy before immunosuppressive therapy W2P

description: Liver biopsy before immunosuppressive therapy (AFFY_W2P) with a Non TOL status


title: Liver biopsy before immunosuppressive therapy W129P

description: Liver biopsy before immunosuppressive therapy (AFFY_W129P) with a TOL status


title: Liver biopsy before immunosuppressive therapy W3P

description: Liver biopsy before immunosuppressive therapy (AFFY_W3P) with a TOL status


title: Human_ThGFP_T360min

description: transcriptomic data to construct a dynamic functional network of human regulatory T cell genes


title: Human_ThGFP_T0min


title: Liver biopsy before immunosuppressive therapy W1P

description: Liver biopsy before immunosuppressive therapy (AFFY_W1P) with a TOL status


title: Jijoye total RNA; 1. Replicate

description: gene expression data


title: Jijoye Ago2-IP; 2. Replicate

description: gene expression data

source_name: Jijoye Ago2-IP

tag: antibody


title: Jijoye Ago2-IP; 1. Replicate

description: gene expression data


title: BL41 B95.8 total RNA; 1. Replicate

description: gene expression data

source_name: BL41 B95.8 total RNA (control)


title: BL41 B95.8 total RNA; 2. Replicate

description: gene expression data


title: Water treated, biological Rep 3

status: Public on Nov 24 2010

city: Lucknow

first: Samir

last: Sawant

state: UP

address: Sikandrabad

department: Plant Molecular Biology Lab

country: India

institute: National Botanical Research Institute

description:
control CEL file: genomic_1.CEL
control CEL file:  genomic_2.CEL
There were total 3 genomic hybridizations have been performed with total 8 replicates i.e. 3 for SA treatment, 3 for water conition and 2 for genomic DNA

hyb_protocol: For hybridization, 7.5 μg of fragmented and labelled DNA target was hybridize onto GeneChip® Arabidopsis Tiling 1.0R array (Reverse) and incubated in a hybridization oven with continuous mixing at 45°C and 60 rpm for 16 h. After hybridization, Arrays were washed and stained in an Affymetrix Fluidics station 450 according to manufacturer’s protocol.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip® 3000 7G scanner and the signals were quantified with the Affymetrix GeneChip® Operating Software (GCOS) to generate CEL files.

data_processing:
Tiling Analysis software (TAS) from Affymetrix technology was used to analyze Tiling Array data (.CEL files) along with three other accessory files namely BPMAP file, GRC file and GFF files.
.bar files  are generated by TAS that contains signal intensity for each probe and which can be read by IGB (Intgrated genome browser)

source_name: Arabiopsis seedling (Col-0)

label_protocol: After fragmentation samples was labelled by incubating it at 37°C for 60 min in a thermal cycler with a labeling master mix containing DNA Labeling Reagent, Terminal deoxynucleotidyl Transferase and 1x Terminal deoxynucleotidyl Transferase buffer as described in the Affymetrix GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (P/N 900812).

growth_protocol: All Arabidopsis seedlings (Col-0) on moist soil were kept at 4°C for 3 days before placing them in the growth chamber.  A. thaliana plants were grown for 2 weeks under controlled environmental conditions at 22±1°C and photoperiod of 16 h light/8 h dark cycle with fluorescent of 120 µmol/m²/sec.

extract_protocol: The nuclei were isolated as described (Li et al. 1998), with slight modifications. The nuclear preparation equivalent to A₂₆₀ of 100 was incubated with micrococcal nuclease (300 units/μl) in a micrococcal nuclease buffer at 37°C for 10 min. The reaction was stopped by adding EGTA. The DNA was extracted and the samples were incubated with RNase A, extracted by phenol: chloroform and precipitated in ethanol. The DNA was separated on 1.5 % agarose gel and fragments of an average size of 150 bp were purified.

treatment_protocol: The salicylic acid (2mM) was used on the 2 week old A. thaliana seedlings (Col-0). The seedlings were floated on water (control) or SA (treated) with incubation for 24 h in light at 22±1°C with gentle agitation.

tag: cultivar

tag: development stage

value: seedling

tag: fraction

value: Mononucleosomal DNA

value: input


title: SA treated, biological Rep 2


title: SA treated, biological Rep 3


title: Water treated, biological Rep 1


title: Water treated, biological Rep 2


title: BL41 Ago2-IP; 1. Replicate

description: gene expression data

source_name: BL41 Ago2-IP


title: BL41 total RNA; 2. Replicate

description: gene expression data

source_name: BL41 total RNA (control)


title: BCBL-1 Ago2-IP; 1. Replicate

description: gene expression data

source_name: BCBL-1 Ago2-IP


title: DG75-eGFP BrdU-IP; 2. Replicate

description: gene expression data

source_name: DG75-eGFP BrdU-IP (control)

value: BrdU


title: DG75-eGFP Ago2-IP; 2. Replicate

description: gene expression data

source_name: DG75-eGFP Ago2-IP


title: DG75-10/12 BrdU-IP; 2. Replicate

description: gene expression data

source_name: DG75-10/12 BrdU-IP (control)


title: DG75-10/12 Ago2-IP; 2. Replicate

description: gene expression data


title: BCBL-1 BrdU-IP; 1. Replicate

description: gene expression data

source_name: BCBL-1 BrdU-IP (control)


title: BL41 B95.8 Ago2-IP; 2. Replicate

description: gene expression data

source_name: BL41 B95.8 Ago2-IP


title: BCBL-1 BrdU-IP; 2. Replicate

description: gene expression data


title: BL41 total RNA; 1. Replicate

description: gene expression data


title: BL41 B95.8 Ago2-IP; 1. Replicate

description: gene expression data


title: DG75-eGFP BrdU-IP; 1. Replicate

description: gene expression data


title: BL41 Ago2-IP; 2. Replicate

description: gene expression data


title: SA treated, biological Rep 1


title: DG75-10/12 Ago2-IP; 1. Replicate

description: gene expression data


title: DG75-10/12 BrdU-IP; 1. Replicate

description: gene expression data


title: BCBL-1 Ago2-IP; 2. Replicate

description: gene expression data


title: DG75-eGFP Ago2-IP; 1. Replicate

description: gene expression data


title: PCN_control shRNA

status: Public on Apr 18 2013

city: Nagoya

first: Shinsuke

last: Ishigaki

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Neurology

country: Japan

institute: Nagoya University School of Medicine

description: RMA expression value derived from Expression Console software; all-exon analysis

hyb_protocol: Samples were hybridized with GeneChip mouse exon 1.0 ST Arrays (Affymetrix) and scanned accoding to the manufacture's protocol.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip 3000 7G

data_processing:
The data were background corrected and normalized using the robust multiarray average (RMA) procedure implemented in the Affymetrix Expression Console software.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dtl.mm9.full.ps

source_name: primary cortical neurons, control shRNA

label_protocol: 100ng of total RNA were used to generate labeled cDNA. Biotinylated DNA probes were prepared using Affymetrix WT Expression kit for Affymetrix Whole Transcript Sense Expression arrays and Affymetrix geneChip WT Terminal Labeling kit according to the manufacture's protocol.

growth_protocol: Mouse fetal brain was taken from C57BL/6 mouse embryos at E15. After removing meninges cortical tissue was dissociated into a single-cell suspension by Sumilon dissociation solution (Sumitomo Bakelite, Tokyo Japan). Cells were plated at a density of 1.5 x 106 cells in a 60 mm-well culture plate with the medium containing 0.5x Sumilon nerve-culture medium (Sumitomo Bakelite), 0.5x Neurobasal medium, 1% FBS, 0.5x B27 supplements (Invitrogen), 0.5x Glutamax, 5 µg/ml of BDNF, 5 µg/ml of CNTF, and 0.5% Pen-Strep. A day after plating (day 2), neurons were supplemented with 10 ng/µl of AraC and incubated overnight.

extract_protocol: Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) followed by DnaseI (Qiagen) treatment.

treatment_protocol: On day 5, neurons were infected with 2 x 1010 copies/well (1.5 x 107 copies/µl) of lentivirus expressing shRNA against mouse Cugbp1 (shCugbp1) or control (shCont). After 4 hr of infection, the virus media was removed. Neurons were then cultured for 6 additional days, and were harvested on day 11 followed by RNA extraction and cDNA synthesis.

tag: strain

tag: developmental stage

value: embryo

tag: age

tag: cell type

value: primary cortical neurons


title: PCN_shRNA Cugbp1

source_name: primary cortical neurons, shRNA Cugbp1

tag: genotype/variation

value: Cugbp1 knockdown


title: Total RNA of BCBL-1 replicate 2

status: Public on Nov 04 2010

description: gene expression data

hyb_protocol: Affymetrix GeneChip Human Gene 1.0 ST arrays were hybridized, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual using the Gene Chip Fluidics Station 450.

scan_protocol: Affymetrix GeneChip® Command Console® Software (AGCC)

data_processing: Expression Console, RMA

source_name: total RNA

label_protocol: 100 ng RNA of each sample was amplified and labeled using the Affymetrix Whole-Transcript (WT) Sense Target Labeling Protocol without rRNA reduction following the manufacturer`s protocol.

growth_protocol: DG75-eGFP, DG75-10/12 and BCBL-1 were cultured in RPMI 1640 medium containing 10% fetal calf serum, 100 IU/ml Penicillin, 100 µg/ml Streptomycin and 2 mM L-Glutamin.

extract_protocol: Cells were culture for 1h in 100 µM 4-thiouridine final concentration (added to cell culture medium), Trizol extraction, Biotinylation and separation of total RNA into nascent and unlabeled preexisting RNA was performed as described by Dölken et al. RNA 2008

tag: cell line


title: Unlabeled RNA of BCBL-1 replicate 3

description: gene expression data

source_name: unlabeled RNA


title: Nascent RNA of BCBL-1 replicate 1

description: gene expression data

source_name: nascent RNA


title: Unlabeled RNA of DG75-10/12 replicate 2

description: gene expression data


title: Total RNA of BCBL-1 replicate 1

description: gene expression data


title: Unlabeled RNA of DG75-10/12 replicate 3

description: gene expression data


title: Total RNA of BCBL-1 replicate 3

description: gene expression data


title: Unlabeled RNA of DG75-eGFP replicate 2

description: gene expression data


title: Nascent RNA of BCBL-1 replicate 2

description: gene expression data


title: Unlabeled RNA of DG75-10/12 replicate 1

description: gene expression data


title: Nascent RNA of BCBL-1 replicate 3

description: gene expression data


title: Unlabeled RNA of BCBL-1 replicate 2

description: gene expression data


title: Nascent RNA of DG75-eGFP replicate 1

description: gene expression data


title: Nascent RNA of DG75-10/12 replicate 3

description: gene expression data


title: Nascent RNA of DG75-eGFP replicate 2

description: gene expression data


title: Unlabeled RNA of DG75-eGFP replicate 1

description: gene expression data


title: Unlabeled RNA of BCBL-1 replicate 1

description: gene expression data

value: 1, CAVE (sample not fitting to other replicates, excluded from analysis)


title: Total RNA of DG75-eGFP replicate 2

description: gene expression data


title: Total RNA of DG75-eGFP replicate 1

description: gene expression data


title: Total RNA of DG75-10/12 replicate 2

description: gene expression data


title: Total RNA of DG75-10/12 replicate 3

description: gene expression data


title: Unlabeled RNA of DG75-eGFP replicate 3

description: gene expression data


title: Nascent RNA of DG75-eGFP replicate 3

description: gene expression data


title: Total RNA of DG75-10/12 replicate 1

description: gene expression data


title: Nascent RNA of DG75-10/12 replicate 2

description: gene expression data


title: Total RNA of DG75-eGFP replicate 3

description: gene expression data


title: Nascent RNA of DG75-10/12 replicate 1

description: gene expression data


title: normal colon 2

status: Public on Oct 06 2010

city: Taipei

first: Chan-Yen

last: Tsai

address: No.155, Sec.2, Linong Street

institute: Yang-Ming University

description: total RNA isolated from normal colon of stage D colorectal carcinoma patient 2

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA through R based affy module

source_name: normal colon from stage D colorectal carcinoma patient 2

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA extracted using standard Trizol protocol, followed by Qiagen RNeasy column clean-up

tag: tissue

value: colon

tag: tumor stage of patient

value: stage D


title: normal colon 1

description: total RNA isolated from normal colon of stage D colorectal carcinoma patient 1

source_name: normal colon from stage D colorectal carcinoma patient 1


title: Liver_normoglycima_no.7

status: Public on Jul 31 2010

city: Kanazawa

first: Hirofumi

last: Misu

address: 13-1 Takaramachi

institute: Kanazawa University

description: Gene expression data from human liver.

hyb_protocol: Ten micrograms of labelled and fragmented cRNA was hybridised onto a Human Genome U133 Plus 2.0 Array (Affymetrix) for 16 h at 45°C.

scan_protocol: Chips were scanned by using GeneChip Scanner3000, Affymetrix.

data_processing: A scanned image was quantified using GCOS version 1.1.1 (GeneChip Operating Software; Affymetrix) with the default parameters for the statistical algorithm and all probe sets scaled to a target intensity of 100.

source_name: Liver, fasting

label_protocol: A total of 100 ng of total RNA was labelled according to the small sample labelling protocol recommended by the manufacturer.

growth_protocol: Hepatic tissues were obtained with percutaneous needle liver biopsy, and immediately frozen in liquid nitrogen and stored at −80°C until use.

extract_protocol: Total RNA was extracted with a kit (Micro RNA Isolation Kit; Stratagene, La Jolla, CA, USA), purified with RNeasy MiniElute Cleanup Kit (Qiagen, Hilden, Germany).

treatment_protocol: Patients with type 2 diabetes were treated with diet therapy alone or insulin; no patients were receiving any oral hypoglycaemic agent. Participants receiving statins, ACE inhibitors or angiotensin II receptor blockers were excluded.

tag: gender

value: female

tag: disease status

value: normal glucose tolerance


title: Liver_normoglycima_no.4

description: Gene expression data from human liver.

value: liver


title: Liver_normoglycima_no.6

description: Gene expression data from human liver.

value: male


title: Liver_normoglycima_no.5

description: Gene expression data from human liver.


title: Liver_normoglycima_no.1

description: Gene expression data from human liver.


title: Liver_normoglycima_no.2

description: Gene expression data from human liver.


title: Liver_normoglycima_no.3

description: Gene expression data from human liver.


title: BL41 60 min p-RNA Rep.2

status: Public on Sep 30 2009

description: unbound, preexisting RNA (p-RNA)

data_processing: GCRMA

source_name: B41 human B-cells

growth_protocol: RPMI, 10% FCS, P/S, 37°C, 5% CO2

treatment_protocol: 60 min 100 µM 4sU

tag: Burkitt lymphoma cell line


title: BL41 60 min tc-RNA Rep.1

description: total cellular RNA (tc-RNA)


title: BL41 60 min p-RNA Rep.3

description: unbound, preexisting RNA (p-RNA)


title: BL41 60 min p-RNA Rep.1

description: unbound, preexisting RNA (p-RNA)


title: BL41 60 min nt-RNA Rep.1

description: newly transcribed RNA (nt-RNA)


title: BL41 60 min tc-RNA Rep.2

description: total cellular RNA (tc-RNA)


title: BL41 60 min tc-RNA Rep.3

description: total cellular RNA (tc-RNA)


title: BL41 60 min nt-RNA Rep.3

description: newly transcribed RNA (nt-RNA)