title: Intestine_C1_3d_4

city: Leioa

first: José María

last: Lacave

state: Bizkaia

address: Sarriena s/n

department: Zoology and Animal Cell Biology

institute: University of the Basque Country

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 1.65 ƒÝg. Volume: 100 uL. Temperature (oC): 65. Duration: 17 hours at 10 rpm in the hybridization oven.

scan_protocol: Scanned on a G2565CA DNA microarray scanner (Agilent Technologies), with ozone-barrier slide covers (Agilent P/N G2505-60550) SCAN C SETTINGS Dye Channel Scan RegionGreen 61 x 21,6 mm Scan resolution (um) 6 Tiff 20 bit

data_processing:
Images (.tiff images) were quantified using Agilent Feature Extraction Software (ver. 10.7.3.1) (Agilent Technologies). The Feature Extraction software (FE) extracts the raw data from Cy3 (Green(g) channel) fluorescence signal (mean signal) from the spot which contains the probes (control features and biological or non control features) and from background. After processing of the raw signal it applies several algorithms for the calculation of the processed signal, which will be used in the analysis, and other useful data for the assessment of the quality of the processed data. The processed signal is corrected for background and microarray processing artifacts (Spatial detrending). For background correction it uses the negative control feature data, which corresponds to sequences with no expected hybridization, and it is an indication of unspecific binding or hybridization.
Raw data from Feature Extraction software was subsequently processed on GeneSpring GX 11.2 (Agilent Technologies). All the .txt raw data files are processed in the same Project, and the software creates a unique txt result file which contains the processed information for all samples (sample data file). That file contains the summarized data per biological feature and per sample.
Experiment Part 1:
Experiment type: Agilent Single Color
Workflow: Advanced workflow
1. Transform all Feature Extraction flags to Absent/Marginal/Present (Compromised/Not detected/Detected in the file) calls, as follows:
– Feature is NOT Positive and significant: ABSENT (Compromised in the file)
– Feature is NOT uniform: ABSENT (Compromised in the file)
– Feature is NOT well above background: ABSENT (Compromised in the file)
– Feature is Saturated: MARGINAL (Not detected)
– Feature is Population outlier: ABSENT (Compromised in the file)
2. Threshold raw signals (lineal data) to 1
3. Summarization: calculate the geometric mean of replicated probes. The resulted summarized lineal data is the “Raw Signal” in result files.
4. Log base2 transformation.
5. Per chip or intra-chip normalization: quantile normalization. The objective is the elimination or correction for the systematic error due to technical variations (sample processing, hybridization and/or washing artifacts, cross-hybridization, scanner settings,… ), that could hide the true biological variation.
6. Mean centering. The mean is centered to 0: for each sample, to each gene value the mean value for all samples for that gene is subtracted. The objective is to make comparable the gene expression for all arrays in the project. The result is the “Normalized Signal” (quantile + mean centering) in result files.
7. Filter Probesets based on Present/Absent calls: Use flag spot information in data files. Entities retained in which 80 % of samples in 1 out of any 6 conditions (3d Control, 3d Ionic, 3d Nano, 3w Control, 3w Ionic, 3w Nano) have Present or Marginal Flag.

organism: Danio rerio

source_name: C1, 3d, Intestine

label_protocol: Amount of nucleic acid labeled: 100 ng. Agilent Protocol One-Color Microarray-Based Gene Expression analysis (Low Input Quick Amp Labeling) Version 6.5 May 2010. Samples are retrotranscribed (first strand synthesis) and labeled using Low imput Quick Amp Labeling kit, One color (Agilent Technologies, Cat. Nº 5190-2305) following manufacturer instructions. First, total RNA is retrotranscribed with AffinityScript Reverse Transcriptase (AffinityScript RT), an engineered thermostable mutant derived from Moloney Murine Leukemia Virus (MMLV) reverse transcriptase, using Oligo dT primers coupled to T7 promoter. Double stranded cDNA synthesized by AffinityScript RT is in vitro transcribed by T7 RNA pol in the presence of either Cy3-CTP or Cy5-CTP fluorophores to generate amplified and labeled cRNA. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen). After labeling and purification, cRNA is quantify with NanoDrop ND-1000 spectrophotometer in order to determine the yield and specific activity of each reaction. Yield: µg of cRNA. Should be > 1.65 µg. Specific activity: pmol Cy3 per µg of cRNA. Should be >6. All the labeled samples where above those limits.

growth_protocol: Zebrafish Wild type AB Tübingen

extract_protocol: Total RNA was extracted following the TRizol® extraction method (ThermoFisher Scientific). Concentration of RNA was measured in a Biophotometer (Eppendorf, Hamburg, Germany). RNA was purified with RNeasy mini kit (Qiagen, Venlo, The Netherlands). In addition, RNA quality was assessed in an Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with a RIN value above 8.1 were used for microarray and qPCR analysis.

treatment_protocol: Samples were dietary exposed to 0.001 mg/L and 0.1 mg/L of PVP-PEI-Ag NPs of 5 nm for 3 and 21 days

value: Intestine

value: Male


title: Intestine_C1_3d_3

status: Public on Mar 21 2017

type: RNA

country: Spain

molecule: total RNA

tag: tissue

tag: gender


title: Intestine_C1_21d_4

source_name: C1, 21d, Intestine


title: Intestine_C1_21d_1


title: Intestine_C1_3d_2


title: Intestine_Control_3d_5

source_name: Control, 3d, Intestine


title: Intestine_Control_3d_3


title: Intestine_C1_21d_2


title: Intestine_Control_21d_2

source_name: Control, 21d, Intestine


title: Intestine_Control_21d_4


title: Liver_C1_21d_5

source_name: C1, 21d, Liver

value: Liver


title: Intestine_C1_3d_1


title: Intestine_Control_21d_5


title: Intestine_Control_3d_4


title: Intestine_Control_3d_1


title: Intestine_Control_3d_2


title: Intestine_Control_21d_3


title: Intestine_C1_3d_5


title: C57BL/6Je/e + NDP-MSH_rep2

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

description: total brain C57BL/6Je/e-6642/4

hyb_protocol: End labeled cDNA was hybridized to Affymetrix Mouse Gene 2.0 ST Gene Expression Microarrays for 16h at 45 °C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturer´s protocol (GeneChip Whole Transcript (WT) Sense Labeling Assay User Manual, Affymetrix, Inc.)

scan_protocol: Gene ChIP Scanner 3000 7G (Affymetrix Inc.); AGCC (Vers. 3.3)

data_processing:
Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probeset were summarized by GeneSpring´s ExonRMA16 algorithm after quantile normalization of probe level signal intensities across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples
probe group file: MoGene-2_0-st.pgf
meta-probeset file: MoGene-2_0-st.mps

label: biotin

organism: Mus musculus

source_name: C57BL/6Je/e + NDP-MSH

label_protocol: Synthesis of biotin labeled cDNA was performed according to the manufacturer´s protocol (WT Plus Reagent Kit; Affymetrix, Inc.). Briefly, 100 ng of total RNA were converted to cDNA. After amplification by in vitro transcription and 2nd cycle synthesis, cDNA was fragmented and biotin labeled by terminal transferase

growth_protocol: Mouse brain, day 14 after MOG-immunization (disease maximum).

extract_protocol: Mice were phenotypically identified as wild-type or mutant (coat color black in wild-type or yellow in C57BL/6Je/e), brain tissue was isolated and snap-frozen in liquid nitrogen, RNA was extracted using the innuPrep RNA kit according to the manufacturer's instructions (Analytik Jena), cDNA was synthesized from 1 μg of total RNA using random hexanucleotide primers and the RevertAid First strand cDNA Synthesis Kit (Thermo Scientific).

treatment_protocol: Intravenous injection of NDP-MSH (5 µg/mouse) at day 8, 10 and 12 after MOG-immunization.

tag: day after immunization

value: d14 (disease maximum)

value: brain

tag: genotype

tag: treatment

value: NDP-MSH


title: ETV6-RUNX1-006

city: Setagaya-ku

first: NOBUTAKA

last: KIYOKAWA

state: Tokyo

department: Pediatric Hematology & Oncology Research

country: Japan

institute: National Research Institute for Child Health & Development

description: Gene expression data from ETV6-RUNX1-positive BCP-ALL

hyb_protocol: Following fragmentation, 5 ug of cDNA were biotinylated and hybridized for 16 hr at 45C on GeneChip Human Genome Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000.

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.

organism: Homo sapiens

source_name: ETV6-RUNX1-positive BCP-ALL

label_protocol: cDNA were prepared using Ovation Pico WTA System V2 (Nugen) according to the the manufacturer's instructions.

extract_protocol: QIAzole extraction of total RNA using miRNA mini kit (Qiagen) was performed according to the manufacturer's instructions.

tag: cell type

value: B-cell precursor ALL (BCP-ALL)


title: Intestine_Control_21d_1


title: Intestine_C1_21d_3


title: Liver_C1_21d_4


title: non-ERG-related_sample 107_microRNA

city: Padova

first: Elena

last: Vendramini

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

description:
MIR_39
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis

hyb_protocol: Labeled RNA were hybridized for 16 hr at 48C on GeneChip miRNA 1.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000

data_processing: The data were normalized using RMA algorithm in R software [www.r-ptoject.org], BioConductor package [www.bioconductor.org]

source_name: non-ERG-related without ERG intragenic deletion

label_protocol: Total RNA (1ug) was labeled using the FlashTag Biotin RNA Labeling Kit (Genisphere LLC)  following manufacturer's instructions.

extract_protocol: White blood cells were isolated through Ficoll-Hypaque density gradient centrifugation. Total RNA was extracted using TRIZOL reagent following manufacturer's instructions.

value: white blood cells

tag: disease state

value: pediatric acute leukemia

value: bone marrow


title: non-ERG-related_sample 98_microRNA

description:
MIR_40
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: Liver_C1_21d_2


title: Liver_C1_21d_3


title: non-ERG-related_sample 97_microRNA

description:
MIR_43
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: ETV6-RUNX1-001


title: non-ERG-related_sample 76_microRNA

description:
MIR_30
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 99_microRNA

description:
MIR_33
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: EP300-ZNF384-005

description: Gene expression data from EP300-ZNF384-positive BCP-ALL

source_name: EP300-ZNF384-positive BCP-ALL


title: non-ERG-related_sample 100_microRNA

description:
MIR_46
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 54_microRNA

description:
MIR_59
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: Liver_C1_3d_4

source_name: C1, 3d, Liver


title: non-ERG-related_sample 51_microRNA

description:
MIR_41
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 55_microRNA

description:
MIR_57
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 44_microRNA

description:
MIR_58
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 45_microRNA

description:
MIR_29
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: Liver_C1_3d_5


title: Liver_C1_21d_1


title: Liver_HFrD_Chrebp_KO

city: Ann Arbor

first: Deqiang

last: Zhang

state: MI

address: 1137 Catherine Street

department: Molecular & Integrative Physiology

country: USA

institute: University of Michigan

description: RNA combined from 6 mice livers

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on [Array], and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267).

scan_protocol: Peg Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267).

data_processing: Data was analyzed using the affy Bioconductor package implemented in the R-statistical environment version 3.1.1. RMA was used to normalize and fit log2 transformed expression values.

source_name: liver of Chrebp null mice fed 70% fructose for 2 weeks

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA

growth_protocol: C57BL/6 mice were maintained on 12 hr/12 hr light/dark cycles with ad lib access to food and water.

extract_protocol: Liver total RNA were extract with RNeasy Mini kit from QiaGen, and RNA of livers of mice of same genotype and treatment were combined

treatment_protocol: Mice older than 2 months were fed 70% fructose diet for indicated time in sample colum

tag: strain


title: non-ERG-related_sample 43_microRNA

description:
MIR_42
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: Liver_C1_3d_3


title: non-ERG-related_sample 30_microRNA

description:
MIR_61
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: Liver_HFrD_WT

description: RNA combined from 4 mice livers

source_name: liver of wildtype mice fed 70% fructose for 2 weeks


title: Liver_WT_HFrD

description: RNA combined from 7 mice livers

source_name: liver of wildtype mice fed 70% fructose for 3 weeks


title: Liver_WT_Chow

description: RNA combined from 7 mice livers

source_name: liver of wildtype mice fed regular chow


title: Liver_C1_3d_2


title: non-ERG-related_sample 39_microRNA

description:
MIR_44
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 29_microRNA

description:
MIR_60
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: 113-ost1-2 alx8-ABA

city: Brisbane

first: Peter

middle: A

last: Crisp

state: QLD

address: John Hines Building (62), The University of Queensland

department: School of Agriculture and Food Science

country: Australia

institute: The University of Queensland

hyb_protocol: Three and a half micrograms of fragmented, biotin labelled ssDNA was hybridised to an Affymetrix Arabidopsis Gene 1.0 ST Array also using the WT plus Reagent kit assay. Arrays were hybridized for 16 hours at 45°C at 60 rpm using an Affymetrix hybridization oven. The arrays were washed according to manufacturer’s instructions on an Affymetrix FS450 fluidics station.

scan_protocol: Arrays were scanned on an Affymetrix Scanner GC3000 7G.

data_processing: Pre-processing and statistical analysis of the Affymetrix Arabidopsis Gene 1.0 ST Arrays was performed in R (v3.1.0) using the Bioconductor packages oligo (v1.28.0) (Carvalho and Irizarry, 2010) and Limma (v3.20.1) (Smyth, 2004; Smyth, 2005) respectively; and also using Affymetrix Power Tools suite (APT). Data quality checks and analysis were also performed using Partek Genomics Solution (PGS) software version 6.6 (default parameters; Partek, St. Louis, www.partek.com) and near identical results were obtained compared to the R workflow. For R analyses (shown in Fig. 3, S4, table S1) raw cel files were read into R and the exon probe sets were background corrected, quantile normalized and expression values were summarized (using the median-polish) to the transcript level by calling the rma() function (Irizarry et al., 2003a, b) with the target=’core’ option (to summarize to gene level features with the highest annotation confidence/evidence). Affymetrix Power Tools were employed to calculate the detection above background (DABG) probability for each probe set. A gene was considered present if at least one half of its constituent exons were assigned a detection p <0.05, only genes that were detected as present in greater than half the sample replicates in at least one sample group were retained for further analysis. Probe sets were further filtered to remove unannotated and control probe sets as well as any probe set reported to cross-hybridize (only probes annotated as crosshyb=1 by Affymetrix were retained), giving a final set of 13,780 detected genes.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana ost1alx8 leaf tissue ABA folar spray 20uM 45 minutes

label_protocol: One hundred nanograms of total RNA was used for the for amplification and labelling using the Affymetrix WT plus Reagent kit assay.

growth_protocol: Seeds were germinated in soil and kept at 4 ºC for three days to synchronize germination. Seedlings were grown at 100-150 µmol photons m-2 s-1, 12 h photoperiod, 21-23 ºC and 50-55 % humidity, unless otherwise stated. The alx8 mutant (Col-0 background) was crossed with abi1-1 (Koornneef et al., 1984), ost1-2 (Mustilli et al., 2002) in the Ler background in order to generate double mutants. Homozygous F2 plants were screened using derived cleavable amplified polymorphic sequence (dCAPS) markers to confirm the presence of individual mutations and sequenced. The Col-0 Ler F1 hybrid was generated as a control and WT refers to the F1 hybrid.

extract_protocol: Total RNA was extracted using the guanidinium thiocyanate-phenol-chloroform extraction method (Chomczynski and Sacchi, 1987) using Trizol (Ambion), DNA removed using TURBO DNase, RNA quality verified using a Bioanalyzer (Agilent Technologies), and spectrophotometric analysis was performed to determine the A260:A280 and A260:A230 ratios. Further RNA quality control and subsequent Microarray analysis were performed at the Ramaciotti Centre for Genomics (The University of New South Wales, Australia).

treatment_protocol: Thirty day-old Col-0 Ler, alx8, ost1-2 and alx8 ost1-2 plants were used for the ABA treatment. Trays containing the plants were placed on top of a copy stand and camera holder inside a custom built box and acclimated to the new conditions (30-40 µmole m-2 s-1, 30-40% humidity) for 45 min. Each plant rosette was sprayed with 400 µl of 0.005% (v/v) Sylwett, 20 µM ABA (dissolved in ethanol), or a control solution (ethanol only), using a Studio Series IS-875 with a 0.5 mm nozzle opening (Iwata). Special care was taken to avoid cross contamination between control and ABA solution while spraying. Leaf temperature was monitored over time using an infra-red (IR) camera FLIR A600-Series, IR lens f=13.1 mm (FLIR Systems AB, Sweden) positioned 30 cm above the plants. The temperature of individual leaves was monitored using the ThermaCAMTM Researcher Pro 2.10 software (FLIR Systems AB). Leaf tissue from four replicates per genotype per treatment were harvested for total RNA extraction after 2 hours of ABA induction.

value: leaf tissue

value: ABA folar spray 20uM 45 minutes


title: ERG-related_ERG-not deleted_sample 26_microRNA

description:
MIR_37
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis

source_name: ERG-related without ERG intragenic deletion


title: ERG-related_ERG-deleted_sample 12_microRNA

description:
MIR_28
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis

source_name: ERG-related with ERG intragenic deletion


title: ERG-related_ERG-deleted_sample 1_microRNA

description:
MIR_31
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: ERG-related_ERG-deleted_sample 2_microRNA

description:
MIR_36
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: ERG-related_ERG-not deleted_sample 25_microRNA

description:
MIR_26
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: ERG-related_ERG-not deleted_sample 17_microRNA

description:
MIR_35
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: 121-ost1-2 alx8-ABA


title: Liver_C1_3d_1


title: 117-ost1-2 alx8-C

source_name: Arabidopsis thaliana ost1alx8 leaf tissue Mock

value: Mock


title: Liver_Control_21d_4

source_name: Control, 21d, Liver


title: Liver_Control_21d_3


title: ERG-related_ERG-not deleted_sample 27_microRNA

description:
MIR_38
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: C57BL/6Je/e + PBS_rep1

description: total brain C57BL/6Je/e-6641/1

source_name: C57BL/6Je/e + PBS

value: PBS


title: 129-ost1-2 alx8-ABA


title: Liver_Control_21d_2


title: 108-ost1-2 alx8-C


title: Liver_Control_3d_5

source_name: Control, 3d, Liver


title: ERG-related_ERG-deleted_sample 7_microRNA

description:
MIR_32
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis


title: Liver_Control_21d_1


title: WT R848-treated Peyer's patch CD8a+ cDC, steady state, replicate 4

city: Marseille

first: Hugues

last: Lelouard

address: parc Scientifique de Luminy case 906

country: France

institute: CIML CNRS UMR 7280

description: Peyer's patch CD8a+ cDC 9h after R848 treatment

hyb_protocol: Following fragmentation and end-labelling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix) interrogating 28.853 genes represented by approximately 27 probes spread across the full length of the gene. The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: Chips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: Raw data (.CEL files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2. CEL files were further processed with Affymetrix Expression Console software version 1.4.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: Mouse Peyer's patch, R848, 9h

label_protocol: Biotinylated double strand cDNA targets were prepared from 2 to 20 ng of total RNA using the NuGEN Ovation Pico WTA System V2 Kit (Cat # 3302) followed by the NuGEN Encore Biotin Module Kit (Cat # 4200) according to manufacturer recommendations.

extract_protocol: Extraction of total RNA was performed using the Qiagen RNeasy Plus Micro Kit following the manufacturer's instructions.

treatment_protocol: Peyer's patches (PP) were collected from 42 C57BL/6 mice per replicate (6–8 week-old). Groups of PP from 3 mice were cut into pieces and digested in 7mL of RPMI containing 100 µg/mL of type 2 collagenase (Worthington) and 140 µg/mL of DNase I (Sigma) for 40 min at room temperature. CD11c+ cells were enriched using anti-CD11c microbeads and the program posselD2 of an autoMACS pro separator according to manufacturer’s instructions (Miltenyi Biotec) before staining and cell sorting using a a FACSAria III (BD Biosciences).

value: Female

tag: age

value: 6 to 8 weeks-old

value: Peyer's patch

tag: main location

value: Interfollicular region (IFR; T cell zone)

value: Dendritic Cell

tag: phenotype


title: WT R848-treated Peyer's patch CD8a+ cDC, steady state, replicate 5


title: Liver_Control_3d_3

value: Liver

value: Male


title: WT R848-treated Peyer's patch CD8a+ cDC, steady state, replicate 2


title: WT R848-treated Peyer's patch CD8a+ cDC, steady state, replicate 3


title: 133-ost1-2 alx8-C


title: MCF-7/ADR

city: shenyang

first: Xiujuan

last: Qu

address: No.155 North Nanjing Street

department: medical oncology

country: China

institute: China Medical University

description: Triple-negative breast cancer cell which pocesses mesenchymal type cell character.

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

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

data_processing: The data were analyzed with Partek Genomics Suite version 6.6 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: human breast cancer cell MCF-7/ADR

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

growth_protocol: The cells were cultured at 37℃ in a humidified atmosphere under 5% CO2.The cells were subcultured every 2-4 days and harvested in the logarithmic phase of growth.

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

treatment_protocol: MCF-7/ADR cells derived from MCF-7 and cultured with 1 ug/ml adriamycin for at least one year and pocessed adriamycin-resistance.

tag: morphology type

value: mesenchymal type of breast cancer cell

tag: pr receptor status

value: negative

tag: er receptor status

tag: her-2 receptor status


title: 136-ost1-2-ABA

source_name: Arabidopsis thaliana ost1 leaf tissue ABA folar spray 20uM 45 minutes


title: WT R848-treated Peyer's patch CD11b+ cDC, steady state, replicate 3

description: Peyer's patch CD11b+ cDC 9h after R848 treatment


title: WT R848-treated Peyer's patch CD8a+ cDC, steady state, replicate 1


title: Liver_Control_3d_1


title: MCF-7

description: Non triple negative breast cancer cell which pocesses epithelial type cell character.

source_name: human breast cancer cell MCF-7

value: epithelial type of breast cancer cell

value: positive


title: 107-ost1-2-C

source_name: Arabidopsis thaliana ost1 leaf tissue Mock


title: WT Peyer's patch TIM-4+ LysoMac, steady state, replicate 2

description: Peyer's patch TIM4+ macrophages at steady state

source_name: Mouse Peyer's patch, steady state

value: Macrophage


title: 116-ost1-2-C


title: WT Peyer's patch TIM-4+ LysoMac, steady state, replicate 1


title: WT Peyer's patch TIM-4+ LysoMac, steady state, replicate 3


title: 110-alx8-ABA

source_name: Arabidopsis thaliana alx8 leaf tissue ABA folar spray 20uM 45 minutes


title: Liver_Control_3d_2


title: WT R848-treated Peyer's patch CD11b+ cDC, steady state, replicate 1


title: 127-alx8-ABA


title: WT Peyer's patch TIM-4- LysoMac, steady state, replicate 1

description: Peyer's patch TIM4- macrophages at steady state

value: Subepithelial dome (SED)


title: 120-ost1-2-ABA

value: leaf tissue


title: WT R848-treated Peyer's patch CD11b+ cDC, steady state, replicate 2


title: 115-alx8-C

source_name: Arabidopsis thaliana alx8 leaf tissue Mock


title: WT Peyer's patch CD8a+ cDC, steady state, replicate 3

description: Peyer's patch CD8a+ cDC at steady state


title: 135-alx8-ABA

value: ABA folar spray 20uM 45 minutes


title: WT Peyer's patch TIM-4- LysoMac, steady state, replicate 2


title: WT Peyer's patch TIM-4- LysoMac, steady state, replicate 3


title: WT Peyer's patch CD8a+ cDC, steady state, replicate 2

description: Peyer's patch CD8a+ cDC at steady state


title: 106-alx8-C

value: Mock


title: WT Peyer's patch CD8a+ cDC, steady state, replicate 1

description: Peyer's patch CD8a+ cDC at steady state


title: WT Peyer's patch DN cDC, steady state, replicate 3

description: Peyer's patch DN cDC at steady state

value: SED and/or IFR


title: 131-alx8-C


title: 118-ColLer-ABA

source_name: Arabidopsis thaliana WT leaf tissue ABA folar spray 20uM 45 minutes

value: WT


title: WT Peyer's patch DN cDC, steady state, replicate 2

description: Peyer's patch DN cDC at steady state

value: Female

value: 6 to 8 weeks-old


title: WT Peyer's patch DN cDC, steady state, replicate 1

description: Peyer's patch DN cDC at steady state

value: Peyer's patch


title: 134-ColLer-ABA


title: 105-ColLer-C

source_name: Arabidopsis thaliana WT leaf tissue Mock


title: NA12878 Genomic DNA Replicate 2 (IlluminaHumanCoreExome)

type: genomic

city: St. Augustine

first: Rajini

last: Haraksingh

address: The University of the West Indies

department: Life Sciences

country: Trinidad and Tobago

institute: The University of the West Indies

description: Genomic DNA extracted from GM12878 cell lines. Genomic DNA obtained from Coriell

hyb_protocol: Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html

data_processing:
Raw data in the form of .idat files from the hybridization of NA12878 genomic DNA to the Illumina Infinium HumanCoreExome v1.1 array were obtained from Illumina Inc. The .idat files were processed using the Genotyping Module of the GenomeStudio 2011.1 software package  (Illumina Inc., San Diego CA 92122, U.S.A.) with default settings according to the manufacturer's user guide. The required manifest and cluster files were downloaded from http://support.illumina.com/array/downloads.html. Processed data were generated in GenomeStudio in the form of final reports with the required format for downstream CNV analysis using the Nexus Copy Number 7.5 software package (BioDiscovery, Hawthorne CA 90250, U.S.A.). Subsequently, CNVs were called using the SNP-FASST2 Segmentation Algorithm in the Nexus Copy Number software package.
The final CNV calls are in the supplementary material of the manuscript.

label: Cy5, Cy3

molecule: genomic DNA

source_name: Blood, B Lymphocyte

extract_protocol: Genomic DNA was extracted from GM12878 cell lines by Coriell Cell Repositories

tag: ethnicity

value: Caucasian

tag: cell line


title: NA12878 Genomic DNA Replicate 1 (IlluminaHumanCoreExome)

scan_protocol: Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html


title: WT Peyer's patch CD11b+ cDC, steady state, replicate 4

description: Peyer's patch CD11b+ cDC at steady state

tag: tissue

value: Interfollicular region (IFR; T cell zone)

value: Dendritic Cell


title: WT Peyer's patch CD11b+ cDC, steady state, replicate 3

tag: gender


title: 114-ColLer-C


title: 126-ColLer-ABA


title: non-ERG-related_sample 101_microRNA

description:
MIR_34
Noncoding RNA expression data from pediatric acute leukemia samples at diagnosis

source_name: non-ERG-related without ERG intragenic deletion

value: white blood cells

value: pediatric acute leukemia

value: bone marrow


title: LoVoDTT0_IgG_Goat

status: Public on Mar 20 2017

type: SRA

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

description: ChIP-seq experiment on cells blocked in early S-phase by double thymidine treadment

library_source: genomic

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: files generated using MACS 1.4

source_name: LoVo

growth_protocol: LoVo (ATCC CCL-229)  colon adenocarcinoma cells were cultured in DMEM supplemented with penicillin/streptomycin and 10% FBS under standard culture conditions.

extract_protocol: Cells were cross-linked by 1% formaldehyde, and DNA was sonicated to 200- 400 bp fragments. Antibodies (5 µg) were added and collected using protein G Sepharose (GE). Cross-links were reversed and proteins digested by incubation with proteinase K at 65 °C overnight. DNA was then purified using Qiagen PCR purification kit.

treatment_protocol: For S-phase synchronization, LoVo cells were arrested in early S phase by double thymidine block essentially as described in (Whitfield et al., 2002). Briefly, cells were cultured to 30 to 40% confluence and washed with PBS. Block medium (DMEM containing 10% FBS and 2 mM thymidine) was applied to cells for 12 h, followed by washing with PBS, and continued culture in culture medium for 8 h. The second thymidine block was applied by changing the medium to the block medium followed by another 12 h of culture before harvesting the cells. Genomic DNA was extracted from the synchronized cells and sequenced as described below. For M-phase synchronization, cells were cultured and incubated in block medium for 12 h as above. Then the block medium was replaced by culture medium (DMEM with 10% FBS) containing 200 ng/ml nocodazole (Sigma), in which cells were cultured for 8 h before harvest.

value: LoVo

value: colon adenocarcinoma

tag: hgn

value: IgG

tag: antibody

value: Santa Cruz Biotechnology, Inc. :sc-2028

tag: control sample

tag: blocking protocol

value: Double Thymidine block

tag: number of peaks, < fdr 5%


title: WT Peyer's patch CD11b+ cDC, steady state, replicate 1

tag: strain

tag: treatment

tag: cell type


title: LoVoSTTnocodazole0_IgG_Goat

description: ChIP-seq experiment on cells synchronized by thymidine block followed by M-phase block by nocodazole treatment

value: Thymidine block + nocodazole


title: LoVoDTT0_CTCF_Goat

value: CTCF

value: Santa Cruz Biotechnology, Inc. :sc-15914 X


title: Spleen cells rep5+6

first: Eva

last: Severinson

address: Svante Arrhenius väg 20C

department: MBW

institute: Stockholm University

hyb_protocol: The labelled DIG-cRNA (10 µg per microarray) was incubated in each microarray hybridization chamber at 55°C for 16 hours. The microarrays were washed. Features that retained bound DIG-labelled cRNA were visualized using the Applied Biosystems Chemiluminescence Detection Kit. Anti-DIG alkaline phosphatase was used to hydrolyse a chemiluminescence substrate to generate light at 458 nm.

scan_protocol: The reaction was detected by the Applied Biosystems 1700 Chemiluninescent Microarray Analyzer.

data_processing: The Mouse Genome Survey Microarray v.2.0 (Applied Biosystems) Microarrays were pre-processed using the R bioconductor package (http://www.r-project.org). Probes with unusual signal patterns were flagged by the scanner and signal strength set to NA (not a number). Arrays showing low correlation between hybridization controls were removed. Missing intensity values were imputed using the nearest neighbour method. The intensity matrix were normalised by RMA normalization.

label: DIG-UTP

source_name: spleen cells

label_protocol: Total RNA was extracted and amplified to digoxigenin (DIG)-labelled cRNA using the Applied Biosystems Chemiluminescent NanoAmp™ RT-IVT Labeling Kit

growth_protocol: Cells were grown in complete RPMI1640 with 10% FCS as detailed in: Gerasimcik, N., Dahlberg, C.I.M., Baptista, M.A.P., Massaad, M.J., Geha, R.S., Westerberg, L.S. and Severinson, E. The Rho GTPase Cdc42 is essential for the activation and function of mature B cells. J. Immunol. 194, 4750, 2015

extract_protocol: Total cellular RNA was isolated using the GenElute Mammalian Total RNA Miniprep Kit (Sigma)

treatment_protocol: As details in: Gerasimcik, N., Dahlberg, C.I.M., Baptista, M.A.P., Massaad, M.J., Geha, R.S., Westerberg, L.S. and Severinson, E. The Rho GTPase Cdc42 is essential for the activation and function of mature B cells. J. Immunol. 194, 4750, 2015

tag: cells

value: spleen cells

value: non-cultured

tag: # of animals


title: Spleen B cells LPS 48hs rep3

description: LPS 1

value: B cells

value: 2 days LPS


title: Spleen B cells LPS 48hs rep1

description: LPS 3


title: Spleen B cells alfa 48hs rep2

description: alfa 2

value: 2 days with anti-CD40+IL-4


title: Spleen B cells alfa 48hs rep3

description: alfa 3


title: Spleen B cells alfa 48hs rep1

description: alfa 1


title: Spleen cells rep3+4


title: NA12878 Genomic DNA Replicate 1 (IlluminaHumanOmniExpressExome)

data_processing:
Raw data in the form of .idat files from the hybridization of NA12878 genomic DNA to the Illumina Infinium HumanOmniExpressExome-8 v1.2  array were obtained from Illumina Inc. The .idat files were processed using the Genotyping Module of the GenomeStudio 2011.1 software package  (Illumina Inc., San Diego CA 92122, U.S.A.) with default settings according to the manufacturer's user guide. The required manifest and cluster files were downloaded from http://support.illumina.com/array/downloads.html. Processed data were generated in GenomeStudio in the form of final reports with the required format for downstream CNV analysis using the Nexus Copy Number 7.5 software package (BioDiscovery, Hawthorne CA 90250, U.S.A.). Subsequently, CNVs were called using the SNP-FASST2 Segmentation Algorithm in the Nexus Copy Number software package.
The final CNV calls are in the supplementary material of the manuscript.
Processed data are final reports exported from GenomeStudio in the required format for downstream analysis in Nexus Copy Number. Columns include Sample Name (blank field - sample is NA12878), Sample ID (corresponding array barcode and sub-field on which sample was hybridized), SNP Name (equivalent to ID REF - unique identifier for each probe on the array), Chr (chromosome containing probe), Position (chromosomal coordinate of probe), Log R Ratio (the base-2 log of the normalized R value over the expected R value for the theta value (interpolated from the R-values of the cluster)), B Allele Freq (B allele theta value of this SNP for the sample, relative to the cluster positions),  GC Score (value between 0 and 1 indicating reliability of genotype call), SNP (Nucleotide substitution for the SNP on the Illumina top strand)

label_protocol: Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html

value: Female

value: Caucasian


title: NA12878 Genomic DNA Replicate 2 (IlluminaHumanOmniExpressExome)


title: NA12878 Genomic DNA Replicate 2 (IlluminaHumanOmniExpress)

data_processing:
Raw data in the form of .idat files from the hybridization of NA12878 genomic DNA to the Illumina Infinium HumanOmniExpress-24 v1.0 array were obtained from Illumina Inc. The .idat files were processed using the Genotyping Module of the GenomeStudio 2011.1 software package  (Illumina Inc., San Diego CA 92122, U.S.A.) with default settings according to the manufacturer's user guide. The required manifest and cluster files were downloaded from http://support.illumina.com/array/downloads.html. Processed data were generated in GenomeStudio in the form of final reports with the required format for downstream CNV analysis using the Nexus Copy Number 7.5 software package (BioDiscovery, Hawthorne CA 90250, U.S.A.). Subsequently, CNVs were called using the SNP-FASST2 Segmentation Algorithm in the Nexus Copy Number software package.
The final CNV calls are in the supplementary material of the manuscript.
Processed data are final reports exported from GenomeStudio in the required format for downstream analysis in Nexus Copy Number. Columns include Sample Name (blank field - sample is NA12878), Sample ID (corresponding array barcode and sub-field on which sample was hybridized), SNP Name (equivalent to ID REF - unique identifier for each probe on the array), Chr (chromosome containing probe), Position (chromosomal coordinate of probe), Log R Ratio (the base-2 log of the normalized R value over the expected R value for the theta value (interpolated from the R-values of the cluster)), B Allele Freq (B allele theta value of this SNP for the sample, relative to the cluster positions),  GC Score (value between 0 and 1 indicating reliability of genotype call), SNP (Nucleotide substitution for the SNP on the Illumina top strand)


title: NA12878 Genomic DNA Replicate 1 (IlluminaHumanOmniExpress)


title: WT Peyer's patch CD11b+ cDC, steady state, replicate 5

tag: age

value: 6 to 8 weeks-old

value: Peyer's patch

tag: main location

value: Interfollicular region (IFR; T cell zone)

value: Dendritic Cell

tag: phenotype


title: WT Peyer's patch CD11b+ cDC, steady state, replicate 2


title: Spleen cells rep1+2


title: Baf3

city: Cincinnati

first: Mohammad

last: Azam

state: OH

address: 3333 Burnet Avenue

department: Division of Experimental Hematology

institute: Cincinnati Childrens Hospital and Medical Center

description: gene expression data from BAF3 parental cell line

hyb_protocol: 2.5 ug of fragmented cDNA were hybridized to Mouse Gene 1.0 ST arrays (Affymetrix). Probe arrays were incubated at 45°C for 17 hrs in the Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix), utilizing the fluidics protocol FS450-0007. The Stain and Antibody solutions are produced by Affymetrix and contained in the Genechip Hybridization Wash and Stain Kit.

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

data_processing: The .cel were created by Affymetrix software. The data were normalized to median of Control Samples BAf3,  Summarization Algorithm: ExonRMA16, Normalization: quantile

label: Biotin

source_name: parental cell line

label_protocol: The Ambion® WT Expression Kit (Life Technologies) combined with the GeneChip® WT Terminal Labeling Kit (Affymetrix), is used to create biotin – labeled sense -strand cDNA targets for hybridization to the Gene 1.0 ST Arrays

growth_protocol: The cell lines were grown in RPMI media supplementad with 10%FBS and and 5% Pen/strep/glutamine 1. BAF3 parental cells were grown with IL-3 supplement while BAF3 cells with DOX inducible BCR-ABL were grown with 500ng/ml DOX in the growth media with or without IL-3 to logarithmic phase.

extract_protocol: RNA was isolated using the miRNeasy Mini Kit  from Qiagen


title: Spleen B cells LPS 48hs rep2

description: LPS 2


title: 130-ColLer-C

value: leaf tissue

tag: genotype

value: WT

value: Mock


title: Baf3+DOX+IL-3

description: gene expression data from Baf3 cell line expressing BCR-ABL grown with IL-3

treatment_protocol: BAF3 parental cells were grown with IL-3 supplement while BAF3 cells with DOX inducible BCR-ABL were grown with 500ng/ml DOX in the growth media with or without IL-3 to logarithmic phase.

tag: cell line


title: Live-NoIL-3

description: gene expression data from BAF3 cell line expressing BCR-ABL grown without IL-3

data_processing: The .cel were created by Affymetrix software. Summarization Algorithm: ExonRMA16, Normalization: Quantile, Baseline Transformation: median of all samples

source_name: Imatinib treated  live Baf3 cell line expressing BCR-ABL grown without IL-3 and Imatinib

growth_protocol: The cell lines were grown in RPMI media supplementad with 10%FBS and and 5% Pen/strep/glutamine.

treatment_protocol: BAF3 cells harboring constitutively expressing BCR-ABL were grown with or without IL-3 supplement and treated with Imatinib (5μm) for 6 hours


title: Baf3+DOX B

source_name: Baf3 cell line expressing BCR-ABL


description: Gene expression data from imatinib treated K562 cells grown with Erythropoetin

hyb_protocol: 2.5 ug of fragmented cDNA were hybridized to Human Gene 1.0 ST arrays (Affymetrix). Probe arrays were incubated at 45°C for 17 hrs in the Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix), utilizing the fluidics protocol FS450-0007. The Stain and Antibody solutions are produced by Affymetrix and contained in the Genechip Hybridization Wash and Stain Kit.

data_processing: The .cel were created by Command Console (Affymetrix). Normalization: Quantile,  Baseline Transformation: median of all samples, Summarization Algorithm:exon RMA16

source_name: Human leukemic cell line_imatinib-treated_grown with Erthropoetin

growth_protocol: The cell lines were grown in RPMI media supplementad with 10%FBS and and 5% Pen/strep/glutamine 1.K562 cells  were grown with and without Erythropoietin.

treatment_protocol: K562 cells  were grown with and without Erythropoietin and treated with Imatinib (2uM) for 6 hours.


title: imatinib treated K562 cells

description: Gene expression data from imatinib treated K562 cells

source_name: Human leukemic cell line_imatinib-treated


title: Baf3+DOX A


title: Live-IL3

source_name: Imatinib treated Live Baf3 cell line expressing BCR-ABL grown with IL-3


title: Healtht thymus control 4

city: Groningen

first: Floris

last: Foijer

address: Antonius Deusinglaan 1

department: European Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description:
This control sample was also used as healthy thymus control sample in Foijer et al, Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):13427-32
5665141048_D
Control sample thymus 4

hyb_protocol: RNA was hybridyzed using Illumina standard protocols

scan_protocol: Slides were scanned using Illumina standard protocols

data_processing: Data were quantile normalized following scanning and analyzed using Bioconductor lumi and limma packages.

label: streptavidin-conjugated Cy3

source_name: Control sample thymus

label_protocol: Biotinylated cRNA was hybridized to llumina Sentrix Bead Chips and next labeled with streptavidin-conjugated Cy3 (Amersham) according to manufacturer’s protocol.

growth_protocol: Mice were sacrificed because of HCA (ageing),  HCC or T-ALL, see for details accompanying paper, Sup. Data 1 for details tumors' genotypes

extract_protocol: Tissue was homogenized using bead-homogenization in Qiagen RNA-easy buffer 1. RNA was then purified using RNA-easy columns using manufacturer's protocols

treatment_protocol: Liver, thymus, or tumors were dissected and stored at -80 in pieces for subsequent analysis

tag: strain background

value: B6-129Sv mixed

tag: genotype/variation

value: wild type

tag: tissue

value: Healtht thymus control

tag: sample type

value: Control


title: T-ALL 7

description:
5665141011_C
T-ALL 56

source_name: T-ALL

value: Mad2f/f p53f/f Lck-Cre+

value: T-ALL

value: Experimental


title: T-ALL 9

description:
5665141011_F
T-ALL 61


title: Healtht thymus control 3

description:
This control sample was also used as healthy thymus control sample in Foijer et al, Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):13427-32
5665141048_C
Control sample thymus 3


title: Healtht thymus control 5

description:
This control sample was also used as healthy thymus control sample in Foijer et al, Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):13427-32
5665141048_E
Control sample thymus 5


title: T-ALL 6

description:
5665141007_D
T-ALL 34


title: T-ALL 8

description:
5665141011_E
T-ALL 60


title: T-ALL 1

description:
5665061082_C
T-ALL 28


title: T-ALL 5

description:
5665141007_B
T-ALL 32


title: T-ALL 2

description:
5665061082_D
T-ALL 29


title: Healtht thymus control 2

description:
This control sample was also used as healthy thymus control sample in Foijer et al, Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):13427-32
5665141048_B
Control sample thymus 2


title: T-ALL 3

description:
5665061082_E
T-ALL 30


title: Healthy liver control 6

description:
5665079065_C
Liver sample 6249

source_name: Liver sample

value: Healthy liver control


title: Healthy liver control 4

description:
5665079065_A
Liver sample 6065


title: Healtht thymus control 1

description:
This control sample was also used as healthy thymus control sample in Foijer et al, Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):13427-32
5665141048_A
Control sample thymus 1


title: Healthy liver control 10

description:
5665079066_A
Liver sample 5890


title: Healthy liver control 9

description:
5665079065_F
Liver sample 6237


title: Healthy liver control 5

description:
5665079065_B
Liver sample 2170


title: Healthy liver control 8

description:
5665079065_E
Liver sample 3441


title: Healthy liver control 2

description:
5665079064_D
Liver sample 3133


title: Healthy liver control 7

description:
5665079065_D
Liver sample 6254


title: Liver tumor 29

description:
5665079064_B
Liver tumor 6381LT5

source_name: Liver tumor

value: Mad2f/f p53f/+ Alb-Cre+

value: Liver tumor


title: Healthy liver control 3

description:
5665079064_E
Liver sample 6077


title: Liver tumor 27

description:
5665079060_F
Liver tumor 6350LT1

value: Mad2f/f p53f/f Alb-Cre+


title: Liver tumor 26

description:
5665079060_E
Liver tumor 6199LT1


title: Healthy liver control 1

description:
5665079064_C
Liver sample 6270


title: Liver tumor 28

description:
5665079064_A
Liver tumor 6381LT1


title: T-ALL 61Th

hyb_protocol: Labeled DNA was hybridyzed to Agilent 244K oligo arrays (mm9 build, design 014695) using manufacturer's standard protocols

scan_protocol: Arrays were scanned on an Agilent 2565BA scanner

data_processing: Data was imported into Agilent Genomc Workbench, quantile normalized and log 2 Cy5/Cy3 ratios were exported to Excel.

source_name: aneuploid T-ALL sample

label_protocol: Tumor DNA and reference DNA were labeled with Cy3 and Cy5 dNTP respectively using Exo Klenow fragment and Agilent random primers using Agilent standard protocols

growth_protocol: We created Mad2 p53 conditional KO mice and inactivated conditional alleles in liver or T-cells using Alb-Cre or Lck-Cre respectively. Mice were followed for tumorigenesis and were sacrificed when gravely ill (in vast majority of cases because of HCC or T-ALL)

extract_protocol: Tissues were homogenized using bead-homogenization in Qiagen DNA-easy buffer 1. DNA was then purified using DNA-easy columns using Qiagen protocols

treatment_protocol: Tumors were dissected and stored at -80 in pieces for subsequent analysis

value: Mad2f/f p53f/f MMTV-Cre+

tag: gender

value: F

tag: cin or non-cin

value: Chromosomal instability (CIN)

tag: tumor/tissue type

value: aneuploid T-ALL

source_name: sex-matched control liver

value: Mad2f/f p53f/+ Lck-Cre sex-matched mixture

value: non-CIN

tag: tumor type/ tissue

value: sex-matched liver (mix several litter mates)


title: T-ALL 60Th


title: Liver tumor 22

description:
5665079060_A
Liver tumor 6510LT1

value: B6-129Sv mixed


title: Liver tumor 23

description:
5665079060_B
Liver tumor 6510LT2


title: Liver tumor 25

description:
5665079060_D
Liver tumor 6499LT1


title: Liver tumor 24

description:
5665079060_C
Liver tumor 6498LT2


title: T-ALL 4

description:
5665141007_A
T-ALL 31


title: Liver tumor 21

description:
5665079059_F
Liver tumor 6509LT4


title: T-ALL 29Th

value: M


title: T-ALL 31Th


title: T-ALL 32Th


title: Liver tumor 20

description:
5665079059_E
Liver tumor 6509LT3


title: Liver tumor 18

description:
5665079059_C
Liver tumor 6347LT4


title: Liver tumor 17

description:
5665079059_B
Liver tumor 6408LT2


title: Liver tumor 19

description:
5665079059_D
Liver tumor 6382LT1


title: Liver tumor 14

description:
5665079058_E
Liver tumor 6326LT3


title: Liver tumor 6509LT3

source_name: aneuploid HCC sample

value: aneuploid HCC

value: Mad2f/f p53f/+ Alb-Cre sex-matched mixture


title: T-ALL 30Th

value: Mad2f/f p53f/f Lck-Cre+


title: T-ALL 56Th


title: Liver tumor 16

description:
5665079059_A
Liver tumor 6408LT1

value: Experimental


title: Liver tumor 12

description:
5665079066_B
Liver tumor 6495LT3


title: T-ALL 28Th


title: Liver tumor 11

description:
5665079058_B
Liver tumor 6451LT3


title: Liver tumor 13

description:
5665079058_D
Liver tumor 6518LT2


title: Liver tumor 6510Lt2


title: Liver tumor 6498LT2


title: Liver tumor 6509Lt4


title: T-ALL 34Th


title: Liver tumor 7

description:
5665079054_D
Liver tumor 6194LT3


title: Liver tumor 6495LT3


title: Liver tumor 6494Lt2


title: Liver tumor 9

description:
5665079054_F
Liver tumor 6376LT1


title: Liver tumor 8

description:
5665079054_E
Liver tumor 6333LT1


title: Liver tumor 6510LT1


title: Liver tumor 10

description:
5665079058_A
Liver tumor 6419LT1


title: Liver tumor 6494LT1


title: Liver tumor 6419Lt1


title: Liver tumor 6451LT3


title: Liver tumor 6410LT2


title: Liver tumor 6518Lt2


title: Liver tumor 3

description:
5665079053_F
Liver tumor 6374LT1


title: Liver tumor 5

description:
5665079054_B
Liver tumor 6410LT1


title: Liver tumor 6

description:
5665079054_C
Liver tumor 6410LT2


title: Liver tumor 1

description:
5665079053_D
Liver tumor 6494LT1


title: Liver tumor 2

description:
5665079053_E
Liver tumor 6494LT2


title: Liver tumor 4

description:
5665079054_A
Liver tumor 6374LT2


title: Liver tumor 6381LT1


title: Liver tumor 6408LT2


title: Liver tumor 6374LT2


title: Liver tumor 6374LT1


title: PB 3

city: Oxford

first: Cheen

last: Khoo

address: John Radcliffe Hospital Oxford

country: United Kingdom

institute: NHSBT

description: Peripheral blood donor 3, grown in parallel, harvested at passage 3

hyb_protocol: miRCURY standard protocol (carried by Exiqon)

source_name: PB ECFCs

growth_protocol: Endothelial colony forming cells were derived from human cord blood and peripheral blood samples.These cells were generated  by culturing the CB and PB mononuclear cells (2 x 107 cells in 6 well collagen coated plates) in 4mls complete EGM-2 medium  supplemented with 10% (v/v) Hyclone heat inactivated fetal bovine serum . Endothelial colonies which formed by 21 days of culture were selected using cloning rings and those from individual CB or PB units were pooled and then passaged in EGM-2 medium.

extract_protocol: Total RNA isolated including small RNAs using Qiagen RNeasy mini kit   and following manufacturer's protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: peripheral blood (PB) derived endothelial colony forming cells (ECFCs)

source_name: Total RNA from common reference pool (samples s1 to s6)

value: common reference pool


title: Liver tumor 6382Lt1


title: Liver tumor 6408LT1

value: Mad2f/f p53f/+ Alb-Cre+


title: PB 2

description: Peripheral blood donor 2, grown in parallel, harvested at passage 3

scan_protocol: miRCURY standard protocol (carried by Exiqon)


title: Liver tumor 15

description:
5665079058_F
Liver tumor 6326LT5

value: Liver tumor


title: CB 3

description: Cord blood donor 3, grown in parallel, harvested at passage 3

data_processing: miRCURY standard protocol (carried by Exiqon)

source_name: CB ECFCs

value: cord blood (CB) derived endothelial colony forming cells (ECFCs)


title: Liver tumor 6347Lt4


title: Biofilm 1

city: Madrid

first: Patricia

last: Romero Lastra

address: Plaza de Ramon y Cajal s/n

institute: Universidad Complutense de Madrid

description: Gene expression after 96h Biofilm 1 sample 1 of 3

hyb_protocol: Preparation of probes and hybridization was performed as described (One-Color Microarray Based Gene Expression Analysis Manual Ver. 6.5, Agilent Technologies) For each hybridization, 600 ng of Cy3 probes were mixed and added to 5 µL of 10x Blocking Agent and Nuclease free water in a 25 µL reaction Then, 25 µL from 2x GExHybridization buffer was added and mixed carefully The samples were placed on ice and quickly loaded onto arrays, hybridized at 65ºC for 17 h in a rotating Agilent hybridization oven After hybridization, microarrays were washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37ºC (1 min).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x15K array slides

data_processing:
Images from Cy3 channel were equilibrated and captured with a high-resolution scanner (Agilent) and spots quantified using Feature Extraction software (Agilent)
Background correction and normalization of data expression were performed using LIMMA

organism: Porphyromonas gingivalis

source_name: Porphyromonas gingivalis culture 96h

label_protocol: Fluorescently labeled cDNA for microarray hybridizations was obtained by using the SuperScript Indirect cDNA Labeling System (Invitrogen)

growth_protocol:
Planktonic cultures of P. gingivalis were grown anaerobically at 37ºC for 24 h in a protein-rich medium containing brain-heart infusion (BHI)
A volume of 1.5 mL of P. gingivalis inoculums (concentration 10^8 CFU/mL) was placed in pre-sterilized polystyrene 24-well tissue culture plates (Greiner Bio-one) with or without the presence of sterile ceramic calcium hydroxyapatite discs

extract_protocol:
After 96 h of incubation, P. gingivalis planktonic and biofilm cells were harvested
Total RNA was extracted from the harvested samples listed above, using the TRIzol® Max Bacterial RNA Isolation Kit (Ambion, Life Technologies, Carlsbad, CA, USA)
RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Plates were incubated in anaerobic conditions at 37°C for 96 h

tag: sampel type

value: biofilm


title: Liver tumor 6410LT1

value: Mad2f/f p53f/f Alb-Cre+

value: Chromosomal instability (CIN)


title: Planktonic 3

description: Gene expression after 96h Planktonic 3 sample 3 of 3

value: planktonic


title: Biofilm 2

description: Gene expression after 96h Biofilm 2 sample 2 of 3


title: Liver tumor 6350LT1

value: F

value: non-CIN


title: Liver tumor 6199LT1

value: sex-matched liver (mix several litter mates)


title: Liver tumor 6326LT3

value: M


title: CB 2

description: Cord blood donor 2, grown in parallel, harvested at passage 3

label_protocol: miRCURY standard protocol (carried by Exiqon)


title: Liver tumor 6381LT5

value: aneuploid HCC


title: Liver tumor 6499LT1

value: Mad2f/f p53f/+ Alb-Cre sex-matched mixture


title: Biofilm 3

description: Gene expression after 96h Biofilm 3 sample 3 of 3


title: Liver tumor 6333LT1


title: Planktonic 2

description: Gene expression after 96h Planktonic 2 sample 2 of 3


title: Liver tumor 6376LT1


title: CB 1

description: Cord blood donor 1, grown in parallel, harvested at passage 3


title: Planktonic 1

description: Gene expression after 96h Planktonic 1 sample 1 of 3


title: Liver tumor 6326LT5


title: miRN_7

status: Public on Mar 19 2017

city: Fukuoka

first: Kohei

last: Miyata

state: FUkuoka

address: 7-45-1 Nanakuma, Jonan-ku

department: Faculty of Medicine

institute: Fukuoka University

description: Benign tumor

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint Human miRNA Microarray Release 16.0, 8x60K; Agilent Technologies) according to the manufacturer's instructions.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. P = Detected; A = Not detected.

source_name: serum, preoperative

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

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

treatment_protocol: Blood samples were obtained just before operation (preoperative) or after 1 month (postoperative) and centrifuged for 10 minutes at 3,000 r.p.m. to separate serum within 24 hours.

value: blood serum

tag: collection timepoint

value: preoperative

tag: diagnosis

value: Paraovarian cyst

tag: histology

value: normal ovary

tag: Stage


title: miRN_6

description: Benign tumor

value: Myoma Uteri

tag: age


title: miRN_5

description: Benign tumor


title: miRS_25_2

description: Progression free survival ≥ 12 months

source_name: serum, postoperative

value: postoperative

value: Ovarian cancer

value: serous adenocarcinoma

value: IIIc


title: miRS_25_1

description: Progression free survival ≥ 12 months


title: miRN_4

description: Benign tumor


title: miRS_19_1

description: Progression free survival < 12 months


title: SNU761_sorafenib_rep3

city: Seoul

first: Jae-Kyung

last: Won

address: 101 Daehak-ro

country: South Korea

institute: Seoul National University Hospital

description:
replicate 3
SAMPLE 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array probes transformed by logarithm and normalized by quantile method.

source_name: HCC cell line SNU761, treated with sorafenib 3 mM for 24 hours

label_protocol: Biotinylated cRNA were prepared with the TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip

extract_protocol: RNA was extracted using RNA-spinTM,  according to the manufacturer’s instructions, and treated with RNase-free DNase I . RNA purity and integrity were evaluated by ND-1000 Spectrophotometer and Agilent 2100 Bioanalyzer.

tag: cell type

value: Hepatocellular carcinoma


title: SNU761_control_rep3

description:
replicate 3
SAMPLE 3

source_name: HCC cell line SNU761, treated with DMSO for 24 hours


title: miRS_15_2

description: Progression free survival ≥ 12 months


title: SNU761_sorafenib_rep1

description:
replicate 1
SAMPLE 4


title: SNU761_sorafenib_rep2

description:
replicate 2
SAMPLE 5


title: miRS_24_1

description: Progression free survival ≥ 12 months

value: immature teratoma

value: Ia


title: Liver tumor 6194LT3

value: Mad2f/f p53f/f Alb-Cre+

value: Chromosomal instability (CIN)

value: non-CIN


title: SNU761_control_rep2

description:
replicate 2
SAMPLE 2


title: miRN_3

description: Benign tumor


title: SNU761_control_rep1

description:
replicate 1
SAMPLE 1


title: miRS_14_1

description: Progression free survival < 12 months


title: miRS_12_2

description: Progression free survival < 12 months

value: IV


title: miRS_12_1

description: Progression free survival < 12 months


title: miRS_18_1

description: Progression free survival < 12 months

value: endometrioid adenocarcinoma


title: miRS_23_1

description: Progression free survival ≥ 12 months

value: blood serum

value: endometrioid adenocarcinoma + mucinous adenocarcinoma

value: Ic


title: miRS_19_2

description: Progression free survival < 12 months


title: miRS_11_2

description: Progression free survival < 12 months


title: miRS_13_1

description: Progression free survival < 12 months

value: preoperative

value: IIb


title: miRS_11_1

description: Progression free survival < 12 months


title: miRS_9_1

description: Progression free survival ≥ 12 months

value: clear cell carcinoma


title: miRS_9_2

description: Progression free survival ≥ 12 months

value: postoperative

value: Ovarian cancer


title: miRS_10_1

description: Progression free survival < 12 months

value: serous adenocarcinoma

value: IIIc


title: Huh7_sorafenib_rep2

description:
replicate 2
SAMPLE 5

source_name: HCC cell line Huh7, treated with sorafenib 3 mM for 24 hours

value: Hepatocellular carcinoma


title: Huh7_sorafenib_rep3

description:
replicate 3
SAMPLE 6


title: miRE_2_1

description: Progression free survival ≥ 12 months


title: miRE_2_2

description: Progression free survival ≥ 12 months


title: miRC_1_2

description: Progression free survival < 12 months

value: serous adenocarcinoma + clear cell carcinoma


title: miRC_1_1

description: Progression free survival < 12 months


title: miRS_6_1

description: Progression free survival < 12 months


title: miRS_6_2

description: Progression free survival < 12 months


title: Huh7_sorafenib_rep1

description:
replicate 1
SAMPLE 4


title: miRS_10_2

description: Progression free survival < 12 months


title: miRS_5_2

description: Progression free survival < 12 months


title: Huh7_control_rep3

description:
replicate 3
SAMPLE 3

source_name: HCC cell line Huh7, treated with DMSO for 24 hours


title: miRS_5_1

description: Progression free survival < 12 months


title: HepG2_sorafenib_rep2

description:
replicate 2
SAMPLE 5

source_name: HCC cell line HepG2, treated with sorafenib 3 mM for 24 hours


title: Huh7_control_rep1

description:
replicate 1
SAMPLE 1


title: Hep3B_sorafenib_rep3

description:
replicate 3
SAMPLE 6

source_name: HCC cell line Hep3B, treated with sorafenib 3 mM for 24 hours


title: Huh7_control_rep2

description:
replicate 2
SAMPLE 2


title: HepG2_sorafenib_rep1

description:
replicate 1
SAMPLE 4


title: miRS_4_2

description: Progression free survival ≥ 12 months

value: IIc


title: NA12878 Genomic DNA Replicate 2 (IlluminaPsychArray)

description: Genomic DNA extracted from GM12878 cell lines. Genomic DNA obtained from Coriell

data_processing:
Raw data in the form of .idat files from the hybridization of NA12878 genomic DNA to the Illumina Psych array were obtained from Illumina Inc. The .idat files were processed using the Genotyping Module of the GenomeStudio 2011.1 software package  (Illumina Inc., San Diego CA 92122, U.S.A.) with default settings according to the manufacturer's user guide. The required manifest and cluster files were downloaded from http://support.illumina.com/array/downloads.html. Processed data were generated in GenomeStudio in the form of final reports with the required format for downstream CNV analysis using the Nexus Copy Number 7.5 software package (BioDiscovery, Hawthorne CA 90250, U.S.A.). Subsequently, CNVs were called using the SNP-FASST2 Segmentation Algorithm in the Nexus Copy Number software package.
The final CNV calls are in the supplementary material of the manuscript.
Processed data are final reports exported from GenomeStudio in the required format for downstream analysis in Nexus Copy Number. Columns include Sample Name (blank field - sample is NA12878), Sample ID (corresponding array barcode and sub-field on which sample was hybridized), SNP Name (equivalent to ID REF - unique identifier for each probe on the array), Chr (chromosome containing probe), Position (chromosomal coordinate of probe), Log R Ratio (the base-2 log of the normalized R value over the expected R value for the theta value (interpolated from the R-values of the cluster)), B Allele Freq (B allele theta value of this SNP for the sample, relative to the cluster positions),  GC Score (value between 0 and 1 indicating reliability of genotype call), SNP (Nucleotide substitution for the SNP on the Illumina top strand)

source_name: Blood, B Lymphocyte

value: Female

tag: ethnicity

value: Caucasian


title: HepG2_control_rep2

description:
replicate 2
SAMPLE 2

source_name: HCC cell line HepG2, treated with DMSO for 24 hours

tag: cell line


title: HepG2_sorafenib_rep3

description:
replicate 3
SAMPLE 6


title: HepG2_control_rep3

description:
replicate 3
SAMPLE 3


title: NA12878 Genomic DNA Replicate 1 (IlluminaPsychArray)


title: PB 1

description: Peripheral blood donor 1, grown in parallel, harvested at passage 3

value: peripheral blood (PB) derived endothelial colony forming cells (ECFCs)

value: common reference pool


title: miRS_4_1

description: Progression free survival ≥ 12 months

value: blood serum


title: HepG2_control_rep1

description:
replicate 1
SAMPLE1


title: Hep3B_sorafenib_rep2

description:
replicate 2
SAMPLE 5


title: ApoE KO HSC, biological rep2

status: Public on Mar 18 2017

city: WORCESTER

first: Lyne

last: Khair

state: MA

address: 368 PLANTATION STREET

department: SURGERY

institute: UMASS MEDICAL SCHOOL

description: microRNA expression in hematopoietic stem cells

hyb_protocol: Following fragmentation, 20 ng of total RNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned by the Affymetrix Scanner 3000(Affymetrix).

data_processing: The scanned images were analyzed using Expression Console Software (version 1.3.1 Affymetrix)

source_name: Hematopoietic stem cells from ApoE KO mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20 ng total RNA

growth_protocol: hematopoietic stem cells were sorted by flow cytometry

extract_protocol: total RNA were isolated by mirVana miRNA isolation kit according to manufacturer's instructions (Applied Biosystems).

value: bone marrow

value: hematopoietic stem cells

tag: genotype

value: ApoE-/-

value: 3 month old mice


title: Hep3B_sorafenib_rep1

description:
replicate 1
SAMPLE 4


title: BTF3-shRNA 2

city: Changsha

first: Qi

last: Liu

address: Western Jiefang Road 61#

institute: First Affiliated Hospital of Hunan Normal University

description: low expression of BTF3

hyb_protocol: The pre-hybridization of HOA v7 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm) and quantify the fluoresence intensity.

data_processing: The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: HCT116 cells were transduced with 10 MOI LV-BTF3-siRNA or LV-negative-siRNA for 16 h in 20% serum medium. After transduction for 72 h, the cells were

tag: transduction

value: 10 MOI LV-BTF3-siRNA

tag: expression levels of ccn3

value: low


title: ApoE KO HSC, biological rep1

tag: tissue


title: Hep3B_control_rep1

description:
replicate 1
SAMPLE 1

source_name: HCC cell line Hep3B, treated with DMSO for 24 hours


title: wt HSC, biological rep2

source_name: Hematopoietic stem cells from WT mice

value: wt


title: wt HSC, biological rep1


title: Negtive-shRNA 2

description: high expression of BTF3

value: LV-negative-siRNA

value: high


title: Hep3B_control_rep3

description:
replicate 3
SAMPLE 3

value: Hepatocellular carcinoma


title: BTF3-shRNA 1

description: low expression of BTF3


title: 3166 - mAdbID:98808

status: Public on Mar 17 2017

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 98808

hyb_protocol: Affymetrix Hybridization Protocol Other: Following fragmentation, 15 micrograms of cRNA was hybridized for 16 hours at 45C on arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affy Scanning Protocol Other: Scanning was performed by the Affymetrix 3000 Scanner.

data_processing:
MAS 5.0 Data Processing Protocol
Calculation Method: The data were analyzed with Microarray Suite version 5.0 (MA S 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 500.

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
Sample RNA Extraction Protocol
Other: Total RNA was extracted using the FastTrack kit from Invitrogen.

tag: disease state

value: Mantle Cell Lymphoma (MCL)

tag: individual


title: Negtive-shRNA 1

description: high expression of BTF3


title: BTF3-shRNA 3

description: low expression of BTF3


title: 2346 - mAdbID:99211

description: mAdb experiment ID: 99211


title: Hep3B_control_rep2

description:
replicate 2
SAMPLE 2


title: Negtive-shRNA 3

description: high expression of BTF3


title: 1799 - mAdbID:97031

description: mAdb experiment ID: 97031


title: 2458 - mAdbID:96336

description: mAdb experiment ID: 96336


title: 2935 - mAdbID:98026

description: mAdb experiment ID: 98026


title: 2881 - mAdbID:98008

description: mAdb experiment ID: 98008


title: 2347 - mAdbID:99210

description: mAdb experiment ID: 99210


title: 2879 - mAdbID:98006

description: mAdb experiment ID: 98006


title: 2357 - mAdbID:96354

description: mAdb experiment ID: 96354


title: 3167 - mAdbID:98809

description: mAdb experiment ID: 98809


title: 2877 - mAdbID:98004

description: mAdb experiment ID: 98004


title: 2913 - mAdbID:98369

description: mAdb experiment ID: 98369


title: 2465 - mAdbID:96331

description: mAdb experiment ID: 96331


title: 2477 - mAdbID:96319

description: mAdb experiment ID: 96319


title: 2406 - mAdbID:96347

description: mAdb experiment ID: 96347


title: 2668 - mAdbID:96303

description: mAdb experiment ID: 96303


title: 2622 - mAdbID:96273

description: mAdb experiment ID: 96273


title: 2561 - mAdbID:96297

description: mAdb experiment ID: 96297


title: 2688 - mAdbID:96248

description: mAdb experiment ID: 96248


title: 2687 - mAdbID:96250

description: mAdb experiment ID: 96250


title: 2667 - mAdbID:96257

description: mAdb experiment ID: 96257


title: 2670 - mAdbID:96255

description: mAdb experiment ID: 96255


title: 1034 - mAdbID:92644

description: mAdb experiment ID: 92644


title: 2328 - mAdbID:93678

description: mAdb experiment ID: 93678


title: 2665 - mAdbID:96259

description: mAdb experiment ID: 96259


title: 2694 - mAdbID:96243

description: mAdb experiment ID: 96243


title: 2330 - mAdbID:91961

description: mAdb experiment ID: 91961


title: 1714 - mAdbID:90884

description: mAdb experiment ID: 90884


title: 2819 - mAdbID:96178

description: mAdb experiment ID: 96178


title: 2323 - mAdbID:91970

description: mAdb experiment ID: 91970


title: 2689 - mAdbID:96247

description: mAdb experiment ID: 96247


title: miRS_15_1

description: Progression free survival ≥ 12 months

value: preoperative

value: Ovarian cancer

value: serous adenocarcinoma

value: IIIc


title: 1889 - mAdbID:88707

description: mAdb experiment ID: 88707


title: 926 - mAdbID:63800

description: mAdb experiment ID: 63800


title: 2119 - mAdbID:89796

description: mAdb experiment ID: 89796


title: 781 - mAdbID:63791

description: mAdb experiment ID: 63791


title: 2739 - mAdbID:96226

description: mAdb experiment ID: 96226


title: 968 - mAdbID:63796

description: mAdb experiment ID: 63796


title: 2699 - mAdbID:96238

description: mAdb experiment ID: 96238


title: 1136 - mAdbID:62899

description: mAdb experiment ID: 62899


title: 2118 - mAdbID:89683

description: mAdb experiment ID: 89683


title: 1888 - mAdbID:88706

description: mAdb experiment ID: 88706


title: 2248 - mAdbID:89697

description: mAdb experiment ID: 89697


title: 1131 - mAdbID:62856

description: mAdb experiment ID: 62856


title: 925 - mAdbID:62898

description: mAdb experiment ID: 62898


title: 1132 - mAdbID:62840

description: mAdb experiment ID: 62840


title: 1142 - mAdbID:62837

description: mAdb experiment ID: 62837


title: 1137 - mAdbID:62836

description: mAdb experiment ID: 62836


title: 1135 - mAdbID:62838

description: mAdb experiment ID: 62838


title: 1128 - mAdbID:62824

description: mAdb experiment ID: 62824


title: 1123 - mAdbID:62822

description: mAdb experiment ID: 62822


title: Haploids and DamP collection Biological Replicate 2 (Selenomethionine 20 uM)

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

institute: Institut Pasteur

description:
Selenometh20uM_exp2
Biological replicate 2 of 3 (Selenomethionine 20 uM)

hyb_protocol: Hybridization was done in Roche RapidHyb buffer at 24°C overnight.

scan_protocol: Genepix 4200AL and GenePix Pro v7

data_processing: The scans were processed using GenePix Pro, v7. The values from the obtained gpr files were filtered to keep only values for spots with an SNR > 10. Next, we performed a loess normalization on groups of probes (UP/DAMP, UP/DELETION, DOWN/DAMP, DOWN/DELETION), followed by aggregation of values for each mutant and a second loess normalization on the aggregated data.

organism: Saccharomyces cerevisiae

source_name: Haploid, homozygous yeast deletion collection + DamP collection (Decourty et al., Cell Rep. 2014) 10 generations with 20 uM Selenomethionine

label_protocol: Cy3 and Cy5 5' tagged oligonucleotides were used to amplify the barcode region with universal primers. PCR products were then mixed, precipitated in the presence of linear poly-acrylamide and prepared for hybridization

growth_protocol: Cells were thawed from -80°C aliquots and left to recover for 9 hours in synthetic complete medium (MMY medium supplemented with 50 mM MES (pH 6), 2% (w/v) glucose 40 mg/l uracil, 80 mg/l adenine, 0.1 mM methionine, 0.1 mM cysteine and 80 mg/l of the other 18 amino acids). An aliquot of the pool of strains was diluted to a DO of 0.002 in 1 liter of the same medium without (control) or with 12 or 20 µM selenomethionine. Cells from each culture were harvested when the OD at 600 nm reached 2 (after 10 generations).

extract_protocol: Genomic DNA was extracted through mechanical lysis (vortexing with glass beads). PCR amplification of the barcode region was followed by a second PCR amplification with Cy3 5' tagged oligonucleotide.

treatment_protocol: Cells in exponential growth were recovered by centrifugation, washed twice in cold water and stored at -80°C until DNA extraction

tag: strain

value: Mix of haploid strains derived from BY4741 (yeast deletion collection)

tag: treatment

value: Selenomethionine

tag: dose

value: 20 uM

source_name: Haploid, homozygous yeast deletion collection + DamP collection (Decourty et al., Cell Rep. 2014) untreated control

value: untreated control


title: Haploids and DamP collection Biological Replicate 3 (Selenomethionine 20 uM)

description:
Selenometh20uM_exp3
Biological replicate 3 of 3 (Selenomethionine 20 uM)


title: Haploids and DamP collection Biological Replicate 1 (Selenomethionine 12 uM)

description:
Selenometh12uM_exp1
Biological replicate 1 of 2 (12 uM Selenomethionine)

source_name: Haploid, homozygous yeast deletion collection + DamP collection (Decourty et al., Cell Rep. 2014) 10 generations with 12 uM Selenomethionine

value: 12 uM


title: Haploids and DamP collection Biological Replicate 3 (16h growth compared with T0)

description:
Growth_test_exp3
Biological replicate 3 of 3 (growth test)

source_name: Haploid, homozygous yeast deletion collection + DamP collection (Decourty et al., Cell Rep. 2014) 16 hours growth

value: 16h growth

source_name: Haploid, homozygous yeast deletion collection + DamP collection (Decourty et al., Cell Rep. 2014) time 0

value: 0h growth


title: Haploids and DamP collection Biological Replicate 1 (Selenomethionine 20 uM)

description:
Selenometh20uM_exp1
Biological replicate 1 of 3 (Selenomethionine 20 uM)


title: Haploids and DamP collection Biological Replicate 1 (16h growth compared with T0)

description:
Growth_test_exp1
Biological replicate 1 of 3 (growth test)


title: Haploids and DamP collection Biological Replicate 2 (16h growth compared with T0)

description:
Growth_test_exp2
Biological replicate 2 of 3 (growth test)


title: 2911 - mAdbID:100750

description: mAdb experiment ID: 100750


title: 2837 - mAdbID:100444

description: mAdb experiment ID: 100444


title: 1011 - mAdbID:100465

description: mAdb experiment ID: 100465


title: 1134 - mAdbID:62835

description: mAdb experiment ID: 62835


title: 1145 - mAdbID:62826

description: mAdb experiment ID: 62826


title: 1129 - mAdbID:62825

description: mAdb experiment ID: 62825


title: 1130 - mAdbID:62834

description: mAdb experiment ID: 62834


title: 2910 - mAdbID:100751

description: mAdb experiment ID: 100751


title: 1121 - mAdbID:62821

description: mAdb experiment ID: 62821


title: Haploids and DamP collection Biological Replicate 2 (Selenomethionine 12 uM)

description:
Selenometh12uM_exp2
Biological replicate 2 of 2 (12 uM Selenomethionine)


title: 2912 - mAdbID:100749

description: mAdb experiment ID: 100749


title: Wheat CS Replica 2 Al treatment

city: Winston-Salem

first: Naike

last: Salvador

state: NC

address: 1 Medical Center Blvd

institute: Wake Forest Baptist Medical Center

description:
Biological replicate 2 of 3. Root apex, wheat, treated with 200 μM AlCl3 for 24h, harvested after 5 days in the growth solution.
0029 wheat CS replica2 (ct-cy3_exp-hy5) 2-12-10.gpr_Exp
raw data file:
0029 wheat CS replica2 (ct-cy3_exp-hy5) 2-12-10.gpr

hyb_protocol: For each hybridization 825 ng of Cy3 and Hiper 5 probes were mixed and was added  11 ul of 10x blocking Agent, 2,2 ul of 25x Fragmentation Buffer and Nuclease free water until 55 ul. The reaction was incubated at 60ºC for exactly 30 minutes to fragment RNA and it was stopped adding the 2xHybridization Buffer. The samples were placed on ice and were loaded onto array as soon as possible. Slides were Agilent White Oligo Microarrays 4x44K (ref. 022297). The arrays was hybridize at 65ºC for 17 hours and then were then washed once for one  minute in GE wash buffer 1 at room temperature and once for one minute in GE Wash Buffer 2 at 37ºC. Arrays were drained with a 2000 rpm spin for 2 min

scan_protocol: Images from Cy3 and Hyper5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots quantified using GenPix software (Axon)

data_processing:
Differentially expressed genes were evaluated by the non-parametric algorithm 'Rank Products' available as RankProd package at Bioconductor, an R language project. This method detects genes that are consistently high ranked in a number of replicated experiments independently of their numerical intensities. The results are provided in the form of p-values defined as the probability that a given gene is ranked in the observed position by chance. The expected false discovery rate was controlled to be less than 5%.
Background correction and normalization of expression data were performed using LIMMA. LIMMA is part of Bioconductor, an R language project. For local background correction the normexp method in LIMMA was used. The resulting log-ratios were print-tip loess normalized for each array. To have similar distribution across arrays and to achieve consistency among arrays, log-ratio values were scaled using as scale estimator the median-absolute-value

organism: Triticum aestivum

source_name: Wheat CSAl treatment

label_protocol: Three biological replicates were independently hybridized for each transcriptomic comparison.Total RNA (1 µg of each) was amplified and aminoallyl-labeled using MessageAmpTM II aRNA kit (Ambion) and 5-(3-aminoallyl)-2’deoxyuridine-5’-triphosphate (aa-dUTP, Ambion) and following the manufacturer´s instructions. For each sample, 3.5 µg of aminoallyl-labeled aRNA was resuspend in 0.1 M Na2CO3 (pH 9.0) and labelled with either Cy3 or Hyper 5 Mono NHS Ester (CyTMDye Post-labelling Reactive Dye Pack, Amersham). The samples were purified following the manufacturer´s instructions for MegaclearTM (Ambion). Cy3 and Hiper 5 incorporation was measured using 1 µl of the probe in a Nanodrop spectrophotometer (Nanodrop Technologies Inc.)

growth_protocol: Seeds were sterilized with 10% (v/v) sodium hypochlorite for 10 min, rinsed with deionized water, and incubated on wet filter paper in the dark for 24h at 4ºC and 24h at room temperature. Seedlings were placed on a styrofoam sheet with a polyethylene net bottom. The styrofoam sheets were floated on a nutrient solution in a plastic tray. Seedlings were grown in aerated medium under controlled environmental conditions (25°C and a 16h photoperiod). Seedlings were grown in the medium described by Aniol, 1981, with the modification of Gallego and Benito (1997). The nutrient solution contained:  CaCl2 0,4 mM, KNO3 0,65 mM, MgCl2.6H2O 0,25 mM, (NH4)2SO4 0,01 mM y NH4NO3 0,04 mM. The pH of the solution was adjusted to 4.0 ± 0.1. Nutrient solution was changed daily. Seedling were grown for 4 days.

extract_protocol: Each replicate composed by nine 1 cm long root tips in liquid nitrogen was homogenizated and pre-extracted using Trizol (following Invitrogen’s instructions). Then, EZNA Plant RNA Kit (Omega Bio-tek) was employed for RNA extraction. To remove genomic DNA, a RNAse free DNAse treatment (Invitrogen) was used.

treatment_protocol: 4 day old seedlings were transferred to the same nutrient solution with or without 200 μM AlCl3 for 24h.

value: 5 days

value: root apex

tag: exposed to

value: 200 μM AlCl3 for 24h


title: Wheat CS Replica 3 Al treatment

description:
Biological replicate 3 of 3. Root apex, wheat, treated with 200 μM AlCl3 for 24h, harvested after 5 days in the growth solution.
0030 wheat CS replica3 (ct-hy5_exp-cy3) 2-12-10.gpr_Exp
raw data file:
0030 wheat CS replica3 (ct-hy5_exp-cy3) 2-12-10.gpr


title: Wheat CS Replica 1 Al treatment

description:
Biological replicate 1 of 3. Root apex, wheat, treated with 200 μM AlCl3 for 24h, harvested after 5 days in the growth solution.
0029 wheat CS replica1 (ct-hy5_exp-cy3) 2-12-10.gpr_Exp
raw data file:
0029 wheat CS replica1 (ct-hy5_exp-cy3) 2-12-10.gpr


title: Wheat CS Replica 2 Control

description:
Biological replicate 2 of 3. Root apex, wheat, untreated, harvested after 5 days in the growth solution.
0029 wheat CS replica2 (ct-cy3_exp-hy5) 2-12-10.gpr_Control
raw data file:
0029 wheat CS replica2 (ct-cy3_exp-hy5) 2-12-10.gpr

source_name: Wheat CS control

value: control solution


title: GQD treated sample 3

city: Suzhou

first: Ming

last: Li

address: No. 199 Ren'ai Road

institute: Soochow University

description: Gene expression of 50 μg/mL GQD-treated HET-1A cells, replicate 3.

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression v3 Microarray (8*60K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with GeneSpring 13.1(Agilent). Probes that had at least 1 out of 2 samples flagged as Detected were maintained.

source_name: GQD treated HET-1A

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: HET-1A cells were maintained in RPMI 1640 medium (Hyclone) supplemented with 10% heat-inactivated fetal calf serum (Gibco), containing 100 U/mL penicillin and 100 U/mL streptomycin and were incubated in a 5% CO2 humidified incubator at 37°C.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1561) following the manufacturer's instructions.

treatment_protocol: HET-1A cells were seeded in 6-cm dishes and treated with 50 μg/mL hydroxyl-modified Graphene quantum dots (GQD) in triplicate. After 24 hours of incubation, cells were harvested with RNAiso Plus (TAKARA). Equivalent volume of ddH2O treated cells were served as controls.

value: Esophageal epithelial cells

value: hydroxyl-modified graphene quantum dots (GQD)


title: Wheat CS Replica 3 Control

description:
Biological replicate 3 of 3. Root apex, wheat, untreated, harvested after 5 days in the growth solution.
0030 wheat CS replica3 (ct-hy5_exp-cy3) 2-12-10.gpr_Control
raw data file:
0030 wheat CS replica3 (ct-hy5_exp-cy3) 2-12-10.gpr


title: GQD treated sample 2

description: Gene expression of 50 μg/mL GQD-treated HET-1A cells, replicate 2.


title: Wheat CS Replica 1 Control

description:
Biological replicate 1 of 3. Root apex, wheat, untreated, harvested after 5 days in the growth solution.
0029 wheat CS replica1 (ct-hy5_exp-cy3) 2-12-10.gpr_Control
raw data file:
0029 wheat CS replica1 (ct-hy5_exp-cy3) 2-12-10.gpr


title: Vehicle treated control sample 3

description: Gene expression of vehicle-treated HET-1A cells, replicate 3.

source_name: Vehicle treated HET-1A

value: vehicle


title: Wheat 6R Replica 2 Control

description:
Biological replicate 2 of 3. Root apex, addition line 6R, untreated, harvested after 5 days in the growth solution.
0028 wheat 6R replica1 (ct-hy5_exp-cy3) 2-12-10.gpr_Control
raw data file:
0028 wheat 6R replica1 (ct-hy5_exp-cy3) 2-12-10.gpr

source_name: Wheat 6R control

tag: line

value: Triticum aestivum secale cereale addition line 6R


title: Wheat 6R Replica 3 Al treatment

description:
Biological replicate 3 of 3. Root apex, addition line 6R, treated with 200 μM AlCl3 for 24h, harvested after 5 days in the growth solution.
0030 wheat 6R replica3 (ct-hy5_exp-cy3) 2-12-10.gpr_Exp
raw data file:
0030 wheat 6R replica3 (ct-hy5_exp-cy3) 2-12-10.gpr

source_name: Wheat 6RAl treatment


title: GQD treated sample 1

description: Gene expression of 50 μg/mL GQD-treated HET-1A cells, replicate 1.


title: Vehicle treated control sample 1

description: Gene expression of vehicle-treated HET-1A cells, replicate 1.


title: Wheat 6R Replica 1 Al treatment

description:
Biological replicate 1 of 3. Root apex, addition line 6R, treated with 200 μM AlCl3 for 24h, harvested after 5 days in the growth solution.
0028 wheat 6R replica2 (ct-cy3_exp-hy5) 2-12-10.gpr_Exp
raw data file:
0028 wheat 6R replica2 (ct-cy3_exp-hy5) 2-12-10.gpr


title: Wheat 6R Replica 2 Al treatment

description:
Biological replicate 2 of 3. Root apex, addition line 6R, treated with 200 μM AlCl3 for 24h, harvested after 5 days in the growth solution.
0028 wheat 6R replica1 (ct-hy5_exp-cy3) 2-12-10.gpr_Exp
raw data file:
0028 wheat 6R replica1 (ct-hy5_exp-cy3) 2-12-10.gpr


title: Wheat 6R Replica 3 Control

description:
Biological replicate 3 of 3. Root apex, addition line 6R, untreated, harvested after 5 days in the growth solution.
0030 wheat 6R replica3 (ct-hy5_exp-cy3) 2-12-10.gpr_Control
raw data file:
0030 wheat 6R replica3 (ct-hy5_exp-cy3) 2-12-10.gpr


title: Vehicle treated control sample 2

description: Gene expression of vehicle-treated HET-1A cells, replicate 2.


title: Wheat 6R Replica 1 Control

description:
Biological replicate 1 of 3. Root apex, addition line 6R, untreated, harvested after 5 days in the growth solution.
0028 wheat 6R replica2 (ct-cy3_exp-hy5) 2-12-10.gpr_Control
raw data file:
0028 wheat 6R replica2 (ct-cy3_exp-hy5) 2-12-10.gpr


title: XIGO_24480

first: Heidi

middle: G

last: Parker

address: 50 South Dr. Rm 5347

department: CGB

institute: NHGRI

description:
SKU_matrix.txt
SKU_signal.txt

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

organism: Canis lupus familiaris

source_name: Xigou_whole blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: origin

value: China

tag: breed

value: Xigou

value: whole blood


title: Wheat 3R Replica 3 Al treatment

description:
Biological replicate 3 of 3. Root apex, addition line 3R, treated with 200 μM AlCl3 for 24h, harvested after 5 days in the growth solution.
0030 wheat 3R replica3 (ct-hy5_exp-cy3) 2-12-10.gpr_Exp
raw data file:
0030 wheat 3R replica3 (ct-hy5_exp-cy3) 2-12-10.gpr

source_name: Wheat 3RAl treatment

value: Triticum aestivum secale cereale addition line 3R

tag: age


title: Wheat 3R Replica 1 Al treatment

description:
Biological replicate 1 of 3. Root apex, addition line 3R, treated with 200 μM AlCl3 for 24h, harvested after 5 days in the growth solution.
0028 wheat 3R replica1 (ct-hy5_exp-cy3) 2-12-10.gpr_Exp
raw data file:
0028 wheat 3R replica1 (ct-hy5_exp-cy3) 2-12-10.gpr


title: Wheat 3R Replica 2 Al treatment

description:
Biological replicate 2 of 3. Root apex, addition line 3R, treated with 200 μM AlCl3 for 24h, harvested after 5 days in the growth solution.
0028 wheat 3R replica2 (ct-cy3_exp-hy5) 2-12-10.gpr_Exp
raw data file:
0028 wheat 3R replica2 (ct-cy3_exp-hy5) 2-12-10.gpr


title: XIGO_24479

description:
SKU_matrix.txt
SKU_signal.txt


title: Wheat 3R Replica 3 Control

description:
Biological replicate 3 of 3. Root apex, addition line 3R, untreated, harvested after 5 days in the growth solution.
0030 wheat 3R replica3 (ct-hy5_exp-cy3) 2-12-10.gpr_Control
raw data file:
0030 wheat 3R replica3 (ct-hy5_exp-cy3) 2-12-10.gpr

source_name: Wheat 3R control


title: XIGO_24481

description:
SKU_matrix.txt
SKU_signal.txt


title: Wheat 3R Replica 2 Control

description:
Biological replicate 2 of 3. Root apex, addition line 3R, untreated, harvested after 5 days in the growth solution.
0028 wheat 3R replica2 (ct-cy3_exp-hy5) 2-12-10.gpr_Control
raw data file:
0028 wheat 3R replica2 (ct-cy3_exp-hy5) 2-12-10.gpr


title: TIBT_30324

description:
SKU_matrix.txt
SKU_signal.txt

source_name: Tibetan Terrier_whole blood

value: North America

value: Tibetan Terrier


title: Wheat 3R Replica 1 Control

description:
Biological replicate 1 of 3. Root apex, addition line 3R, untreated, harvested after 5 days in the growth solution.
0028 wheat 3R replica1 (ct-hy5_exp-cy3) 2-12-10.gpr_Control
raw data file:
0028 wheat 3R replica1 (ct-hy5_exp-cy3) 2-12-10.gpr


title: TIBT_3185

description:
SKU_matrix.txt
SKU_signal.txt


title: TIBT_3186

description:
SKU_matrix.txt
SKU_signal.txt


title: XIGO_24478

description:
SKU_matrix.txt
SKU_signal.txt


title: TIBT_3184

description:
SKU_matrix.txt
SKU_signal.txt


title: TIBT_26260

description:
SKU_matrix.txt
SKU_signal.txt


title: TIBS_5379

description:
SKU_matrix.txt
SKU_signal.txt

source_name: Tibetan Spaniel_whole blood

value: Tibetan Spaniel


title: SCWT_25272

description:
SKU_matrix.txt
SKU_signal.txt

source_name: Soft Coated Wheaten Terrier_whole blood

value: Soft Coated Wheaten Terrier


title: TIBS_5381

description:
SKU_matrix.txt
SKU_signal.txt


title: PUMI_29696

description:
SKU_matrix.txt
SKU_signal.txt

source_name: Pumi_whole blood

value: Pumi