title: A084-POST-Placebo

description: SAMPLE 66


title: borderline serous tumour 17

status: Public on Dec 31 2012

type: genomic

city: London

first: Wei

last: Dai

address: Du Cane Road

department: Sugery and Cancer

country: United Kingdom

institute: Imperial College London

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software methylation module 1.0.5

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: ovarian borderline serous tumour

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted and purified from fresh snap frozen tissue using the the QIAamp DNA Mini kit (Qiagen, West Sussex, UK) according to standard instructions.

tag: tissue

value: ovarian borderline serous tumour


title: Boo Control replicate 2

type: RNA

city: Brisbane

first: Konstantin

last: Shakhbazov

address: Ipswich Road

country: Australia

institute: UQDI

description:
BooV2
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Variance stabilisation and quantile normalisation using lumi package (R/Bioconductor)

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Primary culture of c-Kit enriched bone marrow

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion) was used to make cRNA

growth_protocol: Bone marrow cells were isolated from 4 8-week old Booreana and age matched C57Bl6 mice and enriched for c-Kit expressing cells using MACS CD117 microbeads (Miltenyi). Cells were transduced with retroviral supernatants prepared from MSCV-I-GFP and MSCV-AML1-ETO9a-I-GFP. Cells were transduced by retroviral supernatants by spinoculation using fibronectin (Sigma, F-1141) or Retronectin (Takara) using manufacturer’s guidelines. Cells were cultured in IMDM with 20% fetal calf serum and a cocktail of IL-3, IL-6 and SCF cytokines produced in-house. 48 hours post-transduction, cells were sorted for GFP-positive, c-Kit positive cells on a MoFlo (Beckman Coulter) using an anti-c-Kit PECy7 antibody (eBioscience).

extract_protocol: RNA was extracted with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: genotype/variation

value: Booreana

tag: retrovirus transduction

value: Control

value: Bone marrow


title: Boo Control replicate 3

description:
BooV3
replicate 3


title: A084-PRE-Placebo

city: Ho Chi Minh

first: Nguyen

middle: Hanh

last: Tien

address: 764 Vo Van Kiet

department: Dengue group

country: Viet Nam

institute: Oxford University Clinical Research Unit

description: SAMPLE 65

data_processing: The array intensity values were extracted using GenomeStudio software (v.1.6.0, Illumina Inc., USA) and processed with GeneSpring (v.11.5, Agilent Technologies Inc., USA). First measurements having intensity values less than 5.0 were corrected to 5.0, and then all signals were normalized to the 80th percentile by dividing each value by the 80th percentile value; only genes that were confidently detected in at least 60% of samples in one of the three treatment groups were used for the analysis.

label: Biotin

source_name: PRE-Placebo

label_protocol: RNA was amplified and labeled with biotin using Illumina TotalPrep 96 RNA amplification kit.

extract_protocol: RNA was extracted from blood using PAXgene Blood RNA kit (PreAnalytiX, Switzeland) as instructions of manufacturer.

treatment_protocol: Patients were randomly treated with placebo, low-dose (0.5mg/kg) or high-dose (2mg/kg) of prednisolone. Maximum 3 (pre-treatment (PRE); post-treatment (POST) and follow up (FU) - 1 month since illness onset) and at least 2 samples (pre-treatment and post-treatment) were collected from each patient.

tag: disease status

value: Vietnamese dengue patients

tag: treated with

value: placebo

tag: sample collection time

value: pre-treatment

value: blood

tag: patient id


title: Boo Control replicate 1

description:
BooV1
replicate 1


title: A083-POST-Low dose

description: SAMPLE 63

source_name: POST-Low dose

value: low-dose (0.5mg/kg) of prednisolone

value: post-treatment


title: borderline serous tumour 16


title: Boo AML1-ETO9a replicate 3

description:
BooAE3
replicate 3


title: Boo AML1-ETO9a replicate 4

description:
BooAE4
replicate 4


title: A083-FU-Low dose

description: SAMPLE 64

source_name: FU-Low dose

value: follow up; 1 month after illness-onset


title: A082-FU-Placebo

description: SAMPLE 61

source_name: FU-Placebo


title: Boo AML1-ETO9a replicate 2

description:
BooAE2
replicate 2


title: TBM coinfected with HIV_frozen_tissue 2

city: Bangalore

first: Akhilesh

last: Pandey

email: pandey@jhmi.edu, arivusudar@ibioinformatics.org, sameerkumar.iob@gmail.com, microarray@ibioinformatics.org

state: Karnataka

address: UnitI, Discoverer building, ITPL

country: India

institute: Institute of Bioinformatics

description: Gene expression profile of tuberculous meningitis coinfected with HIV

hyb_protocol: Samples, which have showed specific activity >9 pmol Cy3 per ug and yield > 1600 ug were taken in to a consideration for hybridization.Cyanine-3 labeled cRNA was fragmented and hybridized onto human genome DNA microarrays (G4112F, 4x44 K, Agilent Technologies, Palo Alto, CA). Hybridization was carried out in hybridization chamber for 16 hours at 65C. Subsequently, the arrays were washed using gene expression wash buffers according to the manufacturer’s hybridization protocol (Agilent Oligo Microarray Kit, Agilent Technologies).

scan_protocol: Agilent microarray scanner (G2505B) was used to scan the microarray slides. One color scan settings were used for 4x44K array slides (scan resolution 5 um, dye channel was set to green, green PMT was set to 100%).

data_processing: Agilent feature extraction software was used to processes the images.

source_name: Frontal cortex frozen tissue

label_protocol: From total mRNA, cDNA was synthesized and used as a template to synthesize cRNA. Simultaneous amplification and Cyanine-3 dye was utilized for labeling of cRNA as per the manufacturer’s protocol (Agilent Quick Amp Labeling Kit (Catalog #.51900442, Agilent technologies).  Labelling efficiency and yield of labeled RNA was checked using (NanoDrop® ND-1000).

extract_protocol: Approximately we have used 100 mg of tissue from the normal and infected groups for RNA isolation and the tissues were pulverized in 1 ml of QIAzol lysis reagent using homogenizer. Total RNA extraction and purification was carried out using RNeasy Lipid Tissue Mini kit (Catalog # 74804, QIAGEN, CA 91355, USA) as per manufacturer’s protocol.  RNA quality and yield was calculated by the ratio of absorbance at 260 nm to absorbance at 280 nm.  Integrity of the isolated RNA was checked either by agarose gel electrophoresis or by 2100 Bioanalyzer (Agilent Technologies) that measures the ratio of 28S and 18S ribosomal RNAs to compute the integrity of total mRNA.

value: Frontal cortex

tag: gender

value: Male

tag: age

tag: postmortem delay


title: TBM coinfected with HIV_frozen_tissue 4

value: 4 hrs


title: borderline serous tumour 15


title: borderline serous tumour 14


title: borderline serous tumour 13


title: TBM coinfected with HIV_frozen_tissue 5


title: TBM coinfected with HIV_frozen_tissue 3

value: 12 hrs


title: CellLineSpikeIn_20_MCF7_1

city: San Francisco

first: Mark

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

country: USA

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

hyb_protocol: We combined and precipitated 30 uL Cy3 labeled test DNA, 30 uL Cy5 labeled reference DNA and 100 ug human Cot-1 DNA by adding 0.1 volumes of 3 M sodium acetate (pH 5.2) and 2.5 volumes of ice-cold ethanol. We collected the precipitate by centrifugation  at 14000 rpm for 45 minutes at 4C. We the final hybridization mixture containing 7ul dH20, 14uL  20% SDS, and 49 uL or Master Mix (5 mL ultra pure formamide from Invitrogen, 1g 500000MW Dextran Sulfate, 1mL 20xSSC, 1mL H20). We denatured the hybridization mixture at 73C for 15 min and then incubated the samples at 37C for 2hours to allow the Cot 1 DNA to anneal to repetitive DNA sequeces on both the sample and reference DNA. We exposed our printed arrays to 260000uJoules of UV using StrataLinker and applied a rubber cement ring around each array to form a well. After air drying the rubber cement we added our combined sample/reference hybridization solution onto the array. We placed a silicone gasket around the edge of the wells and laid a clean glass microscope slide on top of the gasket. We clamped the assembly together using binder clips to create an air tight environment. The arrays were incubated or 48-68 hours at 37C on a slowly rocking table (1rpm). After disassembling the hybridization chamber, we rinsed off the excess hybridization fluid with PN buffer (PN: 0.1 M sodium phosphate, 0.1% nonidet P40, pH 8), then washed the arrays once in a solution containing 50% formamide in 2xSSC for 15 min. at 45C and finally in PN buffer at room temperature for 15 min. We removed the ring of rubber cement, drained excess liquid from the arrays, mounted them in a solution containing 90% glycerol, 10% PBS and 1 mM DAPI, and sealed them with a cover slip.

scan_protocol: Arrays were imaged using a custom built CCD array imaging system  and analyzed using the UCSF Spot Program to calculate Cy3/Cy5 ratios.

data_processing: Raw test/ref log2 ratios per spot have been observed in general to exhibit systematic variations of unknown origin across the array. To remove these, an in-house R package ('SpotCorrection'; publication in preparation) was employed. The observed log2 ratios are modeled as the sum of a genomic component (i.e. the desired signal) and a two-dimensional (2D) array component. The genomic and 2D components are iteratively estimated. The estimate of the 2D component after three iterations is then subtracted from the raw ratios. SpotCorrection also includes a relatively subtle correction based on clone GC content. No drastic changes in profiles are observed after correction. The resultant log2 ratios were analyzed by UCSF Sproc to yield the mean and standard deviation of the log2 ratios over replicate spots. The May 2004 freeze of the human genome sequence (hg17) was used to map the array CGH data.

source_name: 20 MCF7 cells isolated from a spike into peripheral blood

label_protocol: BioPrime Array CGH Labeling System (Invitrogen) was used to enzymatically label approximately 600ng of test or reference DNA with Cyanine 3-dCTP or Cyanine 5-dCTP (Amersham), respectively. Briefly, DNA suspended in 11uL of water and 10uL of random prime mix was heated for 10mins at 100C and snap cooled on ice. 2.5uL of 10x-dNTP mix (8uL of 100mM dATP, 8uL of 100mM dGTP, 8uL of 100mM dTTP, 4uL of 100mM dCTP, 2uL 1M Tris, 0.4uL of 0.5M EDTA, and water), 1uL of Cy3 or Cy5 labeled dCTP( 1mM) and 0.6uL Exo-Klenow (40 U/uL) were added to the denatured DNA and incubated for 12 -20 hours at 37C. Unincorporated nucleotides were removed using a Sephadex G-50 spin-columns.

extract_protocol: Magnetic beads coated with EpCAM mAb are used to enrich for tumor cells and then subjected to FACS analysis using differentially labeled mAbs to distinguish tumor cells (EpCAM+) from leukocytes (CD45+) during sorting. Using this protocol, we isolated small pools of highly purified CTCs from breast cancer patients. DNA from Tumor cells sorted in 10uL of TE was amplified using the GenomePlex Single Cell Whole Genome Amplification Kit (Sigma-Aldrich) according to manufacturer’s protocol. The approach was evaluated using breast tumor cell model systems, BT474 and MCF7, and CTCs metastatic breast cancer (MBC) patients. Microdissection and DNA extraction of archival formalin-fixed paraffin-embedded (FFPE) primary tumor were done as previously described in Waldman FM, DeVries S, Chew KL, Moore DH, 2nd, Kerlikowske K, Ljung BM. Chromosomal alterations in ductal carcinomas in situ and their in situ recurrences. J Natl Cancer Inst 2000;92(4):313-20.

treatment_protocol: Array CGH experiments of Circulating Tumor, Primary Tumor, or cell line genomic DNA as test samples and normal human genomic DNA as reference sample.

tag: cell type

tag: assayed molecule

value: Whole genome amplified genomic DNA

source_name: Promega reference Male genomic DNA

value: Whole genome amplified reference male genomic DNA


title: Boo AML1-ETO9a replicate 1

description:
BooAE1
replicate 1


title: borderline serous tumour 18

value: ovarian borderline serous tumour


title: borderline serous tumour 11


title: borderline serous tumour 10


title: borderline serous tumour 12


title: A083-PRE-Low dose

description: SAMPLE 62

source_name: PRE-Low dose


title: A035-POST-Low dose

description: SAMPLE 59


title: A035-PRE-Low dose

description: SAMPLE 58


title: A040-PRE-Placebo

description: SAMPLE 60


title: CellLineSpikeIn_1BT474_2

source_name: 1 BT474 cells isolated from a spike into peripheral blood


title: CellLine_unamplified_MCF7_gDNA

source_name: unamplified genomic DNA isolated from MCF7 cells

value: genomic DNA

value: reference male genomic DNA


title: CellLineSpikeIn_20_MCF7_2

value: MCF7 cells isolated from a spike into peripheral blood


title: A034-POST-Low dose

description: SAMPLE 56

value: Vietnamese dengue patients


title: borderline serous tumour 8


title: A034-FU-Low dose

description: SAMPLE 57


title: ME-15_pcDNA3.1-SOCS4_control_medium_24h_rep3

city: Bern

first: Fredy

last: Siegrist

address: Freiburgstrasse 15

department: Department of Nephrology

country: Switzerland

institute: University Hospital Bern

description: no detectable levels of SOCS4, can be used as vector control

hyb_protocol: 750 ng of biotin labeled, intact cRNA was hybridized to Sentrix HumanRef-8 v3 Expression BeadChips (Illumina) according to the manufacturer’s protocol. Replicates were randomly distributed among slides and positions. Bead arrays were washed and stained using FluoroLink Cy3 Streptavidin (GE Healthcare Life Sciences).

scan_protocol: Fluorescent signal data was collected using a high-resolution scanner system (Illumina iScan) using factory settings for whole genome expression arrays.

data_processing: Scanner images files were processed by software supplied from the manufacturer to probe intensity files and further processed with the GenomeStudio software, gene expression module 1.0.6 (Illumina, Inc.) without normalization and background correction. VST (variance stabilization) transformation 'lumiT()', quantile normalization 'lumiN(, method = quantile)' and statistical analysis were performed with R/Bioconductor software (2.11.1) using the package lumi (1.14.0).

label_protocol: 500 ng total RNA subjected to cDNA synthesis and subsequent in vitro transcribed to biotin labeled cRNA using the Illumina® TotalPrep RNA Amplification Kit (Ambion). cRNA was quantified with QuantIT against ribosomal RNA standard (Invitrogen).

growth_protocol: ME-15 and descendent cell lines were cultured at 37°C in a 5% CO2 atmosphere in RPMI 1640 medium (GIBCO Life Sciences, Paisley, U.K.) supplemented with 10% fetal bovine serum (FBS), L-glutamine (2 mM), sodium pyruvate (1 mM), nonessential amino acids, antibiotics, and 10 mM HEPES buffer. HuH-7 and descendent cell lines were cultured in D-MEM + GlutaMAX™-I containing 10% FBS (D-MEM culture medium). All cell culture reagents were purchased from Invitrogen (GIBCO®).

extract_protocol: Total RNA was extracted from independent triplicates using the Trizol reagent (Sigma) as described previously (Siegrist F et al. 2009 Biol Proced Online 11(1):113-129). RNA was quantified using the Quant-iT™ RiboGreen® RNA Assay (Invitrogen).

treatment_protocol: Roferon (Interferon alpha2a, ROCHE) was diluted in fresh culture medium to a final concentration of 1,000 U/ml and control cultures were grown without cytokine. Cell cultures were incubated at 37°C in a humidified atmosphere containing 5% CO2 for 4 or 24 hours.

tag: cell line

tag: treatment

tag: plasmid

value: pCDNA3.1+NEO SOCS4 A

tag: sentrix barcode

tag: sample section

value: G


title: ME-15_pcDNA3.1-SOCS4_IFNa_1000Uml_24h_rep3

value: F


title: ME-15_pcDNA3.1-SOCS4_IFNa_1000Uml_24h_rep2

value: C


title: ME-15_pcDNA3.1-SOCS4_IFNa_1000Uml_24h_rep1

value: D


title: A030-FU-High dose

description: SAMPLE 54

source_name: FU-High dose

value: high-dose (2mg/kg) of prednisolone

value: follow up; 1 month after illness-onset

tag: tissue

value: blood


title: ME-15_pcDNA3.1-SOCS4_control_medium_24h_rep2

value: H


title: CellLineSpikeIn_1BT474_3

value: BT474 cells isolated from a spike into peripheral blood


title: CellLineSpikeIn_1BT474_1

value: Whole genome amplified genomic DNA


title: A031-PRE-Placebo

description: SAMPLE 55

value: placebo

value: pre-treatment


title: borderline serous tumour 6

value: ovarian borderline serous tumour


title: borderline serous tumour 9


title: A030-POST-High dose

description: SAMPLE 53

source_name: POST-High dose

value: post-treatment


title: CellLineSpikeIn_10_BT474_GP_1

source_name: 10 BT474 cells isolated from a spike into peripheral blood

value: Whole genome amplified reference male genomic DNA


title: CellLineSpikeIn_10_BT474_GP_2


title: borderline serous tumour 5


title: ME-15_pcDNA3.1-SOCS4_control_medium_24h_rep1

value: E


title: CellLineSpikeIn_20_BT474_GP_2

source_name: 20 BT474 cells isolated from a spike into peripheral blood


title: A025-POST-Placebo

description: SAMPLE 50

source_name: POST-Placebo

value: Vietnamese dengue patients


title: CellLineSpikeIn_50_BT474_GP_3

source_name: 50 BT474 cells isolated from a spike into peripheral blood


title: borderline serous tumour 3

source_name: ovarian borderline serous tumour


title: borderline serous tumour 4


title: borderline serous tumour 1


title: ME-15_pcDNA3.1-SOCS4_control_medium_4h_rep3

value: pCDNA3.1+NEO SOCS4 A


title: borderline serous tumour 7


title: A025-PRE-Placebo

description: SAMPLE 49

source_name: PRE-Placebo


title: ME-15_pcDNA3.1-SOCS4_IFNa_1000Uml_4h_rep2


title: A025-FU-Placebo

description: SAMPLE 51


title: ME-15_pcDNA3.1-SOCS4_IFNa_1000Uml_4h_rep1

value: A


title: A030-PRE-High dose

description: SAMPLE 52

source_name: PRE-High dose


title: benign serous tumour 16

source_name: ovarian benign serous tumour

value: ovarian benign serous tumour


title: ME-15_pcDNA3.1-SOCS4_control_medium_4h_rep1

value: B


title: CellLineSpikeIn_50_BT474_GP_2


title: ME-15_pcDNA3.1-SOCS4_IFNa_1000Uml_4h_rep3


title: ME-15_pcDNA3.1-SOCS4_control_medium_4h_rep2

value: G


title: CellLineSpikeIn_20_BT474_GP_1


title: CellLineSpikeIn_50_BT474_GP_1


title: A039-FU-Placebo

description: SAMPLE 48

source_name: FU-Placebo

value: follow up; 1 month after illness-onset


title: CellLineSpikeIn_100_BT474_GP_2

source_name: 100 BT474 cells isolated from a spike into peripheral blood


title: benign serous tumour 15


title: benign serous tumour 13


title: benign serous tumour 14


title: CellLineSpikeIn_500_BT474_GP_2

source_name: 500 BT474 cells isolated from a spike into peripheral blood


title: CellLineSpikeIn_500_BT474_GP_1

source_name: Promega reference Male genomic DNA


title: CellLineSpikeIn_100_BT474_GP_1


title: A039-POST-Placebo

description: SAMPLE 47

value: blood


title: ME-15_pcDNA3.1-SOCS3_IFNa_1000Uml_24h_rep3

value: pCDNA3.1+NEO SOCS3 B


title: benign serous tumour 10


title: benign serous tumour 12


title: CellLine_unamplified_BT474

source_name: unamplified genomic DNA isolated from BT474 cells

value: genomic DNA

value: reference male genomic DNA


title: ME-15_pcDNA3.1-SOCS3_control_medium_24h_rep3


title: A055-PRE-High dose

description: SAMPLE 43

value: high-dose (2mg/kg) of prednisolone


title: A055-FU-High dose

description: SAMPLE 45


title: ME-15_pcDNA3.1-SOCS3_control_medium_24h_rep2

value: C


title: benign serous tumour 11


title: ME-15_pcDNA3.1-SOCS3_IFNa_1000Uml_24h_rep2


title: ME-15_pcDNA3.1-SOCS3_IFNa_1000Uml_24h_rep1

value: H


title: D005-POST-Low dose

description: SAMPLE 41

source_name: POST-Low dose

value: low-dose (0.5mg/kg) of prednisolone

value: post-treatment


title: A055-POST-High dose

description: SAMPLE 44


title: A039-PRE-Placebo

description: SAMPLE 46

value: placebo

value: pre-treatment


title: benign serous tumour 9


title: ME-15_pcDNA3.1-SOCS3_IFNa_1000Uml_4h_rep3

value: E


title: ME-15_pcDNA3.1-SOCS3_IFNa_1000Uml_4h_rep2

value: A


title: D005-FU-Low dose

description: SAMPLE 42

source_name: FU-Low dose

value: Vietnamese dengue patients


title: borderline serous tumour 2

value: ovarian borderline serous tumour


title: D005-PRE-Low dose

description: SAMPLE 40

source_name: PRE-Low dose


title: benign serous tumour 8

value: ovarian benign serous tumour


title: CTC_4009_250CTC_Replicate2_Timepoint_1

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient at timepoint 1

value: Whole genome amplified genomic DNA

value: Whole genome amplified reference male genomic DNA


title: ME-15_pcDNA3.1-SOCS3_control_medium_24h_rep1

value: pCDNA3.1+NEO SOCS3 B


title: PrimaryTumor_462_PT

source_name: Primary tumor

value: Primary tumor


title: CTC_462_20CTC_Timepoint_2

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient at timepoint 2


title: CTC_462_20CTC_Replicate2_Timepoint_1

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient


title: PrimaryTumor_4026_PT


title: A195-FU-Low dose

description: SAMPLE 39

value: follow up; 1 month after illness-onset

value: blood


title: benign serous tumour 7


title: A195-POST-Low dose

description: SAMPLE 38


title: benign serous tumour 6


title: ME-15_pcDNA3.1-SOCS3_control_medium_4h_rep3

value: H


title: PrimaryTumor_4015_PT


title: LymphNode_4015_LN

source_name: Lymph Node

value: Lymph Node


title: PrimaryTumor_4013_PT

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient


title: D021-PRE-Placebo

description: SAMPLE 36


title: ME-15_pcDNA3.1-SOCS3_IFNa_1000Uml_4h_rep1

value: G


title: ME-15_pcDNA3.1-SOCS3_control_medium_4h_rep2


title: benign serous tumour 5


title: A195-PRE-Low dose

description: SAMPLE 37

value: low-dose (0.5mg/kg) of prednisolone


title: benign serous tumour 2


title: benign serous tumour 3


title: TBM coinfected with HIV_frozen_tissue 1

source_name: Frontal cortex frozen tissue

value: Frontal cortex

value: Male


title: ME-15_pcDNA3.1-SOCS1_IFNa_1000Uml_24h_rep2

value: pCDNA3.1+NEO SOCS1 C

value: F


title: ME-15_pcDNA3.1-SOCS1_IFNa_1000Uml_24h_rep3

value: A


title: benign serous tumour 4

value: ovarian benign serous tumour


title: ME-15_pcDNA3.1-SOCS3_control_medium_4h_rep1


title: D020-FU-Placebo

description: SAMPLE 35

value: Vietnamese dengue patients

value: placebo


title: benign serous tumour 1


title: D020-POST-Placebo

description: SAMPLE 34

source_name: POST-Placebo

value: post-treatment


title: D020-PRE-Placebo

description: SAMPLE 33

source_name: PRE-Placebo

value: pre-treatment


title: D012-FU-Placebo

description: SAMPLE 32


title: PEO1, biological replicate 4

source_name: ovarian cancer cell line

value: ovarian cancer cell line isolated from patient before chemotherpay


title: CTC_4013_20CTC_Timepoint_2

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient

value: Whole genome amplified genomic DNA

value: Whole genome amplified reference male genomic DNA


title: PrimaryTumor_4009_PT

value: Primary tumor


title: CTC_303_50CTC_Replicate3_Timepoint_3

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient at timepoint 3


title: CTC_303_50CTC_Replicate2_Timepoint_3


title: CTC_303_50CTC_Replicate1_Timepoint_3


title: CTC_97985_20CTC


title: PEO1, biological replicate 3


title: CTC_303_74CTC_Timepoint_1


title: ME-15_pcDNA3.1-SOCS1_IFNa_1000Uml_24h_rep1

value: G


title: ME-15_pcDNA3.1-SOCS1_control_medium_24h_rep1

value: B


title: PEO1, biological replicate 1, [2]


title: D004-POST-Low dose

description: SAMPLE 28

value: low-dose (0.5mg/kg) of prednisolone

value: blood


title: ME-15_pcDNA3.1-SOCS1_control_medium_24h_rep3

value: pCDNA3.1+NEO SOCS1 C

value: D


title: D004-FU-Low dose

description: SAMPLE 29

value: follow up; 1 month after illness-onset


title: ME-15_pcDNA3.1-SOCS1_IFNa_1000Uml_4h_rep3

value: C


title: PEO1, biological replicate 2, [2]


title: ME-15_pcDNA3.1-SOCS1_control_medium_24h_rep2

value: E


title: D003-FU-Placebo

description: SAMPLE 26

source_name: FU-Placebo

value: Vietnamese dengue patients

value: placebo


title: D012-PRE-Placebo

description: SAMPLE 30

value: pre-treatment


title: D004-PRE-Low dose

description: SAMPLE 27


title: D012-POST-Placebo

description: SAMPLE 31

value: post-treatment


title: CTC_83_20CTC

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient


title: CTC_81_20CTC

value: Whole genome amplified genomic DNA


title: ME-15_pcDNA3.1-SOCS1_IFNa_1000Uml_4h_rep2


title: ME-15_pcDNA3.1-SOCS1_control_medium_4h_rep3

value: F


title: CTC_80_20CTC

value: Whole genome amplified reference male genomic DNA


title: ME-15_pcDNA3.1-SOCS1_IFNa_1000Uml_4h_rep1

value: H


title: CD34

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

institute: Monash University

description:
5529093014_F
normal CD34 positive cells from childhood bone marrow

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2

label: Cy3 and Cy5

source_name: Childhood CD34 positive cells from bone marrow

extract_protocol: Standard cell lysis, proteinase K and phenol/chloroform extraction of genomic DNA from tissue and cell line samples followed by ethanol precipitation and washing. For archived bone marrow smear film samples, cell lysis buffer is applied directly to the microscope slide after removal of coverslip by soaking in 100% xylene. The film is physically scraped off the slide in the presence of cell lysis buffer. Proteinase K treatment and phenol/chloroform extraction is subsequently performed.

tag: disease state

value: normal control

value: fresh tissue (childhood bone marrow)

value: normal CD34 positive cells


title: DONOR2

description:
4686468006_L
normal whole bone marrow from unrelated child Donor 2

source_name: Whole Bone Marrow from Child Donor 2

value: fresh tissue (normal whole bone marrow)


title: neg_frac

description:
5529093014_J
normal CD34 and CD19 negative cells from childhood bone marrow

source_name: Childhood CD34 and CD19 double negattive cells from bone marrow

value: normal CD34 and CD19 negative cells


title: D003-PRE-Placebo

description: SAMPLE 24

value: blood


title: CTC_8001_150CTC

source_name: Promega reference Male genomic DNA


title: D003-POST-Placebo

description: SAMPLE 25


title: ME-15_pcDNA3.1-SOCS1_control_medium_4h_rep1

value: pCDNA3.1+NEO SOCS1 C


title: F235

description:
4686468006_K
remission bone marrow from TEL/AML positive child

source_name: Follow up Bone Marrow from 235

value: remission

value: archived bone marrow smear film


title: CTC_78_20CTC


title: CTC_63_20CTC


title: D002-POST-Low dose

description: SAMPLE 22

source_name: POST-Low dose

value: Vietnamese dengue patients

value: low-dose (0.5mg/kg) of prednisolone


title: ME-15_IFNa_1000Uml_24h_rep2


title: CD19

description:
5529093014_H
normal CD19 postitive cells from childhood bone marrow

source_name: Childhood CD19 positive cells from bone marrow

value: normal CD19 postitive cells


title: DONOR1

description:
4686468006_J
normal whole bone marrow from unrelated child Donor 1

source_name: Whole Bone Marrow from Child Donor 1 replicate 1


title: D002-FU-Low dose

description: SAMPLE 23

source_name: FU-Low dose

value: follow up; 1 month after illness-onset


title: CTC_62_20CTC

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient

value: Whole genome amplified genomic DNA


title: ME-15_IFNa_1000Uml_24h_rep1

value: C


title: A193-POST-Low dose

description: SAMPLE 20

value: post-treatment


title: F216

description:
4686468006_I
remission bone marrow from TEL/AML positive child

source_name: Follow up Bone Marrow from 216


title: R344

description:
4686468006_F
remission bone marrow from TEL/AML positive child

source_name: Remission Bone Marrow from 344


title: ME-15_IFNa_1000Uml_24h_rep3

value: E


title: A193-FU-Low dose

description: SAMPLE 21


title: R114

description:
4686468006_G
remission bone marrow from TEL/AML positive child

source_name: Remission Bone Marrow from 114


title: CTC_56_20CTC

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient

value: Whole genome amplified reference male genomic DNA


title: ME-15_control_medium_24h_rep3


title: A194-FU-High dose

description: SAMPLE 18

source_name: FU-High dose

value: high-dose (2mg/kg) of prednisolone


title: F114

description:
4686468006_E
remission bone marrow from TEL/AML positive child

source_name: Follow up Bone Marrow from 114


title: F088

description:
4686468006_H
remission bone marrow from TEL/AML positive child

source_name: Follow up Bone Marrow from 88


title: L344

description:
4686468006_D
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 344

value: leukaemia


title: CTC_49_9CTC


title: D002-PRE-Low dose

description: SAMPLE 19

source_name: PRE-Low dose

value: pre-treatment


title: ME-15_pcDNA3.1-SOCS1_control_medium_4h_rep2

value: B


title: ME-15_IFNa_1000Uml_4h_rep3

value: G


title: CTC_54_20CTC


title: ME-15_IFNa_1000Uml_4h_rep2

value: D


title: CTC_462_20CTC_Replicate1_Timepoint_1

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient at timepoint 1


title: A194-PRE-High dose

description: SAMPLE 16

source_name: PRE-High dose

value: blood


title: ME-15_control_medium_24h_rep2

value: H


title: ME-15_control_medium_24h_rep1

value: F


title: CTC_47_20CTC

source_name: Promega reference Male genomic DNA


title: D001-FU-Placebo

description: SAMPLE 15

source_name: FU-Placebo

value: Vietnamese dengue patients

value: placebo


title: S344

description:
4686468006_B
remission bone marrow from TEL/AML positive child

value: remission

value: archived bone marrow smear film


title: L133

description:
4686468006_A
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 133


title: F133

description:
4686468006_C
remission bone marrow from TEL/AML positive child

source_name: Follow up Bone Marrow from 133


title: D001-PRE-Placebo

description: SAMPLE 13

source_name: PRE-Placebo


title: CTC_41_20CTC

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient

value: Whole genome amplified genomic DNA


title: A194-POST-High dose

description: SAMPLE 17

source_name: POST-High dose

value: post-treatment


title: R088

description:
4686468004_L
remission bone marrow from TEL/AML positive child

source_name: Remission Bone Marrow from 088


title: ME-15_control_medium_4h_rep3

value: A


title: CTC_4030_8CTC

value: Whole genome amplified reference male genomic DNA


title: ME-15_IFNa_1000Uml_4h_rep1


title: ME-15_control_medium_4h_rep1


title: CTC_40_20CTC


title: R216

description:
4686468004_K
remission bone marrow from TEL/AML positive child

source_name: Remission Bone Marrow from 216


title: ME-15_control_medium_4h_rep2


title: A187-PRE-Placebo

description: SAMPLE 12


title: CTC_4026_7CTC


title: A185-FU-High dose

description: SAMPLE 11

value: high-dose (2mg/kg) of prednisolone

value: follow up; 1 month after illness-onset


title: D001-POST-Placebo

description: SAMPLE 14

source_name: POST-Placebo


title: L088

description:
4686468004_J
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 88 replicate 1

value: leukaemia


title: HuH7_pcDNA3.1-SOCS4_IFNa_1000Uml_24h_rep2

description: no detectable levels of SOCS4, can be used as vector control

value: pCDNA3.1+NEO SOCS4 A

value: G


title: CTC_4019_20CTC

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient


title: L216

description:
4686468004_I
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 216


title: CTC_4017_8CTC


title: CTC_4015_20CTC


title: HuH7_pcDNA3.1-SOCS4_IFNa_1000Uml_24h_rep3

value: D


title: A187-FU-Placebo

description: SAMPLE 10

value: blood


title: CTC_4013_20CTC_Timepoint_1


title: CTC_4009_250CTC_Replicate1_Timepoint_1


title: A189-POST-High dose

description: SAMPLE 8


title: HuH7_pcDNA3.1-SOCS4_IFNa_1000Uml_24h_rep1

value: B


title: CTC_4005_129CTC


title: HuH7_pcDNA3.1-SOCS4_IFNa_1000Uml_4h_rep2


title: A187-POST-Placebo

description: SAMPLE 9

value: Vietnamese dengue patients


title: L143

description:
4686468004_E
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 143


title: HuH7_pcDNA3.1-SOCS4_control_medium_24h_rep1


title: CTC_305_22CTC


title: F084

description:
4686468004_D
remission bone marrow from TEL/AML positive child

source_name: Follow up Bone Marrow from 84


title: F143

description:
4686468004_G
remission bone marrow from TEL/AML positive child

source_name: Follow up Bone Marrow from 143


title: R084

description:
4686468004_B
remission bone marrow from TEL/AML positive child

source_name: Remission Bone Marrow from 84


title: HuH7_pcDNA3.1-SOCS4_IFNa_1000Uml_4h_rep3

value: F


title: L123

description:
4493586003_L
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 123


title: A193-PRE-Low dose

description: SAMPLE 6

source_name: PRE-Low dose

value: low-dose (0.5mg/kg) of prednisolone

value: pre-treatment


title: A192-FU-Low dose

description: SAMPLE 5

source_name: FU-Low dose


title: R235

description:
4686468004_H
remission bone marrow from TEL/AML positive child

source_name: Remission Bone Marrow from 235

value: remission

value: archived bone marrow smear film


title: HuH7_pcDNA3.1-SOCS4_IFNa_1000Uml_4h_rep1

value: E


title: A189-PRE-High dose

description: SAMPLE 7

source_name: PRE-High dose


title: CTC_303_50CTC_Timepoint_2

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient at timepoint 2

value: Whole genome amplified genomic DNA

source_name: Promega reference Male genomic DNA


title: CTC_302_112CTC

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient

value: Whole genome amplified reference male genomic DNA


title: CTC_26_31CTC


title: L119

description:
4493586003_K
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 119


title: CTC_29_20CTC


title: HuH7_pcDNA3.1-SOCS4_control_medium_24h_rep2


title: CTC_22_20CTC


title: A192-PRE-Low dose

description: SAMPLE 3


title: A191-PRE-High dose

description: SAMPLE 1

value: high-dose (2mg/kg) of prednisolone


title: R127

description:
4493586003_J
remission bone marrow from TEL/AML positive child

source_name: Remission Bone Marrow from 127


title: HuH7_pcDNA3.1-SOCS4_control_medium_4h_rep3

value: C


title: REH

description:
4493586003_I
model leukaemia cell line REH

source_name: Model Cell Line REH replicate 1

value: leukaemia control

value: model leukaemia cell line REH


title: HuH7_pcDNA3.1-SOCS4_control_medium_4h_rep1

value: pCDNA3.1+NEO SOCS4 A

value: H


title: L175

description:
4493586003_D
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 175

value: leukaemia


title: HuH7_pcDNA3.1-SOCS3_IFNa_1000Uml_24h_rep3

value: pCDNA3.1+NEO SOCS3 B

value: G


title: CTC_123190_20CTC

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient


title: L127

description:
4493586003_H
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 127


title: CD8EM IL6Rhigh IL7Rhigh 2

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

description: CD8 positive Effector Memory IL-6 Receptor High IL-7 Receptor High T cells

scan_protocol: Illumina BeadScan 500 System

source_name: CD8EM 6high 7high T cells

label_protocol: Refer to the Illumina Gene Expression System Manual

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: CD8+ T

tag: sample number

value: normal

tag: transfection genes


title: HuH7_pcDNA3.1-SOCS3_IFNa_1000Uml_24h_rep1


title: CD8EM IL6Rlow IL7Rhigh 1

description: CD8 positive Effector Memory IL-6 Receptor Low IL-7 Receptor High T cells

source_name: CD8EM 6low 7high T cells


title: HuH7_pcDNA3.1-SOCS4_control_medium_4h_rep2

value: B


title: CD8EM IL6Rlow IL7Rhigh 2


title: HuH7_pcDNA3.1-SOCS3_IFNa_1000Uml_24h_rep2


title: CD8EM IL6Rhigh IL7Rhigh 1


title: A191-POST-High dose

description: SAMPLE 2

source_name: POST-High dose

tag: disease status

value: Vietnamese dengue patients

tag: treated with

value: post-treatment

value: blood


title: CD8EM IL6Rlow IL7Rlow 2

description: CD8 positive Effector Memory IL-6 Receptor Low IL-7 Receptor Low T cells

source_name: CD8EM 6low 7low T cells


title: L114

description:
4493586003_B
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 114

tag: patient id

value: archived bone marrow smear film


title: HuH7_pcDNA3.1-SOCS3_control_medium_24h_rep3

value: F


title: A192-POST-Low dose

description: SAMPLE 4

source_name: POST-Low dose

value: low-dose (0.5mg/kg) of prednisolone

tag: sample collection time


title: CTC_122675_11CTC

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient

value: Whole genome amplified genomic DNA

value: Whole genome amplified reference male genomic DNA


title: CTC_122651_20CTC


title: CTC_123003_20CTC


title: DONOR1_1

description:
4408100017_L
normal whole bone marrow from unrelated child Donor 1

source_name: Whole Bone Marrow from Child Donor 1 replicate 2

value: normal control

value: fresh tissue (normal whole bone marrow)


title: CD8EM IL6Rlow IL7Rlow 1


title: HuH7_pcDNA3.1-SOCS3_control_medium_24h_rep2

value: C


title: HuH7_pcDNA3.1-SOCS3_control_medium_24h_rep1

value: pCDNA3.1+NEO SOCS3 B

value: D


title: MCF-7

description:
4408100017_K
model cancer cell line MCF-7

source_name: Model Cell Line MCF-7

value: cancer control

value: model cancer cell line MCF-7


title: CTC_122504_20CTC


title: L089

description:
4408100017_J
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 89

value: leukaemia


title: K562

description:
4408100017_G
model leukaemia cell line K562

source_name: Model Cell Line K562

value: leukaemia control

value: model leukaemia cell line K562


title: CTC_122286_20CTC

source_name: Promega reference Male genomic DNA


title: HuH7_pcDNA3.1-SOCS3_IFNa_1000Uml_4h_rep2

value: E


title: CTC_122160_20CTC


title: L094

description:
4408100017_F
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 94

value: archived bone marrow smear film


title: L199

description:
4408100017_H
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 199


title: HuH7_pcDNA3.1-SOCS3_IFNa_1000Uml_4h_rep3


title: HuH7_pcDNA3.1-SOCS3_control_medium_4h_rep3

value: A


title: mDC_ND293_cRPMI_6h

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

scan_protocol: Standard Illumina scanning protocol with iScan scanner, Illumina

data_processing: The data were normalized using average normalization with Genome Studio

source_name: Human Whole Blood

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep-96 RNA Amplification Kit

extract_protocol: RNA was extracted with Mirvana™ RNA Isolation Kit. Quality control was performed with Agilent Bioanalyser.

tag: cell population

value: myeloid dendritic cells (mDC)

tag: cell count (10^6)

tag: activation

value: cRPMI

tag: dose

tag: timepoint


title: HuH7_pcDNA3.1-SOCS3_IFNa_1000Uml_4h_rep1

tag: cell line

tag: treatment

value: B


title: mDC_ND307_cRPMI_6h


title: mDC_ND287_Cyclic Glucan 10ug/mL_6h

value: Cyclic Glucan 10ug/mL

value: 10 ug/mL


title: mDC_ND307_Cyclic Glucan_10 ug/mL_6h


title: R175

description:
4493586003_F
remission bone marrow from TEL/AML positive child

source_name: Remission Bone Marrow from 175

value: remission


title: CCRFCEM

description:
4408100017_I
model leukaemia cell line CCRF-CEM

source_name: Model Cell Line CCRF-CEM

value: model leukaemia cell line CCRF-CEM


title: mDC_ND318_cRPMI_6h


title: HuH7_pcDNA3.1-SOCS3_control_medium_4h_rep2

tag: plasmid

value: pCDNA3.1+NEO SOCS3 B

tag: sentrix barcode

value: F


title: CTC_122025_20CTC

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient

tag: cell type

tag: assayed molecule

value: Whole genome amplified genomic DNA

value: Whole genome amplified reference male genomic DNA


title: JURKAT

description:
4408100017_C
model leukaemia cell line JURKAT

source_name: Model Cell Line JURKAT

tag: disease state

value: model leukaemia cell line JURKAT


title: mDC_ND287_LPS_100 ng/mL_6h

value: LPS_100 ng/mL

value: 100 ng/mL


title: L088_1

description:
4408100017_D
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 88 replicate 2

value: leukaemia

tag: tissue


title: HuH7_pcDNA3.1-SOCS1_IFNa_1000Uml_24h_rep2

value: pCDNA3.1+NEO SOCS1 C

tag: sample section

value: E


title: mDC_ND287_cRPMI_6h

value: myeloid dendritic cells (mDC)


title: L102

description:
4408100017_B
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 102

value: archived bone marrow smear film


title: SW48

description:
4408100017_E
model cancer cell line SW48

source_name: Model Cell Line SW48

value: cancer control

value: model cancer cell line SW48


title: HuH7_pcDNA3.1-SOCS1_IFNa_1000Uml_24h_rep1


title: HuH7_pcDNA3.1-SOCS3_control_medium_4h_rep1

value: G


title: mDC_ND318_Cyclic Glucan_10 ug/mL_6h

value: Cyclic Glucan 10ug/mL

value: 10 ug/mL


title: REH2

description:
4408100017_A
model leukaemia cell line REH

source_name: Model Cell Line REH replicate 2

value: leukaemia control

value: model leukaemia cell line REH


title: mDC_ND293_Cyclic Glucan_10 ug/mL_6h


title: L365

description:
5027501055_G
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 365


title: CTC_120821_16CTC

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient

value: Whole genome amplified genomic DNA


title: mDC_ND291_Cyclic Glucan_10 ug/mL_6h


title: HuH7_pcDNA3.1-SOCS1_control_medium_24h_rep2

value: A


title: mDC_ND291_cRPMI_6h

value: cRPMI


title: CTC_121829_20CTC

value: Whole genome amplified reference male genomic DNA


title: HuH7_pcDNA3.1-SOCS1_IFNa_1000Uml_24h_rep3

value: H


title: HuH7_pcDNA3.1-SOCS1_control_medium_24h_rep1

value: pCDNA3.1+NEO SOCS1 C


title: mDC_ND293_LPS_100 ng/mL_6h

value: LPS_100 ng/mL

value: 100 ng/mL


title: mDC_ND318_LPS_100 ng/mL_6h

value: myeloid dendritic cells (mDC)


title: CTC_120660_20CTC


title: mDC_ND307_LPS_100 ng/mL_6h


title: HuH7_pcDNA3.1-SOCS1_control_medium_24h_rep3

value: E


title: CD34.Adult

description:
5027501055_C
normal CD34 positive cells from adult bone marrow

source_name: Adult CD34 positive cells from bone marrow

value: normal control

value: fresh tissue (adult bone marrow)

value: normal CD34 positive cells


title: HuH7_pcDNA3.1-SOCS4_control_medium_24h_rep3

description: no detectable levels of SOCS4, can be used as vector control

value: pCDNA3.1+NEO SOCS4 A


title: R365

description:
5027501055_K
remission bone marrow from TEL/AML positive child

source_name: Remission Bone Marrow from 386

value: remission

value: archived bone marrow smear film


title: CTC_120602_20CTC

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient


title: CTC_120559_6CTC

value: Whole genome amplified genomic DNA


title: CTC_120614_20CTC


title: HuH7_pcDNA3.1-SOCS1_IFNa_1000Uml_4h_rep1

value: D


title: CTC_120489_10CTC


title: HuH7_pcDNA3.1-SOCS1_control_medium_4h_rep3

value: G


title: J82_rep3

city: Miami

first: Avencia

last: Sanchez-Mejias

state: FL

address: 1600 NW 10th Ave

institute: University of Miami

description: Replicate 3

hyb_protocol: Standar Illumina hybridization protocol

scan_protocol: Standar Illumina scanning protocol

data_processing: Quantile normalization algorithm were used to normalised the values of the probe sets within each sample. The software used for normalization was GeneSpring GX v11.0, Agilent Technologies Inc.

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep Amplification Kit.

extract_protocol: Total RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN Rneasy mini kit. Total RNA was quantified with a Nanodrop 8000 Spectrophotometer and quality control was performed with an Agilent Bioanalyser 2100 using the Agilent RNA 6000 Nani kit.

tag: sensitivity to hedgehog

value: Insensitive


title: HuH7_pcDNA3.1-SOCS1_IFNa_1000Uml_4h_rep3

value: A


title: PC14_Fibro-3_Mm

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 46628 probes on the mouse-6 v1.1 were used.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: PC14, NIH 3T3

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: protocol

value: co-culture of MDA-MB-231 and astrocyte cells


title: PC14_Fibro-4_Mm


title: HuH7_pcDNA3.1-SOCS1_IFNa_1000Uml_4h_rep2

value: pCDNA3.1+NEO SOCS1 C


title: L235

description:
4686468004_F
leukaemic bone marrow from TEL/AML positive child

source_name: Leukaemia Bone Marrow from 235

tag: patient id

value: leukaemia


title: HT_rep1

description: Replicate 1

value: HT


title: HT_rep3

description: Replicate 3


title: CTC_120447_20CTC

source_name: Promega reference Male genomic DNA

value: Whole genome amplified reference male genomic DNA


title: J82_rep2

description: Replicate 2


title: PC14_Fibro-2_Mm


title: HuH7_pcDNA3.1-SOCS1_control_medium_4h_rep2


title: HuH7_IFNa_1000Uml_24h_rep3

value: B


title: PC14_Astro-4_Mm

source_name: PC14, astrocytes


title: HT_rep2

description: Replicate 2


title: PC14_Fibro-1_Mm


title: HuH7_IFNa_1000Uml_24h_rep2

value: C


title: T24_rep3

description: Replicate 3

value: Sensitive


title: J82_rep1

description: Replicate 1


title: CTC_120226_11CTC


title: HuH7_pcDNA3.1-SOCS1_control_medium_4h_rep1


title: CTC_120211_5CTC


title: PC14_Astro-2_Mm


title: CTC_121059_20CTC


title: PC14_Astro-1_Mm


title: HuH7_IFNa_1000Uml_24h_rep1


title: CTC_120058_20CTC


title: MDA231_Fibro-4_Mm

source_name: MDA-MB-231, NIH 3T3


title: HuH7_IFNa_1000Uml_4h_rep3


title: HuH7_IFNa_1000Uml_4h_rep2

value: H


title: CTC_120053_20CTC


title: HuH7_control_medium_24h_rep2


title: T24_rep1

description: Replicate 1


title: Vmcub1_rep3

description: Replicate 3


title: Ssa_Diet 10_56d_replicate 5

city: Moncton

first: Francis

last: LeBlanc

state: NB

address: 343 University Ave.

department: Aquatic Animal Health

country: Canada

institute: Fisheries & Oceans Canada

hyb_protocol: Microarray hybridizations were performed using Agilent’s 4 x 44K Atlantic salmon microarray slides containing 4 grids with the same ~ 44 000 features (Design ID 025055), using a one-color approach.  All hybridizations, including washes and drying steps were carried out on a HS4800 automated hybridization station using quad chambers (Tecan, Männedorf, Switzerland). Briefly, slides were initially washed with Agilent’s aOligo aCGH Prehybridization buffer for 1 min at 65°C and injected with a 60 µl of hybridization mix containing 30 µl of fragmentation mix and 30 µl of Agilent’s 2x GEx hybridization Buffer Hi-RPM per chamber.  The injected material was hybridized for 17 hour at 65°C.  Following hybridization slides were washed twice with Agilent’s gene expression wash buffer 1 at 23°C for 1 min, twice with Agilent’s gene expression wash buffer 2 with 0.01 wash buffer additive at 37°C for 1 min and then dried under nitrogen.

scan_protocol: Microarray slides were scanned at a resolution of 5 µm using Agilent’s High Resolution Microarray Scanner (Agilent, CA, USA) using a 20-bit data format and automatic PMT adjustment.

data_processing: The resulting TIFF images were quantified using Agilent’s Feature Extraction software (Agilent, CA, USA). Numerical intensities, descriptive statistics and flag value were computed for each spot and exported in a text file. Spots were considered flagged it they were saturated, not uniform, below background levels and if the background was not uniform. Genes that had a flag on more than 1/3 of the slides used for a particular statistical analysis were filtered out.  The gProcessedSignal values (foreground value minus background value) for each spot were then log2 transformed and normalized between arrays using a median centering approach found in BRBArrayTool version 4.1.0 Beta_2 Release (developed by Dr. Richard Simon and BRB-ArrayTools Development Team).  Statistical analysis was performed on log2 transformed and normalized gProcessedSignal value.

organism: Salmo salar

source_name: Ssa_Diet 10_56d_replicate 5

label_protocol: RNA amplification and labeling for microarray was performed using the one-color Low Input Quick Amp Labeling kit (Agilent, CA, USA) and following the manufacturer’s recommendations. Briefly, 200 ng of each RNA sample was reverse transcribed, amplified and labeled using Cy3 dyes resulting in Cy3 labeled amplified RNA (aRNA). Purification of the labeled aRNA was performed using NucleoSpin RNA clean up columns (Macherey-Nagel, CA, USA) following the manufacturer’s recommendations. Following purification, labeled aRNA samples were then quantified using the NanoDrop 8000 to verify the yield of aRNA and the labeling efficiency. 1.65 µg of each purified aRNA was prepared for hybridization using the fragmentation step described in Agilent’s Low Input Quick Amp labeling kit protocol. Briefly each aRNA was fragmented by mixing 1.65 µg of aRNA in a volume of 22.8 µl, with 6 µl of 10X blocking agent and 1.2 µl of 25X fragmentation buffer and heating the mix at 60°C for 30 min.

extract_protocol: Total RNA from RNAlater preserved salmon liver samples was extracted using TRI reagent (Molecular Research Center, OH, USA) followed by column purification using the NucleoSpin RNA II (Macherey-Nagel, PA, USA) and following the manufacturer’s protocol.  An on column DNase digestion step was performed on each sample.  RNA quantification was performed using a NanoDrop 8000 (Thermo Scientific, DE, USA) and RNA quality and integrity was assessed with the Experion automated electrophoresis system (Bio-Rad, TX, USA).  Only RNA samples with RNA Quality Indicator (RQI) values above 8 were used for analysis.  RNA’s were stored at -70ºC in DEPC treated water containing an RNase inhibitor (Qiagen, ON, Canada) until needed.

tag: diet

value: Shrimp hydrolysate (C)

value: Liver

tag: time


title: HuH7_control_medium_24h_rep3


title: MDA231_Fibro-3_Mm


title: CTC_119982_16CTC

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient


title: HuH7_IFNa_1000Uml_4h_rep1

value: F


title: PC14_Astro-3_Mm


title: Ssa_Diet 10_56d_replicate 6

source_name: Ssa_Diet 10_56d_replicate 6


title: CTC_120018_20CTC

value: Whole genome amplified genomic DNA


title: HuH7_control_medium_24h_rep1


title: Vmcub1_rep2

description: Replicate 2


title: MDA231_Astro-4_Mm

source_name: MDA-MB-231, astrocytes


title: Vmcub1_rep1

description: Replicate 1


title: MDA231_Astro-3_Mm


title: HuH7_control_medium_4h_rep3

value: E


title: MDA231_Fibro-2_Mm


title: MDA231_Fibro-1_Mm


title: CTC_119765_17CTC

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient


title: CTC_119491_20CTC


title: Ssa_Diet 10_56d_replicate 4

source_name: Ssa_Diet 10_56d_replicate 4


title: CTC_119362_4CTC


title: Pseudomonas syringae pv. phaseolicola NPS3121 at low temperature  (Technical Replicate 3)

city: Irapuato

first: Jose Luis

last: Hernandez-Flores

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León

department: Ingeniería Genética

country: Mexico

institute: Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional

hyb_protocol: Labeled probes dried and resuspended in 40 µl of hybridization solution (25% hybridization buffer supplied in the CyScribe kit, 25% nuclease free water and 50% formamide). The probe was immediately applied onto the array and covered with a cover slip (Hybri-slips, Sigma-Aldrich Co. St Louis U.S.A.), hybridized 16 hours at 45°C in a humid hybridization chamber (Corning Incorporated, N.Y., U.S.A). After hybridization, the slides were washed once in solutions 1–4 (wash solution 1: 2% SSC, 0.1% SDS at 45 ºC; wash solution 2: 0.1% SSC, 0.1% SDS; wash solution 3: 0.1% SSC; wash solution 4: 0.01% SSC) for 5 min with gentle stirring/agitation. Washed slides were dried by centrifugation at 1600 r.p.m.

scan_protocol: Slides were scanned with an Axon GenePix 4000 B scanner at a resolution of 10 µm adjusting the laser and gain parameters to obtain similar levels of fluorescence intensity in both channels.

data_processing: Spot intensities were quantified using Axon GenePix Pro 6.0 image analysis software. The mean of the signals and the median of backgrounds were used for further analysis. Raw data were imported into the R 2.2.1 software (http://www.R-project.org). Background correction was done using the method Robust Multichip Analysis "RMA" (Irizarry et al., 2003) whereas normalization of the signal intensities within slides was carried out using the "printtiploess" method (Yang et al., 2002) using the LIMMA package (Smyth et al., 2003, www.bioconductor.org). Normalized data were log2 transformed and then fitted into mixed model ANOVAs (Gibson and Wolfinger, 2004; Wolfinger et al., 2001) using the Mixed procedure. The p-values of the temperature effects were adjusted for by the False Discovery Rate method “FDR” (Benjamini and Hochberg, 1995). Estimates of the expression differences were calculated using the mixed model. Based on these statistical analyses, the spots with tests with an FDR less or equal to 5% and with changes in signal intensity between cultures at 18º C and culture control at 28ºC of 1.5 fold or higher difference were considered as differentially expressed.

organism: Pseudomonas savastanoi pv. phaseolicola

source_name: Pseudomonas syringae pv. phaseolicola NPS3121 grown at 18º C

growth_protocol: To evaluate the effect of the temperature, the culture was incubated at 18 ºC until reached the transition phase (OD600nm 1.0), in which it carried out the RNA extraction.

treatment_protocol: Pre-inoculums (25 mL) of P. syringae pv. phaseolicola were grown in M9 minimal medium overnight at 28 ºC. The cells were washed once with M9 medium and inoculated into 200 mL of M9 minimal medium at optical density (OD 600nm) 0.1.

tag: strain

value: grown at 18º C

source_name: Pseudomonas syringae pv. phaseolicola NPS3121 grown at 28º C

label_protocol: Label protocol Purified total RNA (30 ug) was mixed with 3 uL of random nonamer primers and was incubated at 70ºC for 5 min. Reactions were held at room temperature for 10 min to allow the primers and the RNA template to anneal. To each reaction, the following were added: 1 uL of Cy5/Cy3-dCTP (1 mM) (Amersham Biosciences, Piscataway, NJ, U.S.A.), 2 uL of 0.1 M dithiothreitol, 4 uL of 5X Cyscript buffer, 1 uL of dNTP mixture (15 mM dATP, dTTP, and dGTP; 5 mM dCTP), 1uL of Cy3/Cy5 labeled dUTP and 200 U of CyScript reverse transcriptase. Reactions were incubated at 42ºC for 2 h. CyDye labelled single strand cDNA using the CyScribe GFX Purification Kit (Amersham Biosciences, Piscataway, NJ, U.S.A.) and according to the protocol recommended by the supplier. The purified labeled cDNA was then quantified to have with a Nanodrop equipment to final amount of 150 pg of each labeled cDNA.

growth_protocol: To evaluate the effect of the temperature, the culture was incubated at 28 ºC until reached the transition phase (OD600nm 1.0), in which it carried out the RNA extraction.

extract_protocol: RNA Extraction protocol Total RNA was isolated using Trizol reagent as recommended by the manufacturer (Invitrogen). A second step of purification was performed using RNeasy MinElute spin columns (Qiagen) to remove contaminating DNA. RNAs were eluted in 50 µl of diethylpyrocarbonate (DEPC)-treated water and the concentration was determined using the NanoDrop equipment. RNA integrity was checked by analytical agarose gel electrophoresis.

value: grown at 28º C


title: Pseudomonas syringae pv. phaseolicola NPS3121 at low temperature (Biological Replicate 3)

label_protocol: Label protocol Purified total RNA (30 ug) was mixed with 3 uL of random nonamer primers and was incubated at 70ºC for 5 min. Reactions were held at room temperature for 10 min to allow the primers and the RNA template to anneal. To each reaction, the following were added: 1 uL of Cy5/Cy3-dCTP (1 mM) (Amersham Biosciences, Piscataway, NJ, U.S.A.), 2 uL of 0.1 M dithiothreitol, 4 uL of 5X Cyscript buffer, 1 uL of dNTP mixture (15 mM dATP, dTTP, and dGTP; 5 mM dCTP), 1uL of Cy3/Cy5 labeled dUTP and 200 U of CyScript reverse transcriptase. Reactions were incubated at 42ºC for 2 h. CyDye labelled single strand cDNA using the CyScribe GFX Purification Kit (Amersham Biosciences, Piscataway, NJ, U.S.A.) and according to the protocol recommended by the supplier.

extract_protocol: Total RNA was isolated using Trizol reagent as recommended by the manufacturer (Invitrogen). A second step of purification was performed using RNeasy MinElute spin columns (Qiagen) to remove contaminating DNA. RNAs were eluted in 50 µl of diethylpyrocarbonate (DEPC)-treated water and the concentration was determined using the NanoDrop equipment. RNA integrity was checked by analytical agarose gel electrophoresis


title: Pseudomonas syringae pv. phaseolicola NPS3121 at low temperature  (Technical Replicate 2)


title: Ssa_Diet 10_56d_replicate 2

source_name: Ssa_Diet 10_56d_replicate 2


title: CTC_119468_20CTC


title: Ssa_Diet 10_56d_replicate 1

source_name: Ssa_Diet 10_56d_replicate 1


title: Pseudomonas syringae pv. phaseolicola NPS3121 at low temperature  (Biological Replicate 2)


title: CTC_119373_12CTC


title: MDA231_Astro-1_Mm

value: co-culture of MDA-MB-231 and astrocyte cells


title: HuH7_control_medium_4h_rep2


title: Ssa_Diet 10_56d_replicate 3

source_name: Ssa_Diet 10_56d_replicate 3


title: Ssa_Diet 10_14d_replicate 6

source_name: Ssa_Diet 10_14d_replicate 6


title: EB_2Wk_rep4

city: Mainz

first: Hyobin

last: Jeong

state: Germany

address: Richard shirrmann Str 12.

country: Germany

institute: IMB

description: EBs (embryoid bodies) incubated for 2 weeks in ESC medium.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Illumina BeadScan 500 System.

data_processing: The data were normalised using the quantile normalization method with BeadArray version 1.10 and lumi version 1.8.3 in the R/Bioconductor package.

source_name: Embryoid bodies, 2 weeks

label_protocol: Refer to the Illumina Gene Expression System Manual.

growth_protocol: Human SNUhES3 ESCs (Seoul National University Hospital, Seoul, Korea) were cultured on mitotically-arrested STO feeder cells (ATCC, Manassas, USA) in DMEM/F12 supplemented with 20% knockout serum replacement (KSR) (Invitrogen, Carlsbad, USA), 1 mM nonessential amino acids (Invitogen), 0.1 mM 2-mercaptoethanol (Sigma, St. Lois, USA), and 4 ng/ml basic fibroblast growth factor (Invitrogen). Cells were passaged every 5-7days by mechanical transfer. For the formation of embryoid bodies, colonies of the ESCs were detached by treatment of 2 mg/ml type IV collagenase (Invitrogen) for 30 min and grown as floating spheres on a bacterial culture dish (Kim DS et al. 2010).

extract_protocol: RNA was extracted with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The embryoid bodies were incubated for 1 or 2 weeks in ESC medium without bFGF. The culture medium was changed every 2 days.

value: embryoid bodies (EBs)

tag: incubation time

value: 2 weeks


title: Ssa_Diet 10_14d_replicate 5

source_name: Ssa_Diet 10_14d_replicate 5


title: EB_2Wk_rep3


title: EB_2Wk_rep2


title: CTC_119213_12CTC


title: CTC_120334_20CTC


title: CTC_119202_20CTC


title: Pseudomonas syringae pv. phaseolicola NPS3121 at low temperature  (Technical Replicate 1)


title: CTC_119095_10CTC


title: Ssa_Diet 10_14d_replicate 2

source_name: Ssa_Diet 10_14d_replicate 2


title: Ssa_Diet 10_14d_replicate 3

source_name: Ssa_Diet 10_14d_replicate 3


title: Pseudomonas syringae pv. phaseolicola NPS3121 at low temperature (Biological Replicate 1)

scan_protocol: Slides were scanned with an Axon GenePix 4000 B scanner at a resolution of 10 µm adjusting the laser and gain parameters to obtain similar levels of fluorescence intensity in both channels


title: EB_1Wk_rep4

description: EBs (embryoid bodies) incubated for 1 week in ESC medium.

source_name: Embryoid bodies, 1 week

value: 1 week


title: HuH7_control_medium_4h_rep1


title: Urban Fijian_FJ130187_6904

city: Atlanta

first: artika

middle: Praveeta

last: Nath

email: anath6@gatech.edu, natar210@gmail.com

state: Georgia

address: Boggs Building, 770 State Street Georgia Institute of Technology

department: Biology

institute: Georgia Institute of Technology

description: Sample name: FJ130187_6904

hyb_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization Assay protocol

scan_protocol: Illumina's BeadArray protocol and GenomeStudio (Gene expression Module)

data_processing:
Raw data (namely average bead intensity for each probe from the Illumina Bead Studio) was log2 transformed and then mean-centered across samples and probes standardized to Z score using JMP Genomics 6.0 (SAS Institute, Cary NC).
The 14,343 probes that we routinely find expressed in peripheral blood were retained for analysis, with expression of other transcripts deemed statistically indistinguishable from background.

source_name: Peripheral blood leukocytes

label_protocol: cDNA and cRNA labeling and amplification were all performed using Illumina Whole-Genome Gene Expression Direct Hybridization Assay and the Illumina TotalPrep-96 RNA Amplification Kit. RNA was labeled with Cy3-SA.

extract_protocol: Total RNA was extracted from leukocyte samples using Ambion's Leukolocks kit. Quality control was performed using Agilent's Bioanalyzer.

tag: individual

value: Fijian

tag: environment

value: Urban

tag: gender

value: Male

tag: age

tag: height(cm)

tag: weight (kg)

tag: bmi

value: Peripheral blood

value: leukocytes

tag: rna integrity number


title: EB_2Wk_rep1

tag: cell line

tag: cell type


title: EB_1Wk_rep3


title: Ssa_Diet 10_14d_replicate 1

source_name: Ssa_Diet 10_14d_replicate 1

value: Shrimp hydrolysate (C)

tag: tissue


title: Urban Indian_FJ130188_7637

description: Sample name: FJ130188_7637

value: Indian


title: Ssa_Diet 10_14d_replicate 4

source_name: Ssa_Diet 10_14d_replicate 4

value: Liver


title: Urban Indian_FJ130186_2217

description: Sample name: FJ130186_2217

value: Female


title: CTC_118882_20CTC

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient

tag: assayed molecule

value: Whole genome amplified genomic DNA

source_name: Promega reference Male genomic DNA

value: Whole genome amplified reference male genomic DNA


title: Urban Indian_FJ130185_9727

description: Sample name: FJ130185_9727


title: EB_1Wk_rep2


title: Ssa_Diet 9_56d_replicate 5

source_name: Ssa_Diet 9_56d_replicate 5

value: Shrimp hydrolysate (B)


title: Ssa_Diet 9_56d_replicate 6

source_name: Ssa_Diet 9_56d_replicate 6


title: ES_rep4

description: Undifferentiated SNUhES3 cells.

source_name: Undifferentiated SNUhES3 cells

value: undifferentiated embryonic stem cells (ESCs)


title: EB_1Wk_rep1

value: embryoid bodies (EBs)


title: CTC_118474_20CTC

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient


title: Ssa_Diet 9_56d_replicate 3

source_name: Ssa_Diet 9_56d_replicate 3


title: CTC_118177_20CT


title: Ssa_Diet 9_56d_replicate 4

source_name: Ssa_Diet 9_56d_replicate 4


title: Urban Indian_FJ130184_4882

description: Sample name: FJ130184_4882


title: CTC_117938_20CTC


title: CTC_117908_7CTC


title: CTC_117932_20CTC


title: Ssa_Diet 9_56d_replicate 1

source_name: Ssa_Diet 9_56d_replicate 1


title: ES_rep1

description: Undifferentiated SNUhES3 cells.


title: CTC_117719_20CTC


title: Urban Indian_FJ130180_9995

description: Sample name: FJ130180_9995


title: Ssa_Diet 9_56d_replicate 2

source_name: Ssa_Diet 9_56d_replicate 2


title: CTC_117673_20CTC


title: Urban Indian_FJ130181_6571

description: Sample name: FJ130181_6571


title: Urban Fijian_FJ130182_4415

description: Sample name: FJ130182_4415


title: Urban Indian_FJ130183_4361

description: Sample name: FJ130183_4361


title: Ssa_Diet 9_14d_replicate 6

source_name: Ssa_Diet 9_14d_replicate 6


title: Veraison_sh_2

city: Stellenbosch

first: Daniel

last: Jacobson

address: Victoria Street

country: South Africa

institute: Stellenbosch University

hyb_protocol: Hybridization was performed by MoGene (St. Louis, MO), according to the instructions and recommendations of the supplier (NimbleGen).

scan_protocol: Scanning was performed by MoGene (St. Louis, MO), according to the instructions and recommendations of the supplier (NimbleGen).

data_processing: The raw data was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction

organism: Vitis vinifera

source_name: Berry tissue, Veraison, EL-34

label_protocol: Labeling was performed by MoGene (St. Louis, MO), according to the instructions and recommendations of the supplier (NimbleGen).

extract_protocol: RNA Extracted as in Reid et al., BMC Plant Biology 2006, 6:27 and cleaned with the use of an RNeasy Mini Kit column

tag: developmental stage

value: Veraison, EL-34


title: ES_rep2

description: Undifferentiated SNUhES3 cells.


title: Harvest_sh_1

source_name: Berry tissue, Ripe, EL-38

value: Ripe, EL-38


title: Ssa_Diet 9_14d_replicate 4

source_name: Ssa_Diet 9_14d_replicate 4

tag: diet


title: Urban Indian_FJ130177_2345

description: Sample name: FJ130177_2345


title: Urban Indian_FJ130179_7789

description: Sample name: FJ130179_7789


title: Veraison_sh_1


title: Veraison_sh_3


title: Ssa_Diet 9_14d_replicate 5

source_name: Ssa_Diet 9_14d_replicate 5

tag: time


title: T24_rep2

description: Replicate 2

tag: sensitivity to hedgehog

value: Sensitive


title: ES_rep3

description: Undifferentiated SNUhES3 cells.


title: Ssa_Diet 9_14d_replicate 3

source_name: Ssa_Diet 9_14d_replicate 3


title: Urban Fijian_FJ130175_6300

description: Sample name: FJ130175_6300

source_name: Peripheral blood leukocytes

value: Fijian

value: Urban


title: CTC_117568_20CTC


title: Urban Indian_FJ130176_8562

description: Sample name: FJ130176_8562

value: Peripheral blood


title: Ssa_Diet 9_14d_replicate 2

source_name: Ssa_Diet 9_14d_replicate 2


title: Green_sh_2

source_name: Berry tissue, Green, EL-31

value: Green, EL-31


title: CTC_117255_20CTC

source_name: Promega reference Male genomic DNA


title: CTC_117252_20CTC


title: CTC_117228_20CTC


title: Urban Indian_FJ130174_3016

description: Sample name: FJ130174_3016

value: Male

value: leukocytes


title: Urban Fijian_FJ130173_2368

description: Sample name: FJ130173_2368


title: Ssa_Diet 8_56d_replicate 6

source_name: Ssa_Diet 8_56d_replicate 6

value: Herring milt hydrolysate

value: Liver


title: Green_sh_1


title: Green_sh_3


title: Ssa_Diet 9_14d_replicate 1

source_name: Ssa_Diet 9_14d_replicate 1


title: Ssa_Diet 8_56d_replicate 5

source_name: Ssa_Diet 8_56d_replicate 5


title: CTC_116990_8CTC

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient


title: Urban Indian_FJ130172_5445

description: Sample name: FJ130172_5445

value: Indian


title: Ssa_Diet 8_56d_replicate 4

source_name: Ssa_Diet 8_56d_replicate 4


title: Ssa_Diet 8_56d_replicate 3

source_name: Ssa_Diet 8_56d_replicate 3


title: stimulated  vs stimulated  97_FTV_Low 4

city: Seattle

first: Ramsey

last: Saleem

state: Washington

address: 307 Westlake Ave N

institute: Seattle Biomedical Research

hyb_protocol: Labeled cRNA was hybridized to the Rhesus Macaque (V2) Gene Expression 4x44K Microarray (Agilent) in the appropriate combinations, including dye-flip and self versus self controls.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
After scanning the arrays, data was background subtracted and the probe signal normalized both within the array and between the arrays, using the limma package in Bioconductor.

organism: Cercocebus atys

source_name: DN T-cells

label_protocol: cRNA was synthesized from total RNA and Cy3/Cy5 labeled using the Agilent Low Input Quick Amp Labeling procedure, as per the manufacturer’s instructions.

growth_protocol: Pure population of double negative and CD4 T cells were isolated by a step-wise magnetic bead isolation (Miltenyi) using bead specific for non-human primate antigens. Briefly, we stained PBMC with CD4-Microbead to isolate CD4 cells and treated the flow-through with CD8-PE and CD16-PE followed by anti-PE Microbeads for CD8 and CD16 depletion. This CD4-CD8-CD16- flow-through was then positive selected for CD3+ cells with CD3-Biotin and anti-biotin Microbead to obtain, CD3+CD4-CD8- (double negative T cells). Purity was checked after each isolation and further experiments were carried out only with >98% pure populations. Cells were rested overnight prior to functional analyses.

extract_protocol: Cells were collected post-stimulation and immediately lysed in RLT buffer (Qiagen) for RNA extraction. RNA was isolated using RNeasy mini kit (Qiagen) and genomic DNA was removed on-column.

treatment_protocol: 1 million purified T cells were stimulated with anti-CD3 (3mg/ml) and anti-CD28 (1mg/ml) in 200ul of complete RPMI at 37oC for 4 hrs.

tag: cd4 status

value: Low

tag: treatment

value: Stimulated with CD3/CD28 antibodies

value: Double Negative (CD4-/CD8-) T-cells

tag: infection

value: SIV


title: Urban Fijian_FJ130171_6375

description: Sample name: FJ130171_6375

tag: individual

tag: environment

tag: gender

value: Female


title: Urban Indian_FJ130170_8076

description: Sample name: FJ130170_8076

tag: age

tag: height(cm)

tag: weight (kg)


title: unstimulated  vs unstimulated  97_FTV_Low 3

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

value: Unstimulated


title: CTC_116986_10CTC

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient

value: Whole genome amplified genomic DNA

value: Whole genome amplified reference male genomic DNA


title: CTC_116917_20CTC


title: Urban Fijian_FJ130169_0220

description: Sample name: FJ130169_0220

value: Fijian

value: Urban

tag: bmi

tag: rna integrity number


title: Urban Fijian_FJ130168_4170

description: Sample name: FJ130168_4170

tag: tissue

value: Peripheral blood

tag: cell type


title: CTC_116875_20CTC

tag: assayed molecule


title: Ssa_Diet 8_56d_replicate 2

source_name: Ssa_Diet 8_56d_replicate 2

tag: diet


title: Ssa_Diet 8_14d_replicate 6

source_name: Ssa_Diet 8_14d_replicate 6

tag: time


title: unstimulated  vs stimulated  97_FTV_Low 1


title: Rural Fijian_FJ130206_5715

description: Sample name: FJ130206_5715

value: Rural

value: Male


title: Urban Indian_FJ130167_4551

description: Sample name: FJ130167_4551

value: leukocytes


title: stimulated  vs stimulated  96_FBR_Low 4


title: unstimulated  vs unstimulated  96_FBR_Low 3


title: Ssa_Diet 8_14d_replicate 5

source_name: Ssa_Diet 8_14d_replicate 5

value: Herring milt hydrolysate

value: Liver


title: stimulated  vs unstimulated  97_FTV_Low 2

value: Low


title: stimulated  vs unstimulated  96_FBR_Low 2

value: Stimulated with CD3/CD28 antibodies


title: unstimulated  vs unstimulated  95_FKN_Normal 3

value: Normal

value: Double Negative (CD4-/CD8-) T-cells


title: CTC_116326_20CTC


title: CTC_116564_9CTC


title: Urban Fijian_FJ130202_0788

description: Sample name: FJ130202_0788

value: Female


title: CTC_116437_7CTC


title: Ssa_Diet 8_14d_replicate 4

source_name: Ssa_Diet 8_14d_replicate 4


title: Ssa_Diet 8_14d_replicate 3

source_name: Ssa_Diet 8_14d_replicate 3


title: Rural Fijian_FJ130204_4919

description: Sample name: FJ130204_4919


title: stimulated  vs unstimulated  95_FKN_Normal 2

value: SIV

value: Unstimulated


title: stimulated  vs stimulated  95_FKN_Normal 4


title: unstimulated  vs stimulated  96_FBR_Low 1


title: CTC_115015_8CTC

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient

value: Whole genome amplified genomic DNA


title: CTC_114319_16CTC

value: Whole genome amplified reference male genomic DNA


title: Rural Fijian_FJ130194_9954

description: Sample name: FJ130194_9954

value: Fijian


title: Ssa_Diet 8_14d_replicate 2

source_name: Ssa_Diet 8_14d_replicate 2


title: Rural Fijian_FJ130207_1544

description: Sample name: FJ130207_1544

source_name: Peripheral blood leukocytes

value: Peripheral blood


title: Urban Fijian_FJ130193_2942

description: Sample name: FJ130193_2942

value: Urban


title: Ssa_Diet 8_14d_replicate 1

source_name: Ssa_Diet 8_14d_replicate 1


title: Ssa_Diet 7_56d_replicate 6

source_name: Ssa_Diet 7_56d_replicate 6

value: Herring immature roe


title: CTC_115397_20CTC

source_name: Promega reference Male genomic DNA


title: CTC_112456_20CTC


title: Urban Fijian_FJ130195_8750

description: Sample name: FJ130195_8750

value: leukocytes


title: unstimulated  vs stimulated  73_FNV_Normal 4


title: stimulated  vs unstimulated  73_FNV_Normal 3


title: unstimulated  vs stimulated  95_FKN_Normal 1


title: Urban Fijian_FJ130190_6362

description: Sample name: FJ130190_6362


title: Ssa_Diet 7_56d_replicate 4

source_name: Ssa_Diet 7_56d_replicate 4


title: Urban Fijian_FJ130198_8538

description: Sample name: FJ130198_8538


title: stimulated  vs stimulated  73_FNV_Normal 2


title: CTC_110329_18CTC


title: Ssa_Diet 7_56d_replicate 3

source_name: Ssa_Diet 7_56d_replicate 3


title: Ssa_Diet 7_56d_replicate 5

source_name: Ssa_Diet 7_56d_replicate 5


title: Urban Indian_FJ130205_5982

description: Sample name: FJ130205_5982

value: Indian

value: Male


title: Ssa_Diet 7_56d_replicate 1

source_name: Ssa_Diet 7_56d_replicate 1

value: Liver


title: Ssa_Diet 7_56d_replicate 2

source_name: Ssa_Diet 7_56d_replicate 2


title: CTC_108_7CTC

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient


title: unstimulated  vs unstimulated  73_FNV_Normal 1

source_name: DN T-cells


title: CTC_108913_20CTC


title: CTC_104_18CTC


title: Rural Fijian_FJ130203_5330

description: Sample name: FJ130203_5330

value: Rural


title: Ssa_Diet 7_14d_replicate 5

source_name: Ssa_Diet 7_14d_replicate 5


title: Autonomous adenomas 75 vs adjacent tissues of the same patient [mRNA]

city: Anderlecht

first: sebastien

last: floor

state: Bruxelles

address: Route de Lennik 808

country: Belgium

institute: IRIBHM - ULB

description: Up-regulation of NIS in the Tumors compared to the adjacent tissues

hyb_protocol: hybridized for 16–18 h at 65°C

scan_protocol: the slides were scanned using a GenePix 4000B scanner (Axon, Sunnyvale, CA)

data_processing: A Normex + offset background correction and LOESS normalization were carried out by using functions of the LIMMA 3.4.5 package for the R 2.8.1 language. Data points were removed when intensity values for both dyes were below 200% of the background and absent calls were removed before subsequent statistical analyses.

label: Cy5, Cy3

source_name: autonomous adenomas

label_protocol: After RNA amplification (using Amino Allyl MessageAmp II aRNA amplification kit, Ambion, Austin, TX), 8 µg of aRNA were labelled, fragmented

extract_protocol: total RNA was extracted using a TRIzol Reagent kit (Invitrogen) followed by purification on RNeasy columns (Qiagen, Hilden, Germany)

treatment_protocol: tissues were immediately dissected, placed on ice, snap-frozen in liquid nitrogen, and stored at -80°C until processing

value: autonomous adenomas

tag: tumor number

value: AA 75

label: Cy3, Cy5

source_name: Adjacent tissues

value: Adjacent tissues


title: Autonomous adenomas 78 vs adjacent tissues of the same patient [mRNA]

value: AA 78


title: Ssa_Diet 7_14d_replicate 4

source_name: Ssa_Diet 7_14d_replicate 4


title: Urban Indian_FJ130200_6010

description: Sample name: FJ130200_6010

value: Female


title: Rural Fijian_FJ130191_1861

description: Sample name: FJ130191_1861


title: Rural Fijian_FJ130201_8564

description: Sample name: FJ130201_8564


title: Rural Fijian_FJ130197_5532

description: Sample name: FJ130197_5532


title: Urban Indian_FJ130192_5358

description: Sample name: FJ130192_5358


title: Autonomous adenomas 70 vs adjacent tissues of the same patient [mRNA]

value: AA 70


title: Lin+_KRNxG7_sorted

city: Saint Louis

first: Kwadwo

last: Oduro Jnr

address: 4940 Parkview Place, Room 1024

department: Pathology and Immunology

institute: Washington University School of Medicine

description: KRNxG7 Mature cells

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45degC on Mouse 430 2.0  Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix GeneChip Command Console 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: Mouse bone marrow Lin+ cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

growth_protocol: KSL cells or Lin+ cells were primary cells sorted from 6-7 week old arthritic (KRNxG7) or control (KRN) or control (B6xG7) mice. No ex-vivo growth of cells.

extract_protocol: RNA was extracted and purified using Arcturus Picopure RNA kit (Applied Biosystems) according to manufacturing instructions followed by linear amplification.

treatment_protocol: No ex-vivo treatment of sorted cells prior to RNA extraction. Sorted cells were stored at -80 deg celsius.

tag: strain

tag: genotype/variation

value: KRNxG7 (KRN mice crossed with G7 mice)

tag: disease state

value: arthritic

value: male + female

value: 6-7 weeks old

value: Lin+ cells


title: Ssa_Diet 7_14d_replicate 6

source_name: Ssa_Diet 7_14d_replicate 6

value: Herring immature roe


title: Ssa_Diet 7_14d_replicate 3

source_name: Ssa_Diet 7_14d_replicate 3


title: Autonomous adenomas 68 vs adjacent tissues of the same patient [mRNA]

value: AA 68


title: Autonomous adenomas 71 vs adjacent tissues of the same patient [mRNA]

value: AA 71


title: CTC_117535_6CTC

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient

value: Whole genome amplified genomic DNA

value: Whole genome amplified reference male genomic DNA


title: Autonomous adenomas 67 vs adjacent tissues of the same patient [mRNA]

value: autonomous adenomas

value: AA 67


title: Autonomous adenomas 61 vs adjacent tissues of the same patient [mRNA]

value: AA 61

value: Adjacent tissues


title: Urban Fijian_FJ130199_7900

description: Sample name: FJ130199_7900

source_name: Peripheral blood leukocytes

tag: individual

value: Fijian

value: Urban

value: Male

value: Peripheral blood

value: leukocytes


title: Lin+_KRN_sorted

description: KRN Mature cells

value: KRN (KRN TCR transgenic mice on a C57BL/6 background)

value: control

value: male + female

value: 6-7 weeks old


title: Ssa_Diet 7_14d_replicate 2

source_name: Ssa_Diet 7_14d_replicate 2

value: Herring immature roe

value: Liver


title: Lin+_B6xG7_sorted

description: B6xG7 Mature cells

value: B6xG7 (F1 of C57BL/6 mice crossed with G7 mice)

value: Lin+ cells


title: Ssa_Diet 7_14d_replicate 1

source_name: Ssa_Diet 7_14d_replicate 1


title: 150 minutes after Notch activation vs unactivated pool trial 4

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

institute: University  of Cambridge

description: 150' Notch activation trial 4 - dye swap

hyb_protocol: Co-hybridisation of sample vs reference control to long oligonucleotides microarrays (Flychip FL003; GEO platform accession GPL8244) was performed for 16 hours at 51°C using a GeneTac hybridisation station (Digilab Genomic Solutions Inc). Post hybridisation washes were performed according to the slide manufacturer’s recommendation.  Detailed protocols for array spotting, labelling, hybridisation and washes are available at http://www.flychip.org.uk/protocols/.

scan_protocol: Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/)

data_processing: Spot finding and quantitation via the Dapple package. The R package limma (SMYTH and SPEED 2003) was used to normalize the arrays. For each array, the background intensity level of the array image was first adjusted before loess normalization was applied to the MA values of the array. The intensities of the two channels of all 72 arrays (4 replicates at 18 time points) were then quantile normalized, such that the intensities all had the same empirical distribution. Missing values arise because genes are not expressed or there is poor quality on the array.

organism: Drosophila melanogaster

source_name: 150' after Notch activation - trial 4

label_protocol: 45 µg of sample or reference pool RNA was mixed with 1.5 µM anchored oligo(dT)23 (Sigma) and incubated at 65°C for 10 minutes. Reverse transcription was performed in the presence of 1nmol fluorescently labelled Cy3- or Cy5-dCTP (GE Healthcare) and 20U RNAsin (Promega) with 400U SuperScript III (Life Technologies) at 46°C for 2 hours. The product was purified using Sephadex G50 columns (GE Healthcare). Samples from trials #1 and #3 were labelled with Cy5 and trails #2 and #4 as dye-swap with Cy3.

growth_protocol: DmD8 cells were cultured in Schneiders medium (Invitrogen) supplemented with 10% FBS (Sigma), 5ug/ml insulin (Sigma) and 5% penicillin / streptomycin (Sigma) according to standard protocols.

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 150 minutes before washing out EDTA using normal culture media.

tag: cell line

value: 150 minutes after a 5 minute activation with EDTA

tag: time trial

source_name: reference pool - trial 4

extract_protocol: RNA was extracted from cells by removing media and incubating cells in TRI-reagent (Ambion) for 5 minutes. RNA was then purified by extracting with chloroform and precipitating with isopropanol before resuspension in DEPC treated water. DNA was removed by treating with DNase (DNA-free kit - Ambion). For each trial 50 µg of the untreated RNA sample of each time point was pooled to create a trial specific reference sample.

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. For control samples, media was replaced with fresh media to mimic the addition and removal of EDTA in corresponding experimental samples.

value: pool of unactivated cells from 0-150 minutes


title: KSL cells_KRN_sorted

description: KRN KSL

source_name: Mouse bone marrow KSL cells

tag: gender

tag: age

value: KSL cells


title: Rural Fijian_FJ130208_4056

description: Sample name: FJ130208_4056

tag: environment

value: Rural

tag: height(cm)

tag: weight (kg)


title: KSL cells_KRNxG7_sorted

description: KRNxG7 KSL

value: KRNxG7 (KRN mice crossed with G7 mice)

value: arthritic


title: Rural Fijian_FJ130196_7404

description: Sample name: FJ130196_7404

value: Fijian

value: Male

tag: bmi

tag: tissue

tag: rna integrity number


title: Ssa_Diet 8_56d_replicate 1

source_name: Ssa_Diet 8_56d_replicate 1

tag: diet

value: Herring milt hydrolysate


title: Ssa_Diet 6_56d_replicate 4

source_name: Ssa_Diet 6_56d_replicate 4

value: Sea cucumber internal organs

tag: time


title: Ssa_Diet 6_56d_replicate 5

source_name: Ssa_Diet 6_56d_replicate 5


title: Urban Fijian_FJ130189_9700

description: Sample name: FJ130189_9700

value: Urban

value: Peripheral blood

tag: cell type

value: leukocytes


title: Ssa_Diet 6_56d_replicate 6

source_name: Ssa_Diet 6_56d_replicate 6


title: control1 [CW2011060316]

city: Boston

first: Christopher

middle: A

last: Walsh

state: MA

address: 3 Blackfan Circle

department: Genetics

institute: Children's Hospital Boston

description:
Gene expression data from cells that show a decrease in ZNF335
long term

hyb_protocol: hybridized at 45C for 16hours according to Genechip 3 IVT Express Kit User Manual

scan_protocol: Affymetrix Genechip scanner 3000 to scan the arrays

data_processing: D chip analysis

source_name: control knockdown in mouse neurons from E14.5 harvested at P0

label_protocol: labeling of RNA was done with biotinylated ribonucleotide according to Genechip 3 IVT Express Kit User Manual

extract_protocol: Qiagen total RNA kit

tag: developmental stage

tag: strain

tag: time point

value: long term (5 days post knockdown)


title: Chip-28 Para Wk0 R1blue & RD+Vern R4red

city: Fargo

first: Munevver

last: Dogramaci

state: ND

address: 1605 Albrecht Blvd N

institute: USDA-ARS

scan_protocol: Microarray hybridization was visualized using a GenePix 4000B scanner and probe intensities and background were quantified using GenePix 6.0 software (Molecular Devices, Sunnyvale, California, USA).

data_processing: A quality control value of "1" was assigned to all probes that had intensity values greater than 2 times the standard deviation over average of the negative control and empty probe intensities (after deleting 1% of the most intense negative/empty probe values). Intensity values of control spots (a total of 1455 spots including 3X SSC, blanks, and mouse) from MA chips were removed before bioinformatics. In this submission, the original "GPR" files include information for the control spots, while the Sample data tables include information only for the spots that were used for data analyses (a total of: 23937). Raw signal intensities of all DNA-containing spots were up-loaded into the GeneMaths XT 5.1 microarray data analysis program (Applied Maths Inc., Austin, TX, USA) for normalization following the "Layer/Normalization/Arrays" path with default settings (Offset: Average; Scaling: Standard deviation), and for statistical analysis and clustering of the dataset. Hybridization intensities were log2 transformed, and arrays were centered and normalized against each other; technical replicates within each biological replicate were averaged.

organism: Euphorbia esula

source_name: Paradormant crown buds

label_protocol: For microarray hybridizations, labeled cDNAs were prepared from 30 µg of total RNA using the Alexa Fluor cDNA labeling kit (Invitrogen, Carlsbad, CA, USA) according to manufacturer's protocols. Labeled cDNAs were hybridized to a custom made 23K element microarray that contained 19,808 unigenes from a leafy spurge EST database (Anderson et al. 2007) and an additional 4,129 unigenes from a cassava EST database (Lokko et al. 2007). Comparison of gene expression between samples was accomplished using a rolling circle dye swap hybridization scheme (Churchill 2002) to provide every biological replicate with technical replicates. In this experiment, each of the four biological replicates included two technical replicates.

growth_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype 1984-ND001 and maintained in a greenhouse as described by Anderson and Davis (2004). Shoot cuttings were grown in No. 1 Ray Leach Cone-tainers (Stuewe and Sons Inc. Corvallis, OR, USA) in the greenhouse for three months prior to application of experimental treatments. The greenhouse was set at 25°C with a 16 h:8 h day:night photoperiod. Average daily light fluencies were approximately 350 μmol m-2 s-1 and 400 W high-pressure sodium lamps were used as to extend the day-length. Each treatment was replicated four times, and thirty plants were used per biological replication. Prior to the start of each experiment, plants were randomly chosen from the greenhouse and acclimated in a growth chamber (PGR15 Model of Conviron, Winnipeg, Canada) for one week at 27°C, 16 h:8 h day:night photoperiod. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation.

extract_protocol: At the end of each treatment, crown bud samples were collected, flash froze in liquid N2, and stored at -80°C until RNA extraction. Crown bud samples were ground to a fine powder in liquid N2, and RNA was extracted from approximately one gram of tissue according to the pine tree RNA extraction protocol (Chang et al. 1993). RNA quality and quantity was confirmed by spectrophotometry and agarose gel electrophoresis.

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents paradormant crown buds (Para-0 week) used as controls.

tag: species

value: Leafy spurge

value: crown buds

tag: treatment

value: controls

source_name: Paradormant crown buds exposed to ramp down in temperature under constant photoperiod for 12 weeks, then vernalized

treatment_protocol:
We previously established conditions for induction and release of dormancy phases under controlled environments (Doğramacı et al. 2010, 2011; Foley et al. 2009). To induce endodormancy, paradormant plants were subjected to a ramp-down in temperature (27°C → 10°C) and photoperiod (16 h → 8 h light), i.e., RDtp, for 12 weeks. In this study, to distinguish the individual effects of temperature and photoperiod on molecular networks involved in endodormancy induction, we compared three-month old paradormant plants subjected to a ramp-down in temperature (27°C → 10°C) under constant photoperiod (16 h light) for 12 weeks (i.e., RDt) to RDtp plants. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation. Samples were collected after 3, 6, 9, 12 week during RDt treatment. Additionally, a set of paradormant plants were kept under constant temperature and light (27°C, 16 h light) as a control (Para-0 week); we also maintained a set of paradormant plants, as a second control, in the greenhouse and collected samples at the end of 12 weeks of RDt treatment (Para-12 week).
This sample represents crown buds collected from plants exposed to ramp down in temperature for 12 weeks under constant light, and then exposed to vernalizing cold treatment (5-7°C for 8 weeks).

value: 12 weeks, then vernalized


title: SiRNA knockdown 3 [CW2011060315]

description:
Gene expression data from control
long term

source_name: ZNF335 knockdown of cells at E14.5 harvested at P0


title: Ssa_Diet 6_56d_replicate 3

source_name: Ssa_Diet 6_56d_replicate 3

value: Liver


title: 150 minutes after Notch activation vs unactivated pool trial 2

description: 150' Notch activation trial 2 - dye swap

source_name: 150' after Notch activation - trial 2

extract_protocol: RNA was extracted from cells by removing media and incubating cells in TRI-reagent (Ambion) for 5 minutes. RNA was then purified by extracting with chloroform and precipitating with isopropanol before resuspension in DEPC treated water. DNA was removed by treating with DNase (DNA-free kit - Ambion).

tag: cell line

value: 150 minutes after a 5 minute activation with EDTA

tag: time trial

source_name: reference pool - trial 2

value: pool of unactivated cells from 0-150 minutes


title: MDA231_Astro-2_Mm

source_name: MDA-MB-231, astrocytes

tag: protocol

value: co-culture of MDA-MB-231 and astrocyte cells


title: 150 minutes after Notch activation vs unactivated pool trial 1

description: 150' Notch activation trial 1

source_name: reference pool - trial 1

source_name: 150' after Notch activation - trial 1

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 0 minutes before washing out EDTA using normal culture media.


title: Ssa_Diet 6_56d_replicate 1

source_name: Ssa_Diet 6_56d_replicate 1


title: 150 minutes after Notch activation vs unactivated pool trial 3

description: 150' Notch activation trial 3

source_name: reference pool - trial 3

source_name: 150' after Notch activation - trial 3


title: control3 [CW2011060318]


title: 120 minutes after Notch activation vs unactivated pool trial 4

description: 120' Notch activation trial 4 - dye swap

source_name: 120' after Notch activation - trial 4

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 120 minutes before washing out EDTA using normal culture media.

value: 120 minutes after a 5 minute activation with EDTA

source_name: reference pool - trial 4


title: SiRNA knockdown 2 [CW2011060314]


title: Ssa_Diet 6_56d_replicate 2

source_name: Ssa_Diet 6_56d_replicate 2


title: SiRNA knockdown 1 [CW2011060313]


title: KSL cells_B6xG7_sorted

description: B6xG7 KSL

source_name: Mouse bone marrow KSL cells

tag: genotype/variation

value: B6xG7 (F1 of C57BL/6 mice crossed with G7 mice)

tag: disease state

value: control

tag: gender

value: male + female

tag: age

value: 6-7 weeks old

value: KSL cells