title: A098-PRE-Low dose

description: SAMPLE 213

source_name: PRE-Low dose

value: pre-treatment


title: 20070628_A.4.RhoGAP1A RNAi 05/12/2007

status: Public on Dec 31 2012

type: RNA

city: Cambridge

first: Michael

last: Baym

state: MA

address: MIT 32-G572 / 32 Vassar St.

department: Mathematics

country: USA

institute: MIT

description:
20070628_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

hyb_protocol: The aRNA mixtures were fragmented in a solution of 40 mM Tris-Acetate pH8.1, 100 mM KOAc, 30 mM MgOAc) at 95°C for 20 minutes, then placed on ice. Hybridization to Combimatrix CustomArrayä microarrays was performed as described by the manufacturer at 45°C for 18 hours under gentle rotation in a Fisher Biotech Hybridization Incubator under gentle rotation. Following hybridization and washing, arrays were blocked in 2XPBS, 0.1% Tween-20, 1% Acetylated BSA (Sigma) for 15 minutes at room temperature (RT), and subsequently incubated with Streptavidin-Alexa Fluor 647 (Molecular Probes) at final concentration of 1 μg/ml in the blocking solution for 30 minutes at RT while protected from light. Two subsequent washing steps were then performed at RT for 5 minutes using 2X PBS, 0.1% Tween-20 followed by 2 rounds of washing using 2X PBS with no detergent.

scan_protocol: Arrays were scanned using the Axon Genepix 4000B scanner.

data_processing: Median expression was extracted, spatial artifacts were removed by iterative surface-fit, features were averaged by probe sequence, and Loess-normalized with span=0.4.

label: biotin

molecule: total RNA

organism: Drosophila melanogaster

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGAP1A RNAi

label_protocol: The Ambion MegaScript Kit was used to produce biotin-labeled antisense RNA (aRNA) by combining Biotin-11-UTP (PerkinElmer) and Biotin-CTP (PerkinElmer) with unlabelled UTP and CTP in a molar ratio of 1:3. Biotin-labeled aRNA was purified using the Qiagen RNeasy kit.

growth_protocol: Drosophila S2R+ cells were cultured in Schneider’s media (Sigma), supplemented with 10% Fetal Bovine Serum (SAFC Biosciences), and Penicillin-Streptomycin (Gibco).

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen) as directed by the manufacturer. Double-stranded cDNA incorporating a T7 RNA Polymerase promoter site was prepared from total RNA using the Roche Applied Sciences Microarray cDNA Synthesis Kit and purified using the Qiagen QIAquick purification kit.

treatment_protocol: RNAi experiments were performed by transfecting S2R+ cells with specific dsRNAs in combination with actin-GAL4 and UAS-GFP plasmids. Alternatively, cells were transfected with actin-GAL4 and UAS-GFP plasmids in addition to plasmids encoding activated forms of Rho-family GTPases, RhoGEFs, or RhoGAPs. All transfections were performed using Effectene Reagent (Qiagen). Following plasmid/RNAi transfection, cells were incubated for 5 days at room temperature. S2R+ cells were transfected in batches of 4-6 over the course of several months.

tag: cell line

tag: cell line derivation

value: late stage embryos


title: 20070621_A.4.RhoGAP1A RNAi 05/12/2007

description:
20070621_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: A097-POST-High dose

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 211

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

organism: Homo sapiens

source_name: POST-High dose

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

tag: sample collection time

value: post-treatment

tag: tissue

value: blood

tag: patient id


title: MEF_p53(-/-)_transformed_rep2

city: Singapore

first: Kanaga

last: Sabapathy

state: Singapore

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Centre Singapore

description: 193P 2312-6ER.CEL

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials as per manufactorere's instructions

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Partek software (v.6.5). Quantile normalization uisng GC-RMS method, gene level expression were summarized from the quantile normalized data.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

organism: Mus musculus

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Nalgene)

extract_protocol: Early passage primary MEFs and the coresponding E1A/Ras transformed clones were used.  Total RNA was extracted from all samples using Trizol and further purified by RNeasy RNA extraction kit (Qiagen).  cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Nalgene).

tag: strain background

value: C57BL6/129 hybrid

tag: genotype/variation

tag: cell type

value: Mouse Embryonic Fibroblasts

tag: transformed with

tag: state

value: transformed


title: A096-POST-Placebo

description: SAMPLE 209

source_name: POST-Placebo

value: placebo


title: MEF_p53(246/-)_primary_rep1

description: 193P 2336-4.CEL

value: primary


title: 20070621_A.3.RhoBTB (GTPase) RNAi 05/12/2007

description:
20070621_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoBTB RNAi


title: 20070621_A.2.RhoL (GTPase) RNAi 05/12/2007

description:
20070621_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoL RNAi


title: MEF_p53(-/-)_transformed_rep3

description: 193P 2312-10ER.CEL


title: 20070411_B.4.Rac1 RNAi 04/11/2007

description:
20070411_B_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and Rac1 RNAi


title: A096-PRE-Placebo

description: SAMPLE 208

source_name: PRE-Placebo


title: MEF_p53(-/-)_primary_rep3

description: 193P 2312-10.CEL


title: MEF_p53(-/-)_transformed_rep1

description: 193P 2312-2ER.CEL


title: A094-FU-Low dose

description: SAMPLE 207

source_name: FU-Low dose

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

value: follow up; 1 month after illness-onset


title: 20070411_B.1.GFP April 11 2007

description:
20070411_B_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP


title: 20070411_B.3.Rho1 RNAi 04/11/2007

description:
20070411_B_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and Rho1 RNAi


title: 20070411_B.2.Rho1 RNAi 04/11/2007

description:
20070411_B_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20070411_A.2.Rac1 RNAi 04/11/2007

description:
20070411_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20070411_A.4.Rho1 RNAi 04/11/2007

description:
20070411_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20070621_A.1.GFP May 12 2007

description:
20070621_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: A094-PRE-Low dose

description: SAMPLE 205


title: A094-POST-Low dose

description: SAMPLE 206

source_name: POST-Low dose


title: 20061218_B.4.Cdc42 RNAi G8 10/12/06

description:
20061218_B_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and Cdc42 RNAi


title: 20061218_B.3.Cdc42 RNAi D21 10/12/06

description:
20061218_B_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: Bcells_tumor_p53(246/-)_rep6

source_name: B cells_tumor_p53(246/-)

extract_protocol: B cells were isolated by magnetic immuno-depletion method (MACS) and genotyped.  Total RNA was extracted from all samples using Trizol and further purified by RNeasy RNA extraction kit (Qiagen).  cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Nalgene).

tag: genotype of the cells

tag: tissue origin

value: lymph nodes

value: Myc-induced B lymphoma cells

tag: b cell type

value: tumorous


title: MEF_p53(-/-)_primary_rep2

description: 193P 2312-6.CEL


title: MEF_p53(-/-)_primary_rep1

description: 193P 2312-2.CEL


title: Bcells_tumor_p53(-/-)_rep5

source_name: B cells_tumor_p53(-/-)


title: A093-FU-Low dose

description: SAMPLE 204


title: 20070411_A.3.Rac1 RNAi 04/11/2007

description:
20070411_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20061218_B.1.***GFP December 10

description:
20061218_B_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: Bcells_tumor_p53(-/-)_rep6


title: A093-PRE-Low dose

description: SAMPLE 202


title: 20070411_A.1.GFP April 11 2007

description:
20070411_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: A092-FU-High dose

description: SAMPLE 201

source_name: FU-High dose


title: A093-POST-Low dose

description: SAMPLE 203


title: A092-PRE-High dose

description: SAMPLE 199

source_name: PRE-High dose


title: Bcells_tumor_p53(-/-)_rep4


title: 20061218_A.1.GFP December 6

description:
20061218_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: A090-FU-High dose

description: SAMPLE 198


title: 20061218_A.3.Cdc42 RNAi  G8_B 06/12/06

description:
20061218_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20061218_A.2.Cdc42 RNAi  G8_A 06/12/06

description:
20061218_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20060622_B.3.RhoGEF4 RNAi

description:
20060622_B_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGEF4 RNAi


title: Bcells_tumor_p53(246/-)_rep4


title: 20060622_B.4.trio (RhoGEF) RNAi

description:
20060622_B_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and trio RNAi


title: 20061218_B.2.Rho1 RNAi  ****06/12/06

description:
20061218_B_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: A092-POST-High dose

description: SAMPLE 200

source_name: POST-High dose


title: Bcells_tumor_p53(246/-)_rep3


title: Bcells_tumor_p53(246/-)_rep5


title: 20061218_A.4.Cdc42 RNAi  D21_A 06/12/06

description:
20061218_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: Bcells_tumor_p53(-/-)_rep2


title: A090-POST-High dose

description: SAMPLE 197


title: A089-POST-Placebo

description: SAMPLE 195

source_name: POST-Placebo


title: 20060622_B.2.RhoGAP19D RNAi

description:
20060622_B_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGAP19D RNAi


title: 20060622_A.4.pbl (RhoGEF) RNAi

description:
20060622_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and pbl RNAi


title: 20060622_B.1.GFP June 10

description:
20060622_B_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20060621_A.4.CG15611 (RhoGEF)

description:
20060621_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and CG15611 RNAi


title: 20060622_A.1.GFP June 10

description:
20060622_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20060622_A.3.p190RhoGAP RNAi

description:
20060622_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and p190RhoGAP RNAi


title: 20060622_A.2.CG30115 (RhoGEF) RNAi

description:
20060622_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and CG30115 RNAi


title: 20060621_A.1.GFP June 10

description:
20060621_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP


title: 20060621_A.2.Cdep (RhoGEF) RNAi

description:
20060621_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and Cdep RNAi


title: Bcells_tumor_p53(246/-)_rep2


title: 20060528_B.4.Rho F30L overexpress

description:
20060528_B_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding RhoF30L (constitutively active)


title: Bcells_tumor_p53(-/-)_rep3


title: Bcells_normal_p53(246/-)_rep2

description: 193P 2581.CEL

source_name: B cells_normal_p53(246/-)

value: spleen

value: B cells

value: normal


title: A088-FU-Placebo

description: SAMPLE 193

source_name: FU-Placebo

value: Vietnamese dengue patients


title: 20060528_B.3.Rac F28L overexpress

description:
20060528_B_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding RacF28L (constitutively active)

value: late stage embryos


title: A090-PRE-High dose

description: SAMPLE 196

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

value: pre-treatment


title: Bcells_tumor_p53(-/-)_rep1

source_name: B cells_tumor_p53(-/-)

value: C57BL6/129 hybrid


title: A089-PRE-Placebo

description: SAMPLE 194

source_name: PRE-Placebo

value: blood


title: 20060528_B.1.GFP May 26

description:
20060528_B_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20060528_B.2.CG30456 (RhoGEF) RNAi

description:
20060528_B_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and 30456 RNAi


title: Bcells_normal_p53(-/-)_rep2

description: 193P 2571.CEL

source_name: B cells_normal_p53(-/-)


title: 20060528_A.4.CG10188 (RhoGEF) RNAi

description:
20060528_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and CG10188 RNAi


title: Bcells_tumor_p53(246/-)_rep1

source_name: B cells_tumor_p53(246/-)


title: 20060621_A.3.CG14045 (RhoGEF) RNAi

description:
20060621_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and CG14045 RNAi


title: 20060528_A.1.GFP May 26

description:
20060528_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20060528_A.3.RhoGAP100F RNAi

description:
20060528_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGAP100F RNAi


title: 20060528_A.2.RhoGAP93B RNAi

description:
20060528_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGAP93B RNAi


title: Bcells_normal_p53(246/-)_rep1

description: 193P 2319.CEL


title: A088-POST-Placebo

description: SAMPLE 192

source_name: POST-Placebo

value: post-treatment


title: thymus_p53(-/-)mdm2(-/-)_rep2

data_processing:
Data were processed using Partek software (v.6.5). Quantile normalization using GC-RMS method, gene level expression were summarized from the quantile normalized data.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: p53(-/-)mdm2(-/-)_normal thymus

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: All samples were snap frozen in liquid N2. Total RNA was extracted from all samples using Trizol and further purified by RNeasy RNA extraction kit (Qiagen). Samples were then treated with the RiobMinus rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

tag: genotype

tag: age

value: 4-5 weeks

value: Thymus


title: Bcells_normal_p53(-/-)_rep1

description: 193P 2271.CEL


title: A141-FU-High dose

description: SAMPLE 189

source_name: FU-High dose


title: 20060526_B.4.RhoL (GTPase) RNAi

description:
20060526_B_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and MTL RNAi

tag: cell line


title: A088-PRE-Placebo

description: SAMPLE 191

value: placebo


title: A142-PRE-Low dose

description: SAMPLE 190

source_name: PRE-Low dose

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


title: A141-PRE-High dose

description: SAMPLE 187

source_name: PRE-High dose


title: A141-POST-High dose

description: SAMPLE 188

source_name: POST-High dose


title: 20060526_B.3.RhoBTB (GTPase) RNAi

description:
20060526_B_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoBTB RNAi

tag: cell line derivation


title: 20060526_B.2.MTL (GTPase) RNAi

description:
20060526_B_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: thymus_p53(-/-)mdm2(-/-)_rep1


title: 20060526_A.4.RhoGEF64C RNAi

description:
20060526_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGAP64C RNAi


title: 20060526_B.1.GFP May 26

description:
20060526_B_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP


title: thymus_p53(246/246)mdm2(+/+)_rep3


title: 20060526_A.1.GFP May 26

description:
20060526_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20060613_A.4.CG10188 (RhoGEF) RNAi

description:
20060613_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20060526_A.3.RhoGAP54D RNAi

description:
20060526_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGAP54D RNAi


title: 20060526_A.2.RhoGAP50C RNAi

description:
20060526_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGAP50C RNAi


title: thymus_p53(246/246)mdm2(+/+)_rep1


title: thymus_p53(246/246)mdm2(+/+)_rep2


title: thymus_p53(-/-)mdm2(+/+)_rep3

source_name: p53(-/-)mdm2(+/+)_normal thymus


title: 20060613_A.1.GFP May 26

description:
20060613_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: thymus_p53(-/-)mdm2(+/+)_rep2


title: A140-POST-Placebo

description: SAMPLE 185

tag: disease status


title: 20060613_A.3.RhoGAP100F RNAi

description:
20060613_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: A140-PRE-Placebo

description: SAMPLE 184

source_name: PRE-Placebo

tag: treated with


title: A140-FU-Placebo

description: SAMPLE 186

source_name: FU-Placebo

tag: sample collection time

value: follow up; 1 month after illness-onset


title: A137-FU-High dose

description: SAMPLE 183

tag: tissue


title: A137-POST-High dose

description: SAMPLE 182

tag: patient id


title: 20060610_A.4.RhoGEF64C RNAi

description:
20060610_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20060610_A.2.RhoGAP50C RNAi

description:
20060610_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20060610_A.1.GFP May 26

description:
20060610_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20060610_A.3.RhoGAP54D RNAi

description:
20060610_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: thymus_p53(246/246)mdm2(-/-)_rep2

tag: strain background


title: A137-PRE-High dose

description: SAMPLE 181


title: 20060613_A.2.RhoGAP93B RNAi

description:
20060613_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: A136-FU-Low dose

description: SAMPLE 180

source_name: FU-Low dose


title: 20060501_A.4.sifFL.over

description:
20060501_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding full-length Sif


title: 20060424_A.3.oncoPbl.over

description:
20060424_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding N-terminally truncated Pbl


title: 20060424_A.4.RhoGEF64C.over

description:
20060424_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding N-terminally truncated RhoGEF64C


title: 20060501_A.1.S2Rp.GFPGAL4

description:
20060501_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20060501_A.3.oncoSif.over

description:
20060501_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding N-terminally truncated Sif (constitutively active)


title: 20060501_A.2.sif

description:
20060501_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and sif RNAi


title: thymus_p53(246/246)mdm2(-/-)_rep1


title: 20060424_A.2.RhoGAP1A.over

description:
20060424_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding RhoGAP1A


title: 20060424_A.1.S2Rp.GFPGAL4

description:
20060424_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: A136-POST-Low dose

description: SAMPLE 179

source_name: POST-Low dose


title: A136-PRE-Low dose

description: SAMPLE 178

source_name: PRE-Low dose


title: A133-FU-Low dose

description: SAMPLE 177


title: 20060422_B.4.RhoGAP84C RNAi

description:
20060422_B_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGAP84C RNAi


title: 20060422_B.1.S2Rp.GFPGAL4

description:
20060422_B_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20060422_B.3.RhoGAP71E RNAi

description:
20060422_B_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGAP71E RNAi


title: A133-POST-Low dose

description: SAMPLE 176


title: 20060422_A.4.RhoGAP16F

description:
20060422_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGA16F RNAi


title: 20060422_A.2.RhoGAP1A

description:
20060422_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGAP1A RNAi


title: 20060422_B.2.69C RNAi

description:
20060422_B_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and GAP69C (ArfGAP) RNAi


title: 20060422_A.3.RhoGAP5A

description:
20060422_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGAP5A RNAi


title: A132-FU-Low dose

description: SAMPLE 174


title: 20060422_A.1.S2Rp.GFPGAL4

description:
20060422_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP


title: RARE_KO_RA_8hr_3

city: New York

first: Kristian

middle: Bruun

last: Laursen

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

description:
SAMPLE 21
replicate 3

data_processing: The data were normalized using quantile normalisation with GeneSpring 12.5 (Agilent)

label_protocol: Total RNA from each sample was labeled using the Illumina Total Prep RNA Amplification kit (Ambion) and fragmented according to the manufacturer’s instructions.

extract_protocol: RNA was extracted with Trizol reagent in accordance with the prescribed protocol. Quality control was performed with RNA 6000 NanoAssay and a Bioanalyzer 2100 (Agilent).

value: ESC

tag: genotype/variation

tag: treatment

value: RA

tag: time


title: 20060401_B.4.sif

description:
20060401_B_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: RARE_KO_RA_24hr_2

description:
SAMPLE 23
replicate 2

tag: cell type


title: RARE_KO_RA_24hr_3

description:
SAMPLE 24
replicate 3


title: RARE_KO_RA_24hr_1

description:
SAMPLE 22
replicate 1


title: 20060401_B.2.RacV12.over

description:
20060401_B_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding RacV12 (constitutively active)


title: 20060401_B.3.RhoGAP92B

description:
20060401_B_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGAP92B RNAi


title: RARE_KO_RA_8hr_1

description:
SAMPLE 19
replicate 1


title: thymus_p53(-/-)mdm2(+/+)_rep1

source_name: p53(-/-)mdm2(+/+)_normal thymus


title: RARE_KO_RA_8hr_2

description:
SAMPLE 20
replicate 2


title: A132-POST-Low dose

description: SAMPLE 173


title: RARE_KO_RA_1hr_3

description:
SAMPLE 18
replicate 3


title: RARE_KO_RA_1hr_2

description:
SAMPLE 17
replicate 2


title: A133-PRE-Low dose

description: SAMPLE 175


title: A131-FU-Placebo

description: SAMPLE 171

source_name: FU-Placebo


title: A132-PRE-Low dose

description: SAMPLE 172


title: RARE_KO_RA_1hr_1

description:
SAMPLE 16
replicate 1


title: A131-POST-Placebo

description: SAMPLE 170

source_name: POST-Placebo


title: 20060401_B.1.RhoV14.over

description:
20060401_B_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding RhoV14 (constitutively active)


title: 20060401_A.4.RhoGEF3

description:
20060401_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding RhoGEF3


title: 20060401_A.3.oncoGEF3.over

description:
20060401_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding N-terminally truncated RhoGEF3


title: 20060401_A.1.S2Rp.GFPGAL4

description:
20060401_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 080306_A.4.Rac1Rho1

description:
080306_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and Rac1 + Rho1 RNAi


title: 080306_A.2.S2Rp.GFPGAL4

description:
080306_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 080306_A.3.Rac1

description:
080306_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and Rac1 RNAi


title: 270206_B.2.CG3799 RNAi

description:
270206_B_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and CG3799 RNAi


title: 270206_B.3.oncoSif.over

description:
270206_B_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding N-terminally truncated Sif (constitutively active)


title: 270206_B.4.Sif.over

description:
270206_B_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding full-length sif


title: 270206_B.1.S2Rp.GFPGAL4

description:
270206_B_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 080306_A.1.Rho1

description:
080306_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and Rho1 RNAi


title: A131-PRE-Placebo

description: SAMPLE 169

source_name: PRE-Placebo


title: RARE_KO_Ctrl_2

description:
SAMPLE 14
replicate 2

value: EtOH


title: A129-FU-High dose

description: SAMPLE 168

source_name: FU-High dose


title: A031-FU-Placebo

description: SAMPLE 164


title: 270206_A.4.CG3799.over

description:
270206_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding full-length CG3799


title: 270206_A.3.oncoCG3799.over

description:
270206_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding N-terminally truncated CG3799


title: 270206_A.2.CG3799

description:
270206_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: CCE_WT_RA_24hr_3

description:
SAMPLE 12
replicate 3


title: 270206_A.1.S2Rp.GFPGAL4

description:
270206_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP


title: RARE_KO_Ctrl_3

description:
SAMPLE 15
replicate 3


title: A035-FU-Low dose

description: SAMPLE 165

source_name: FU-Low dose


title: CCE_WT_RA_24hr_1

description:
SAMPLE 10
replicate 1


title: A031-POST-Placebo

description: SAMPLE 163


title: A036-PRE-High dose

description: SAMPLE 166

source_name: PRE-High dose


title: A129-POST-High dose

description: SAMPLE 167

source_name: POST-High dose


title: CCE_WT_RA_8hr_2

description:
SAMPLE 8
replicate 2


title: A027-PRE-Placebo

description: SAMPLE 161


title: A027-POST-Placebo

description: SAMPLE 162

source_name: POST-Placebo


title: Glycerol and Glucose anaerobic GG_anaerob_d2_2

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: Following fragmentation, 4 microg of cDNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: RMA summarization

organism: Mycobacterium tuberculosis

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA (Prokaryotic Expression Analysis, Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol

tag: carbon source

value: Glycerol and Glucose

value: anaerobic


title: A019-FU-High dose

description: SAMPLE 160

value: Vietnamese dengue patients


title: Glycerol and Glucose anaerobic GG_anaerob_d2_1


title: CCE_WT_RA_8hr_1

description:
SAMPLE 7
replicate 1


title: Glycerol and Glucose aerobic GG_aerob_d2_1

value: aerobic


title: CCE_WT_Ctrl_3

description:
SAMPLE 3
replicate 3


title: A012-PRE-High dose

description: SAMPLE 157

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


title: A005-POST-High dose

description: SAMPLE 155


title: CCE_WT_RA_1hr_3

description:
SAMPLE 6
replicate 3


title: A012-POST-High dose

description: SAMPLE 158


title: Glycerol and Glucose aerobic GG_aerob_d2_3


title: CCE_WT_RA_1hr_2

description:
SAMPLE 5
replicate 2


title: CCE_WT_Ctrl_1

description:
SAMPLE 1
replicate 1


title: PCI-35 S100A4 exp.2

city: Sendai

first: yuriko

last: saiki

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Molecular Pathology

country: Japan

institute: Tohoku University School of Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: Pancreatic cancer cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp labeling kit one color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were cultured with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Studio City, CA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: To overexpress S100A4 protein, the expression vector was transfected in pancreatic cancer cell lines using lipofectamine 2000 reagent (Invitrogen) according to the methods by the suppliers. An empty pcDNA6/Myc-His plasmid was also transfected as a control.

tag: expression vector


title: RARE_KO_Ctrl_1

description:
SAMPLE 13
replicate 1


title: Glycerol and Glucose aerobic GG_aerob_d2_2


title: PCI-35 S100A4 exp.1


title: CCE_WT_Ctrl_2

description:
SAMPLE 2
replicate 2


title: A036-FU-High dose

description: SAMPLE 154


title: A036-POST-High dose

description: SAMPLE 153


title: Rbpj;MyoD mutant rep7

city: Berlin

first: Dominique

last: Bröhl

state: Berlin

address: Robert-Rössle-Str. 10

department: Research Program Function and Dysfunction of the Nervous System

institute: Max-Delbrück-Center for Molecular Medicine

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio software (version 2010.1) with the Gene Expression Module (version 1.6.0).

source_name: embryonic back muscle progenitor cells

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion) and the RNeasy MinElute Cleanup Kit (Qiagen)

growth_protocol: Muscle progenitor cells were purified by FACS sorting from primary samples for transcription analysis.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with the RNeasy MinElute Cleanup Kit (Qiagen) in accordance with the prescribed protocol provided with the kit.

tag: strain

value: mixed C57BL/6, 129/Sv and 129/Ola.

value: skeletal muscle

value: progenitor cell

tag: developmental stage


title: A019-POST-High dose

description: SAMPLE 159

value: post-treatment

value: blood


title: Rbpj;MyoD mutant rep6

tag: genotype


title: PCI-43 S100A4 exp.2

tag: cell line


title: CCE_WT_RA_24hr_2

description:
SAMPLE 11
replicate 2


title: A009-PRE-High dose

description: SAMPLE 156

value: pre-treatment


title: A032-POST-Low dose

description: SAMPLE 152

source_name: POST-Low dose


title: PCI-43 S100A4 exp.1


title: CCE_WT_RA_1hr_1

description:
SAMPLE 4
replicate 1


title: Glycerol and Glucose anaerobic GG_anaerob_d2_3


title: PCI-35 control mock exp.2


title: Rbpj;MyoD mutant rep4


title: Rbpj;MyoD mutant rep5


title: A022-POST-High dose

description: SAMPLE 148


title: A027-FU-Placebo

description: SAMPLE 149

source_name: FU-Placebo

value: placebo


title: Rbpj;MyoD mutant rep1


title: A014-PRE-Low dose

description: SAMPLE 146

source_name: PRE-Low dose

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


title: Rbpj;MyoD mutant rep3


title: PCI-35 control empty exp.2

value: empty


title: A022-PRE-High dose

description: SAMPLE 147


title: A029-PRE-High dose

description: SAMPLE 150


title: DnMaml;MyoD mutant rep7


title: PCI-43 control mock exp.1


title: Rbpj;MyoD mutant rep2


title: PCI-43 control empty exp.1


title: A032-PRE-Low dose

description: SAMPLE 151


title: A012-FU-High dose

description: SAMPLE 145

value: follow up; 1 month after illness-onset


title: A009-FU-High dose

description: SAMPLE 144


title: DnMaml;MyoD mutant rep8


title: DnMaml;MyoD mutant rep6


title: siARHGAP21_3 / siControl_3 biol. Rep. 3; techn. Rep. 1

city: Campinas

first: Mariana

last: Lazarini

state: São Paulo

address: Rua Carlos Chagas, num 480

department: Hematology and Hemotherapy Center

country: Brazil

institute: University of Campinas

description: Biological replicate 3 of 3. PC-3 siControl cells replica 3 labeled with Cy3 x PC-3 siARHGAP21 cells replica 3 labeled with Cy5

hyb_protocol: Samples were combined and hybridize on a custom oligoarray with 4 x 44k elements produced by Agilent Technologies (GPL4133), the hybridization and washing steps were perfomed according to agilent instructions.

scan_protocol: Slides were scanned on a GenePix 4000 B scanner (Molecular Devices, Sunnyvale, CA, USA). Fluorescence intensities were extracted using Feature Extraction (FE) software (version 9.0; Agilent).

data_processing: Data was extracted using Feature Extraction software (Agilent Technologies), the intensities were LOWESS normalized. Agilent software was used.

source_name: PC-3 prostate adenocarcinoma cell line control

label_protocol: 500ng of total RNA were amplified and labeled with Cy3 or Cy5 using the Agilent Low RNA Input Fluorescent Linear Amplification Kit PLUS, two-Color (Agilent Technologies) according to the manufacturer's recommendations.

growth_protocol: PC-3 cells were cultured in RPMI containing 10% fetal bovine serum with penicillin/streptomycin and maintained at 37ºC, 5% CO2.

extract_protocol: Total RNA from PC-3 siARHGAP21 and siControl cells was extracted using Trizol (Invitrogen, Carlsbad, CA, USA), according to the manufacturer's instructions.  RNA was purified with Qiagen®, RNeasyTM Micro Kit and integrity of the RNAs was analyzed with Agilent 2100 Eletrophoresis Bioanalyser (Agilent Technologies, Santa Clara, CA).

treatment_protocol: PC-3 cells were transfected with a pool of 4 siRNAs targeting ARHGAP21 (5´-GAAAAUAGCAGAUCGGUUAUU-3´, 5´-GAUGAUAAAUGGCGAGAUUUU-3´, 5´-GGAUCUAAUUAGUCGAAGAUU-3´, 5´-GCACAGAGAUGCUACCGAAUU-3´) or a pool of 4 siRNA control (5´-UGGUUUACAUGUCGACUAA-3´, 5´-UGGUUUACAUGUUGUGUGA-3´, 5´-UGGUUUACAUGUUUUCUGA-3´, 5´-UGGUUUACAUGUUUUCCUA-3´) from ThermoFisher Scientific (Lafayette, CO, USA). Briefly, the cells were plated at 70% confluence and transfected using Lipofectamine 2000 reagent according to the manufacturer´s instructions. Cells were collected 72 hours after transfection.

tag: gender

value: male

tag: expression

value: siControl

source_name: PC-3 prostate adenocarcinoma cell line silenced for ARHGAP21


title: DnMaml;MyoD mutant rep5


title: siARHGAP21_1 / siControl_1 biol. Rep. 1; techn. Rep. 2

description: Biological replicate 1 of 3. PC-3 siControl cells replica 1 labeled with Cy5 x PC-3 siARHGAP21 cells replica 1 labeled with Cy3


title: siARHGAP21_2 / siControl_2 biol. Rep. 2; techn. Rep. 1

description: Biological replicate 2 of 3. PC-3 siControl cells replica 2 labeled with Cy3 x PC-3 siARHGAP21 cells replica 2 labeled with Cy5


title: siARHGAP21_3 / siControl_3 biol. Rep. 3; techn. Rep. 2

description: Biological replicate 3 of 3. PC-3 siControl cells replica 3 labeled with Cy5 x PC-3 siARHGAP21 cells replica 3 labeled with Cy3


title: A009-POST-High dose

description: SAMPLE 143

tag: disease status

tag: treated with


title: siARHGAP21_2 / siControl_2 biol. Rep. 2; techn. Rep. 2

description: Biological replicate 2 of 3. PC-3 siControl cells replica 2 labeled with Cy5 x PC-3 siARHGAP21 cells replica 2 labeled with Cy3


title: DnMaml;MyoD mutant rep4

tag: tissue


title: 13969465 - IR71 KO repet3 vs Col-0 repet3

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA in diferent mutants?

hyb_protocol: Col-0 repet3 Cy5 / IR71 KO repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: Col-0 repet3

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

growth_protocol: flower - Temperature: 22°C Light: Long day

extract_protocol: Col-0 repet3:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: wild type

tag: age

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

source_name: IR71 KO repet3

extract_protocol: IR71 KO repet3:10ug. (Qiagen_RNeasy.pdf)

value: ir71 ko n°3 mutant


title: siARHGAP21_1 / siControl_1 biol. Rep. 1; techn. Rep. 1

description: Biological replicate 1 of 3. PC-3 siControl cells replica 1 labeled with Cy3 x PC-3 siARHGAP21 cells replica 1 labeled with Cy5


title: A129-PRE-High dose

description: SAMPLE 142

value: Vietnamese dengue patients

tag: sample collection time

tag: patient id


title: DnMaml;MyoD mutant rep3

tag: cell type


title: A126-POST-High dose

description: SAMPLE 140


title: MeOH_4h_replicate_5

city: Fougères

first: Perrine

last: Zeller

address: la haute marche-javené

department: UTC

institute: ANSES

hyb_protocol: Hybridization, washing and drying of the microarray were performed in a HS4800 Pro Hybridization station (Tecan). Washing was performed with the Gene Expression Wash Pack (Agilent) and drying with the Stabilization and Drying Solution (Agilent).

scan_protocol: The slides were scanned with an Innoscan 900AL scanner (Innopsys, Toulouse, France).

data_processing: The raw data were normalized and scaled with the lowess algorithm. The median sample (median of all samples) were used for fitting of a non-linear normalization curve.

source_name: Caco-2 cells, MeOH, 4h

label_protocol: RNA samples were converted to aminoallyl-RNA (aRNA) using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion) prior to labeling with either Cy3 or Cy5 dye using the Quick Amp Labeling Kit (Agilent).

growth_protocol: The Caco-2 cells (ATCC HTB-37), passages 30-33, were cultured in GlutaMAX minimum essential medium (MEM) with 1% non-essential amino acids, penicillin (50 IU/mL) and streptomycin (50 μg/mL) (InVitrogen) and supplemented with 10% fetal calf serum (FCS, InVitrogen). Cells were grown in 75 cm² flasks at 37°C in an atmosphere containing 5% CO2 and subcultured twice a week. To obtain differentiated Caco-2 cells, the cells were seeded into 12-wells plates (60× 103 cells/cm²) and maintained 24 days in 10% FCS culture medium with a medium change every 2 or 3 days.

extract_protocol: Total RNA of each replicate was extracted by standard TRIzol RNA extraction protocol (InVitrogen). The RNA integrity and quantity were assessed with the Agilent 2100 Bioanalyzer. Only the RNA samples with a RIN (RNA Integrity Number) above 8 were considered further for the transcriptomic study.

treatment_protocol: Differentiated Caco-2 cells were exposed to different concentrations of MC-RR or MC-LR treatment in free FCS culture medium for either 4 or 24 hours.

value: colon adenocarcinoma cells

tag: differentiation state

value: differentiated

tag: treatment

value: MeOH

tag: treatment duration


title: 13969459 - Col-0 repet1 vs IR71 KO repet1

hyb_protocol: IR71 KO repet1 Cy5 / Col-0 repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: IR71 KO repet1

extract_protocol: IR71 KO repet1:10ug. (Qiagen_RNeasy.pdf)

tag: genotype/variation

source_name: Col-0 repet1

extract_protocol: Col-0 repet1:10ug. (Qiagen_RNeasy.pdf)


title: 13969463 - IR71 KO repet2 vs Col-0 repet2

hyb_protocol: Col-0 repet2 Cy5 / IR71 KO repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col-0 repet2

extract_protocol: Col-0 repet2:10ug. (Qiagen_RNeasy.pdf)

source_name: IR71 KO repet2

extract_protocol: IR71 KO repet2:10ug. (Qiagen_RNeasy.pdf)


title: 13969462 - Col-0 repet2 vs IR71 KO repet2

hyb_protocol: IR71 KO repet2 Cy5 / Col-0 repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MeOH_4h_replicate_4


title: A126-PRE-High dose

description: SAMPLE 139

source_name: PRE-High dose

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


title: A126-FU-High dose

description: SAMPLE 141

source_name: FU-High dose


title: MyoD mutant rep17

tag: strain

value: mixed C57BL/6, 129/Sv and 129/Ola.

tag: genotype

value: MyoD-/-

value: skeletal muscle

value: progenitor cell

tag: developmental stage


title: MeOH_4h_replicate_1

tag: cell line


title: MyoD mutant rep18


title: 13969464 - Col-0 repet3 vs IR71 KO repet3

hyb_protocol: IR71 KO repet3 Cy5 / Col-0 repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: A125-PRE-High dose

description: SAMPLE 136

tag: disease status

value: pre-treatment

value: blood


title: MeOH_4h_replicate_2


title: DnMaml;MyoD mutant rep2


title: A125-FU-High dose

description: SAMPLE 138

tag: treated with


title: MeOH_24h_replicate_5

source_name: Caco-2 cells, MeOH, 24h


title: MeOH_4h_replicate_3


title: MyoD mutant rep16

tag: tissue


title: CCE_WT_RA_8hr_3

description:
SAMPLE 9
replicate 3

value: ESC

value: RA

tag: time


title: DnMaml;MyoD mutant rep1


title: MyoD mutant rep15


title: (cr)-CSdt7BS young spike-rep2

city: Yokohama

first: Kanako

last: Kawaura

address: Maioka-cho 641-12

institute: Kihara Institute for Biological Research, Yokohama City University

description: cytoplasmic substitution line of Chinese Spring having the Aegilops crassa cytoplasm with ditelosomic chromosome 7BS, replicate 2

hyb_protocol: Hybridization of the Cy3-labeled cRNA to the microarrays and washing were performed using a Gene Expression Hybridization kit and Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Signal intensities were detected by Feature Extraction software (Agilent Technologies). Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is XDR Hi 100% and XDR Li 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent Agilent Technologies) using default parameters(protocol GE1-v5_95) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Triticum aestivum

source_name: (cr)-CSdt7BS young spike

label_protocol: A Cy3 labeled cRNA probe were prepared using a Low RNA Input Linear Amp Kit (Agilent Technologies), and microarray hybridization was performed following the recommended protocol.

growth_protocol: Plants were grown in the experimental field.

extract_protocol: Total RNA was extracted using ISOGEN (Nippon-gene). Total RNA quality was checked with an Agilent 2100 Bioanalyzer.

treatment_protocol: Nothing

tag: cultivar

value: Chinese Spring

value: young spike

tag: line

value: pistillody


title: (cr)-CSdt7BS young spike-rep1

description: cytoplasmic substitution line of Chinese Spring having the Aegilops crassa cytoplasm with ditelosomic chromosome 7BS, replicate 1


title: A125-POST-High dose

description: SAMPLE 137

source_name: POST-High dose

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

tag: sample collection time

value: post-treatment


title: MeOH_24h_replicate_4


title: 13969460 - IR71 KO repet1 vs Col-0 repet1

hyb_protocol: Col-0 repet1 Cy5 / IR71 KO repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

value: wild type

tag: age

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

value: ir71 ko n°3 mutant


title: MyoD mutant rep12

source_name: embryonic back muscle progenitor cells

tag: cell type


title: A124-POST-Placebo

description: SAMPLE 134

source_name: POST-Placebo

value: Vietnamese dengue patients

value: placebo

tag: patient id


title: A124-FU-Placebo

description: SAMPLE 135

source_name: FU-Placebo

value: follow up; 1 month after illness-onset


title: A124-PRE-Placebo

description: SAMPLE 133

source_name: PRE-Placebo


title: MyoD mutant rep13

value: mixed C57BL/6, 129/Sv and 129/Ola.


title: MyoD mutant rep14

value: MyoD-/-


title: A174-FU-High dose

description: SAMPLE 131

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


title: MeOH_24h_replicate_2

value: colon adenocarcinoma cells

tag: differentiation state

value: differentiated

tag: treatment

value: MeOH

tag: treatment duration


title: Glioblastoma FFPE-GBM

type: genomic

city: Scottsdale

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

hyb_protocol: All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to 400k CGH arrays (Agilent Technologies, Santa Clara, CA) for 40 hours in a rotating 65°C oven.

scan_protocol: All microarray slides were scanned using an Agilent 2565C DNA scanner, and the images were analyzed with Agilent Feature Extraction version 10.7 using default settings.

data_processing: The aCGH data was assessed with a series of QC metrics, dye normalized and centralized, and then analyzed using an aberration detection algorithm (ADM2) which is included in Agilent Genomic Workbench 6.5 software. The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average log ratio) of the genomic interval and to the square root of the number of probes in the interval.

molecule: genomic DNA

source_name: FFPE tissue, glioblastoma

label_protocol: Genomic DNAs from sorted FFPE samples were amplified using the Ovation® WGA FFPE System from NuGEN® Technologies (San Carlos, CA). DNA was processed in accordance with the Ovation® WGA FFPE standard protocol with an alternate T7 endonuclease fragmentation step. Resulting amplified product was either used as template for aCGH analysis or processed with the Nugen Encore ds-DNA module according to the supplier's instructions in order to generate double-stranded end repaired DNA as input for library suitable for next-generation sequencing. Extracted fresh frozen sourced genomic DNA was amplified using the phi29 based Illustra GenomiPhi V2 Amplification kit from GE Healthcare Bio-sciences Corp (Piscataway, NJ) according to our published protocols. A 100 ng aliquot of pooled 46,XX DNA (Promega, Madison, WI) was amplified with the matching amplification protocol to generate a suitable reference for each aCGH experiment using amplified DNA template. In all cases, the quality of the amplification product was assessed by gel electrophoresis.  Fresh frozen phi29 amplified and FFPE non-amplified DNAs were treated with DNAse 1 prior to Klenow-based labeling. High molecular weight phi29 templates were digested for 30 minutes while the smaller fragmented FFPE samples were digested for only 1 minute. In each case, 1ul of 10x DNase 1 reaction buffer and 2ul of DNase 1 dilution buffer were added to 7ul of DNA sample and incubated at room temperature,  then transferred to 70°C for 30 minutes to deactivate DNase 1. In contrast, the amplified FFPE sourced DNAs do not require DNase 1 treatment prior to Klenow-based labeling. Sample and reference templates were then labeled with Cy-5 dUTP and Cy-3 dUTP, respectively, using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols.

growth_protocol: None.

extract_protocol: DNA from sorted nuclei was extracted using an amended protocol from the QIAamp® DNA Micro Kit from Qiagen (Valencia, CA). Briefly, each sorted sample was resuspended in 180ul buffer ATL and 20ul proteinase K, then incubated for 3 hours at 56°C for complete lysis. Samples were bound and washed according to QIAamp® DNA Micro Kit instructions, eluted into 50ul of H20, then precipitated overnight with 5ul 3 M sodium acetate and 180 ul 100% EtOH. Each sample was then centrifuged for 30 minutes at 20,000 x g, and washed in 1 ml of 70% EtOH for 30 minutes at 20,000 x g. The samples were carefully decanted and the DNA pellet was dried by speed vacuum then resuspended in a small volume (e.g. 10-50ul) of H20 for final concentrations suitable for accurate quantification.

treatment_protocol: Excess paraffin was removed with a scalpel from either side of 40-60um scrolls. Sectioning samples reduces accumulation of debris during the sorting process. Each sectioned piece was collected into individual microcentrifuge tubes, then washed three times with 1 ml Xylene for 5 minutes to remove remaining paraffin. Each sample was rehydrated in sequential ethanol washes (100% 5 minutes x2, then 95%, 70%, 50% and 30% ethanol) and washed 2 times in 1ml 1 mM EDTA pH 8.0. A 1 ml aliquot of 1 mM EDTA pH 8.0 was added to the samples and incubated at 95oC for 80 minutes to facilitate the removal of protein cross-links present in FFPE tissue. Samples were then cooled to room temperature for > 5 minutes, followed by addition of 300 ul PBS pH 7.4 and gentle centrifugation for 2 minutes at 3.6 x g. The supernatant was carefully removed and the pellet washed three times with 1 ml PBS pH 7.4/0.5mM CaCl2 to remove EDTA. Each sample was digested overnight (6-17 hours) in 1ml of a freshly prepared enzymatic cocktail containing 50 units/ml of collagenase type 3, 80 units/ml of purified collagenase, and 100 units/ml of hyaluronidase in PBS pH 7.4/0.5mM CaCl2 buffer. Each enzyme was rehydrated with PBS pH 7.4/0.5mM CaCl2 buffer, then stored at -200C immediately prior to addition to the cocktail mixture. Following overnight digestion, 500 ul NST was added to each sample to facilitate pelleting. Samples were centrifuged for 5 minutes at 3000 x g, after which pellets were resuspended in 750 ul of NST/10% fetal bovine serum and then passed through a 25 G needle 10-20 times. The samples were filtered through a 35 um mesh and collected into a 5 ml Polypropylene round bottom tube. The mesh was rinsed with an additional 750 ul of NST/10% fetal bovine serum and placed on ice while processing remaining samples. The total volume in the tube for each sample was approximately 1.5 ml. An equal volume of 20ug/ml DAPI was added to each tube to achieve a final concentration of 10ug/ml DAPI prior to flow sorting with a BD Influx cytometer with ultraviolet excitation (Becton-Dickinson, San Jose, CA). The optimal settings for sorting FFPE samples with the Influx sorter were as follows: Drop formation was achieved with piezzo amplitude of 6-10 volts and a drop frequency of 30 khertz. The sort mode was set to purity yield with a drop delay of 31.5-32. Sheath fluid pressure was typically 17-18 psi with a 100 um nozzle. For single parameter DNA content assays, DAPI emission was collected at >450nm. DNA content and cell cycle were then analyzed using the software program MultiCycle (Phoenix Flow Systems, San Diego, CA).

value: glioblastoma

tag: sample type

value: formalin-fixed paraffin-embedded tissue

source_name: Normal 46,XX reference

value: commercial pooled reference


title: CS young spike-rep1

description: Chinese Spring, replicate 1

source_name: CS young spike

value: Chinese Spring

value: young spike

value: normal


title: MC-RR_50µM_4h_replicate_3

source_name: Caco-2 cells, MC-RR 50 µM, 4h

tag: cell line

value: microcystin RR

tag: treatment dose

value: 50 µM


title: MyoD mutant rep9

tag: strain

tag: genotype

value: skeletal muscle

value: progenitor cell

tag: developmental stage


title: A174-POST-High dose

description: SAMPLE 130

tag: disease status

value: Vietnamese dengue patients

tag: treated with

value: post-treatment

tag: tissue

value: blood


title: MyoD mutant rep10

value: mixed C57BL/6, 129/Sv and 129/Ola.

value: MyoD-/-


title: MyoD mutant rep11


title: brain O2 21% vs. brain O2 10% array 8

city: Urbana

first: Mark

middle: Robert

last: Band

state: IL

address: 1201 W. Gregory Dr

department: Biotechnology

institute: University of Illinois

hyb_protocol: Agilent hybridization protocol

scan_protocol: Axon 4000B GenePix 6.1

data_processing:
Feature Extraction software- GenePix 6.1
Data from each slide was background corrected and Lowess normalized

organism: Nannospalax galili

source_name: Spalax brain 21% oxygen

label_protocol: Agilent Low input 2 color labeling kit

extract_protocol: RNA isolated with Trizol

value: brain

tag: time

value: control

source_name: Spalax brain 10% oxygen


title: MeOH_24h_replicate_3

value: colon adenocarcinoma cells

value: differentiated

value: MeOH


title: MC-RR_50µM_4h_replicate_4


title: A176-PRE-Low dose

description: SAMPLE 132

source_name: PRE-Low dose

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

tag: sample collection time

value: pre-treatment


title: MeOH_24h_replicate_1


title: A174-PRE-High dose

description: SAMPLE 129

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


title: CS young spike-rep2

description: Chinese Spring, replicate 2

tag: cultivar

value: Chinese Spring

value: young spike

tag: line

value: normal


title: MC-RR_50µM_4h_replicate_2

tag: cell type

value: microcystin RR

value: 50 µM


title: MyoD mutant rep8

value: skeletal muscle

value: progenitor cell


title: brain O2 10% vs. brain O2 10% array 7


title: MyoD mutant rep7

value: mixed C57BL/6, 129/Sv and 129/Ola.


title: MC-RR_50µM_4h_replicate_1

tag: differentiation state


title: A166-POST-High dose

description: SAMPLE 127

value: Vietnamese dengue patients

value: post-treatment

value: blood

tag: patient id


title: brain O2 6% vs. brain O2 3% array 6

source_name: Spalax brain 6% oxygen

value: brain

tag: treatment

source_name: Spalax brain 3% oxygen


title: A163-POST-Low dose

description: SAMPLE 124

source_name: POST-Low dose


title: MC-RR_100µM_4h_replicate_5

source_name: Caco-2 cells, MC-RR 100 µM, 4h

value: colon adenocarcinoma cells

value: differentiated

tag: treatment duration


title: A166-PRE-High dose

description: SAMPLE 126

source_name: PRE-High dose


title: A163-FU-Low dose

description: SAMPLE 125

source_name: FU-Low dose

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

value: follow up; 1 month after illness-onset


title: brain O2 3% vs. brain O2 3% array 5


title: MyoD mutant rep6

source_name: embryonic back muscle progenitor cells

value: MyoD-/-


title: MC-RR_100µM_4h_replicate_2

tag: cell line


title: A166-FU-High dose

description: SAMPLE 128

source_name: FU-High dose

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


title: MC-RR_100µM_4h_replicate_3

tag: treatment dose


title: MyoD mutant rep5

tag: strain


title: MyoD mutant rep4

tag: genotype


title: MC-RR_100µM_4h_replicate_1


title: MC-RR_100µM_4h_replicate_4


title: brain O2 6% vs. brain O2 3% array 2

source_name: Spalax brian 6% oxygen


title: MyoD mutant rep3

tag: developmental stage


title: MyoD mutant rep2


title: A161-FU-High dose

description: SAMPLE 122

tag: disease status


title: A161-POST-High dose

description: SAMPLE 121

source_name: POST-High dose

tag: treated with


title: MC-RR_10µM_4h_replicate_4

source_name: Caco-2 cells, MC-RR 10 µM, 4h

value: 10 µM


title: brain O2 21% vs. brain O2 10% array 4

source_name: Spalax brian 21% oxygen

tag: tissue

value: control


title: muscle O2 10% vs. muscle O2 10% array 7

source_name: Spalax muscle 10% oxygen

value: muscle

tag: time


title: MyoD heterozygous rep4

value: MyoD+/-


title: MyoD mutant rep1

value: skeletal muscle


title: A163-PRE-Low dose

description: SAMPLE 123

tag: sample collection time

value: pre-treatment


title: brain O2 3% vs. brain O2 21% array 1

source_name: Spalax brian 3% oxygen


title: MC-RR_10µM_4h_replicate_3

value: microcystin RR


title: MyoD heterozygous rep3

value: mixed C57BL/6, 129/Sv and 129/Ola.

value: progenitor cell


title: brain O2 10% vs. brain O2 6% array 3

source_name: Spalax brian 10% oxygen


title: A005-FU-High dose

description: SAMPLE 119

value: Vietnamese dengue patients

value: blood


title: MyoD heterozygous rep1


title: MyoD heterozygous rep2


title: A006-PRE-Low dose

description: SAMPLE 120


title: A001-POST-Placebo

description: SAMPLE 118

source_name: POST-Placebo

value: placebo

value: post-treatment


title: muscle O2 21% vs. muscle O2 10% array 4

source_name: Spalax muscle 21% oxygen

label_protocol: Agilent low input 2-color amplification kit


title: muscle O2 10% vs. muscle O2 21% array 8


title: muscle O2 10% vs. muscle O2 6% array 3

source_name: Spalax muscle 6% oxygen


title: muscle O2 6% vs. muscle O2 3% array 6

source_name: Spalax muscle 3% oxygen


title: muscle O2 6% vs. muscle O2 3% array 2


title: wild type rep8

value: wild type


title: wild type rep9


title: MC-RR_10µM_4h_replicate_2

value: colon adenocarcinoma cells

value: differentiated


title: MC-RR_5µM_24h_replicate_3

source_name: Caco-2 cells, MC-RR 5 µM, 24h

value: 5 µM


title: D032-POST-Placebo

description: SAMPLE 115


title: P3_exposed_60min_rep4

city: Helsinki

first: Heidi

middle: J

last: Hyytiäinen

address: Agnes Sjöbergin katu 2

department: Dep. of Food Hygiene and Environmental Health

country: Finland

institute: University of Helsinki

description:
5_D
Aray slot: 253307710002_2_4
Ciprofloxacin-resistant variant of 81-176.

hyb_protocol: Each Cy3-labelled cDNA (600 ng) was hybridized at 65°C to a custom chip (Design ID 33077, Agilent Technologies) by using the Gene Expression Hybridization Kit according to manufacturer recommendations (Agilent). Washings were performed with the Gene Expression Wash Pack (Agilent) containing added 0.005% Triton X-102 and Stabilization and Drying solution (Agilent).

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2565CA) with scan profile AgilentHD_GX_1Color. The scanned images were analyzed with Feature Extraction Software 10.7.1 (Agilent) using protocol GE1_107_Sep09 and Grid 033077_D_F_20110318.

data_processing: The data set was normalized using quantile normalization with limma in R.

organism: Campylobacter jejuni subsp. jejuni 81-176

source_name: P3, 1 hr, 8 µg/ml ciprofloxacin

label_protocol: cDNA synthesis was performed for four independent biological replicates of each RNA sample, and the samples were processed by one-color microarray-based prokaryote analysis protocol according to the manufacturer's instructions (FairPlay III Labeling, Agilent Technologies). 5 ug total RNAs were labeled with the One Color RNA Spike-In Kit (Agilent) following measurement with NanoDrop ND-200 to control specific activity of Cy3-labelled cDNA.

growth_protocol: C. jejuni was grown 16 hours in 250 ml Mueller-Hinton (MH) broth at 37°C under a microaerobic atmosphere with agitation at 100 rpm.

extract_protocol: Bacterial cells (10 ml) were mixed with two volumes of the RNA stabilization reagent RNAprotect (Qiagen). The samples were further processed according to manufacturer's instructions (Qiagen) and stored at -70°C before RNA extraction. Total RNA was extracted using the RNeasy Mini Kit according to manufacturer's instructions (Qiagen). A second DNase treatment with 2 U of TURBO DNase (Ambion INC, Austin, TX, USA) was performed following a RNA cleanup by the RNeasy Mini Kit.

treatment_protocol: Bacterial cells grown for 16 hours were divided into two equal portions: 125 ml (unexposed control) and 125 ml with added ciprofloxacin (8 µg/ml). The cultures were further incubated 1 hour at 37°C in a microaerobic atmosphere with agitation.

tag: strain/background

tag: genotype/variation

value: P3 variant

tag: phenotype

value: ciprofloxacin resistant

value: ciprofloxacin


title: D029-FU-Low dose

description: SAMPLE 113

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

value: follow up; 1 month after illness-onset


title: wild type rep7

value: skeletal muscle

tag: cell type


title: P3_unexposed_60min_rep4

description:
5_C
Aray slot: 253307710002_2_3
Ciprofloxacin-resistant variant of 81-176.

source_name: P3, 1 hr, 0 µg/ml ciprofloxacin


title: D029-POST-Low dose

description: SAMPLE 112

source_name: POST-Low dose

tag: patient id


title: muscle O2 3% vs. muscle O2 21% array 5

value: muscle

tag: treatment

value: control


title: MC-RR_10µM_4h_replicate_5

tag: differentiation state

value: microcystin RR

value: 10 µM

tag: treatment duration


title: MC-RR_5µM_24h_replicate_2

tag: cell line

tag: treatment dose


title: D032-FU-Placebo

description: SAMPLE 116

source_name: FU-Placebo

value: Vietnamese dengue patients

value: blood


title: MC-RR_10µM_24h_replicate_5

source_name: Caco-2 cells, MC-RR 10 µM, 24h


title: muscle O2 3% vs. muscle O2 21% array 1

data_processing:
Feature Extraction software- GenePix 6.1
Data from each slide was background corrected and Lowess normalized using Limma.


title: MC-RR_5µM_24h_replicate_1


title: wild type rep6

source_name: embryonic back muscle progenitor cells

tag: strain

value: mixed C57BL/6, 129/Sv and 129/Ola.

tag: genotype

value: progenitor cell


title: WT_exposed_60min_rep4

description:
5_B
Aray slot: 253307710002_2_2
Ciprofloxacin-susceptible wild-type.

source_name: WT, 1 hr, 8 µg/ml ciprofloxacin

value: WT

value: ciprofloxacin susceptible


title: MC-RR_10µM_24h_replicate_4

value: colon adenocarcinoma cells

value: differentiated


title: wild type rep10

value: wild type

tag: developmental stage


title: A001-PRE-Placebo

description: SAMPLE 117

source_name: PRE-Placebo

tag: disease status

tag: treated with

value: placebo

value: pre-treatment


title: MC-RR_10µM_4h_replicate_1

source_name: Caco-2 cells, MC-RR 10 µM, 4h


title: MC-RR_5µM_24h_replicate_5

value: 5 µM


title: WT_unexposed_60min_rep4

description:
5_A
Aray slot: 253307710002_2_1
Ciprofloxacin-susceptible wild-type.

source_name: WT, 1 hr, 0 µg/ml ciprofloxacin


title: P3_exposed_60min_rep3

description:
4_D
Aray slot: 253307710002_1_4
Ciprofloxacin-resistant variant of 81-176.

value: P3 variant

value: ciprofloxacin resistant

value: ciprofloxacin


title: wild type rep4

tag: tissue

value: skeletal muscle


title: D028-FU-Low dose

description: SAMPLE 110

source_name: FU-Low dose

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

tag: sample collection time

value: follow up; 1 month after illness-onset


title: MC-RR_5µM_24h_replicate_4

value: microcystin RR


title: MC-RR_10µM_24h_replicate_3

value: 10 µM


title: WT_exposed_60min_rep3

description:
4_B
Aray slot: 253307710002_1_2
Ciprofloxacin-susceptible wild-type.

tag: strain/background


title: wild type rep3

value: mixed C57BL/6, 129/Sv and 129/Ola.

value: progenitor cell


title: wild type rep2


title: MC-RR_1µM_24h_replicate_5

source_name: Caco-2 cells, MC-RR 1 µM, 24h

value: 1 µM


title: D032-PRE-Placebo

description: SAMPLE 114

value: Vietnamese dengue patients

value: blood


title: WT_unexposed_60min_rep3

description:
4_A
Aray slot: 253307710002_1_1
Ciprofloxacin-susceptible wild-type.

tag: genotype/variation

value: WT

value: ciprofloxacin susceptible


title: wild type rep5

value: wild type


title: A005-PRE-High dose

description: SAMPLE 108

source_name: PRE-High dose

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

value: pre-treatment


title: P3_exposed_60min_rep2

description:
2_D
Aray slot: 253307710001_2_4
Ciprofloxacin-resistant variant of 81-176.

value: P3 variant

tag: phenotype

value: ciprofloxacin resistant


title: MC-RR_10µM_24h_replicate_2

tag: cell type

value: colon adenocarcinoma cells

value: differentiated


title: D029-PRE-Low dose

description: SAMPLE 111

source_name: PRE-Low dose

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

tag: patient id


title: wild type rep1

value: skeletal muscle


title: D028-POST-Low dose

description: SAMPLE 109

value: post-treatment


title: MC-RR_10µM_24h_replicate_1

tag: treatment

value: microcystin RR

value: 10 µM


title: A004-POST-Low dose

description: SAMPLE 107


title: P3_unexposed_60min_rep3

description:
4_C
Aray slot: 253307710002_1_3
Ciprofloxacin-resistant variant of 81-176.


title: MC-RR_1µM_24h_replicate_4

tag: differentiation state

value: 1 µM


title: MC-RR_1µM_24h_replicate_3

tag: treatment duration


title: A064-POST-Placebo

description: SAMPLE 106

source_name: POST-Placebo

value: Vietnamese dengue patients

value: placebo


title: Olig2 Cells, Normal Brain Total RNA, Replicate 3

first: Karim

last: Helmy

state: NY

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

description: OPC Total C

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Non-normalized data is background subtracted; Normalized data is background subtracted, filtered for only probes with detection p-value<0.05 in all samples, quantile normalized in Partek Genomics software and log2 transformed.

label_protocol: Illumina TotalPrep RNA Amplification manufacturer protocol

extract_protocol: For collection of total cellular RNA, normal brain or grossly-dissected tumor tissue was dissociated into a single cell suspension with papain and GFP+ cells were collected by FACS (Becton-Dickinson Aria Cell Sorter). Sorted cells were collected with Trizol-LS (Invitrogen), chloroform extracted, precipitated with sodium acetate in isopropanol overnight, and purified with Qiagen RNeasy MinElute Cleanup Kit. Ribosome-bound RNA was immunoprecipitated with anti-GFP conjugated magnetic beads from mechanically-homogenized tissue and purified as above. Tissue samples were divided equally for total and ribosome-bound RNA to generate paired datasets.

tag: fraction

value: Total RNA


title: Olig2 Cells, Normal Brain Total RNA, Replicate 2

description: OPC Total B


title: Olig2 Cells, Normal Brain Total RNA, Replicate 4

description: OPC Total D


title: Olig2 Cells, Normal Brain Total RNA, Replicate 1

description: OPC Total A


title: WT_exposed_60min_rep2

description:
2_B
Aray slot: 253307710001_2_2
Ciprofloxacin-susceptible wild-type.

value: WT

value: ciprofloxacin susceptible

value: ciprofloxacin


title: P3_unexposed_60min_rep2

description:
2_C
Aray slot: 253307710001_2_3
Ciprofloxacin-resistant variant of 81-176.


title: WT_exposed_60min_rep1

description:
1_B
Aray slot: 253307710001_1_2
Ciprofloxacin-susceptible wild-type.


title: Olig2 Cells, Normal Brain Ribosome-bound RNA, Replicate 2

description: OPC IP B

value: Ribosome-bound RNA


title: Olig2 Cells, Normal Brain Ribosome-bound RNA, Replicate 3

description: OPC IP C


title: Olig2 Cells, Normal Brain Ribosome-bound RNA, Replicate 1

description: OPC IP A


title: A061-FU-High dose

description: SAMPLE 104

hyb_protocol: Standard Illumina hybridization protocol

source_name: FU-High dose

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

value: follow up; 1 month after illness-onset

value: blood


title: MC-RR_1µM_24h_replicate_1

tag: cell line

value: colon adenocarcinoma cells

value: differentiated

tag: treatment dose


title: A064-PRE-Placebo

description: SAMPLE 105

value: pre-treatment


title: A061-POST-High dose

description: SAMPLE 103

source_name: POST-High dose

value: post-treatment


title: P3_unexposed_60min_rep1

description:
1_C
Aray slot: 253307710001_1_3
Ciprofloxacin-resistant variant of 81-176.

value: P3 variant

value: ciprofloxacin resistant


title: A054-PRE-Low dose

description: SAMPLE 102

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


title: P3_exposed_60min_rep1

description:
1_D
Aray slot: 253307710001_1_4
Ciprofloxacin-resistant variant of 81-176.

source_name: P3, 1 hr, 8 µg/ml ciprofloxacin


title: WT_unexposed_60min_rep1

description:
1_A
Aray slot: 253307710001_1_1
Ciprofloxacin-susceptible wild-type.


title: MC-LR_50µM_4h_replicate_4

source_name: Caco-2 cells, MC-LR 50 µM, 4h

value: microcystin LR

value: 50 µM


title: WT_unexposed_60min_rep2

description:
2_A
Aray slot: 253307710001_2_1
Ciprofloxacin-susceptible wild-type.


title: A047-POST-High dose

description: SAMPLE 100

value: Vietnamese dengue patients


title: MC-RR_1µM_24h_replicate_2

value: microcystin RR

value: 1 µM


title: MC-LR_50µM_4h_replicate_3


title: Olig2 Cells, Normal Brain Ribosome-bound RNA, Replicate 4

description: OPC IP D


title: A047-FU-High dose

description: SAMPLE 101


title: MC-LR_50µM_4h_replicate_5


title: A047-PRE-High dose

description: SAMPLE 99


title: MC-LR_50µM_4h_replicate_1


title: Olig2 Cells, PDGF/PTEN-deleted Glioma Total RNA, Replicate 4

description: Cre Total G174

value: Total RNA


title: MC-LR_50µM_4h_replicate_2


title: Olig2 Cells, PDGF/PTEN-deleted Glioma Total RNA, Replicate 3

description: Cre Total G168


title: A040-FU-Placebo

description: SAMPLE 98

value: placebo


title: A040-POST-Placebo

description: SAMPLE 97


title: Olig2 Cells, PDGF/PTEN-deleted Glioma Total RNA, Replicate 2

description: Cre Total G126


title: Olig2 Cells, PDGF/PTEN-deleted Glioma Total RNA, Replicate 1

description: Cre Total G121


title: Olig2 Cells, PDGF Glioma Total RNA, Replicate 3

description: PDGF Total G47


title: A123-FU-Placebo

description: SAMPLE 96


title: MC-LR_100µM_4h_replicate_5

source_name: Caco-2 cells, MC-LR 100 µM, 4h


title: Olig2 Cells, PDGF Glioma Total RNA, Replicate 4

description: PDGF Total G53


title: Olig2 Cells, PDGF/PTEN-deleted Glioma Ribosome-bound RNA, Replicate 1

description: Cre IP G121

value: Ribosome-bound RNA


title: MC-LR_100µM_4h_replicate_4


title: Olig2 Cells, PDGF/PTEN-deleted Glioma Ribosome-bound RNA, Replicate 4

description: Cre IP G174


title: Olig2 Cells, PDGF/PTEN-deleted Glioma Ribosome-bound RNA, Replicate 2

description: Cre IP G126


title: MC-LR_100µM_4h_replicate_3


title: Olig2 Cells, PDGF Glioma Total RNA, Replicate 2

description: PDGF Total G34


title: Olig2 Cells, PDGF Glioma Total RNA, Replicate 1

description: PDGF Total G3


title: A123-PRE-Placebo

description: SAMPLE 94


title: MC-LR_10µM_4h_replicate_1

source_name: Caco-2 cells, MC-LR 10 µM, 4h

value: 10 µM


title: A121-POST-Placebo

description: SAMPLE 89

value: blood


title: A122-FU-Low dose

description: SAMPLE 93

value: follow up; 1 month after illness-onset


title: Olig2 Cells, PDGF/PTEN-deleted Glioma Ribosome-bound RNA, Replicate 3

description: Cre IP G168


title: A122-PRE-Low dose

description: SAMPLE 91


title: A123-POST-Placebo

description: SAMPLE 95


title: MC-LR_100µM_4h_replicate_1

value: colon adenocarcinoma cells

value: differentiated


title: MC-LR_10µM_4h_replicate_5


title: MC-LR_10µM_4h_replicate_4


title: MC-LR_10µM_4h_replicate_2


title: MC-LR_10µM_4h_replicate_3


title: MC-LR_100µM_4h_replicate_2


title: A121-PRE-Placebo

description: SAMPLE 88

value: pre-treatment


title: MC-LR_5µM_24h_replicate_5

source_name: Caco-2 cells, MC-LR 5 µM, 24h

value: 5 µM


title: A122-POST-Low dose

description: SAMPLE 92

source_name: POST-Low dose

value: post-treatment


title: A121-FU-Placebo

description: SAMPLE 90

source_name: FU-Placebo


title: Olig2 Cells, PDGF Glioma Ribosome-bound RNA, Replicate 4

description: PDGF IP G53


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

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: samples were hybridized using Corning Pronto! Microarray Hybridization Kit

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: Hy5, Hy3

source_name: autonomous adenomas

label_protocol: total RNA was labelled using the miRCURY LNA microRNA Power Labelling Kit (Hy3/Hy5) (Exiqon, Copenhagen, Denmark), according to the manufacturer’s protocol. Labeled RNA was purified on a miRNeasy column (Qiagen)

extract_protocol: total RNA was extracted using a TRIzol Reagent kit (Invitrogen) followed by purification on miRNeasy 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 adenoma

tag: tumor number

value: HN 78

label: Hy3, Hy5

source_name: Adjacent tissues

value: Adjacent tissue


title: Olig2 Cells, PDGF Glioma Ribosome-bound RNA, Replicate 2

description: PDGF IP G34


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

value: HN 70


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

value: HN 71


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

value: HN 75


title: A120-FU-Placebo

description: SAMPLE 87

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

value: Vietnamese dengue patients


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

value: HN 61


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

value: HN 67


title: Olig2 Cells, PDGF Glioma Ribosome-bound RNA, Replicate 3

description: PDGF IP G47

value: Ribosome-bound RNA


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

value: HN 68


title: Olig2 Cells, PDGF Glioma Ribosome-bound RNA, Replicate 1

description: PDGF IP G3


title: MC-LR_5µM_24h_replicate_1

value: microcystin LR


title: MC-LR_5µM_24h_replicate_4

value: colon adenocarcinoma cells


title: A120-PRE-Placebo

description: SAMPLE 85

source_name: PRE-Placebo

value: placebo

value: blood


title: D026-FU-Low dose

description: SAMPLE 83

source_name: FU-Low dose

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

value: follow up; 1 month after illness-onset


title: D028-PRE-Low dose

description: SAMPLE 84

value: pre-treatment


title: D026-POST-Low dose

description: SAMPLE 82

value: post-treatment


title: MC-LR_5µM_24h_replicate_3

value: differentiated

value: 5 µM


title: A120-POST-Placebo

description: SAMPLE 86


title: MC-LR_10µM_24h_replicate_4

source_name: Caco-2 cells, MC-LR 10 µM, 24h

value: 10 µM


title: air-breathing E18.5 Mutant lung rep1

city: Mainz

first: Hyobin

last: Jeong

state: Germany

address: Richard shirrmann Str 12.

institute: IMB

description: Air MT

scan_protocol: standard protocol for Illumina BeadScan 500 System

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

source_name: lung tissue

label_protocol: standard protocol as outlined in the Illumina Gene Expression System Manual

growth_protocol: preparation of whole mouse lung tissue at E18.5

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.

tag: strain

tag: age

value: embryonic 18.5 day

value: lung

value: air

tag: genotype

value: snx5 null


title: air-breathing E18.5 Mutant lung rep2

description: Air MT

tag: tissue


title: MC-LR_5µM_24h_replicate_2


title: D025-FU-Placebo

description: SAMPLE 80

tag: disease status

value: Vietnamese dengue patients

tag: treated with

tag: sample collection time


title: D026-PRE-Low dose

description: SAMPLE 81

source_name: PRE-Low dose


title: MC-LR_10µM_24h_replicate_5


title: air-breathing E18.5 Wild lung rep2

description: Air WT

value: wild type


title: air-breathing E18.5 Wild lung rep1

description: Air WT


title: MC-LR_10µM_24h_replicate_3

value: microcystin LR


title: E18.5 Mutant lung rep1

description: non-Air WT

value: non-air


title: D025-POST-Placebo

description: SAMPLE 79

source_name: POST-Placebo

value: placebo


title: D025-PRE-Placebo

description: SAMPLE 78

value: blood


title: MC-LR_10µM_24h_replicate_2

value: colon adenocarcinoma cells


title: MC-LR_1µM_24h_replicate_5

source_name: Caco-2 cells, MC-LR 1 µM, 24h

value: 1 µM


title: D024-FU-High dose

description: SAMPLE 77

source_name: FU-High dose

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

value: follow up; 1 month after illness-onset


title: E18.5 Mutant lung rep2

description: non-Air WT


title: low grade serous tumour 12

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

source_name: ovarian low grade 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.

value: ovarian low grade serous tumour


title: MC-LR_10µM_24h_replicate_1

value: differentiated


title: low grade serous tumour 10


title: low grade serous tumour 11


title: D024-POST-High dose

last: Tien

address: 764 Vo Van Kiet

institute: Oxford University Clinical Research Unit

description: SAMPLE 76

source_name: POST-High dose

value: post-treatment


title: low grade serous tumour 9


title: E18.5 Wild lung rep2

description: non-Air WT

value: embryonic 18.5 day


title: WT Control replicate 4

city: Brisbane

first: Konstantin

last: Shakhbazov

address: Ipswich Road

country: Australia

institute: UQDI

description:
WTV4
replicate 4

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

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: wildtype

tag: retrovirus transduction

value: Control

value: Bone marrow


title: low grade serous tumour 7


title: MC-LR_1µM_24h_replicate_4

tag: cell type


title: MC-LR_1µM_24h_replicate_3

tag: treatment


title: D021-FU-Placebo

city: Ho Chi Minh

first: Nguyen

description: SAMPLE 74

value: Vietnamese dengue patients

tag: patient id


title: low grade serous tumour 8


title: MC-LR_1µM_24h_replicate_1

tag: differentiation state

tag: treatment duration


title: low grade serous tumour 6


title: WT Control replicate 3

description:
WTV3
replicate 3


title: D024-PRE-High dose

description: SAMPLE 75

source_name: PRE-High dose

value: pre-treatment


title: E18.5 Wild lung rep1

description: non-Air WT

value: lung

value: wild type


title: MC-LR_1µM_24h_replicate_2

tag: cell line

value: microcystin LR


title: D021-POST-Placebo

description: SAMPLE 73

value: placebo

value: blood


title: EtOH_4h_replicate_5

source_name: Caco-2 cells, EtOH, 4h

value: colon adenocarcinoma cells

value: EtOH


title: A086-POST-Low dose

description: SAMPLE 71

source_name: POST-Low dose

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


title: WT Control replicate 2

description:
WTV2
replicate 2


title: low grade serous tumour 5

value: ovarian low grade serous tumour


title: WT Control replicate 1

description:
WTV1
replicate 1


title: EtOH_4h_replicate_3

value: differentiated


title: EtOH_4h_replicate_4


title: EtOH_4h_replicate_2


title: A086-PRE-Low dose

description: SAMPLE 70


title: low grade serous tumour 3


title: low grade serous tumour 4


title: WT AML1-ETO9a replicate 4

description:
WTAE4
replicate 4


title: A085-POST-High dose

description: SAMPLE 69

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

value: post-treatment


title: A085-PRE-High dose

description: SAMPLE 68


title: low grade serous tumour 2


title: low grade serous tumour 1


title: WT AML1-ETO9a replicate 3

description:
WTAE3
replicate 3

value: wildtype


title: EtOH_4h_replicate_1


title: EtOH_24h_replicate_4

source_name: Caco-2 cells, EtOH, 24h


title: A084-FU-Placebo

description: SAMPLE 67

source_name: FU-Placebo

value: follow up; 1 month after illness-onset


title: WT AML1-ETO9a replicate 2

description:
WTAE2
replicate 2

value: Bone marrow


title: borderline serous tumour 19

source_name: ovarian borderline serous tumour

value: ovarian borderline serous tumour


title: WT AML1-ETO9a replicate 1

description:
WTAE1
replicate 1


title: A086-FU-Low dose

description: SAMPLE 72

value: Vietnamese dengue patients


title: Boo Control replicate 4

description:
BooV4
replicate 4

value: Booreana

value: Control


title: EtOH_24h_replicate_3


title: EtOH_24h_replicate_1


title: EtOH_24h_replicate_2