title: Erythroid Prog B Thal Day 14 5

description:
Sample_Name: S11
Sample_Group: Thal5_D14
Sentrix_ID: 8795274088
Sentrix_Position: K
Group_Classification: Thal_Day14
HSC_DFU_Batch_no: HSC_DFU_Batch2
cRNA_batch_no: cRNA_Batch2


title: Erythroid Prog B Thal Day 7 5

status: Public on Oct 28 2014

type: RNA

city: Perth

first: Luke

last: Forster

state: WA

address: Hopsital Ave

department: Haematology

country: Australia

institute: PathWest

description:
Sample_Name: S5
Sample_Group: Thal5_D7
Sentrix_ID: 8795274088
Sentrix_Position: E
Group_Classification: Thal_Day7
HSC_DFU_Batch_no: HSC_DFU_Batch2
cRNA_batch_no: cRNA_Batch1

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina Illumina iScan protocol

data_processing:
The data was normalized using loess normalization using the limma R package within Bioconductor

Normalization/filtering steps were as follows:
1) First we removed intensity gradients in the arrays using the bead array HULK function
2) We then log transformed the data
3) Following this we utilised the bead array normaliseIllumina function using ?quantile? as the method of normalisation
4) Lastly, we filtered the probes against the illuminaHumanv4.db and removed probes that had no match, Non value associated with them  or were flagged as BAD by the bead array  normaliseIllumina function.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Erythroid Progenitor

label_protocol: Ambion Illumina RNA TotalPrep RNA amplification kit

extract_protocol: Ambion miRvana miRNA isolation kit

tag: subject group

value: β-thalassaemia patient

tag: gender

value: male

tag: mutation

tag: tissue

value: peripheral blood

tag: cell type

value: haematopoietic cells

tag: time in culture

value: 7 days


title: Erythroid Prog Control Day 14 1

description:
Sample_Name: S7
Sample_Group: CtlC1_D14
Sentrix_ID: 8795274088
Sentrix_Position: G
Group_Classification: Control_Day14
HSC_DFU_Batch_no: HSC_DFU_Batch1
cRNA_batch_no: cRNA_Batch2

value: Healthy Control

value: 14 days


title: Erythroid Prog Control Day 7 6

description:
Sample_Name: S15
Sample_Group: CtlC6_D7
Sentrix_ID: 8795274108
Sentrix_Position: C
Group_Classification: Control_Day7
HSC_DFU_Batch_no: HSC_DFU_Batch3
cRNA_batch_no: cRNA_Batch3

value: female


title: Erythroid Prog Control Day 7 5

description:
Sample_Name: S14
Sample_Group: CtlC5_D7
Sentrix_ID: 8795274108
Sentrix_Position: B
Group_Classification: Control_Day7
HSC_DFU_Batch_no: HSC_DFU_Batch2
cRNA_batch_no: cRNA_Batch3


title: Lung of vehicle-treated rat after 8W, replicate 3

city: Allschwil

first: Axel

last: Klenk

address: Hegenheimermattweg 91

department: Research Informatics

country: Switzerland

institute: Idorsia Pharmaceuticals Ltd.

hyb_protocol: a pool of 825 ng of Cy3 labeled aRNA (examined sample) and 825 ng of Cy5 labeled aRNA rat reference (Agilent, Austin TX, USA) were hybridized using the Agilent Hybridization kit (Agilent, Austin TX, USA) according to the manufacturer's instructions. Hybridization was performed for 17 hours and washed according to Agilent's instructions.

scan_protocol: Scanned on an Agilent G2505B scanner using Agilent scan control (version 7.0) Images were quantified using Agilent Feature Extraction Software (version 10.5.5.1).

data_processing: BioConductor package vsn was used for variance-stabilizing normalization and glog transformation

organism: Rattus norvegicus

label_protocol: 200 ng of totRNA were labeled using the Low Input Quick Amp Labeling kit (Agilent, Austin TX, USA) following the manufacturer's instructions.

extract_protocol: total RNA extracted  using MagMAX-96 for microarrays kit (Life technologies, Foster City CA, USA ) following the manufacturer's instructions

value: Lung

tag: treatment

value: VEHICLE

tag: time

value: 8 WEEKS

source_name: Stratagene Reference

value: Pool of 14 rat cell types


title: Erythroid Prog Control Day 7 3

description:
Sample_Name: S3
Sample_Group: CtlC3_D7
Sentrix_ID: 8795274088
Sentrix_Position: C
Group_Classification: Control_Day7
HSC_DFU_Batch_no: HSC_DFU_Batch3
cRNA_batch_no: cRNA_Batch1


title: Lung of vehicle-treated rat after 4W, replicate 1

value: 4 WEEKS


title: Erythroid Prog Control Day 7 4

description:
Sample_Name: S13
Sample_Group: CtlC4_D7
Sentrix_ID: 8795274108
Sentrix_Position: A
Group_Classification: Control_Day7
HSC_DFU_Batch_no: HSC_DFU_Batch1
cRNA_batch_no: cRNA_Batch3


title: Lung of vehicle-treated rat after 8W, replicate 1


title: Lung of bleomycin-treated rat after 3D, replicate 5

value: BLEOMYCIN

value: 3 DAYS


title: NMOB-Cont-48hr-2

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

country: Netherlands

institute: ErasmusMC

description: PC3 incubated 48hrs with NoDex control (no cells) condition replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was background subtracted, vst transformation and a quantile normalization was applied. Probes that were detected at least once in the experiments (illumina detection p-value <0.01), were considered to be expressed and further analyzed for differential expression using Limma.

label_protocol: cDNA and Biotinylated cRNA were prepared with the Illumina Totalprep RNA Amplification kit (Ambion)

growth_protocol: SV-HFOs (Source for vesicle production) were cultured in alphaMEM, 20mM HEPES, strep/pen, 1.8 mM CaCl2, 2% depleted-FCS, 10 mM beta-glycerophosphate, with or without 100 nM dexamethasone. PC3 cells were cultured in alphaMEM, strep/pen, 1.8 mM CaCl2, 10% FCS

extract_protocol: Total RNA extracted using Trizol (invitrogen)

treatment_protocol: SV-HFO extracellular vesicles were isolated by a series of centrifugation steps (1500 rpm 5', 4500 rpm 10', 20000g 30', 100000g 1h) from conditioned medium of SV-HFOs cultured in serum-free growth medium overnight in p175 flask. EV pellet was re-suspended in 100ul filtered-PBS. 20000 PC3 cells were treated with 20 ul extracellular vesicles. PC3 RNA was extracted after 4h, 24h and 28h EV treatment. Controls were cell-free serum-free SV-HFO growth media with or without dexamethasone treated the same way as the conditioned media.

value: male (caucasian)

tag: developmental stage

value: 62 yr adult

value: prostate

tag: tumor stage

value: grade IV

tag: cell passage

value: passage 92

value: NoDex control (no cells) condition

value: 48 hrs

tag: cell line


title: MOB-Cont-48hr-2

description: PC3 incubated 48hrs with Dex control (no cells) condition replicate 2

value: Dex control (no cells) condition


title: Lung of untreated rat after 3D, replicate 2

value: NAIVE (UNTREATED)


title: Erythroid Prog Control Day 7 1

description:
Sample_Name: S1
Sample_Group: CtlC1_D7
Sentrix_ID: 8795274088
Sentrix_Position: A
Group_Classification: Control_Day7
HSC_DFU_Batch_no: HSC_DFU_Batch1
cRNA_batch_no: cRNA_Batch1

value: Healthy Control

value: male

value: peripheral blood

value: haematopoietic cells

value: 7 days


title: NMOB-Cont-48hr-1

description: PC3 incubated 48hrs with NoDex control (no cells) condition replicate 1


title: MOB-EV-48hr-1

description: PC3 incubated 48hrs with vesicles from Dex condition replicate 1

value: vesicles from Dex condition


title: MOB-Cont-48hr-1

description: PC3 incubated 48hrs with Dex control (no cells) condition replicate 1


title: Lung of vehicle-treated rat after 3D, replicate 2

value: Lung

value: VEHICLE

value: Pool of 14 rat cell types


title: Lung of bleomycin-treated rat after 2W, replicate 3

value: BLEOMYCIN

value: 2 WEEKS


title: Lung of vehicle-treated rat after 8W, replicate 4

value: 8 WEEKS


title: MOB-EV-48hr-2

description: PC3 incubated 48hrs with vesicles from Dex condition replicate 2

value: male (caucasian)

value: 62 yr adult

value: prostate

value: grade IV

value: passage 92


title: Erythroid Prog Control Day 7 2

description:
Sample_Name: S2
Sample_Group: CtlC2_D7
Sentrix_ID: 8795274088
Sentrix_Position: B
Group_Classification: Control_Day7
HSC_DFU_Batch_no: HSC_DFU_Batch2
cRNA_batch_no: cRNA_Batch1

value: Healthy Control


title: NMOB-EV-48hr-1

description: PC3 incubated 48hrs with vesicles from NoDex condition replicate 1

value: vesicles from NoDex condition

value: 48 hrs


title: Lung of bleomycin-treated rat after 3W, replicate 1

value: 3 WEEKS


title: Lung of vehicle-treated rat after 4W, replicate 5

value: 4 WEEKS


title: MOB-Cont-24hr-1

description: PC3 incubated 24hrs with Dex control (no cells) condition replicate 1

value: Dex control (no cells) condition

value: 24 hrs


title: NMOB-Cont-24hr-1

description: PC3 incubated 24hrs with NoDex control (no cells) condition replicate 1

value: NoDex control (no cells) condition


title: Lung of vehicle-treated rat after 2W, replicate 4

value: Lung

value: VEHICLE

value: Pool of 14 rat cell types


title: Lung of vehicle-treated rat after 8W, replicate 2

value: 8 WEEKS


title: Lung of vehicle-treated rat after 3W, replicate 5


title: Lung of bleomycin-treated rat after 1W, replicate 4

value: BLEOMYCIN

value: 1 WEEKS


title: Lung of bleomycin-treated rat after 4W, replicate 1


title: Lung of bleomycin-treated rat after 2W, replicate 1

value: 2 WEEKS


title: Lung of bleomycin-treated rat after 6W, replicate 3

value: 6 WEEKS


title: Lung of bleomycin-treated rat after 3W, replicate 2


title: Lung of bleomycin-treated rat after 1W, replicate 5


title: MOB-Cont-24hr-2

description: PC3 incubated 24hrs with Dex control (no cells) condition replicate 2

value: male (caucasian)

value: 62 yr adult

value: prostate

value: grade IV

value: passage 92


title: Lung of vehicle-treated rat after 3W, replicate 2

value: 3 WEEKS


title: Lung of bleomycin-treated rat after 6W, replicate 4


title: NMOB-EV-48hr-2

description: PC3 incubated 48hrs with vesicles from NoDex condition replicate 2

value: vesicles from NoDex condition

value: 48 hrs


title: Lung of bleomycin-treated rat after 4W, replicate 4

value: 4 WEEKS


title: Lung of bleomycin-treated rat after 1W, replicate 3

value: Lung


title: Lung of vehicle-treated rat after 2W, replicate 5

value: VEHICLE


title: Lung of vehicle-treated rat after 6W, replicate 1

value: Pool of 14 rat cell types


title: NMOB-Cont-4hr-2

description: PC3 incubated 4hrs with NoDex control (no cells) condition replicate 2

value: NoDex control (no cells) condition

value: 4 hrs


title: MOB-Cont-4hr-2

description: PC3 incubated 4hrs with Dex control (no cells) condition replicate 2

value: Dex control (no cells) condition


title: NMOB-Cont-4hr-1

description: PC3 incubated 4hrs with NoDex control (no cells) condition replicate 1


title: MOB-EV-4hr-1

description: PC3 incubated 4hrs with vesicles from Dex condition replicate 1

value: vesicles from Dex condition


title: NMOB-EV-4hr-1

description: PC3 incubated 4hrs with vesicles from NoDex condition replicate 1


title: MOB-EV-24hr-1

description: PC3 incubated 24hrs with vesicles from Dex condition replicate 1

value: 24 hrs


title: MOB-Cont-4hr-1

description: PC3 incubated 4hrs with Dex control (no cells) condition replicate 1

value: male (caucasian)


title: Lung of vehicle-treated rat after 1W, replicate 4

value: 1 WEEKS


title: Lung of bleomycin-treated rat after 6W, replicate 5

value: BLEOMYCIN

value: 6 WEEKS


title: MOB-EV-24hr-2

description: PC3 incubated 24hrs with vesicles from Dex condition replicate 2

value: 62 yr adult

value: prostate

value: grade IV

value: passage 92


title: NMOB-EV-24hr-2

description: PC3 incubated 24hrs with vesicles from NoDex condition replicate 2

value: vesicles from NoDex condition


title: Erythroid Prog B Thal Day 14 3

description: Thal3_D14; 8795274108_L

data_processing: The data was normalized using loess normalization using the lumi R package within the brb-ArrayTools software

source_name: erythroid progenitor_B Thal_day 14

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

extract_protocol: Total RNA was isolated and purified using the Ambion mirVana miRNA Isolation Kit. This was followed by DNase I treatment using the Ambion DNA-free kit. All performed according to the manufatcurer's protocol. Quality control was performed with Agilent Bioanalyser.

value: β-thalassaemia patient

value: male

value: peripheral blood

value: haematopoietic cells

value: 14 days


title: NMOB-EV-4hr-2

description: PC3 incubated 4hrs with vesicles from NoDex condition replicate 2

value: 4 hrs


title: Lung of vehicle-treated rat after 4W, replicate 4

value: Lung

value: VEHICLE

value: 4 WEEKS

value: Pool of 14 rat cell types


title: Lung of bleomycin-treated rat after 8W, replicate 5

value: BLEOMYCIN

value: 8 WEEKS


title: Lung of bleomycin-treated rat after 8W, replicate 2


title: NMOB-EV-24hr-1

description: PC3 incubated 24hrs with vesicles from NoDex condition replicate 1

value: male (caucasian)

value: 62 yr adult

value: 24 hrs


title: Erythroid Prog B Thal Day 14 1

description: Thal1_D14; 8795274108_J

value: female


title: Erythroid Prog B Thal Day 14 2

description: Thal2_D14; 8795274108_K


title: Lung of bleomycin-treated rat after 4W, replicate 5


title: Lung of bleomycin-treated rat after 1W, replicate 2

value: 1 WEEKS


title: Lung of bleomycin-treated rat after 8W, replicate 1


title: Cocultivation at 8 hrs, biological rep1_root

city: London

first: Ze-Chun

last: Yuan

state: Ontario

address: 1391 Sanford Street

department: Microbiology

country: Canada

institute: Southern Crop Protection and Food Research Center, Agricultre and Agri-Foods Canada

description: Gene expression data from roots of 3-week-old seedlings co-cultivated with A. tumefaciens C58 for eight hours in a hydroponic system.

hyb_protocol: 12.5μg of fragmented end-labeled aRNA was hybridized for 16 hours at 45°C to Arabidopsis Genome ATH1 arrays for five cycles in 2x SSC and three cylces in 0.1x SSC.

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

data_processing: The data were analzyed using the Affymetrix Command Console v3.2.4 using the RMA algorithm.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana (3-week-old seedlings) inoculated

label_protocol: Single stranded amplified RNA (aRNA) was prepared from 500 ng of total RNA as per the Affymetrix 3' IVT Express kit manual (Affymetrix, Santa Clara, CA).

growth_protocol: Arabidopsis seedlings were spotted onto semi-solid Murashige-Skoog plates for germination and growth in 16/8 hour light-dark periods with 24/18 degrees celsius. At 3 weeks, seedlings were transferd into hydroponic system and sustained by liquid MS media.

extract_protocol: Qiagen Plant RNeasy column based extraction was performed according to the manufacturere's protocol.

treatment_protocol: Seedlings were inoculated with Agrobacterium tumefaciens C58 (5μL at an OD600 1.5) and cocultivated for 8 hours.

value: Root

tag: cultivar

tag: age

value: 3-week-old Arabidopsis thaliana Col-0 seedlings


title: Lung of vehicle-treated rat after 1W, replicate 3


title: Cocultivation at 8 hrs, biological rep2_root


title: Erythroid Prog B Thal Day 14 5

description: Thal5_D14; 8795274088_K

value: β-thalassaemia patient

value: male

value: peripheral blood


title: Erythroid Prog B Thal Day 14 4

description: Thal4_D14; 8795274088_J

value: haematopoietic cells

value: 14 days


title: Erythroid Prog B Thal Day 14 6

description: Thal6_D14; 8795274088_L


title: NMOB-Cont-24hr-2

description: PC3 incubated 24hrs with NoDex control (no cells) condition replicate 2

value: prostate

value: grade IV

value: passage 92

value: NoDex control (no cells) condition


title: Mock cocultivation at 8 hrs, biological rep2_root

source_name: Arabidopsis thaliana (3-week-old seedlings) mock inoculated


title: Lung of vehicle-treated rat after 3D, replicate 5

value: Lung

value: VEHICLE

value: 3 DAYS

value: Pool of 14 rat cell types


title: Lung of bleomycin-treated rat after 6W, replicate 1

value: BLEOMYCIN

value: 6 WEEKS


title: Erythroid Prog B Thal Day 7 2

description: Thal2_D7; 8795274108_E

source_name: erythroid progenitor_B Thal_day 7

value: female

value: 7 days


title: Erythroid Prog B Thal Day 7 3

description: Thal3_D7; 8795274108_F

value: β-thalassaemia patient


title: Mock cocultivation at 8 hrs, biological rep1_root

value: Root

value: 3-week-old Arabidopsis thaliana Col-0 seedlings


title: Lung of bleomycin-treated rat after 2W, replicate 2

value: 2 WEEKS


title: Lung of vehicle-treated rat after 3D, replicate 3


title: Erythroid Prog B Thal Day 7 1

description: Thal1_D7; 8795274108_D

value: peripheral blood

value: haematopoietic cells


title: Cocultivation at 8 hrs, biological rep2_leaf

value: Leaf


title: Lung of vehicle-treated rat after 6W, replicate 3


title: Mock cocultivation at 8 hrs, biological rep1_leaf


title: Lung of vehicle-treated rat after 3W, replicate 1

value: 3 WEEKS


title: Erythroid Prog B Thal Day 7 6

description: Thal6_D7; 8795274088_F


title: Lung of bleomycin-treated rat after 2W, replicate 5


title: Erythroid Prog B Thal Day 7 5

description: Thal5_D7; 8795274088_E

value: male


title: Lung of vehicle-treated rat after 3D, replicate 1

value: Lung


title: Lung of untreated rat after 3D, replicate 1

value: NAIVE (UNTREATED)


title: Lung of bleomycin-treated rat after 8W, replicate 3

value: 8 WEEKS


title: Cocultivation at 8 hrs, biological rep1_leaf


title: Lung of vehicle-treated rat after 6W, replicate 5

value: VEHICLE

value: Pool of 14 rat cell types


title: Mock cocultivation at 8 hrs, biological rep2_leaf


title: Erythroid Prog Control Day 14 6

description: CtlC6_D14; 8795274108_I

source_name: erythroid progenitor_control_day 14

value: Healthy Control

value: 14 days


title: Erythroid Prog B Thal Day 7 4

description: Thal4_D7; 8795274088_D

value: 7 days


title: Lung of bleomycin-treated rat after 2W, replicate 4

value: BLEOMYCIN


title: Lung of vehicle-treated rat after 4W, replicate 2

value: 4 WEEKS


title: Erythroid Prog Control Day 14 4

description: CtlC4_D14; 8795274108_G


title: Lung of bleomycin-treated rat after 3D, replicate 2

value: 3 DAYS


title: Lung of vehicle-treated rat after 3D, replicate 4


title: Lung of vehicle-treated rat after 6W, replicate 4

value: 6 WEEKS


title: Erythroid Prog Control Day 14 3

description: CtlC3_D14; 8795274088_I

value: peripheral blood


title: Lung of vehicle-treated rat after 6W, replicate 2


title: Lung of vehicle-treated rat after 1W, replicate 5

value: 1 WEEKS


title: Slide 347265

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 1

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of rokA mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: cells

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown in AM17 medium (M17 medium + 10mM ascorbic acid) and harvested at OD600 of 0.15.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: genotype/variation

value: ulaR mutant

value: Wild type


title: Slide 347287

description: Sample 2


title: Lung of bleomycin-treated rat after 4W, replicate 3


title: Lung of vehicle-treated rat after 2W, replicate 1

value: 2 WEEKS


title: Erythroid Prog Control Day 14 2

description: CtlC2_D14; 8795274088_H

value: male

value: haematopoietic cells


title: Lung of bleomycin-treated rat after 1W, replicate 1

value: Lung


title: Erythroid Prog Control Day 14 5

description: CtlC5_D14; 8795274108_H

value: female


title: Lung of vehicle-treated rat after 4W, replicate 3

value: VEHICLE

value: Pool of 14 rat cell types


title: Erythroid Prog Control Day 7 5

description: CtlC5_D7; 8795274108_B

source_name: erythroid progenitor_control_day 7

value: Healthy Control


title: Erythroid Prog Control Day 7 4

description: CtlC4_D7; 8795274108_A

value: 7 days


title: Erythroid Prog Control Day 7 2

description: CtlC2_D7; 8795274088_B


title: Erythroid Prog Control Day 7 3

description: CtlC3_D7; 8795274088_C


title: Lung of bleomycin-treated rat after 3D, replicate 1

value: BLEOMYCIN


title: Erythroid Prog Control Day 7 6

description: CtlC6_D7; 8795274108_C


title: overexpressed polQ timing 2

type: genomic

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

country: France

institute: CNRS/ Université de Paris

hyb_protocol: The hybridization was performed according to the manufacturer instructions on 4× 180K human microarray (SurePrint G3 Human CGH Microarray Kit, 4x180K, AGILENT Technologies, genome reference Hg18) that covers the whole genome with one probe every 13 Kb (11 KB in RefSeq sequences).

scan_protocol: Microarrays were scanned with an Agilent's High-Resolution C Scanner using a resolution of 2 µm and the autofocus option.

data_processing: Feature extraction was performed with the Feature Extraction 9.1 software (Agilent technologies). For each experiment, the raw data sets were automatically normalized by the Feature extraction software. Analysis was performed with the Agilent Genomic Workbench 5.0 software.

molecule: genomic DNA

source_name: neosynthetized DNA in early S phase

label_protocol: Microarray hybridization requires a minimum of 500 ng of DNA and to obtain sufficient specific immunoprecipited DNA, whole genome amplification was conducted (WGA, Sigma). To be sure that this step does not introduce bias, an after WGA qPCR was performed to confirm the specific enrichment in each fractions S1 and S2. After amplification, early and late neo-synthesized DNA were labeled with Cy3 and Cy5 ULS molecules (Genomic DNA labeling Kit, Agilent) as recommended by the manufacturer.

growth_protocol: Modified Eagle Medium with GlutaMAX™ I, High glucose, Sodium Pyruvate (Gibco, Life technologies, Paisley, UK), supplemented with 10% Foetal Bovine Serum (Lonza, Basel, CH), penicillin (100U/ml) and streptomycin (100µg/ml) (Gibco) at 37°C, 5% CO2 and 5% O2 (standard culture conditions).

extract_protocol: cells were incubated with BrdU (50µM) for one hour, then collected, washed three times in PBS, fixed in 75% ethanol, and stored at −20°C. Fixed cells were re-suspended in PBS first with RNAse (0.5 mg/ml) and then with propidium iodide (PI) (50 µg/ml) following by an incubation of 30 min at room temperature. 80,000 cells were sorted in two fractions S1 and S2 using INFLUX 500 (Cytopeia purchased by BD Biosciences) corresponding to Early and Late fractions respectively. Neo-synthesized DNA was immunoprecipited by BrdU antibodies (Anti BrdU Pure, BD Biosciences, # 347580) as described by Hiratani et al 2008. To control the quality of enrichment of early and late fractions in S1 and S2, qPCR was performed with CAV2 oligonucleotides (early control) and with bgGRM8 oligonucleotides (late control).

treatment_protocol: overexpressed PolQ cells are stable cells that overexpress PolQ gene

value: overexpressed PolQ

tag: growth phase

value: early S phase

source_name: neosynthetized DNA in late S phase

value: late S phase


title: Lung of vehicle-treated rat after 8W, replicate 5

value: 8 WEEKS


title: siRNA ESR1-siRNA FOXL2-1

city: GIF SUR YVETTE

first: Adrien

last: Georges

address: CEA/SACLAY

institute: CNRS

hyb_protocol: Nimblegen in-house protocol

scan_protocol: Nimblegen in-house protocol

data_processing: log2 transformation-75th percentile normalisation (from Nimblegen .call global gene expression file)

organism: Mus musculus

source_name: Primary mouse ovarian follicle cells, 9 days post dissection

label_protocol: Nimblegen in-house protocol

growth_protocol: The ovaries of 8-week old female Swiss mice were dissected and digested in DMEM/F-12 medium (Gibco) containing 1mg/mL collagenase (Sigma-Aldrich), 0,5mg/mL BSA (Sidma-Aldrich) and 2000 U/mL DNase I (Thermo-Fisher), in a ratio of 500µL per ovary, at 37°C for 30 min. Ovaries were progressively dispersed during digestion using pipette tips of decreasing size to flush the organ debris. The mix was then diluted in 10 volumes of DMEM/F-12 medium, filtered using a 500 µm membrane, spinned at 300 g. The pellet was rinsed in cold PBS and spinned again, and the pelleted debris were resuspended in a PBS/Ficoll mix of density 1.10. A PBS/Ficoll gradient was made by depositing PBS/Ficoll layers of density 1.08, 1.07, 1.06, 1.05, 1.03 and 1. The gradient was spinned at 1500 g for 20min, and 1 mL fractions were collected and diluted in 5 mL culture medium (i.e. DMEM/F-12 supplemented with 4% FBS, 1% Insulin-Transferrin-Selenium-X supplement, 1% Penicillin-Streptomycine (Gibco) and 10-7M androstenedione (Sigma-Aldrich). We then manually collected intact preantral follicles, characterized by the presence of several layers of granulosa cells around the oocyte and the absence of antrum. They mainly migrated to the 1.07/1.06 and 1.06/1.05 interfaces. Follicles were then rinsed, transferred to culture plates and grown overnight. On day 1, they were dispersed using trypsin and then cultured in monolayers. Culture medium was changed on day 3, and cells were passed on days 5 and 7.

extract_protocol: Trizol extraction

treatment_protocol: cells were seeded 18 h before transfection in 12-well plates. For transfection, cell medium was replaced with a premade Mix containing 500 µL Optimem (Gibco), a total of 12 pmol of siRNAs (2 x 6pmol in the case of simultaneous knockdown), 200 ng pDsRed plasmid (Clontech) and 2µL Lipofectamine 2000 (Life Technologies). 6h after transfection, 1.5 mL of culture medium was added to each well, and cells were then grown for 24h before lysis in 500 µL Trizol reagent (Life Technologies).

tag: strain

value: Swiss

value: Female

value: ovary

value: cells from preantral follicles maintained 9-days in culture (mostly granulosa cells)

tag: biological material provider

value: JANVIER SAS

tag: mrna targeted by 1st sirna

tag: mrna targeted by 2nd sirna

tag: biological replica #


title: Lung of vehicle-treated rat after 1W, replicate 1

tag: tissue

value: 1 WEEKS


title: Erythroid Prog Control Day 7 1

description: CtlC1_D7; 8795274088_A

tag: subject group

tag: gender

value: male

tag: mutation

value: peripheral blood

tag: cell type

value: haematopoietic cells

tag: time in culture


title: siRNA NR5A1-siRNA FOXL2-2


title: siRNA ESR1-siRNA CONTROL-1


title: control replication timing 1

value: control


title: Lung of vehicle-treated rat after 2W, replicate 2

value: Lung

tag: treatment

value: VEHICLE

tag: time

value: 2 WEEKS

value: Pool of 14 rat cell types


title: Lung of bleomycin-treated rat after 6W, replicate 2

value: BLEOMYCIN

value: 6 WEEKS


title: Erythroid Prog Control Day 14 1

description: CtlC1_D14; 8795274088_G

value: Healthy Control

value: 14 days


title: siRNA AR-siRNA FOXL2-1

value: Swiss

value: Female

value: Ar


title: siRNA ESR1-siRNA CONTROL-2

value: ovary

value: cells from preantral follicles maintained 9-days in culture (mostly granulosa cells)

value: JANVIER SAS


title: Lung of bleomycin-treated rat after 3W, replicate 4

value: 3 WEEKS


title: Lung of vehicle-treated rat after 3W, replicate 4


title: overexpressed polQ timing 1

tag: cell line

value: overexpressed PolQ

value: early S phase

value: late S phase


title: control replication timing 2

value: control


title: muzzle_skin_UoL_rep1

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

country: USA

institute: The Jackson Laboratory

hyb_protocol: Ten micrograms of biotin-labeled and fragmented cDNAs were hybridized onto 1.0 ST GeneChip™ arrays (Affymetrix) for 16 hours at 45°C. Post-hybridization staining and washing was done according to the manufacturer's protocols using a Fluidics Station 450 instrument (Affymetrix).

scan_protocol: The arrays were scanned with a GeneChip® Scanner 3000 laser confocal slide scanner. The images were quantified using GCOS 1.0 software (GeneChip® Operating Software, Affymetrix).

data_processing: Two separate gene array experiments were done at two institutions, The Jackson Laboratory and University of Louisville, concurrently. One compared dorsal skin lesion, trichoblastomas, with tail skin papillomas and the respective normal skin. The second compared the dorsal skin lesions to papillomas on the face and the respective normal skin. For each experiment, average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.2) software using the RMA method which incorporates convolution background correction, sketch-quantile normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm.

source_name: muzzle, unaffected skin

label_protocol: Following reverse transcription with an oligo(dT)-T7 primer (Affymetrix, Santa Clara, CA), double-stranded cDNA was synthesized with the GeneChip Expression 3’–Amplification One-cycle kit (Affymetix). In an in vitro transcription (IVT) reaction with T7 RNA polymerase, the cDNA was amplified and labeled with biotinylated nucleotides (Affymetrix).

extract_protocol: Total RNA was isolated by standard TRIzol methods, and quality assessed using a 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA)

treatment_protocol: For cutaneous inoculation, small areas of skin (0.5 cm2 on the muzzle, dorsal back and/or tail) were scarified with a 20 gauge needle. One µl of the MmuPV1 cell-free homogenate was applied at each site. For maximum efficiency of infection, the scarified skin was then gently rubbed with the side of pipet tip. Mice were observed on a daily basis. When lesions approached 1 cm in diameter, in accordance with IACUC regulations, mice were euthanized and tumors were collected.

tag: location

value: muzzle

tag: tissue type

value: unaffected skin


title: siRNA AR-siRNA FOXL2-2

tag: age


title: muzzle_skin_UoL_rep2

tag: strain


title: Lung of bleomycin-treated rat after 3W, replicate 5

value: Lung

value: BLEOMYCIN

value: Pool of 14 rat cell types


title: muzzle_skin_UoL_rep3


title: Lung of vehicle-treated rat after 1W, replicate 2

value: VEHICLE

value: 1 WEEKS


title: Lung of bleomycin-treated rat after 3D, replicate 4

value: 3 DAYS


title: muzzle_tumor_UoL_rep2

source_name: muzzle, papilloma

value: papilloma


title: muzzle_tumor_UoL_rep3


title: Lung of vehicle-treated rat after 3W, replicate 3


title: dorsal_skin_UoL_rep3

source_name: dorsal, unaffected skin

value: dorsal


title: siRNA CONTROL-siRNA CONTROL-2

value: Swiss

value: Female

value: ovary

value: cells from preantral follicles maintained 9-days in culture (mostly granulosa cells)

tag: biological material provider


title: muzzle_tumor_UoL_rep1


title: dorsal_skin_UoL_rep1


title: siRNA NR5A1-siRNA CONTROL-1

value: JANVIER SAS

tag: mrna targeted by 1st sirna


title: siRNA CONTROL-siRNA FOXL2-1

tag: mrna targeted by 2nd sirna


title: siRNA NR2C1-siRNA CONTROL-2

tag: biological replica #


title: siRNA ESR2-siRNA FOXL2-2

tag: tissue


title: Lung of bleomycin-treated rat after 3D, replicate 3


title: siRNA ESR2-siRNA FOXL2-1


title: dorsal_skin_UoL_rep2


title: siRNA CONTROL-siRNA FOXL2-2


title: dorsal_tumor_UoL_rep3

source_name: dorsal, trichoblastoma

value: trichoblastoma


title: Lung of bleomycin-treated rat after 4W, replicate 2

value: 4 WEEKS


title: Lung of bleomycin-treated rat after 3W, replicate 3

value: 3 WEEKS


title: Lung of untreated rat after 3D, replicate 3

value: NAIVE (UNTREATED)


title: Fat control_RNA pool

city: Cologne

first: Helen

last: Künstlinger

address: Kerpener Str. 62

department: Institute of Pathology

country: Germany

institute: University Hospital Cologne

description: Gene expression in RNA pool of 8 healthy fat tissue samples

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent technologies, Santa Clara CA / US). 1.65 µg Cy3-labeled fragmented cRNA in hybridization buffer were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent's recommended hybridization chamber and oven. After hybridization, microarrays were washed with Agilent Gene Expression Wash Buffer 1 (1 min, room temperature) followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (1 min, 37°C) and a final washing step with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies, Santa Clara CA / US).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. Signal intensities from the single-experiment raw data lists were normalized by dividing the intensity values by their median. These normalized signal inetnsities are joined to a common table (normalized data_matrix.xlsx).

label_protocol: To produce Cy3-labeled cRNA, 0.5 µg of each total RNA sample were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies, Santa Clara CA / US) following the manufacturer's protocol. Yields of cRNA and the dye-incorporation rate were measured with the NanoDrop-1000 spectrophotometer (Thermo Fisher scientific Inc., Waltham MA / US).

extract_protocol: Total RNA was extracted using the miRNeasy mini kit (Qiagen, Hilden / GER) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer  (Thermo Fisher scientific Inc., Waltham MA / US) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA / US).

treatment_protocol: Tissue of primary myxoid liposarcomas and healthy fat tissue samples were cryo-conserved. All samples were histologically characterized by an experienced pathologist and specific DDIT3 translocation was proven in myxoid liposarcoma samples by FISH and RT-PCR.

value: Cryo-conserved healthy fat tissue

tag: rearrangement


title: Lung of bleomycin-treated rat after 8W, replicate 4

value: Lung

value: BLEOMYCIN

value: 8 WEEKS


title: siRNA NR5A1-siRNA FOXL2-1

tag: gender


title: siRNA NR2C1-siRNA FOXL2-2


title: dorsal_tumor_UoL_rep2


title: Myxoid liposarcoma_MLS 01

description: Gene expression in primary myxoid liposarcoma sample

source_name: primary myoid liposarcoma tissue

value: Cryo-conserved tumor tissue


title: siRNA NR2C1-siRNA CONTROL-1


title: tail_skin_JAX_rep3

source_name: tail, unaffected skin

value: tail

value: unaffected skin


title: siRNA AR-siRNA CONTROL-2

value: Ar


title: dorsal_tumor_UoL_rep1

value: dorsal


title: tail_skin_JAX_rep2


title: Myxoid liposarcoma_MLS 15


title: siRNA ESR2-siRNA CONTROL-1

value: Swiss

value: Female


title: Myxoid liposarcoma_MLS 16


title: Myxoid liposarcoma_MLS 14


title: tail_tumor_JAX_rep3

source_name: tail, papilloma

value: papilloma


title: siRNA ESR1-siRNA FOXL2-2

value: ovary

value: cells from preantral follicles maintained 9-days in culture (mostly granulosa cells)

value: JANVIER SAS


title: dorsal_skin_JAX_rep1


title: siRNA AR-siRNA CONTROL-1


title: dorsal_skin_JAX_rep3


title: siRNA NR2C1-siRNA FOXL2-1


title: siRNA ESR2-siRNA CONTROL-2


title: Myxoid liposarcoma_MLS 12


title: tail_skin_JAX_rep1


title: dorsal_skin_JAX_rep2


title: dorsal_tumor_JAX_rep3

value: trichoblastoma


title: siRNA NR5A1-siRNA CONTROL-2


title: siRNA CONTROL-siRNA CONTROL-1


title: Myxoid liposarcoma_MLS 13


title: Normal 3

city: Göttingen

first: Michael

last: Zeisberg

address: Robert-Koch-Street 40

department: Nephrology/Rheumatology

institute: University Medical Center Göttingen

hyb_protocol: The biotinylated cDNA is added to a hybridization solution with several biotinylated control oligos and hybridized to an Affymetrix Mouse Expression Array 430 2.0 Chip overnight at 45°C. The chips are then washed in the Affymetrix Fluidics Station 400 to remove unhybridized cDNA that didn't bind to its complimentary probe. The bound cDNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: The GeneChips were scanned with a GeneChip Scanner 3000 7G equipped for High Resolution, which records the location and magnitude of fluorescent emissions given off when the scanner excites a cDNA bound to its complimentary oligo.

data_processing: The data was normalized at the probe intensity level using dChip2006, with the baseline being set by the array with median signal intensity, MZ2007091209 (Normal 1). A broad comparison analysis was performed to look for differences in expression profiles between the control and IRI-fibroblasts, yielding the normalized data values for the entire probe set. Examination of the data quality metrics showed some variation within the groups. Two samples from each group were selected for use in further analysis, due to their identical median intensity values, comparable percent present values, and 3’/5’ internal control ratios for GAPDH and β-actin expression, in order to ensure quality in the data and calculations. The microarray data was assembled and submitted to the NCBI GEO database to be made freely available in accordance with the MIAME convention.

source_name: Biotinylated cDNA, sham (control) kidney

label_protocol: Biotinylation cDNA was prepared with the NuGEN FL-Ovation cDNA Biotin Module V2 Kit according to manufacturer's instructions from 5.0ug of cDNA.

growth_protocol: Mice were 6 months old at time of experiment, no special prepartions; after ischemia reperfusion surgery, 0.05mg/kg Buprenorphine was admiinistered 1-2x daily to provide post-operative pain relief

extract_protocol: Total RNA was isolated from the FSP1-GFP+ sorted cells with the Qiagen miRNeasy Kit, then amplified with the NuGen WT-Ovation Pico RNA Amplification System, both according to manufacturer's specifications.

treatment_protocol: 5 Male FSP-GFP1 positive mice underwent Ischemia Reperfusion surgery, in which the renal artery and vein of the animal's left kidney are clamped using an 85g pressure micro clamp for 45 minutes, then released. After three days, the mice were sacrificed, and a single cell suspension was generated from the kidneys by subsequent mincing, collagenase digestion and filtration. FSP1-GFP+ cells were isolated by FACS sorting of the single cell suspensions, and a portion of the isolated cells were culture on plastic to confirm they were in fact FSP1-GFP positive fibroblasts by their displaying of typical fibroblast morphology.

tag: genetic background

tag: transgenic strain

value: Male

value: 6 months

value: Kidney

tag: group

value: Control (Non-ischemic Kidney)


title: tail_tumor_JAX_rep2


title: Normal 2


title: Myxoid liposarcoma_MLS 11


title: dorsal_tumor_JAX_rep2


title: dorsal_tumor_JAX_rep1


title: Ischemic 3

source_name: Biotinylated cDNA, d:3 post-IRI kidney

tag: treatment

value: Ischemia Reperfusion Surgery - Clamped left renal artery and vein for 45 minutes, then clamp is removed; acute kidney injury peaks day 3, almost completely heals by day 10

tag: days since surgery

value: Post-ischemia (Reperfused Kidney)


title: Ischemic 4


title: Normal 1


title: Ischemic 5


title: tail_tumor_JAX_rep1

value: tail


title: heart_normal_rep3.

city: Beijing

first: Jian

last: Zhou

address: Gongtinan Road 8

country: China

institute: Chaoyang Hospital

description:
normal heart rhythm
SAMPLE 10

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: GenomeStudio software V2011.1.

label: Cy5 and Cy3

source_name: left atrium,normal

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from left atrium samples using Qiagen DNeasy Kit according to standard instructions

value: left atrium

tag: condition

value: normal

tag: tag

value: male


title: heart_normal_rep4.

description:
normal heart rhythm
SAMPLE 11

value: female


title: Ischemic 1


title: Human umbilical cord mesenchymal stem cells cultured in serum free medium, biological rep 3

city: Tianjin

first: Youwei

last: Wang

state: --- Select One ---

address: 92 Weijin Road

department: Medical College

institute: Tianjin University

hyb_protocol: According to the protocol from Affymetrix, bio-tagged cRNA were fragmented and hybridized to Human Genome U133 Plus 2.0 containing over 47,000 transcripts.

scan_protocol: After hybridizing, the arrays were washed, stained by Affymetrix Fluidics Station 450 and scanned by GeneChip Scanner 3000.

data_processing: The intensity values of different microarray were normalized and log2 transformed using RMA gene core algorithm provided by Expression Console (Affymetrix).

label_protocol: one µg of total RNA was used to synthesize double-stranded cDNA and then produced biotin-tagged cRNA using the MessageAmpTM II aRNA Amplification Kit.

growth_protocol: hUC-MSCs were cultured on tissue culture surface with serum-containing medium which contained 10% fetal bovine serum or on a chemical treated cell culture surface with a chemical defined serum free medium, at 37℃ and 5% CO2. After reaching 90% confluence, hUC-MSCs were detached and subcultured at a ratio of 1:3 till reaching senescence.

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

treatment_protocol: hUC-MSCs were detached from flask by enzyme.

tag: growth protocol

value: serum free medium


title: Ischemic 2

tag: age


title: Human umbilical cord mesenchymal stem cells cultured in serum free medium, biological rep 2


title: Human umbilical cord mesenchymal stem cells cultured in serum containing medium, biological rep 3

value: serum containing medium


title: donor4_CD4+CD8+CD3-

status: Public on Oct 27 2014

city: Gent

first: Annelynn

last: Wallaert

address: De Pintelaan 185

country: Belgium

institute: UGent

description: Gene expression of CD4+CD8+CD3- T-cell subsets of donor4

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to teh array for 17 hours at 65°C in a rotating 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner with SureScan High-Resolution Technology using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the VSN-package (Bioconductor)

source_name: donor4, CD4+CD8+CD3-

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labling kit (Agilent) according to the manufacturer's instructions, followed by miRNeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was harvested with the miRNeasy mini kit (Qiagen) with Dnase treatment on-column.

treatment_protocol: CD34 MACS purified thymocytes were labeled with CD34, CD1 and CD4 to sort CD34+CD1-CD4- and CD34+CD1+CD4+ thymocytes, while CD4+CD8+CD3- and CD4+CD8+CD3+ were sorted following CD4, CD8 and CD3 labeling of a total thymus suspension.

tag: t cell subset


title: heart_normal_rep1.

description:
normal heart rhythm
SAMPLE 8


title: Human umbilical cord mesenchymal stem cells cultured in serum containing medium, biological rep 1


title: donor5_CD4+CD8+CD3+

description: Gene expression of CD4+CD8+CD3+ T-cell subsets of donor5

source_name: donor5, CD4+CD8+CD3+


title: Human umbilical cord mesenchymal stem cells cultured in serum free medium, biological rep 1


title: donor4_CD4+CD8+CD3+

description: Gene expression of CD4+CD8+CD3+ T-cell subsets of donor4

source_name: donor4, CD4+CD8+CD3+


title: donor3_CD4+CD8+CD3+

description: Gene expression of CD4+CD8+CD3+ T-cell subsets of donor3

source_name: donor3, CD4+CD8+CD3+


title: donor5_CD34+ MACS

description: Gene expression of CD34+ T-cell subset of donor5

source_name: donor5, CD34+ MACS


title: heart_atrial fibrilation_rep7.

description:
atrial fibrillation
SAMPLE 7

value: atrial fibrillation, permanent


title: donor2_CD4+CD8+CD3+

description: Gene expression of CD4+CD8+CD3+ T-cell subset of donor2

source_name: donor2, CD4+CD8+CD3+


title: donor3_CD34+CD1-CD4-

description: Gene expression of CD34+CD1-CD4- T-cell subset of donor3

source_name: donor3, CD34+CD1-CD4-


title: Human umbilical cord mesenchymal stem cells cultured in serum containing medium, biological rep 2


title: donor5_CD4+CD8+CD3-

description: Gene expression of CD4+CD8+CD3- T-cell subsets of donor5

source_name: donor5, CD4+CD8+CD3-


title: donor3_CD34+CD1+CD4+

description: Gene expression of CD34+CD1+CD4+ T-cell subset of donor3

source_name: donor3, CD34+CD1+CD4+


title: donor4_CD34+ MACS

description: Gene expression of CD34+ T-cell subset of donor4

source_name: donor4, CD34+ MACS


title: heart_atrial fibrilation_rep1.

description:
atrial fibrillation
SAMPLE 1


title: donor2_CD34+CD1+CD4+

description: Gene expression of CD34+CD1+CD4+ T-cell subset of donor2

source_name: donor2, CD34+CD1+CD4+


title: heart_atrial fibrilation_rep2.

description:
atrial fibrillation
SAMPLE 2


title: heart_normal_rep2.

description:
normal heart rhythm
SAMPLE 9


title: OP9_GFP_donor4

description: Gene expression of CD34+ cells after a 48h coculture with an OP9-GFP feeder layer.

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating 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).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the VSN-package (Bioconductor) and background correction was performed during the normalization process, selecting those probes detecting a 2 times higher expression than the average of the DarkCorner probes in at least 60% of the samples one treatment.

source_name: CD34+, OP9-GFP, donor4

treatment_protocol: CD34+ thymocytes were purified out of pediatric thymus samples using MACS and seeded onto confluent OP9-GFP (control) or OP9-DLL1 plates for 48h in α-MEM media supplemented with 20% heat-inactivated FCS plus 100U penicilin, 100 µg/ml streptomycin, 2 mM L-glutamine and cytokines SCF, Flt-3 and IL-7 at 5 ng/ml each.

tag: co-culture


title: OP9_GFP_donor2

source_name: CD34+, OP9-GFP, donor2


title: heart_atrial fibrilation_rep6.

description:
atrial fibrillation
SAMPLE 6


title: OP9_DLL1_donor4

description: Gene expression of CD34+ cells after a 48h coculture with an OP9-DLL1 feeder layer.

source_name: CD34+, OP9-DLL1, donor4


title: heart_atrial fibrilation_rep4.

description:
atrial fibrillation
SAMPLE 4


title: donor2_CD34+CD1-CD4-

description: Gene expression of CD34+CD1-CD4- T-cell subset of donor2

source_name: donor2, CD34+CD1-CD4-


title: OP9_GFP_donor3

source_name: CD34+, OP9-GFP, donor3


title: OP9_DLL1_donor3

source_name: CD34+, OP9-DLL1, donor3


title: OP9_DLL1_donor2

source_name: CD34+, OP9-DLL1, donor2


title: ALLSIL_DMSO_48h

description: Gene expression after 48h DMSO treatment of ALL-SIL cell line

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating  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).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the VSN-package (Bioconductor) and background correction was performed during the normalization process, selecting those probes detecting a 10% higher expression than the negative control probes of the array design in at least one treatment.

source_name: ALLSIL, DMSO, 48h

growth_protocol: Cells were grown in RPMI supplemented with 10% or 20% (ALL-SIL)  fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

treatment_protocol: Cells were seeded at 1*10^6 cells/ml and treated with either DMSO or 1 µM of Compound E. Cells were harvested 12 and 48h after treatment.

tag: cell line

value: ALL-SIL

value: DMSO

tag: time


title: OP9_GFP_donor1

source_name: CD34+, OP9-GFP, donor1


title: heart_atrial fibrilation_rep5.

description:
atrial fibrillation
SAMPLE 5


title: TALL1_DMSO_48h

description: Gene expression after 48h DMSO treatment of TALL-1 cell line

source_name: TALL1, DMSO, 48h


title: ALLSIL_GSI_48h

description: Gene expression after 48h GSI treatment of ALL-SIL cell line

source_name: ALLSIL, GSI, 48h

value: GSI


title: DND41_GSI_48h

description: Gene expression after 48h GSI treatment of DND-41 cell line

source_name: DND41, GSI, 48h


title: DND41_DMSO_48h

description: Gene expression after 48h DMSO treatment of DND-41 cell line

source_name: DND41, DMSO, 48h


title: OP9_DLL1_donor1

source_name: CD34+, OP9-DLL1, donor1


title: heart_atrial fibrilation_rep3.

description:
atrial fibrillation
SAMPLE 3


title: TALL1_DMSO_12h

description: Gene expression after 12h DMSO treatment of TALL-1 cell line

source_name: TALL1, DMSO, 12h


title: ALLSIL_GSI_12h

description: Gene expression after 12h GSI treatment of ALL-SIL cell line

source_name: ALLSIL, GSI, 12h


title: DND41_GSI_12h

description: Gene expression after 12h GSI treatment of DND-41 cell line

source_name: DND41, GSI, 12h


title: TALL1_GSI_12h

description: Gene expression after 12h GSI treatment of TALL-1 cell line

source_name: TALL1, GSI, 12h


title: HPBALL_GSI_48h

description: Gene expression after 48h GSI treatment of HPB-ALL cell line

source_name: HPBALL, GSI, 48h

value: HPB-ALL


title: HPBALL_DMSO_48h

description: Gene expression after 48h DMSO treatment of HPB-ALL cell line

source_name: HPBALL, DMSO, 48h


title: DND41_DMSO_12h

description: Gene expression after 12h DMSO treatment of DND-41 cell line

source_name: DND41, DMSO, 12h


title: HPBALL_GSI_12h

description: Gene expression after 12h GSI treatment of HPB-ALL cell line

source_name: HPBALL, GSI, 12h


title: ALLSIL_DMSO_12h

description: Gene expression after 12h DMSO treatment of ALL-SIL cell line

source_name: ALLSIL, DMSO, 12h


title: CUTLL1_DMSO_48h_3

description: Gene expression after 48h DMSO treatment of CUTLL1 cell line replicate 3

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the VSN-package (Bioconductor) and background correction was performed during the normalization process, selecting those probes detecting a 10 % higher expression than the negative control probes of the array design in at least one treatment.

source_name: CUTLL1, DMSO, 48h, 3

growth_protocol: Cells were grown in RPMI supplemented with 20% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin


title: TALL1_GSI_48h

description: Gene expression after 48h GSI treatment of TALL-1 cell line

source_name: TALL1, GSI, 48h


title: HPBALL_DMSO_12h

description: Gene expression after 12h DMSO treatment of HPB-ALL cell line

source_name: HPBALL, DMSO, 12h


title: CUTLL1_DMSO_48h_2

description: Gene expression after 48h DMSO treatment of CUTLL1 cell line replicate 2

source_name: CUTLL1, DMSO, 48h, 2


title: CUTLL1_GSI_12h_3

description: Gene expression after 12h GSI treatment of CUTLL1 cell line replicate 3

source_name: CUTLL1, GSI, 12h, 3


title: CUTLL1_GSI_48h_3

description: Gene expression after 48h GSI treatment of CUTLL1 cell line replicate 3

source_name: CUTLL1, GSI, 48h, 3


title: CUTLL1_GSI_12h_2

description: Gene expression after 12h GSI treatment of CUTLL1 cell line replicate 2

source_name: CUTLL1, GSI, 12h, 2


title: CUTLL1_DMSO_12h_3

description: Gene expression after 12h DMSO treatment of CUTLL1 cell line replicate 3

source_name: CUTLL1, DMSO, 12h, 3


title: donor3_CD4+CD8+CD3-

description: Gene expression of CD4+CD8+CD3- T-cell subset of donor3

source_name: donor3, CD4+CD8+CD3-


title: CUTLL1_GSI_48h_2

description: Gene expression after 48h GSI treatment of CUTLL1 cell line replicate 2

source_name: CUTLL1, GSI, 48h, 2


title: CUTLL1_DMSO_48h_1

description: Gene expression after 48h DMSO treatment of CUTLL1 cell line replicate 1

source_name: CUTLL1, DMSO, 48h, 1


title: CUTLL1_DMSO_12h_2

description: Gene expression after 12h DMSO treatment of CUTLL1 cell line replicate 2

source_name: CUTLL1, DMSO, 12h, 2


title: CUTLL1_GSI_12h_1

description: Gene expression after 12h GSI treatment of CUTLL1 cell line replicate 1

source_name: CUTLL1, GSI, 12h, 1


title: CUTLL1_GSI_48h_1

description: Gene expression after 48h GSI treatment of CUTLL1 cell line replicate 1

source_name: CUTLL1, GSI, 48h, 1


title: CUTLL1_DMSO_12h_1

description: Gene expression after 12h DMSO treatment of CUTLL1 cell line replicate 1

source_name: CUTLL1, DMSO, 12h, 1


title: TALL_JS_63

description: Gene expression of T-ALL patient bone marrow sample

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: bone marrow

tag: disease state

value: T-ALL

tag: sample type

value: bone marrow sample


title: TALL_JS_60

description: Gene expression of T-ALL patient blood sample

source_name: blood

value: blood sample


title: TALL_JS_61


title: TALL_JS_59


title: TALL_JS_57


title: TALL_JS_62


title: TALL_JS_64


title: TALL_JS_58


title: TALL_JS_55


title: TALL_JS_54


title: TALL_JS_56


title: TALL_JS_52


title: TALL_JS_53

description: Gene expression of T-ALL patient EM sample

source_name: EM

value: EM sample


title: TALL_JS_50


title: TALL_JS_51


title: TALL_JS_49


title: TALL_JS_47


title: TALL_JS_48


title: TALL_JS_46


title: TALL_JS_45


title: TALL_JS_44


title: TALL_JS_43


title: USC.DISC.MIBC193

city: vancouver

first: Mohammed

last: Alshalalfa

state: bc

address: water st

institute: GenomeDx

description:
muscle_invasive_bladder_cancer_primary_193
celfile_group_name: Mitra2014-BladderRec-tst

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using fRMA software package (Bioconductor)
probe group file: HuEx-1_0-st-v1.r2.pgf

source_name: primary muscle-invasive bladder cancer FFPE tissue sample

label_protocol: RNA was amplified, fragmented and biotinylated using the Ovation FFPE system v 2.0 (NuGEN)

extract_protocol: not provided

tag: tissue type


title: USC.DISC.MIBC190

description:
muscle_invasive_bladder_cancer_primary_190
celfile_group_name: Mitra2014-BladderRec-tst

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: USC.DISC.MIBC192

description:
muscle_invasive_bladder_cancer_primary_192
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC188

description:
muscle_invasive_bladder_cancer_primary_188
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC186

description:
muscle_invasive_bladder_cancer_primary_186
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC194

description:
muscle_invasive_bladder_cancer_primary_194
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC189

description:
muscle_invasive_bladder_cancer_primary_189
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC191

description:
muscle_invasive_bladder_cancer_primary_191
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC182

description:
muscle_invasive_bladder_cancer_primary_182
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC195

description:
muscle_invasive_bladder_cancer_primary_195
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC196

description:
muscle_invasive_bladder_cancer_primary_196
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC178

description:
muscle_invasive_bladder_cancer_primary_178
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC181

description:
muscle_invasive_bladder_cancer_primary_181
celfile_group_name: Mitra2014-BladderRec-tst


title: TALL_JS_42


title: TALL_JS_40


title: USC.DISC.MIBC199

description:
muscle_invasive_bladder_cancer_primary_199
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC179

description:
muscle_invasive_bladder_cancer_primary_179
celfile_group_name: Mitra2014-BladderRec-tst


title: TALL_JS_39

description: Gene expression of T-ALL patient bone marrow sample


title: TALL_JS_41


title: TALL_JS_37

description: Gene expression of T-ALL patient blood sample


title: USC.DISC.MIBC180

description:
muscle_invasive_bladder_cancer_primary_180
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC187

description:
muscle_invasive_bladder_cancer_primary_187
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC177

description:
muscle_invasive_bladder_cancer_primary_177
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC197

description:
muscle_invasive_bladder_cancer_primary_197
celfile_group_name: Mitra2014-BladderRec-tst


title: TALL_JS_36


title: USC.DISC.MIBC176

description:
muscle_invasive_bladder_cancer_primary_176
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC174

description:
muscle_invasive_bladder_cancer_primary_174
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC173

description:
muscle_invasive_bladder_cancer_primary_173
celfile_group_name: Mitra2014-BladderRec-trn


title: TALL_JS_35


title: TALL_JS_34


title: USC.DISC.MIBC183

description:
muscle_invasive_bladder_cancer_primary_183
celfile_group_name: Mitra2014-BladderRec-tst


title: TALL_JS_33


title: TALL_JS_38


title: TALL_JS_32


title: USC.DISC.MIBC185

description:
muscle_invasive_bladder_cancer_primary_185
celfile_group_name: Mitra2014-BladderRec-tst


title: TALL_JS_31


title: USC.DISC.MIBC175

description:
muscle_invasive_bladder_cancer_primary_175
celfile_group_name: Mitra2014-BladderRec-trn


title: TALL_JS_29


title: TALL_JS_28


title: TALL_JS_27


title: TALL_JS_26


title: TALL_JS_25


title: TALL_JS_24


title: USC.DISC.MIBC184

description:
muscle_invasive_bladder_cancer_primary_184
celfile_group_name: Mitra2014-BladderRec-tst


title: TALL_JS_30


title: TALL_JS_23


title: TALL_JS_22


title: USC.DISC.MIBC167

description:
muscle_invasive_bladder_cancer_primary_167
celfile_group_name: Mitra2014-BladderRec-trn


title: TALL_JS_20


title: TALL_JS_21


title: USC.DISC.MIBC198

description:
muscle_invasive_bladder_cancer_primary_198
celfile_group_name: Mitra2014-BladderRec-trn


title: TALL_JS_19


title: USC.DISC.MIBC165

description:
muscle_invasive_bladder_cancer_primary_165
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC162

description:
muscle_invasive_bladder_cancer_primary_162
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC172

description:
muscle_invasive_bladder_cancer_primary_172
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC171

description:
muscle_invasive_bladder_cancer_primary_171
celfile_group_name: Mitra2014-BladderRec-trn


title: TALL_JS_17

description: Gene expression of T-ALL patient bone marrow sample


title: TALL_JS_16

description: Gene expression of T-ALL patient blood sample


title: TALL_JS_18


title: USC.DISC.MIBC168

description:
muscle_invasive_bladder_cancer_primary_168
celfile_group_name: Mitra2014-BladderRec-trn


title: TALL_JS_13


title: TALL_JS_15


title: USC.DISC.MIBC169

description:
muscle_invasive_bladder_cancer_primary_169
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC164

description:
muscle_invasive_bladder_cancer_primary_164
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC160

description:
muscle_invasive_bladder_cancer_primary_160
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC163

description:
muscle_invasive_bladder_cancer_primary_163
celfile_group_name: Mitra2014-BladderRec-trn


title: TALL_JS_14


title: USC.DISC.MIBC157

description:
muscle_invasive_bladder_cancer_primary_157
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC159

description:
muscle_invasive_bladder_cancer_primary_159
celfile_group_name: Mitra2014-BladderRec-trn


title: TALL_JS_12


title: USC.DISC.MIBC161

description:
muscle_invasive_bladder_cancer_primary_161
celfile_group_name: Mitra2014-BladderRec-trn


title: TALL_JS_11


title: USC.DISC.MIBC156

description:
muscle_invasive_bladder_cancer_primary_156
celfile_group_name: Mitra2014-BladderRec-trn


title: TALL_JS_9


title: TALL_JS_8


title: TALL_JS_10


title: USC.DISC.MIBC155

description:
muscle_invasive_bladder_cancer_primary_155
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC158

description:
muscle_invasive_bladder_cancer_primary_158
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC170

description:
muscle_invasive_bladder_cancer_primary_170
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC154

description:
muscle_invasive_bladder_cancer_primary_154
celfile_group_name: Mitra2014-BladderRec-trn


title: TALL_JS_6


title: USC.DISC.MIBC151

description:
muscle_invasive_bladder_cancer_primary_151
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC150

description:
muscle_invasive_bladder_cancer_primary_150
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC153

description:
muscle_invasive_bladder_cancer_primary_153
celfile_group_name: Mitra2014-BladderRec-trn


title: TALL_JS_4

description: Gene expression of T-ALL patient blood sample


title: TALL_JS_7


title: TALL_JS_1

description: Gene expression of T-ALL patient bone marrow sample


title: USC.DISC.MIBC152

description:
muscle_invasive_bladder_cancer_primary_152
celfile_group_name: Mitra2014-BladderRec-trn


title: TALL_JS_2


title: TALL_JS_3


title: USC.DISC.MIBC146

description:
muscle_invasive_bladder_cancer_primary_146
celfile_group_name: Mitra2014-BladderRec-tst


title: TALL_JS_5


title: USC.DISC.MIBC147

description:
muscle_invasive_bladder_cancer_primary_147
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC166

description:
muscle_invasive_bladder_cancer_primary_166
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC149

description:
muscle_invasive_bladder_cancer_primary_149
celfile_group_name: Mitra2014-BladderRec-trn


title: 4458_MUT

description: Gene expression of blood from a T-ALL patient with mutant NOTCH1

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed with the VSN-package (Limma) and during the normalization preocess, probes were selected that detected a 10 % higher expression than the negative control probes of the array design in at least one treatment.

value: T-cell acute lymphoblastic leukemia

value: mutant


title: 4925_MUT


title: USC.DISC.MIBC148

description:
muscle_invasive_bladder_cancer_primary_148
celfile_group_name: Mitra2014-BladderRec-trn


title: 4449_MUT


title: 4436_MUT


title: USC.DISC.MIBC136

description:
muscle_invasive_bladder_cancer_primary_136
celfile_group_name: Mitra2014-BladderRec-trn


title: 4472_MUT


title: 4471_MUT


title: 4443_MUT


title: USC.DISC.MIBC141

description:
muscle_invasive_bladder_cancer_primary_141
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC137

description:
muscle_invasive_bladder_cancer_primary_137
celfile_group_name: Mitra2014-BladderRec-trn


title: 4470_WT

description: Gene expression of blood from a T-ALL patient with wild type NOTCH1

value: WT


title: 4424_WT


title: USC.DISC.MIBC138

description:
muscle_invasive_bladder_cancer_primary_138
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC135

description:
muscle_invasive_bladder_cancer_primary_135
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC143

description:
muscle_invasive_bladder_cancer_primary_143
celfile_group_name: Mitra2014-BladderRec-trn


title: 4441_WT


title: USC.DISC.MIBC142

description:
muscle_invasive_bladder_cancer_primary_142
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC140

description:
muscle_invasive_bladder_cancer_primary_140
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC134

description:
muscle_invasive_bladder_cancer_primary_134
celfile_group_name: Mitra2014-BladderRec-trn


title: 4444_WT


title: 4437_WT


title: 4461_WT


title: 4442_WT


title: 4448_WT


title: 500 μM_MNU_Replicate_3

city: Bilthoven

first: Mirjam

middle: M

last: Schaap

address: Antonie van Leeuwenhoeklaan 9

institute: RIVM

description: quality control: approved

hyb_protocol: According to the protocol provided with the Affymetrix 3'IVT Express Labeling Kit  According to the protocol provided with the Affymetrix 3'IVT Express Labeling Kit (#901229)

scan_protocol: According to Affymetrix protocols, using a GeneChip HT Array Plate Scanner (Affymetrix)

data_processing: The raw data were subjected to a set of quality control checks. After passing array quality control, the arrays were annotated according to de Leeuw et al. (2008) and expression values were calculated using the robust multi-array average (RMA) algorithm (Affy package, version 1.22.0; Irizarry et al. 2003) available from the Bioconductor project (http://www.bioconductor.org) for the R statistical language (http://cran.r-project.org)). The normalized data was statistically analyzed for differential gene expression using a mixed linear model with coefficients for block (random) and each experimental group (fixed) (Smyth 2004; Wolfinger et al. 2001). A contrast analysis was applied to compare each exposure with the corresponding vehicle control. For hypothesis testing, a permutation-based Fs test was used (Cui et al. 2005). False discovery rate (FDR) correction was performed globally across all contrasts according to Storey and Tibshirani (2003). Only the annotated genes were used for further analysis.

source_name: Embryonic stem cells

label_protocol: Biotins labeled cRNA samples were prepared as described in the Affymetrix GeneChip HT 3” IVT Express Technical Manual (Affymetrix) using 200 ng of purified total RNA as template for the reaction.

growth_protocol: Wild type mouse embryonic stem cells (ESC) (B4418 of C57Bl/6 genetic background) were maintained on mitomycin-C treated mouse embryonic fibroblast (MEF) feeders in ES complete medium. Exposure experiments were conducted with ESC cells at passage three (P3), which were cultured on 0.1% (w/v) gelatin-coated plates or wells (Greiner) in ES-BRL medium. To obtain third passage cells, ESC were re-seeded from MEF feeder layers to gelatin-coated plates and subsequently passed twice on gelatin-coated plates or wells. Cultures were incubated at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol: RNA was extracted using QIAzol and purified using the miRNeasy mini kit and the QIAcube (Qiagen), according to the manufacturer’s protocol.

treatment_protocol: Mouse embryonic stem cells were exposed for 8 hours to the chemicals. Control cells were vehicle-treated (DMSO or PBS, 0.5%). After 8 hours of exposure, cells were collected in 1 ml RNAprotect (QIAgen) and stored at -80˚C for RNA isolation.

tag: cell type

value: Embryonic stem cells

tag: strain

value: B4418 of C57BL/6 background

tag: chemical

value: N-Methyl-N-nitrosourea

tag: abbreviation

value: MNU

tag: concentration

value: 500 μM MNU


title: USC.DISC.MIBC145

description:
muscle_invasive_bladder_cancer_primary_145
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC139

description:
muscle_invasive_bladder_cancer_primary_139
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC132

description:
muscle_invasive_bladder_cancer_primary_132
celfile_group_name: Mitra2014-BladderRec-tst


title: 100 μM_DEM_Replicate_3

description: quality control: approved

value: Diethyl maleate

value: DEM

value: 100 μM DEM


title: USC.DISC.MIBC129

description:
muscle_invasive_bladder_cancer_primary_129
celfile_group_name: Mitra2014-BladderRec-tst


title: 5 μM_ETP_Replicate_3

description: quality control: approved

value: Etoposide

value: ETP

value: 5 μM ETP


title: USC.DISC.MIBC131

description:
muscle_invasive_bladder_cancer_primary_131
celfile_group_name: Mitra2014-BladderRec-tst


title: 50 μM_MEN_Replicate_3

description: quality control: approved

value: Menadion

value: MEN

value: 50 μM MEN


title: USC.DISC.MIBC144

description:
muscle_invasive_bladder_cancer_primary_144
celfile_group_name: Mitra2014-BladderRec-tst

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: 5 μM_CSPT_Replicate_3

description: quality control: approved

value: Cisplatin

value: CSPT

value: 5 μM CSPT


title: 2 mM_DIDP_Replicate_3

description: quality control: approved

value: Embryonic stem cells

value: B4418 of C57BL/6 background

value: Diisodecyl phtalate

value: DIDP

value: 2 mM DIDP


title: USC.DISC.MIBC130

description:
muscle_invasive_bladder_cancer_primary_130
celfile_group_name: Mitra2014-BladderRec-tst


title: 10 μM_LAC_Replicate_3

description: quality control: approved

value: Lead Acetate

value: LAC

value: 10 μM LAC


title: 2 mM_D-M_Replicate_3

description: quality control: approved

value: D-mannitol

value: D-M

value: 2 mM D-M


title: USC.DISC.MIBC128

description:
muscle_invasive_bladder_cancer_primary_128
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC124

description:
muscle_invasive_bladder_cancer_primary_124
celfile_group_name: Mitra2014-BladderRec-tst


title: 80 μM_BPA_Replicate_3

description: quality control: approved

value: Bisphenol A

value: BPA

value: 80 μM BPA


title: 2 μM_SAR_Replicate_3

description: quality control: approved

value: Sodium Arsenite

value: SAR

value: 2 μM SAR


title: USC.DISC.MIBC121

description:
muscle_invasive_bladder_cancer_primary_121
celfile_group_name: Mitra2014-BladderRec-tst

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: 0.5 nM_CA_Replicate_3

description: quality control: approved

value: Embryonic stem cells

value: B4418 of C57BL/6 background

value: Calyculin A

value: CA

value: 0.5 nM CA


title: USC.DISC.MIBC125

description:
muscle_invasive_bladder_cancer_primary_125
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC120

description:
muscle_invasive_bladder_cancer_primary_120
celfile_group_name: Mitra2014-BladderRec-tst


title: 250 nM_TBTO_Replicate_3

description: quality control: approved

value: Tributyltinoxide

value: TBTO

value: 250 nM TBTO


title: USC.DISC.MIBC123

description:
muscle_invasive_bladder_cancer_primary_123
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC133

description:
muscle_invasive_bladder_cancer_primary_133
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC117

description:
muscle_invasive_bladder_cancer_primary_117
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC127

description:
muscle_invasive_bladder_cancer_primary_127
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC119

description:
muscle_invasive_bladder_cancer_primary_119
celfile_group_name: Mitra2014-BladderRec-tst


title: 3 mM_PB_Replicate_3

description: quality control: approved

value: Phenobarbital

value: PB

value: 3 mM PB


title: 3 mM_TCE_Replicate_3

description: quality control: approved

value: TCE

value: 3 mM TCE


title: USC.DISC.MIBC110

description:
muscle_invasive_bladder_cancer_primary_110
celfile_group_name: Mitra2014-BladderRec-tst


title: 3 mM_CT_Replicate_3

description: quality control: approved

value: Carbon Tetrachloride

value: CT

value: 3 mM CT


title: USC.DISC.MIBC112

description:
muscle_invasive_bladder_cancer_primary_112
celfile_group_name: Mitra2014-BladderRec-tst

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: Rat synovium_after human mesenchymal stem cells mix_rep1

city: Tokyo

first: Nobutake

last: Ozeki

address: 1-5-45 Yushima, Bunkyo-ku

department: Department of Joint Surgery and Sports Medicine

country: Japan

institute: Tokyo Medical and Dental University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression Console Version1.1 (EC1.1) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Rat synovium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (3'IVT Expression Analysis Technical Manual, 2008, Affymetrix)

growth_protocol: Rat synovium was harvested and digested with collagenase after human mesenchymal stem cells injection

extract_protocol: RNA was extracted using TRIZol solution (Invitrogen) and High Pure RNA Isolation Kit (Roche Applied Sciences)

treatment_protocol: After injection of human synovial mesenchymal stem cells into the rat knee joint, rat synovium was harvested for the extraction of RNA. Human mesenchymal stem cells mixed rat synovium was used as a control.

value: Lewis

tag: protocol

value: human mesenchymal stem cells mixed with rat synovium

tag: tissue

value: rat synovium


title: USC.DISC.MIBC114

description:
muscle_invasive_bladder_cancer_primary_114
celfile_group_name: Mitra2014-BladderRec-tst


title: Rat synovium_after human mesenchymal stem cells injection_rep1

value: human mesenchymal stem cells injected into rat knee joint


title: USC.DISC.MIBC113

description:
muscle_invasive_bladder_cancer_primary_113
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC118

description:
muscle_invasive_bladder_cancer_primary_118
celfile_group_name: Mitra2014-BladderRec-tst


title: 100 μM_CF_Replicate_3

description: quality control: approved

value: Embryonic stem cells

value: B4418 of C57BL/6 background

value: Clofibrate

value: CF

value: 100 μM CF


title: 100 nM_TCDD_Replicate_3

description: quality control: approved

value: TCDD

value: 100 nM TCDD


title: 25 μM_ARO_Replicate_3

description: quality control: approved

value: Aroclor 1254

value: ARO

value: 25 μM ARO


title: USC.DISC.MIBC111

description:
muscle_invasive_bladder_cancer_primary_111
celfile_group_name: Mitra2014-BladderRec-tst


title: 5 μM_TCPOBOP_Replicate_3

description: quality control: approved

value: TCPOBOP

value: 5 μM TCPOBOP


title: 250 μM_WY_Replicate_3

description: quality control: approved

value: WY

value: 250 μM WY


title: USC.DISC.MIBC108

description:
muscle_invasive_bladder_cancer_primary_108
celfile_group_name: Mitra2014-BladderRec-tst

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: USC.DISC.MIBC109

description:
muscle_invasive_bladder_cancer_primary_109
celfile_group_name: Mitra2014-BladderRec-trn


title: 5 μM_HCE_Replicate_3

description: quality control: approved

value: Heptachlor epoxide

value: HCE

value: 5 μM HCE


title: USC.DISC.MIBC126

description:
muscle_invasive_bladder_cancer_primary_126
celfile_group_name: Mitra2014-BladderRec-tst


title: 50 μM_HCH_Replicate_3

description: quality control: approved

value: Embryonic stem cells

value: B4418 of C57BL/6 background

value: β-Hexachlorocyclohexane

value: HCH

value: 50 μM HCH


title: USC.DISC.MIBC106

description:
muscle_invasive_bladder_cancer_primary_106
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC115

description:
muscle_invasive_bladder_cancer_primary_115
celfile_group_name: Mitra2014-BladderRec-tst


title: 10 μM_CsA_Replicate_3

description: quality control: approved

value: Cyclosporin A

value: CsA

value: 10 μM CsA


title: PBS_Replicate_5

description: quality control: approved

value: PBS


title: 10 μM_FK506_Replicate_3

description: quality control: approved

value: Tacrolimus


title: PBS_Replicate_6

description: quality control: approved


title: USC.DISC.MIBC122

description:
muscle_invasive_bladder_cancer_primary_122
celfile_group_name: Mitra2014-BladderRec-tst


title: DMSO_Replicate_6

description: quality control: approved

value: DMSO

value: 0,5 % DMSO


title: DMSO_Replicate_5

description: quality control: approved


title: sip53_TNF_rep3

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

data_processing: GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.9 was used and cubic spline normalization was applied to the data.

source_name: p53 siRNA, TNFa treated

label_protocol: standard labeling protocol with biotin wirh Cy3-streptavidin

growth_protocol: MDA-MB-231 were routinely grown in DMEM with 10% FBS, with L-glutamine and pen/strep antibiotics.

extract_protocol: RNA was extracted with Qiazol reagent (Qiagen), following the protocol provided by the manufacturer. RNA integrity was checked by formaldehyde agarose gel electrophoresis. Purity and concentration were determined on a Nanodrop spectrophotometer.

treatment_protocol: Cells were transfected with control (siC) or p53 (sip53) siRNA. 48 hours after transfection, cells were grown in DMEM 0.1% FBS with or without TNF-alpha (10ng/ml) for additional 20 hours.

tag: genotype/variation

value: mutp53 depletion

tag: agent

value: TNFa


title: sip53_TNF_rep2


title: USC.DISC.MIBC116

description:
muscle_invasive_bladder_cancer_primary_116
celfile_group_name: Mitra2014-BladderRec-tst

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: sip53_TNF_rep1


title: 500 μM_MNU_Replicate_2

description: quality control: approved

value: N-Methyl-N-nitrosourea

value: MNU

value: 500 μM MNU


title: sip53_NT_rep3

source_name: p53 siRNA, untreated

value: untreated


title: 0.5 μM_MMC_Replicate_2

description: quality control: approved

value: Embryonic stem cells

value: B4418 of C57BL/6 background

value: Mitomycin C

value: MMC

value: 0.5 μM MMC


title: sip53_NT_rep1


title: USC.DISC.MIBC107

description:
muscle_invasive_bladder_cancer_primary_107
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC104

description:
muscle_invasive_bladder_cancer_primary_104
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC101

description:
muscle_invasive_bladder_cancer_primary_101
celfile_group_name: Mitra2014-BladderRec-tst


title: 100 μM_DEM_Replicate_2

description: quality control: approved

value: Diethyl maleate

value: DEM

value: 100 μM DEM


title: sip53_NT_rep2


title: siC_TNF_rep3

source_name: control siRNA, TNFa treated

value: control


title: 50 μM_MEN_Replicate_2

description: quality control: approved

value: Menadion

value: MEN

value: 50 μM MEN


title: USC.DISC.MIBC99

description:
muscle_invasive_bladder_cancer_primary_99
celfile_group_name: Mitra2014-BladderRec-tst

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: siC_NT_rep3

source_name: control siRNA, untreated


title: USC.DISC.MIBC103

description:
muscle_invasive_bladder_cancer_primary_103
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC100

description:
muscle_invasive_bladder_cancer_primary_100
celfile_group_name: Mitra2014-BladderRec-tst


title: siC_TNF_rep2

value: TNFa


title: USC.DISC.MIBC98

description:
muscle_invasive_bladder_cancer_primary_98
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC105

description:
muscle_invasive_bladder_cancer_primary_105
celfile_group_name: Mitra2014-BladderRec-tst


title: siC_NT_rep2


title: siC_TNF_rep1


title: siC_NT_rep1


title: pre-RASP SEB exposed samples 8

city: Fort Detrick

first: seid

last: muhie

state: MD

address: 568 Doughten Dr

department: Systems Biology Enterprise

institute: USACEHR

description: pre-RASP SEB exposed samples 8 of 9

hyb_protocol: The slides were hybridized at 60ºC for 16 h (for cDNA microarrays and Trizol® isolated RNA)

scan_protocol: Hybridized slides were scanned and recorded using a GenePix® Pro 4000B (Axon Instruments Inc., Union City, CA) optical scanner, and the images were digitized using GenePix® 6.0 software (Axon Instruments Inc, Union City, CA).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: pooled whole human tissue cell line

label_protocol: RNA was reverse transcribed and labeled using Micromax Tyramide Signal Amplification (TSA) Labeling and Detection Kit (Perkin Elmer, Inc., Waltham, MA) following the manufacturer’s protocol.

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

treatment_protocol: RASP trainees underwent extreme stressor condtions which simulated an intense battlefield scenario for more than 8 weeks; and Isolated Leucocytes (~ 106 cells/ml in RPMI 1640 and 10 % human AB serum media) were treated with SEB toxin to a final concentration of 100 ng/ml and SEB treated cells were incubated for 6 hours at 37 ºC and 5% CO2.

tag: reference

value: Strategen universal reference RNA Cat. No. 740000

source_name: leukocytes

value: WBCs (leukocytes)

value: pre-RASP SEB exposed


title: 5 μM_ETP_Replicate_2

description: quality control: approved

value: Embryonic stem cells

value: Etoposide

value: ETP

value: 5 μM ETP


title: pre-RASP SEB exposed samples 6

description: pre-RASP SEB exposed samples 6 of 9


title: pre-RASP SEB exposed samples 9

description: pre-RASP SEB exposed samples 9 of 9


title: pre-RASP SEB exposed samples 7

description: pre-RASP SEB exposed samples 7 of 9


title: USC.DISC.MIBC96

description:
muscle_invasive_bladder_cancer_primary_96
celfile_group_name: Mitra2014-BladderRec-tst


title: 2 mM_DIDP_Replicate_2

description: quality control: approved

value: B4418 of C57BL/6 background

value: Diisodecyl phtalate

value: DIDP

value: 2 mM DIDP


title: pre-RASP SEB exposed samples 4

description: pre-RASP SEB exposed samples 4 of 9


title: pre-RASP SEB exposed samples 3

description: pre-RASP SEB exposed samples 3 of 9


title: 5 μM_CSPT_Replicate_2

description: quality control: approved

value: Cisplatin

value: CSPT

value: 5 μM CSPT


title: USC.DISC.MIBC95

description:
muscle_invasive_bladder_cancer_primary_95
celfile_group_name: Mitra2014-BladderRec-trn


title: pre-RASP SEB exposed samples 5

description: pre-RASP SEB exposed samples 5 of 9


title: USC.DISC.MIBC93

description:
muscle_invasive_bladder_cancer_primary_93
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC97

description:
muscle_invasive_bladder_cancer_primary_97
celfile_group_name: Mitra2014-BladderRec-tst


title: pre-RASP SEB exposed samples 2

description: pre-RASP SEB exposed samples 2 of 9


title: 80 μM_BPA_Replicate_2

description: quality control: approved

value: Bisphenol A

value: BPA

value: 80 μM BPA


title: USC.DISC.MIBC89

description:
muscle_invasive_bladder_cancer_primary_89
celfile_group_name: Mitra2014-BladderRec-tst

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: post-RASP SEB exposed samples 12

description: post-RASP SEB exposed samples 12 of 15

value: Strategen universal reference RNA Cat. No. 740000

value: WBCs (leukocytes)

value: post-RASP SEB exposed


title: post-RASP SEB exposed samples 14

description: post-RASP SEB exposed samples 14 of 15


title: USC.DISC.MIBC90

description:
muscle_invasive_bladder_cancer_primary_90
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC87

description:
muscle_invasive_bladder_cancer_primary_87
celfile_group_name: Mitra2014-BladderRec-trn


title: pre-RASP SEB exposed samples 1

description: pre-RASP SEB exposed samples 1 of 9

value: pre-RASP SEB exposed


title: post-RASP SEB exposed samples 13

description: post-RASP SEB exposed samples 13 of 15


title: USC.DISC.MIBC102

description:
muscle_invasive_bladder_cancer_primary_102
celfile_group_name: Mitra2014-BladderRec-tst


title: post-RASP SEB exposed samples 11

description: post-RASP SEB exposed samples 11 of 15


title: 2 μM_SAR_Replicate_2

description: quality control: approved

value: Embryonic stem cells

value: Sodium Arsenite

value: SAR

value: 2 μM SAR


title: 2 mM_D-M_Replicate_2

description: quality control: approved

value: B4418 of C57BL/6 background

value: D-mannitol

value: D-M

value: 2 mM D-M


title: 10 μM_LAC_Replicate_2

description: quality control: approved

value: Lead Acetate

value: LAC

value: 10 μM LAC


title: post-RASP SEB exposed samples 9

description: post-RASP SEB exposed samples 9 of 15


title: 0.5 nM_CA_Replicate_2

description: quality control: approved

value: Calyculin A

value: CA

value: 0.5 nM CA


title: post-RASP SEB exposed samples 10

description: post-RASP SEB exposed samples 10 of 15

value: Strategen universal reference RNA Cat. No. 740000

value: WBCs (leukocytes)


title: USC.DISC.MIBC83

description:
muscle_invasive_bladder_cancer_primary_83
celfile_group_name: Mitra2014-BladderRec-trn

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: post-RASP SEB exposed samples 8

description: post-RASP SEB exposed samples 8 of 15

value: post-RASP SEB exposed


title: USC.DISC.MIBC86

description:
muscle_invasive_bladder_cancer_primary_86
celfile_group_name: Mitra2014-BladderRec-trn


title: post-RASP SEB exposed samples 6

description: post-RASP SEB exposed samples 6 of 15


title: post-RASP SEB exposed samples 5

description: post-RASP SEB exposed samples 5 of 15


title: post-RASP SEB exposed samples 7

description: post-RASP SEB exposed samples 7 of 15


title: 4 nM_OA_Replicate_2

description: quality control: approved

value: Embryonic stem cells

value: Okadaic Acid

value: OA

value: 4 nM OA


title: 250 nM_TBTO_Replicate_2

description: quality control: approved

value: B4418 of C57BL/6 background

value: Tributyltinoxide

value: TBTO

value: 250 nM TBTO


title: 3 mM_TCE_Replicate_2

description: quality control: approved

value: TCE

value: 3 mM TCE


title: USC.DISC.MIBC94

description:
muscle_invasive_bladder_cancer_primary_94
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC92

description:
muscle_invasive_bladder_cancer_primary_92
celfile_group_name: Mitra2014-BladderRec-tst


title: USC.DISC.MIBC84

description:
muscle_invasive_bladder_cancer_primary_84
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC85

description:
muscle_invasive_bladder_cancer_primary_85
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC88

description:
muscle_invasive_bladder_cancer_primary_88
celfile_group_name: Mitra2014-BladderRec-trn


title: post-RASP SEB exposed samples 4

description: post-RASP SEB exposed samples 4 of 15


title: post-RASP SEB exposed samples 15

description: post-RASP SEB exposed samples 15 of 15


title: post-RASP SEB exposed samples 3

description: post-RASP SEB exposed samples 3 of 15


title: post-RASP SEB exposed samples 1

description: post-RASP SEB exposed samples 1 of 15


title: USC.DISC.MIBC91

description:
muscle_invasive_bladder_cancer_primary_91
celfile_group_name: Mitra2014-BladderRec-tst


title: 3 mM_CT_Replicate_2

description: quality control: approved

value: Carbon Tetrachloride

value: CT

value: 3 mM CT


title: post-RASP SEB exposed samples 2

description: post-RASP SEB exposed samples 2 of 15

value: Strategen universal reference RNA Cat. No. 740000


title: USC.DISC.MIBC81

description:
muscle_invasive_bladder_cancer_primary_81
celfile_group_name: Mitra2014-BladderRec-trn


title: 3 mM_PB_Replicate_2

description: quality control: approved

value: Phenobarbital

value: PB

value: 3 mM PB


title: 5 μM_TCPOBOP_Replicate_2

description: quality control: approved

value: Embryonic stem cells

value: TCPOBOP

value: 5 μM TCPOBOP


title: pre-RASP control samples 36

description: pre-RASP control samples 36 of 36

value: WBCs (leukocytes)

value: pre-RASP control


title: pre-RASP control samples 35

description: pre-RASP control samples 35 of 36


title: pre-RASP control samples 34

description: pre-RASP control samples 34 of 36


title: pre-RASP control samples 33

description: pre-RASP control samples 33 of 36


title: pre-RASP control samples 32

description: pre-RASP control samples 32 of 36


title: 25 μM_ARO_Replicate_2

description: quality control: approved

value: B4418 of C57BL/6 background

value: Aroclor 1254

value: ARO

value: 25 μM ARO


title: pre-RASP control samples 31

description: pre-RASP control samples 31 of 36


title: pre-RASP control samples 30

description: pre-RASP control samples 30 of 36


title: pre-RASP control samples 29

description: pre-RASP control samples 29 of 36


title: USC.DISC.MIBC82

description:
muscle_invasive_bladder_cancer_primary_82
celfile_group_name: Mitra2014-BladderRec-trn

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: pre-RASP control samples 28

description: pre-RASP control samples 28 of 36


title: 100 μM_CF_Replicate_2

description: quality control: approved

value: Clofibrate

value: CF

value: 100 μM CF


title: pre-RASP control samples 26

description: pre-RASP control samples 26 of 36

value: Strategen universal reference RNA Cat. No. 740000


title: pre-RASP control samples 27

description: pre-RASP control samples 27 of 36


title: pre-RASP control samples 25

description: pre-RASP control samples 25 of 36


title: USC.DISC.MIBC78

description:
muscle_invasive_bladder_cancer_primary_78
celfile_group_name: Mitra2014-BladderRec-trn


title: 250 μM_WY_Replicate_2

description: quality control: approved

value: WY

value: 250 μM WY


title: 5 μM_HCE_Replicate_2

description: quality control: approved

value: Heptachlor epoxide

value: HCE

value: 5 μM HCE


title: pre-RASP control samples 24

description: pre-RASP control samples 24 of 36


title: pre-RASP control samples 22

description: pre-RASP control samples 22 of 36


title: USC.DISC.MIBC79

description:
muscle_invasive_bladder_cancer_primary_79
celfile_group_name: Mitra2014-BladderRec-trn


title: 50 μM_HCH_Replicate_2

description: quality control: approved

value: Embryonic stem cells

value: β-Hexachlorocyclohexane

value: HCH

value: 50 μM HCH


title: 10 μM_CsA_Replicate_2

description: quality control: approved

value: B4418 of C57BL/6 background

value: Cyclosporin A

value: CsA

value: 10 μM CsA


title: pre-RASP control samples 21

description: pre-RASP control samples 21 of 36

value: WBCs (leukocytes)

value: pre-RASP control


title: pre-RASP control samples 20

description: pre-RASP control samples 20 of 36


title: pre-RASP control samples 19

description: pre-RASP control samples 19 of 36


title: pre-RASP control samples 18

description: pre-RASP control samples 18 of 36


title: PBS_Replicate_4

description: quality control: approved

value: PBS


title: 100 nM_TCDD_Replicate_2

description: quality control: approved

value: TCDD

value: 100 nM TCDD


title: pre-RASP control samples 17

description: pre-RASP control samples 17 of 36

value: Strategen universal reference RNA Cat. No. 740000


title: pre-RASP control samples 16

description: pre-RASP control samples 16 of 36


title: pre-RASP control samples 15

description: pre-RASP control samples 15 of 36


title: USC.DISC.MIBC77

description:
muscle_invasive_bladder_cancer_primary_77
celfile_group_name: Mitra2014-BladderRec-trn

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: USC.DISC.MIBC76

description:
muscle_invasive_bladder_cancer_primary_76
celfile_group_name: Mitra2014-BladderRec-trn


title: 10 μM_FK506_Replicate_2

description: quality control: approved

value: Tacrolimus


title: PBS_Replicate_3

description: quality control: approved


title: pre-RASP control samples 14

description: pre-RASP control samples 14 of 36


title: pre-RASP control samples 13

description: pre-RASP control samples 13 of 36


title: DMSO_Replicate_4

description: quality control: approved

value: DMSO

value: 0,5 % DMSO


title: USC.DISC.MIBC75

description:
muscle_invasive_bladder_cancer_primary_75
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC74

description:
muscle_invasive_bladder_cancer_primary_74
celfile_group_name: Mitra2014-BladderRec-trn


title: pre-RASP control samples 11

description: pre-RASP control samples 11 of 36


title: pre-RASP control samples 10

description: pre-RASP control samples 10 of 36


title: pre-RASP control samples 12

description: pre-RASP control samples 12 of 36


title: pre-RASP control samples 9

description: pre-RASP control samples 9 of 36


title: 500 μM_MNU_Replicate_1

description: quality control: approved

value: Embryonic stem cells

value: N-Methyl-N-nitrosourea

value: MNU

value: 500 μM MNU


title: 0.5 μM_MMC_Replicate_1

description: quality control: approved

value: B4418 of C57BL/6 background

value: Mitomycin C

value: MMC

value: 0.5 μM MMC


title: USC.DISC.MIBC80

description:
muscle_invasive_bladder_cancer_primary_80
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC72

description:
muscle_invasive_bladder_cancer_primary_72
celfile_group_name: Mitra2014-BladderRec-trn


title: pre-RASP control samples 8

description: pre-RASP control samples 8 of 36

value: WBCs (leukocytes)

value: pre-RASP control


title: USC.DISC.MIBC70

description:
muscle_invasive_bladder_cancer_primary_70
celfile_group_name: Mitra2014-BladderRec-trn


title: pre-RASP control samples 6

description: pre-RASP control samples 6 of 36


title: pre-RASP control samples 23

description: pre-RASP control samples 23 of 36


title: USC.DISC.MIBC71

description:
muscle_invasive_bladder_cancer_primary_71
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC67

description:
muscle_invasive_bladder_cancer_primary_67
celfile_group_name: Mitra2014-BladderRec-trn


title: pre-RASP control samples 5

description: pre-RASP control samples 5 of 36


title: 100 μM_DEM_Replicate_1

description: quality control: approved

value: Diethyl maleate

value: DEM

value: 100 μM DEM


title: 50 μM_MEN_Replicate_1

description: quality control: approved

value: Menadion

value: MEN

value: 50 μM MEN


title: USC.DISC.MIBC73

description:
muscle_invasive_bladder_cancer_primary_73
celfile_group_name: Mitra2014-BladderRec-trn

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: pre-RASP control samples 3

description: pre-RASP control samples 3 of 36

value: Strategen universal reference RNA Cat. No. 740000


title: pre-RASP control samples 4

description: pre-RASP control samples 4 of 36


title: pre-RASP control samples 2

description: pre-RASP control samples 2 of 36


title: post-RASP stress samples 43

description: post-RASP stress samples 43  of 43

value: post-RASP stress


title: DMSO_Replicate_3

description: quality control: approved

value: Embryonic stem cells

value: DMSO

value: 0,5 % DMSO


title: pre-RASP control samples 1

description: pre-RASP control samples 1 of 36


title: post-RASP stress samples 42

description: post-RASP stress samples 42  of 43