title: Bladder_Tumour_7 [mouse]

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA using RMAExpress.

source_name: bladder tumour

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

extract_protocol: Extraction of total RNA was performed with RNeasy Qiagen Kit according to the manufacturer's instructions.

tag: strain/background

value: FVB

value: bladder tumour

value: infected with Adeno-Cre


title: HCC-1954_Ctrl_2

status: Public on Oct 02 2014

type: RNA

city: Andover

first: Zoltan

last: Dezso

state: MA

address: 4 Corporate dr

country: USA

institute: Eisai Inc

description: vehicle

hyb_protocol: We used manufacture recommened protocol (Affymetrix). Arrays were washed and stained using Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000

data_processing: Gene chips were analyzed using Affymetrix Microarray Analysis Suite (MAS) version 5. RMA normalization was performed using Affymetrix Power Tools version 1.12.0.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HCC-1954 Control

label_protocol: Biotinylated fragmenetd cRNA was used.

growth_protocol: Cell lines were growing in growth media recommanded by ATCC.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen).

treatment_protocol: Treated with eribulin and paclitaxel at 10xIC50 conc. for 24 hours. IC50 determinded in growth inhibitation assay for cell line separately.

tag: cell line

tag: cell type

value: breast cancer


title: HDAC2 siRNA_4_HepG2 [HDAC2 siRNA subset]

city: Copenhagen

first: Jesper

middle: B

last: Andersen

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: Copenhagen University

description: SAMPLE 32

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed by means of  Genome Studio v2011.1 from illumina, Inc. The background noise was substrated and quantile normalization was applied.

label_protocol: Biotinylated cRNA were prepared using Ambion Totalprep RNA Amplification kit for Illumina arrays

extract_protocol: Total RNA was extracted using Qiagen mini kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.

tag: subset

value: HDAC2 siRNA subset

value: HB cell line HepG2

tag: treatment

value: HDAC2 siRNA


title: HCC-1954_Ctrl_1

description: vehicle


title: Control 4_HepG2 [HDAC2 siRNA subset]

description: SAMPLE 28

value: scrambled siRNA


title: Bladder_Tumour_6 [mouse]

organism: Mus musculus

tag: genotype/variation

tag: tissue


title: Bladder_Tumour_3 [mouse]


title: Control 2_HepG2 [HDAC2 siRNA subset]

description: SAMPLE 26


title: Control 1_HepG2 [HDAC2 siRNA subset]

description: SAMPLE 25


title: HCC-1954_Ctrl_3

description: vehicle


title: Bladder_Tumour_5 [mouse]


title: MCF-7_PTX_3

description: drug

source_name: MCF-7 Paclitaxel_24h


title: Bladder_Tumour_4 [mouse]


title: HDAC2 siRNA_2_Huh7 [HDAC2 siRNA subset]

description: SAMPLE 22

value: HCC cell line Huh7


title: fibroblast_cultured_8days_rep1

city: Beijing

first: yuan

middle: Yuan

last: Du

address: Yihe Yuan Road 5

country: China

institute: Department of Cell Biology and Genetics, College of Life Sciences, Peking University

hyb_protocol: Hybridized to a mouse Oligo Microarray (Phalanx Mouse OneArray® v2, Phalanx Biotech) according to the manufacturer's protocol.

scan_protocol: After hybridization, arrays were scanned using GenePix 4000B scanner (Molecular Devices) and processed using the GenePix Pro 6.0 software (Molecular Devices).

data_processing: After removing control probes, a 14/33 presence call (SNR>=5 and foreground-background>0) was used to filter probes for the 33 microarrays, resulting in 12733 probes for further quantile normalization. The median of each sample was used for hierarchical clustering. Complete-linkage hierarchical clustering was performed using cluster 3.0 (written by Michael Eisen, Stanford University) with Spearman rank correlation coefficient as gene distances measurement and Pearson correlation coefficient as sample distances measurement.

source_name: fibroblast of newborn mouse (less than 3days)

label_protocol: Total mRNA from NBF1, NBF2, ICM1, ICM2, cm1, cm2 cells were labeled with Cy5.

extract_protocol: Total cellular RNA was extracted with TRIzol reagent (Sigma). Genomic DNA were removed with DNAase(Ambion), and 1ug RNA of each sample were used for reverse transcription with EasyScript Reverse Transcriptase (TransGen), according to the manufacturer's instructions. PCR amplification was performed using 2× EasyTaq SuperMix (TransGen).

treatment_protocol: In brief, the limbs and tails of neonatal mice were cut off, and the neonatal mouse skin was carefully peeled. The isolated neonatal mouse skin was then incubated in Collagenase type Ⅳ (2mg/ml, Gibco) for 2hrs at 37℃. After incubation, the epiderm was carefully removed from the surface of the skin. The remaining tissues were dissociated and minced into 1mm pieces, which were then resuspended by Dulbecco’s Modified Eagle Medium (DMEM, Hyclone), containing 10% Fetal bovine serum (Hyclone), 2x penicillin/streptomycin (Invitrogen). The isolated neonatal skin fibroblasts were collected by flowing through cell strainers.

tag: strain

value: ICR

tag: gender

value: female

tag: age

value: 3 days

value: skin


title: Normal_Bladder_6 [mouse]

source_name: non-tumoral bladder mucosa

value: wild type

value: non-tumoral bladder mucosa

value: infected with Adeno-GFP


title: MCF-7_PTX_2

description: drug


title: MCF-7_PTX_1

description: drug


title: HDAC2 siRNA_1_Huh7 [HDAC2 siRNA subset]

description: SAMPLE 21


title: Bladder_Tumour_2 [mouse]


title: Control 3_HepG2 [HDAC2 siRNA subset]

description: SAMPLE 27


title: HDAC2 siRNA_4_Huh7 [HDAC2 siRNA subset]

description: SAMPLE 24


title: HDAC2 siRNA_3_Huh7 [HDAC2 siRNA subset]

description: SAMPLE 23


title: MCF-7_ERI_1

description: drug

source_name: MCF-7 Eribulin_24h


title: Normal_Bladder_4 [mouse]


title: Normal_Bladder_5 [mouse]


title: Control 2_Huh7 [HDAC2 siRNA subset]

description: SAMPLE 18


title: MCF-7_ERI_2

description: drug


title: Normal_Bladder_3 [mouse]


title: Control 3_Huh7 [HDAC2 siRNA subset]

description: SAMPLE 19


title: Control 4_Huh7 [HDAC2 siRNA subset]

description: SAMPLE 20


title: MCF-7_Ctrl_3

description: vehicle

source_name: MCF-7 Control


title: Normal_Bladder_2 [mouse]


title: Normal_Bladder_1 [mouse]


title: Bladder_Tumour_1 [mouse]


title: MCF-7_ERI_3

description: drug


title: MCF-7_Ctrl_1

description: vehicle


title: Control 1_Huh7 [HDAC2 siRNA subset]

description: SAMPLE 17


title: T47D_PTX_3

description: drug

source_name: T47D Paclitaxel_24h


title: SAHA 3_HepG2 [SAHA subset]

description: SAMPLE 15

value: SAHA subset

value: SAHA


title: T47D_PTX_2

description: drug


title: MCF-7_Ctrl_2

description: vehicle


title: SAHA 1_HepG2 [SAHA subset]

description: SAMPLE 13


title: SAHA 2_HepG2 [SAHA subset]

description: SAMPLE 14


title: Kidney cortex treated captopril rep2

city: Montreal

first: Timothy

middle: L

last: Reudelhuber

state: Quebec

address: 110 Avenue des Pins Ouest

country: Canada

institute: IRCM

description: Treatment replicate 2

data_processing: The data were normalized using the quantile normalization function in FlexArray, from the R Bioconductor package lumi.

source_name: Mouse kidney cortex

label_protocol: standard Illumina protocol

growth_protocol: Mice were housed in groups and given free access to food and water

extract_protocol: RNA was extracted with Trizol reagent.

treatment_protocol: Eleven week-old male C57BL6 mice were treated with captopril at 10 mg/kg/day in drinking water for 7 days.

value: captopril

value: kidney cortex

value: 12 wk

value: male


title: Kidney cortex treated captopril rep1

description: Treatment replicate 1


title: T47D_ERI_3

description: drug

source_name: T47D Eribulin_24h

value: breast cancer


title: T47D_PTX_1

description: drug


title: Kidney cortex control rep2

description: Control replicate 2

value: control


title: Control 2_HepG2 [SAHA subset]

description: SAMPLE 10

value: HB cell line HepG2

value: DMSO


title: Kidney cortex treated captopril rep3

description: Treatment replicate 3


title: T47D_Ctrl_2

description: vehicle

source_name: T47D Control


title: Control 4_HepG2 [SAHA subset]

description: SAMPLE 12


title: Control 1_HepG2 [SAHA subset]

description: SAMPLE 9


title: T47D_ERI_2

description: drug


title: T47D_Ctrl_1

description: vehicle


title: T47D_ERI_1

description: drug


title: Bladder_Tumour_28 [human]

data_processing:
The data were analyzed with RMA using RMAExpress.
Meta-probeset file: HuGene-1_0-st-v1.r4.mps

value: bladder tumour

tag: disease status

value: bladder cancer patient

tag: pik3ca mutation status

value: WT

tag: pik3ca cn status

tag: fgfr3 mutation

tag: tumor recurrence

value: yes


title: SAHA 4_Huh7 [SAHA subset]

description: SAMPLE 8

value: HCC cell line Huh7


title: Bladder_Tumour_26 [human]

value: no


title: T47D_Ctrl_3

description: vehicle


title: Control 3_HepG2 [SAHA subset]

description: SAMPLE 11


title: Kidney cortex control rep3

description: Control replicate 3


title: Bladder_Tumour_27 [human]


title: ZRT_PTX_3

description: drug

source_name: ZRT Paclitaxel_24h

value: ZRT


title: Bladder_Tumour_25 [human]


title: ZRT_PTX_2

description: drug


title: SAHA 2_Huh7 [SAHA subset]

description: SAMPLE 6

value: SAHA subset


title: SAHA 3_Huh7 [SAHA subset]

description: SAMPLE 7

value: SAHA


title: Normal_Bladder_10 [human]

value: non-tumoral bladder mucosa


title: Normal_Bladder_9 [human]


title: ZRT_PTX_1

description: drug


title: SAHA 1_Huh7 [SAHA subset]

description: SAMPLE 5


title: ZRT_ERI_3

description: drug

source_name: ZRT Eribulin_24h


title: Control 3_Huh7 [SAHA subset]

description: SAMPLE 3


title: ZRT_ERI_2

description: drug


title: ZRT_Ctrl_2

description: vehicle

source_name: ZRT Control


title: Bladder_Tumour_24 [human]


title: Bladder_Tumour_17 [human]


title: Bladder_Tumour_10 [human]


title: Bladder_Tumour_16 [human]


title: Bladder_Tumour_20 [human]


title: Control 1_Huh7 [SAHA subset]

description: SAMPLE 1


title: Control 2_Huh7 [SAHA subset]

description: SAMPLE 2


title: ZRT_ERI_1

description: drug


title: Bladder_Tumour_23 [human]


title: ZRT_Ctrl_1

description: vehicle


title: Control 4_Huh7 [SAHA subset]

description: SAMPLE 4


title: Limbal fibroblast cells-cultured-2

city: Dublin

first: colin

last: clarke

address: Dublin City University

country: Ireland

institute: Dublin City University

description: LFC_2 cultures demonstrated fibroblast cell morphology with elongated, spindle-shaped cells and monolayer formation.

hyb_protocol: 5.5 μg of fragmented ssDNA was processed according to the manufacturers' instructions using the GeneChip® WT Terminal  Labeling and Hybridization kit (P/N 702808). 100µl of hybridisation coctail was added to the arrays and they were hybridised for 16 hours at 45°C and 60 rpm. Arrays were subsequently washed (Affymetrix Fluidics Station 450) and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on an Affymetrix GCS GeneChip GeneArray scanner. Resulting data was analysed using GCOS, dCHIP, and GeneSpring (Agilent Technologies).

data_processing: All microarray data were called using the robust multichip average method (RMA)

label: Biotin

source_name: Limbal fibroblast cells, cultured

label_protocol: 300 ng of each specimen was amplified and labelled using the Affymetrix GeneChip WT cDNA Synthesis and Amplification Kit, (Affymetrix; 900652) according to the manufacturer’s instructions (http://www.affymetrix.com/estore/esearch/search.jsp?Ntt=genechip+WT+cDNA+synthesis+and+amplification+kit&basic=1).

growth_protocol: AMLE cultures were initiated using donor cadaveric limbal tissue within ten days of biologic death. Limbal rings were dissected and limbal explants (2×2×0.25mm) cultured on fresh frozen human amniotic membrane (Transplant Service Foundation, Spain; Code-30102-619). To prepare the amniotic membrane for limbal explant culture; cryo-preserved amniotic membrane was thawed, freezing-medium aspirated, nitrocellulose paper removed and membranes washed in PBS and incubated with trypsin/EDTA (20 min., 37°C). Cell scrapers (Costar-Corning, Corning, NY) were used to remove amniotic epithelium and mucus from the membrane. The amniotic membrane was held taut by wrapping around a sterile glass slide and limbal explants placed on the de-epithelialised surface. Explants were cultured in supplemented epithelial growth medium; 3:1 DMEM/HAM F12 (Sigma Aldrich, St. Louis, MO), 10% FCS (Invitrogen-Gibco, Grand Island, NY),  5μg /ml insulin, 10ng/ml rhEGF,  100ng/ml cholera toxin, 0.4μg /ml hydrocortisone,1E-9M triiodothyronine (Sigma Aldrich, St. Louis, MO). All cultures were incubated at 37 °C, 5% CO2 with media aspiration every 2-3 days until confluent.  CE samples were isolated from donor cadaveric corneal buttons within ten days of biologic death. Upon receipt, the blunt edge of a scalpel blade (Swann-Morton, Sheffield, UK) was used to separate corneal epithelial tissue. Separation of the corneal epithelial sheet was confirmed using a Nikon Eclipse TS100 microscope (Nikon, Melville, NY). LFC samples were initiated using donor cadaveric limbal tissue within ten days of biologic death. Limbal rings were dissected and limbal explants (0.5×0.5×0.25mm) cultured on tissue culture-treated plastic (Costar-Corning, Corning, NY) using DMEM (Sigma Aldrich, St. Louis, MO) supplemented with 10% FCS (Invitrogen-Gibco, Grand Island, NY). All cultures were incubated at 37 °C, 5% CO2 with media aspiration every 2-3 days until confluent.

extract_protocol: Total RNA was isolated from cell samples using Qiagen RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration was verified using a Nanodrop spectrophotometer (ND-1000, Labtech International, UK), and RNA integrity verified using a 2100 Bioanalyser (Agilent, CA, USA).

treatment_protocol: Samples were stored at −70°C/–80°C prior to RNA isolation

tag: pathology

value: Normal

value: Limbal fibroblast cells

tag: cultured


title: Hs578T_PTX_3

description: drug

source_name: Hs578T Paclitaxel_24h


title: 28C-28B_Rep3

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

description:
28C-28B_Rep3
Biological replicate 2
Biological replicate 2
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.

hyb_protocol: Hybridization and post-hybridization washing using Hybridization Systems Kit (Roche NimbleGen) and Wash Buffer Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com

scan_protocol: Image acquisition with Axon GenePix 4200A Professional scanner, 5 micron resolution.

data_processing: Raw signal intensities extracted with NimbleScan 2.4 Software (Roche NimbleGen) as PAIR files.

organism: Daphnia pulex

source_name: whole body

label_protocol: ds cDNA labeled using NimbleGen Dual Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com

tag: phenotype

value: heat tolerant

value: heat sensitive


title: Hs578T_PTX_2

description: drug

tag: cell line

value: breast cancer


title: Hs578T_PTX_1

description: drug

tag: cell type


title: Limbal fibroblast cells-cultured-3

description: LFC_3 cultures demonstrated fibroblast cell morphology with elongated, spindle-shaped cells and monolayer formation.


title: Hs578T_ERI_3

description: drug

source_name: Hs578T Eribulin_24h


title: Hs578T_ERI_2

description: drug


title: Central corneal button-not cultured-3

description: CE_3 demonstrated stratified corneal epithelial cell morphology with small, tightly packed, cobble-shaped cells on the basal layer and larger squamous cells on apical layers. CE_3 tissue is 5-7 cell layers thick.

source_name: Central corneal button, not cultured

value: Central corneal button


title: Hs578T_Ctrl_3

description: vehicle

source_name: Hs578T Control


title: Hs578T_ERI_1

description: drug


title: 28B-28E_Rep3

description:
28B-28E_Rep3
Biological replicate 2
Biological replicate 2
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: Kidney cortex control rep1

description: Control replicate 1

value: control

value: kidney cortex

value: 12 wk

value: male


title: Central corneal button-not cultured-1

description: CE_1 demonstrated stratified corneal epithelial cell morphology with small, tightly packed, cobble-shaped cells on the basal layer and larger squamous cells on apical layers. CE_1 tissue is 5-7 cell layers thick.


title: Central corneal button-not cultured-2

description: CE_2 demonstrated stratified corneal epithelial cell morphology with small, tightly packed, cobble-shaped cells on the basal layer and larger squamous cells on apical layers. CE_2 tissue is 5-7 cell layers thick.


title: SAHA 4_HepG2 [SAHA subset]

description: SAMPLE 16

tag: subset

value: HB cell line HepG2


title: 28E-28K_Rep3

description:
28E-28K_Rep3
Biological replicate 2
Biological replicate 2
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.

tag: treatment


title: Hs578T_Ctrl_2

description: vehicle


title: Limbal fibroblast cells-cultured-1

description: LFC_1 cultures demonstrated fibroblast cell morphology with elongated, spindle-shaped cells and monolayer formation.

value: yes


title: Hs578T_Ctrl_1

description: vehicle


title: Patient-derived xenograft ETP-ALL-3

city: Sydney

first: Santi

last: Suryani

state: NSW

address: Level 5 Lowy Cancer Research Centre Gate 9 High St

department: Leukaemia Biology

country: Australia

institute: Children's Cancer Institute Australia for Medical Research

description: patient-derived xenograft cells

data_processing: The data were max-collapsed, log2-transformed and quantile normalised using GenePattern

source_name: Patient-derived xenograft cells

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA kit for Illumina arrays

extract_protocol: RNA was extracted with a combination of Trizol reagent and QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: host strain

value: NOD/SCID

tag: age at injection

value: xenograft cells Injected at 6-10 weeks

value: Xenograft cells (>95% hCD45+ cells) from mouse spleens

tag: xenograft

value: ETP-ALL


title: Amniotic membrane expanded limbal epithelium-cultured-3

description: AMLE_3 cultures demonstrated stratified corneal epithelial cell morphology with small, tightly packed, cobble-shaped cells on the basal layer and larger squamous cells on apical layers. AMLE_3 tissues were 2-3 cell layers thick.

source_name: Amniotic membrane expanded limbal epithelium, cultured

tag: tissue

value: Amniotic membrane-expanded limbal epithelium


title: Bladder_Tumour_22 [human]

source_name: bladder tumour

value: bladder tumour

value: bladder cancer patient

value: WT

value: no


title: Bladder_Tumour_19 [human]


title: Bladder_Tumour_21 [human]


title: Amniotic membrane expanded limbal epithelium-cultured-2

description: AMLE_2 cultures demonstrated stratified corneal epithelial cell morphology with small, tightly packed, cobble-shaped cells on the basal layer and larger squamous cells on apical layers. AMLE_2 tissues were 2-3 cell layers thick.

value: Normal


title: 18B-18C_Rep3

description:
18B-18C_Rep3
Biological replicate 2
Biological replicate 2
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.

value: heat sensitive

value: heat tolerant


title: Patient-derived xenograft T-ALL-42

description: patient-derived xenograft cells

value: T-ALL


title: Patient-derived xenograft T-ALL-47

description: patient-derived xenograft cells


title: Amniotic membrane expanded limbal epithelium-cultured-1

description: AMLE_1 cultures demonstrated stratified corneal epithelial cell morphology with small, tightly packed, cobble-shaped cells on the basal layer and larger squamous cells on apical layers. AMLE_1 tissues were 2-3 cell layers thick.


title: BT-549_PTX_3

description: drug

source_name: BT-549 Paclitaxel_24h

value: breast cancer


title: Patient-derived xenograft T-ALL-43

description: patient-derived xenograft cells


title: BT-549_PTX_2

description: drug


title: 28C-18C_Rep3

description:
28C-18C_Rep3
Biological replicate 2
Biological replicate 2
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: 18K-18E_Rep3

description:
18K-18E_Rep3
Biological replicate 2
Biological replicate 2
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: 18K-28K_Rep3

description:
18K-28K_Rep3
Biological replicate 2
Biological replicate 2
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: 18C-18K_Rep3

description:
18C-18K_Rep3
Biological replicate 2
Biological replicate 2
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: BT-549_PTX_1

description: drug


title: BT-549_ERI_3

description: drug

source_name: BT-549 Eribulin_24h


title: Bladder_Tumour_18 [human]


title: BT-549_ERI_2

description: drug


title: 18E-18B_Rep3

description:
18E-18B_Rep3
Biological replicate 2
Biological replicate 2
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: 28E-28B_Rep2

description:
28E-28B_Rep2
Biological replicate 3
Biological replicate 3
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: Bladder_Tumour_15 [human]


title: 18B-28B_Rep3

description:
18B-28B_Rep3
Biological replicate 2
Biological replicate 2
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: 28E-18E_Rep3

description:
28E-18E_Rep3
Biological replicate 2
Biological replicate 2
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: 28K-28E_Rep2

description:
28K-28E_Rep2
Biological replicate 3
Biological replicate 3
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: BT-549_ERI_1

description: drug


title: Patient-derived xenograft T-ALL-44

description: patient-derived xenograft cells


title: 28B-28C_Rep2

description:
28B-28C_Rep2
Biological replicate 3
Biological replicate 3
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: Patient-derived xenograft ETP-ALL-1

description: patient-derived xenograft cells


title: Bladder_Tumour_12 [human]


title: Patient-derived xenograft BCP-ALL-7

description: patient-derived xenograft cells

value: BCP-ALL


title: Bladder_Tumour_13 [human]


title: Patient-derived xenograft T-ALL-27

description: patient-derived xenograft cells


title: BT-549_Ctrl_3

description: vehicle

source_name: BT-549 Control


title: Bladder_Tumour_14 [human]


title: BT-549_Ctrl_2

description: vehicle


title: BT-549_Ctrl_1

description: vehicle


title: Patient-derived xenograft BCP-ALL-11

description: patient-derived xenograft cells


title: 28K-28C_Rep3

description:
28K-28C_Rep3
Biological replicate 2
Biological replicate 2
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: Patient-derived xenograft MLL-ALL-7

description: patient-derived xenograft cells

value: MLL-ALL


title: Bladder_Tumour_8 [human]


title: 28C-28K_Rep2

description:
28C-28K_Rep2
Biological replicate 3
Biological replicate 3
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: Bladder_Tumour_7 [human]


title: Patient-derived xenograft T-ALL-16

description: patient-derived xenograft cells


title: Bladder_Tumour_11 [human]

value: yes


title: MDA-MB-436_PTX_3

description: drug

source_name: MDA-MB-436 Paclitaxel_24h


title: MDA-MB-436_ERI_3

description: drug

source_name: MDA-MB-436 Eribulin_24h


title: 18B-18E_Rep2

description:
18B-18E_Rep2
Biological replicate 3
Biological replicate 3
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: MDA-MB-436_PTX_1

description: drug


title: 18C-28C_Rep2

description:
18C-28C_Rep2
Biological replicate 3
Biological replicate 3
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: MDA-MB-436_ERI_2

description: drug


title: Bladder_Tumour_9 [human]


title: Patient-derived xenograft BCP-ALL-10

description: patient-derived xenograft cells

value: NOD/SCID


title: Patient-derived xenograft T-ALL-30

description: patient-derived xenograft cells

value: xenograft cells Injected at 6-10 weeks


title: Patient-derived xenograft BCP-ALL-19

description: patient-derived xenograft cells

value: Xenograft cells (>95% hCD45+ cells) from mouse spleens


title: Bladder_Tumour_6 [human]


title: 28K-18K_Rep2

description:
28K-18K_Rep2
Biological replicate 3
Biological replicate 3
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: 18K-18C_Rep2

description:
18K-18C_Rep2
Biological replicate 3
Biological replicate 3
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: Bladder_Tumour_5 [human]


title: 18E-18K_Rep2

description:
18E-18K_Rep2
Biological replicate 3
Biological replicate 3
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: MDA-MB-436_ERI_1

description: drug


title: 18E-28E_Rep2

description:
18E-28E_Rep2
Biological replicate 3
Biological replicate 3
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: Patient-derived xenograft T-ALL-8

description: patient-derived xenograft cells


title: MDA-MB-436_Ctrl_3

description: vehicle

source_name: MDA-MB-436 Control


title: Patient-derived xenograft ETP-ALL-2

description: patient-derived xenograft cells

value: ETP-ALL


title: Bladder_Tumour_3 [human]


title: Bladder_Tumour_4 [human]


title: Bladder_Tumour_2 [human]


title: Patient-derived xenograft BCP-ALL-2

description: patient-derived xenograft cells


title: 28B-28E_Rep1

description:
28B-28E_Rep1
Biological replicate 1
Biological replicate 1
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: MDA-MB-436_Ctrl_2

description: vehicle


title: Patient-derived xenograft MLL-ALL-1

description: patient-derived xenograft cells


title: Patient-derived xenograft MLL-ALL-6

description: patient-derived xenograft cells


title: 28C-28B_Rep1

description:
28C-28B_Rep1
Biological replicate 1
Biological replicate 1
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: Patient-derived xenograft T-ALL-3

description: patient-derived xenograft cells


title: 28B-18B_Rep2

description:
28B-18B_Rep2
Biological replicate 3
Biological replicate 3
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: MDA-MB-436_Ctrl_1

description: vehicle


title: 18C-18B_Rep2

description:
18C-18B_Rep2
Biological replicate 3
Biological replicate 3
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: Normal_Bladder_8 [human]

source_name: non-tumoral bladder mucosa

value: non-tumoral bladder mucosa


title: Bladder_Tumour_1 [human]

value: bladder tumour


title: CAL-51_PTX_2

description: drug

source_name: CAL-51 Paclitaxel_24h


title: Normal_Bladder_7 [human]

value: bladder cancer patient


title: CAL-51_PTX_3

description: drug


title: Patient-derived xenograft BCP-ALL-17

description: patient-derived xenograft cells


title: 28E-28K_Rep1

description:
28E-28K_Rep1
Biological replicate 1
Biological replicate 1
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: Patient-derived xenograft MLL-ALL-8

description: patient-derived xenograft cells


title: CAL-51_ERI_3

description: drug

source_name: CAL-51 Eribulin_24h


title: CAL-51_PTX_1

description: drug


title: 28K-28C_Rep1

description:
28K-28C_Rep1
Biological replicate 1
Biological replicate 1
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: Normal_Bladder_5 [human]


title: 18B-18C_Rep1

description:
18B-18C_Rep1
Biological replicate 1
Biological replicate 1
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: Normal_Bladder_4 [human]


title: Patient-derived xenograft T-ALL-33

description: patient-derived xenograft cells


title: Patient-derived xenograft T-ALL-31

description: patient-derived xenograft cells


title: 18C-18K_Rep1

description:
18C-18K_Rep1
Biological replicate 1
Biological replicate 1
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: Patient-derived xenograft T-ALL-32

description: patient-derived xenograft cells


title: 18K-18E_Rep1

description:
18K-18E_Rep1
Biological replicate 1
Biological replicate 1
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: CAL-51_Ctrl_3

description: vehicle

source_name: CAL-51 Control


title: CAL-51_ERI_2

description: drug


title: Normal_Bladder_3 [human]

value: WT


title: CAL-51_ERI_1

description: drug


title: Normal_Bladder_2 [human]


title: CAL-51_Ctrl_2

description: vehicle


title: Patient-derived xenograft MLL-ALL-5

description: patient-derived xenograft cells


title: Patient-derived xenograft BCP-ALL-4

description: patient-derived xenograft cells


title: Normal_Bladder_1 [human]


title: 28C-18C_Rep1

description:
28C-18C_Rep1
Biological replicate 1
Biological replicate 1
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.

source_name: whole body


title: 18E-18B_Rep1

description:
18E-18B_Rep1
Biological replicate 1
Biological replicate 1
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: CAL-51_Ctrl_1

description: vehicle


title: MDA-MB-436_PTX_2

description: drug


title: 18K-28K_Rep1

description:
18K-28K_Rep1
Biological replicate 1
Biological replicate 1
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: CON_iTreg_4 Days_rep3

city: Shanghai

first: Lingyun

last: Zhang

address: 280 Chongqing South Road

institute: Shanghai Institute of Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine

description: Gene expression after 4 Day cultured with anti-CD3,anti-CD28,TGF-β,IL-2 in RPMI 1640 medium

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Con-CD4+ Naïve T cell,4days,induced Treg, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: mouse CD4+ Naive T cell isolation, spleens were removed, teased into cell-single suspensions and filtered through a 40 μm cell strainer (BD, USA).Naïve CD4+CD25-Foxp3gfp-CD62Lhi T cells were sorted by FACSAria III (BD bioscience).

extract_protocol: RNA was prepared using the miRNeasy Micro Kit ((Cat#217084, QIAGEN, GmBH, Germany)) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The medium used for T cell cultures was RPMI-1640 (Gibco) supplemented with 10% heat-inactivated FBS (Gibco), 2 mM L-glutamine (Gibco), 100 U/ml penicillin, 100 μg/ml streptomycin, and 5 mM β-mercaptoethanol (Gibco, USA). The CD4+ Naïve T cells were stimulated with plate-bound anti-CD3 (5 μg/ml) plus soluble anti-CD28 (2 μg/ml) under iTreg cell differentiation conditions (mTGF-β1, 5 ng/ml and rmIL-2, 40 ng/ml; R&D Systems).

tag: background strain

tag: cell

value: iTreg

value: mouse spleen


title: CON_iTreg_4 Days_rep2

department: Shanghai Institute of Immunology, Institute of Medical Sciences

source_name: Con-CD4+ Naïve T cell,4days,induced Treg, replicate 2


title: 18B-28B_Rep1

description:
18B-28B_Rep1
Biological replicate 1
Biological replicate 1
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.


title: Normal_Bladder_6 [human]

tag: disease status

tag: pik3ca mutation status


title: AtGNL_LLM_AAAox (Col)_repB

city: Freising-Weihenstephan

first: Claus

last: Schwechheimer

address: WZW - Lehrstuhl Systembiologie der Pflanzen, Am Hochanger 4

country: Germany

institute: Claus Schwechheimer

description:
AtGNL_LLM/AAAox-B
Replicate B

hyb_protocol: The probes were hybridized to Agilent-021169 arrays in rotating hybridization chambers (Agilent Technologies) and incubated at 65 °C for 17 h overnight in a hybridization oven. Subsequently, the arrays were washed according to manufacturer's instructions. 1.65 µg of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 µL of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-021169 Arabidopsis Arrays (G2519F) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed following the manufacturer's protocol for washing with Stabilization and Drying Solution.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 021169_D_F_20111220) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: 10-day-old seedlings, AtGNL_LLM/AAAox

label_protocol: Cy3-labeled cRNA was prepared from 150 ng total RNA.

growth_protocol: Arabidopsis thaliana (Col-0) and transgenic seedlings were grown in 120 µE white light on 1/2 MS medium at 22 °C for 10 days in continuous light.

extract_protocol: Total RNA was prepared using the Macherey-Nagel Nucleo Spin RNA Plant Kit from three biological replicate samples.

treatment_protocol: Does not apply.

tag: ecotype/background

tag: genotype/variation

value: YFP:HA AtGNL_LLM/AAAox

value: seedlings

tag: developmental stage

value: 10-day-old seedlings


title: Patient-derived xenograft MLL-ALL-2

description: patient-derived xenograft cells

source_name: Patient-derived xenograft cells


title: CKO_iTreg_4 Days_rep2

source_name: CKO-CD4+ Naïve T cell,4days,induced Treg, replicate 2


title: Patient-derived xenograft T-ALL-29

description: patient-derived xenograft cells

value: T-ALL


title: AtGNL_LLM_AAAox (Col)_repC

description:
AtGNL_LLM/AAAox-C
Replicate C


title: Patient-derived xenograft MLL-ALL-3

description: patient-derived xenograft cells


title: Patient-derived xenograft MLL-ALL-14

description: patient-derived xenograft cells


title: CKO_iTreg_4 Days_rep1

source_name: CKO-CD4+ Naïve T cell,4days,induced Treg, replicate 1


title: AtGNL_LLM_AAAox (Col)_repA

description:
AtGNL_LLM/AAAox-A
Replicate A


title: 28E-18E_Rep1

description:
28E-18E_Rep1
Biological replicate 1
Biological replicate 1
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.

value: heat sensitive


title: AtGNC_LLM_AAAox (Col)_repB

description:
AtGNC_LLM/AAAox-B
Replicate B

source_name: 10-day-old seedlings, AtGNC_LLM/AAAox

value: YFP:HA AtGNC_LLM/AAAox


title: CKO_iTreg_4 Days_rep3

source_name: CKO-CD4+ Naïve T cell,4days,induced Treg, replicate 3


title: mouse cecum microbiota to mouse transfer, biological rep 3

city: St Louis

first: Henning

last: Seedorf

address: 4444 Forest Park Blvd

institute: Washington University

description: Gene expression data from tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a mouse cecum

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 plus 2/Mouse 430 2.0  Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as described in the manuscript.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

growth_protocol: Germfree mice were gavaged with microbiota from various sources and maintained on the same diet for ~28 days in plastic isolators.

extract_protocol: Proximal colon was homgenized in RLT buffer. RNA was extracted using RNeasy mini kit.

treatment_protocol: At the terminal time point animals were sacrificed and the colon was removed. The proximal part of the colon was snap-frozen in liquid nitrogen and stored at -80C until further processing.

tag: strain

tag: gender

value: male

tag: age

value: 12-16 weeks

value: colon


title: AtGNC_LLM_AAAox (Col)_repC

description:
AtGNC_LLM/AAAox-C
Replicate C


title: TRS-HGPS-shBRD4 rep3

city: Bethesda

first: Patricia

last: Fernandez Ferri

state: MD

address: 41 Library Drive, B513

institute: NCI/NIH

description: Replica 3

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files from Affymetrix were imported into Partek Genomics Suite (Partek Incorporated) and RMA normalized. Analysis of variance (ANOVA) with false discovery correction (FDR) was performed and differentially expressed genes (DEG) were defined as genes having ≥ 2-fold change of expression in pair-wise comparisons, with an FDR-corrected P value <0.05, unless otherwise stated (unadjusted p value).

source_name: TRS-HGPS2 cells in which BRD4 has been stably knocked-down (shBRD4-3)

label_protocol: standard Affymetrix protocol

growth_protocol: Not applicable

extract_protocol: RNA was extracted using the RNAeasy kit (Qiagen)

treatment_protocol: Not applicable

tag: cell type


title: AtGNCox (Col)_repC

description:
AtGNCox-C
Replicate C

source_name: 10-day-old seedlings, AtGNCox

value: YFP:HA AtGNCox


title: mouse cecum microbiota to mouse transfer, biological rep 2

source_name: tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a mouse cecum


title: mouse cecum microbiota to mouse transfer, biological rep 1


title: AtGNCox (Col)_repB

description:
AtGNCox-B
Replicate B


title: TRS-HGPS-shBRD4 rep2

description: Replica 2

source_name: TRS-HGPS2 cells in which BRD4 has been stably knocked-down (shBRD4-2)


title: TRS-HGPS-shBRD4 rep1

description: Replica 1

source_name: TRS-HGPS2 cells in which BRD4 has been stably knocked-down (shBRD4-1)


title: termite hindgut microbiota to mouse transfer, biological rep 3

description: Gene expression data from tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a termite hindgut


title: AtGNC_LLM_AAAox (Col)_repA

description:
AtGNC_LLM/AAAox-A
Replicate A


title: AtGNCox (Col)_repA

description:
AtGNCox-A
Replicate A


title: TRS-HGPS2 rep1

description: Replica 1

source_name: HGPS dermal fibroblasts transformed by retroviral introduction of TERT, HRAS and SV40 T antigens (Hahn et al 1999)


title: termite hindgut microbiota to mouse transfer, biological rep 2

source_name: tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a termite hindgut


title: TRS-WT2 rep2

description: Replica 2

source_name: WT dermal fibroblasts transformed by retroviral introduction of TERT, HRAS and SV40 T antigens (Hahn et al 1999)


title: wild type (Col_0)_repA

description:
Col-A
Replicate A

source_name: 10-day-old seedlings, WT

value: wild type


title: termite hindgut microbiota to mouse transfer, biological rep 1


title: soil microbiota to mouse transfer, biological rep 3

description: Gene expression data from tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a soil


title: soil microbiota to mouse transfer, biological rep 2

source_name: tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a soil


title: TRS-HGPS2 rep2

description: Replica 2

value: HGPS dermal fibroblasts transformed by retroviral introduction of TERT, HRAS and SV40 T antigens (Hahn et al 1999)


title: wild type (Col_0)_repC

description:
Col-C
Replicate C


title: tongue microbiota to mouse transfer, biological rep 3

description: Gene expression data from tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a tongue


title: BdGATA6ox (Col)_rep1

description:
BdGATA6ox-1
Replicate 1

source_name: 10-day-old seedlings, BdGATA6ox

value: YFP:HA BdGATA6ox


title: soil microbiota to mouse transfer, biological rep 1


title: CON_iTreg_4 Days_rep1

source_name: Con-CD4+ Naïve T cell,4days,induced Treg, replicate 1


title: T. gondii spor. oocysts Bio Rep 3

city: Pittsburgh

first: Jon

middle: P

last: Boyle

state: PA

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

description: Transcript abundance data from T. gondii oocysts (containing RNA from both sporozoites and unsporulated oocysts)

hyb_protocol: Standard protocol using 17 micrograms of labeled cRNA

scan_protocol: Standard protocol

data_processing: To permit analysis of hybridization data for two species, custom Affymetrix Chip Description Files (CDF) were generated that contained only probes that had perfect matches to sequences in the T. gondii VEG (ToxoDB) and H. hammondi HhGer041 genomes using BLASTN.  The expression module of the chip contains 11 probes for each of 8,058 T. gondii genes, and 6,294 of these genes had at least one probe that perfectly matched the T. gondii VEG and H. hammondi HhGer041 genomes.  A custom script (written in Perl and available upon request) was written to generate the CDF file.  Raw CEL files for the H. hammondi and T. gondii VEG oocyst hybridizations were analyzed using the Affy package implemented in R statistical software, and all data were normalized (“constant” method) and log2 transformed using “median polishing”.  To identify genes with significantly different abundance between species, we used Rank Products with a false-discovery rate of 1/100 as implemented in the MeViewer Module of the TM4 Microarray Software Suite.  Genes were deemed to be significantly different in abundance if the adjusted P-value was ≤ 0.01.  Gene ontology (GO) analyses of differentially-expressed transcripts were calculated with GeneMerge (45) as described previously (46).  GO categories were deemed significantly enriched if they had adjusted P-values ≤ 0.05.

organism: Toxoplasma gondii

source_name: T. gondii spor. oocysts Bio Rep 3

label_protocol: Biotinylated cRNA were prepared using the Illumina Total Prep RNA labeling kit as per instructions from 5 micrograms of total RNA.

growth_protocol: Unsporulated oocysts were collected from the feces of infected cats and sporulated in 2% sulfuric acid

extract_protocol: Sporulated oocysts from H. hammondi HhGER041 and T. gondii VEG were produced as described above and sporulated in 2% sulfuric acid at 4°C.  Sporulated oocysts of both species were kept at 4°C for ~20 d prior to RNA harvest.  To isolate RNA ~80 million oocysts per species were washed with HBSS, treated with 10% bleach, and sporocysts were released using glass beads as above for DNA isolation.  Sporulation efficiency was ~40% for both T. gondii and H. hammondi oocysts.  Pellets were resuspended in mL Trizol Reagent (Invitrogen) by pipetting, and passed serially through 25 and 27 gauge needles.  Preparations were centrifuged for 1 min at 5000 x g, supernatants were chloroform extracted and RNA was precipitated according to the manufacturer's instructions.  Pellets were resuspended in RNase-free water, extracted with phenol:chloroform:isoamyl alcohol (25:24:1), and re-precipitated with 0.7 volumes of isopropanol in the presence of 0.3 M sodium acetate (pH 5.2).  Pellets were washed with 75% ethanol and resuspended in RNase-free water.  Samples were labeled for array hybridization using the Illumina® TotalPrep RNA Amplification Kit (Applied Biosystems, Carlsbad, CA). Labeled cRNA samples were hybridized using Toxoplasma 169 chips (Available through the University of Pennsylvania Genomics Core Facility (37)).  Three separate RNA isolations were performed for each species and hybridized separately.

treatment_protocol: Sporulated oocysts were quantified using a hemacytometer, and washed multiple times in HBSS to remove the sulfuric acid.  Oocysts were treated for 30 min with 10% bleach in PBS, and then washed again in HBSS to remove any residual bleach.

value: VEG


title: tongue microbiota to mouse transfer, biological rep 2

source_name: tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a tongue


title: BdGATA6ox (Col)_rep2

description:
BdGATA6ox-2
Replicate 2


title: T. gondii spor. oocysts Bio Rep 2

source_name: T. gondii spor. oocysts Bio Rep 2


title: tongue microbiota to mouse transfer, biological rep 1


title: BdGATA6ox (Col)_rep3

description:
BdGATA6ox-3
Replicate 3


title: AtGATA17ox (Col)_rep3

description:
AtGATA17ox-3
Replicate 3

source_name: 10-day-old seedlings, AtGATA17ox

value: YFP:HA AtGATA17ox


title: AtGATA17ox (Col)_rep2

description:
AtGATA17ox-2
Replicate 2


title: human feces microbiota to mouse transfer, biological rep 3

description: Gene expression data from tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a human feces


title: TRS-WT2 rep1

description: Replica 1

value: WT dermal fibroblasts transformed by retroviral introduction of TERT, HRAS and SV40 T antigens (Hahn et al 1999)


title: human feces microbiota to mouse transfer, biological rep 2

source_name: tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a human feces


title: AtGATA17ox (Col)_rep1

description:
AtGATA17ox-1
Replicate 1


title: human feces microbiota to mouse transfer, biological rep 1


title: H. hammondi spor. oocysts Bio Rep 3

description: Transcript abundance data from H. hammondi  oocysts (containing RNA from both sporozoites and unsporulated oocysts)

organism: Hammondia hammondi

source_name: H. hammondi spor. oocysts Bio Rep 3


title: T. gondii spor. oocysts Bio Rep 1

source_name: T. gondii spor. oocysts Bio Rep 1


title: H. hammondi spor. oocysts Bio Rep 2

source_name: H. hammondi spor. oocysts Bio Rep 2


title: skin microbiota to mouse transfer, biological rep 3

description: Gene expression data from tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a skin


title: H. hammondi spor. oocysts Bio Rep 1

source_name: H. hammondi spor. oocysts Bio Rep 1


title: GNLox (Col)_rep2

description:
AtGNLox-2
Replicate 2

source_name: 10-day-old seedlings, AtGNLox

value: YFP:HA AtGNLox


title: wild type (Col_0)_rep3

description:
Col-3
Replicate 3


title: microbial mat microbiota to mouse transfer, biological rep 3

description: Gene expression data from tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a microbial mat


title: skin microbiota to mouse transfer, biological rep 2

source_name: tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a skin


title: GNLox (Col)_rep1

description:
AtGNLox-1
Replicate 1


title: wild type (Col_0)_repB

description:
Col-B
Replicate B


title: wild type (Col-0)_rep1

description:
Col-1
Replicate 1

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 µL of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-021169 Arabidopsis Arrays (G2519F) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed following the manufacturer's protocol for washing with Stabilization and Drying Solution.


title: microbial mat microbiota to mouse transfer, biological rep 2

source_name: tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a microbial mat


title: skin microbiota to mouse transfer, biological rep 1


title: zebrafish gut microbiota to mouse transfer, biological rep 2

description: Gene expression data from tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a zebrafish gut


title: microbial mat microbiota to mouse transfer, biological rep 1


title: zebrafish gut microbiota to mouse transfer, biological rep 1

description: Gene expression data from tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a  zebrafish gut


title: zebrafish gut microbiota to mouse transfer, biological rep 3

source_name: tissue of the proximal colon of a formerly germfree mouse  ~28 days after gavage with a microbiota from a zebrafish gut


title: Rice spl5 mutant with many lesions,biological rep1

city: JinHua

first: JIN

last: BIN

state: ZheJiang

address: YingBin Road 688#

department: College of Chemistry & Life Sciences

institute: Zhejiang Normal University

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix, US) in Hybridization Oven 645 (Affymetrix, US) and Fluidics Station 450 (Affymetrix, US) followed the manufacturer’ s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Affymetrix, US) and Command Console Software 3.1 (Affymetrix, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, US).

organism: Oryza sativa

source_name: spl5 mutant with many lesions (ML)

label_protocol: Total RNAs were amplified, labeled and purified by using GeneChip® 3’IVT Express Kit (Affymetrix, US) strictly followed the instructions of manufacturer to obtain biotin labeled cRNA.

growth_protocol: Rice plants were grown in a chamber under a 12h-light (28℃) and 12h-dark (24℃) cycle in hydroponic culture.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Life technologies, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, US). Qualified total RNA was further purified by RNeasy mini kit (QIAGEN, Germany) and RNase-Free DNase Set (QIAGEN, Germany).

value: spl5 mutant

value: 60 days old

tag: lesion formation

value: many lesions (ML), leaf area with 70-80% lesions

value: leaf


title: Rice WT-ZF802,biological rep2

source_name: Wild-type (WT) control, Zhefu802

tag: variety

value: wild type (control)


title: Rice WT-ZF802,biological rep1


title: Rice spl5 mutant with many lesions,biological rep2


title: Rice spl5 mutant with few lesions,biological rep1

source_name: spl5 mutant with few lesions (FL)

value: few lesions (FL), leaf area with 10-20% lesions


title: GFP-SAS siAkt1-22

status: Public on Oct 01 2014

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

country: Japan

institute: Ehime University Graduate School of Medicine

hyb_protocol: 7.5 µg fragmented and labeled aRNA were hybridized for 16h at 45℃ on Human Genome U219 Array Strip. Array Strip was washed and stained in the GeneAtlasTM fluidics station.

scan_protocol: Array Strip was scanned in the GeneAtlasTM imaging station.

data_processing:
The robust multichip average (RMA) method was used background correction and normalization.
GeneSpring GX 12.1 software computed normalized signal intensity (log2).

source_name: GFP-SAS, siAkt1-22

label_protocol: 10 ng of total RNA was labeled using a GeneAtlasTM 3'IVT Express Kit Assay (Affymetrix) according to the manufacturer's instructions.

growth_protocol: GFP-SAS cells were incubated in a humidified atomosphere of 95% air and 5% CO2 at 37℃

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

treatment_protocol: GFP-SAS cells were treated with 10 nM of siNT, siAkt1-22, or siAkt1-58 for 24 h.

value: Tongue

tag: cell line

value: SAS human tongue carcinoma cell line

value: Knockdown of Akt1


title: PB CD34+ cells from PMF patient 5776 (GEP)

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: Peripheral Blood CD34+ cells from PMF patient

hyb_protocol: Regarding GEP, fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays, according to the standard protocol supplied by Affymetrix (GeneAtlas 3’ IVT Express Kit, P/N 702833 Rev. 4). As for miEP, tagged RNA was hybridized to the Affymetrix Genechip miRNA array 2.0 using manufacturer's recommendations (FlashTag™ Biotin HSR RNA Labeling Kit, P/N 703095 Rev. 1). The miRNA arrays were washed and stained by GeneChip Hybridization, Wash and Stain Kit (Affymetrix) with Fluidic Station 450 using fluidic script FS450_003.

scan_protocol: Affymetrix HG-U219 array strips were finally scanned using GeneAtlas Scanner.  Affymetrix Genechip miRNA arrays 2.0 were scanned using the Affymetrix GCS3000 7G Scanner.

data_processing: Gene expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

source_name: PMF Peripheral Blood CD34+ Cells

label_protocol: Gene expression profiling (GEP) and miRNA expression profiling (miEP) were performed on the same RNA preparation. As regards GEP, biotinylated cRNA were prepared according to the standard GeneAtlas 3’IVT Express Kit protocol from 100ng of  total RNA (P/N 702833 Rev. 4, Affymetrix). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the cRNA sample concentration.As for miEP, total RNA (100ng for samples) were labeled using the FlashTag® Biotin HSR kit (Affymetrix).

growth_protocol: CD34+ cells were purified from 30–50 ml of PB collected from PMF patients, from 150 ml of PB from G-CSF untreated healthy donors, or from 5 ml of BM aspirates, all obtained in preservative free heparin.  Mononuclear cells were separated over a Ficoll-Paque gradient (Lympholyte; Cederlane Labs) and processed through two sequential steps of immunomagnetic CD34  selection (Miltenyi Biotec, Bergisch Gladbach,Germany,http://www.miltenyibiotec.com). Purity of the isolated CD34+ cell population was evaluated by flow cytometry after labeling with PE-HPCA2 anti-CD34 monoclonal antibody (BD Biosciences) and was always > 95%.

extract_protocol: CD34+ cells were purified from Peripheral Blood of PMF patients and immediately  lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA). Total RNA from CD34+ cells was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations for Purification of Total RNA, Including Small RNAs, from Animal Cells. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

tag: supplier

value: Vannucchi

value: MPD

tag: disease

value: PMF

value: pos

value: PB


title: GFP-SAS siNT

source_name: GFP-SAS, siNT

tag: tissue

value: control


title: PB CD34+ cells from PMF patient 5793 (GEP)

value: neg


title: PB CD34+ cells from PMF patient 5782 (GEP)


title: PB CD34+ cells from PMF patient 5719 (GEP)


title: Rice spl5 mutant with few lesions,biological rep2


title: PB CD34+ cells from PMF patient 5775 (GEP)


title: Tumor xenograft control (rep2)

type: genomic

city: Indianapolis

first: Horacio

last: Cardenas

state: IN

address: 980 West Walnut Street

institute: Indiana University

description: Ovarian cancer xenografts grown in mice treated with carboplatin and then with diluent control during tumor recurrence.

hyb_protocol: DNA was amplified, fragmented, and hybridized to Illumina Infinium HumanMethylation450 BeadChip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Arrays were imaged with HiScan Reader using recommended Illumina scanner settings.

data_processing:
GenomeStudio v2011.2 with Methylation module v1.8.5
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: peritoneal tumor

label_protocol: Standard Infinium HD Methylation Assay Protocol

growth_protocol: Peritoneal tumors xenografts were grown in athymic nude mice

extract_protocol: Genomic DNA was extracted and purified from cells using Qiagen QiaAMP kit according to standard instructions.

tag: tumor type

value: ovarian cancer xenograft

tag: treatment


title: PB CD34+ cells from PMF patient 5578 (GEP)


title: PB CD34+ cells from PMF patient 5566 (GEP)


title: PB CD34+ cells from PMF patient 5760 (GEP)


title: PB CD34+ cells from PMF patient 5408 (GEP)


title: GFP-SAS siAkt1-58

source_name: GFP-SAS, siAkt1-58


title: Tumor xenograft SGI-110 treated (rep1)

description: Ovarian cancer xenografts grown in mice treated with carboplatin and then with SGI-110 during tumor recurrence.

value: demethylating agent SGI-110


title: Tumor xenograft control (rep1)


title: Tumor Xenograft SGI-110 treated (rep2)


title: Tumor xenograft control (rep3)


title: PB CD34+ cells from PMF patient 5024 (GEP)


title: PB CD34+ cells from PMF patient 5196 (GEP)


title: PB CD34+ cells from PMF patient 5757 (GEP)


title: PB CD34+ cells from PMF patient 5396 (GEP)


title: PB CD34+ cells from PMF patient 5415 (GEP)


title: PB CD34+ cells from PMF patient 5017 (GEP)


title: PB CD34+ cells from PMF patient 4771 (GEP)


title: PB CD34+ cells from PMF patient 5008 (GEP)


title: PB CD34+ cells from PMF patient 4831 (GEP)


title: PB CD34+ cells from PMF patient 5035 (GEP)


title: PB CD34+ cells from PMF patient 5005 (GEP)


title: Tumor xenograft SGI-110 treated (rep3)


title: PB CD34+ cells from Healthy Donor Buffy Coat 18 (GEP)

description: Buffy Coat Peripheral Blood CD34+ cells from healthy donor

source_name: CTR Peripheral Blood Buffy Coat CD34+ Cells

value: CTR

value: PB CTR


title: PB CD34+ cells from Healthy Donor Buffy Coat 7 (GEP)


title: PB CD34+ cells from Healthy Donor Buffy Coat 4 (GEP)


title: PB CD34+ cells from Healthy Donor Buffy Coat 5 (GEP)


title: PB CD34+ cells from Healthy Donor Buffy Coat 8 (GEP)


title: PB CD34+ cells from Healthy Donor Buffy Coat 17 (GEP)


title: PB CD34+ cells from Healthy Donor Buffy Coat 15 (GEP)


title: PB CD34+ cells from Healthy Donor Buffy Coat 11 (GEP)


title: PB CD34+ cells from Healthy Donor Buffy Coat 16 (GEP)


title: PB CD34+ cells from Healthy Donor Buffy Coat 6 (GEP)


title: PB CD34+ cells from Healthy Donor Buffy Coat 2 (GEP)


title: PB CD34+ cells from PMF patient PV_46 (GEP)

value: Barosi


title: PB CD34+ cells from Healthy Donor Buffy Coat 10 (GEP)


title: PB CD34+ cells from Healthy Donor Buffy Coat 9 (GEP)


title: PB CD34+ cells from PMF patient PV_41 (GEP)


title: PB CD34+ cells from Healthy Donor Buffy Coat 1 (GEP)


title: PB CD34+ cells from Healthy Donor Buffy Coat 3 (GEP)


title: PB CD34+ cells from Healthy Donor Buffy Coat 14 (GEP)


title: PB CD34+ cells from PMF patient PV_27 (GEP)


title: PB CD34+ cells from PMF patient PV_22 (GEP)


title: PB CD34+ cells from PMF patient PV_13 (GEP)


title: PB CD34+ cells from PMF patient BG_7 (GEP)

value: Rambaldi


title: PB CD34+ cells from PMF patient PV_12 (GEP)


title: PB CD34+ cells from PMF patient PV_40 (GEP)


title: PB CD34+ cells from PMF patient PV_29 (GEP)


title: PB CD34+ cells from PMF patient PV_21 (GEP)


title: PB CD34+ cells from PMF patient PV_47 (GEP)


title: sea cucumber respiratory tree 2 NA_002

city: QINGDAO

first: Muyan

last: Chen

address: 5 YUSHAN ROAD

institute: Ocean University of China

description: S02 13H-Cy3

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.

organism: Apostichopus japonicus

source_name: Apostihopus japonicus respiratory tree

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

extract_protocol: Total RNA from each tissue sample was extracted using miRNeasy Mini kit (Qiagen) according to the manufacturer’s instructions.

value: normal respiratory tree


title: sea cucumber respiratory tree 4 DA_001

description: S04 22H-Cy3

value: degenerated respiratory tree


title: sea cucumber respiratory tree 3 NA_003

description: S03 14H-Cy3


title: sea cucumber respiratory tree 5 DA_002

description: S05 23H-Cy3


title: sea cucumber respiratory tree 6 DA_003

description: S06 28H-Cy3


title: sea cucumber respiratory tree 1 NA_001

description: S01 3H-Cy3


title: PB CD34+ cells from PMF patient BG_2 (GEP)


title: PB CD34+ cells from PMF patient BG_6 (GEP)