title: SpnD39_aerobic_vs_anaerobic_rep1

city: Bloomington

first: Ho-Ching

middle: Tiffany

last: Tsui

state: IN

address: 1001 E. Third St.

institute: Indiana University

description: Independent biological replicate, dye swap

hyb_protocol: Performed as per microarray manufacturer’s recommendations (OciChip Application Guide from Ocimum Biosolutions). Fluorescently-labeled cDNAs were resuspended in the manufacturer’s salt-based hybridization buffer. Samples were heated for 3 min at 95C, then chilled on ice for 3 min before application to the microarray slide. Slides were hybridized at 42C overnight (~18 hrs). Slides were washed sequentially for 5 min in the following buffers pre-warmed to 30C: Buffer 1, 2X SSC, 0.1% SDS; Buffer 2, 1X SSC; Buffer 3, 0.1X SSC.

scan_protocol: Microarray slides were scanned on an Axon GenePix 4200A microarray scanner at 532 nm and 635nm. Slides were scanned at gain settings which balanced the signal acquired in both channels (pixel ratio~1.0). Images were analysed using GenePix Pro 5.0 software (molecular Devices)

data_processing: Data were normalized with BASE (Bioarray Software Environment) using the Lowess normalization method without background subtraction.

organism: Streptococcus pneumoniae

source_name: IU1690, S. pneumoniae bacterial strain D39

label_protocol: Single strand cDNA synthesis and direct labeling performed using 30 micrograms of total RNA and superscript II reverse transcriptase (Invitrogen) as per microarray manufacturer’s recommendations (OciChip Application Guide from Ocimum Biosolutions)

growth_protocol: Bacterial strains were grown statically in brain heart infusion media (Bacto BHI, Becton Dickinson) at 37ºC and aerobic condition of 5% CO2 and 95% air overnight. Overnight (~15 hrs) aerobic cultures that were in log phase (O.D620nm ~0.1-0.3) were diluted to an O.D620nm ~0.005 in 25 ml’s of BHI media in 50 ml conical tubes and grown at 37ºC and an atmosphere of 5% CO2. Growth was monitored by change in OD620 (13mm cuvette) as measured in a Spectronic 20 spectrophotometer.

extract_protocol: Total RNA was extracted from exponentially growing cultures (OD620~0.2) using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification using the RNAeasy mini kit (Qiagen) as described in Robertson et al, J. Bact (2002) 184:3508-3520

value: IU1690, S. pneumoniae serotype II capsulated bacterial strain D39

tag: growth condition

value: aerobic condition

growth_protocol: All anaerobic procedures were carried out in a Coy anaerobic chamber (www.coylab.com) that maintain an atmosphere of 2.0% hydrogen, 7% CO2  and 91% nitrogen. To prepare anaerobic media, 200 ml of BHI media in 250 ml glass bottle with loose cap was equilibrated in the Coy anaerobic chamber for 15 hours. The same overnight aerobic culture used for aerobic growth conditions was similarly diluted into equilibrated anaerobic media and incubated at 37ºC in the Coy anaerobic chamber. Growth was monitored by change in OD620 (13mm cuvette) as measured in a Spectronic 20 spectrophotometer.

extract_protocol: Cultures grown to OD620~0.2 was removed from the anaerobic hood and added immediately (less than 10 seconds in aerobic condition) to boiling lysis buffer. The same extraction procedures were used for both aerobic and anaerobic conditions.

value: anaerobic condition


title: SpnD39_aerobic_vs_anaerobic rep2

status: Public on Dec 08 2016

type: RNA

department: Biology

country: USA

molecule: total RNA

tag: strain


title: stegm-00394: AML1-ETO_Amx_d4-2

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

label: biotin

organism: Homo sapiens

source_name: Bone marrow

tag: disease state

value: Acute Myeloid Leukemia

tag: cell line


title: SpnD39_aerobic_vs_anaerobic rep3

source_name: IU1781, S. pneumoniae bacterial strain D39 rpsL1

value: IU1781, S. pneumoniae serotype II capsulated bacterial strain D39 rpsL1, streptomycin resistant


title: Control Veh-Rep7

status: Public on Dec 07 2016

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
251485077085_1_3
Gene expression after 6 hours of vehicle (H20) treatment

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: primary macrophages_Control Veh

label_protocol: Gene expression analysis was conducted using Agilent Whole Human Genome 4x44 multiplex format oligo arrays (014850) (Agilent Technologies) following the Agilent 1-color microarray-based gene expression analysis protocol. Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Peripheral blood mononuclear cells (~4x106) were plated in 10 ml total volume of X-Vivo medium supplemented with 10% human serum and 100 IU of penicillin and 100 mg/ml of streptomycin. The cells were cultured in the X-VIVO medium for 7 days with the medium being replaced every 3-4 days.

extract_protocol: Total RNA was isolated from cells using the QIAGEN RNeasy mini-kit (including DNase treatment) following the manufacturer’s instructions.

treatment_protocol: Eight days after cells were plated, the cells were treated with 100 nM dexamethasone or vehicle (H2O) for 6 hours.

tag: snp

value: non-carrier

tag: tissue/cell type

value: peripheral blood mononuclear cells differentiated to macrophages

tag: treated with

value: vehicle for 6 hours


title: Control DEX-Rep7

description:
251485077085_1_4
Gene expression after 6 hours of glucocorticoid (dexamethasone,DEX) treatment

source_name: primary macrophages_Control DEX

value: 100 nM dexamethasone (DEX) for 6 hours


title: Control DEX-Rep5

description:
251485077084_1_4
Gene expression after 6 hours of glucocorticoid (dexamethasone,DEX) treatment


title: Control DEX-Rep4

description:
251485077082_1_4
Gene expression after 6 hours of glucocorticoid (dexamethasone,DEX) treatment


title: Control Veh-Rep5

description:
251485077084_1_3
Gene expression after 6 hours of vehicle (H20) treatment


title: Control DEX-Rep3

description:
251485077082_1_2
Gene expression after 6 hours of glucocorticoid (dexamethasone,DEX) treatment


title: Control Veh-Rep3

description:
251485077082_1_1
Gene expression after 6 hours of vehicle (H20) treatment


title: N363S Veh-Rep6

description:
251485077094_1_1
Gene expression after 6 hours of vehicle (H20) treatment

source_name: primary macrophages_N363S Veh

value: N363S carrier


title: Control Veh-Rep6

description:
251485077085_1_1
Gene expression after 6 hours of vehicle (H20) treatment


title: N363S Veh-Rep4

description:
251485077086_1_1
Gene expression after 6 hours of vehicle (H20) treatment


title: N363S Veh-Rep5

description:
251485077086_1_3
Gene expression after 6 hours of vehicle (H20) treatment


title: N363S DEX-Rep6

description:
251485077094_1_2
Gene expression after 6 hours of glucocorticoid (dexamethasone,DEX) treatment

source_name: primary macrophages_N363S DEX


title: Control Veh-Rep2

description:
251485072637_1_3
Gene expression after 6 hours of vehicle (H20) treatment


title: N363S Veh-Rep2

description:
251485072642_1_1
Gene expression after 6 hours of vehicle (H20) treatment


title: Control Veh-Rep1

description:
251485072637_1_1
Gene expression after 6 hours of vehicle (H20) treatment


title: N363S Veh-Rep7

description:
251485077088_1_3
Gene expression after 6 hours of vehicle (H20) treatment


title: N363S DEX-Rep7

description:
251485077094_1_3
Gene expression after 6 hours of glucocorticoid (dexamethasone,DEX) treatment


title: Control Veh-Rep4

description:
251485077082_1_3
Gene expression after 6 hours of vehicle (H20) treatment


title: N363S Veh-Rep3

description:
251485072642_1_3
Gene expression after 6 hours of vehicle (H20) treatment


title: N363S DEX-Rep4

description:
251485077086_1_2
Gene expression after 6 hours of glucocorticoid (dexamethasone,DEX) treatment


title: Control DEX-Rep2

description:
251485072637_1_4
Gene expression after 6 hours of glucocorticoid (dexamethasone,DEX) treatment


title: N363S DEX-Rep2

description:
251485072642_1_2
Gene expression after 6 hours of glucocorticoid (dexamethasone,DEX) treatment


title: N363S DEX-Rep5

description:
251485077086_1_4
Gene expression after 6 hours of glucocorticoid (dexamethasone,DEX) treatment


title: N363S Veh-Rep1

description:
251485072641_1_3
Gene expression after 6 hours of vehicle (H20) treatment


title: Control DEX-Rep6

description:
251485077085_1_2
Gene expression after 6 hours of glucocorticoid (dexamethasone,DEX) treatment


title: Control DEX-Rep1

description:
251485072637_1_2
Gene expression after 6 hours of glucocorticoid (dexamethasone,DEX) treatment


title: Aged  RVLM biological replicate 3 technical replicate 2

city: El Paso

first: Sivasai

last: Balivada

state: Texas

address: 4th floor, Bioscience research building

institute: University of Texas at El Paso

hyb_protocol: Labeled samples were hybridized onto whole rat genome microarray for 17hrs at 65°C in a rotator oven, washed following Agilent protocols.

scan_protocol: Hybridized arrays were scanned in an Agilent Technologies Array Scanner, G2505A (Agilent Technologies, CA).

data_processing:
Hybridization signal intensities from microarrays were extracted with Agilent Feature Extraction Software, version 9.5.1.1. (Agilent Technologies, CA). Signal intensities were normalized with a Z-Score transformation after removing positive controls, negative controls, replicate probe values and average probe signal intensity values <0
Signal intensities were normalized with a Z-Score transformation after removing positive controls, negative controls, replicate probe values and average probe signal intensity values <0

organism: Rattus norvegicus

source_name: aged RVLM

label_protocol: Briefly, 200 ng of total RNA from each sample was labeled with Cy-3 using the Low Input Quick Amp Labeling Kit (product # 5190-2305, Agilent Technologies, CA) following the manufacturer’s protocol.  The labeled RNA samples were tested for cRNA quantity and Cy-3 specific activity by NanoDrop ND-1000 UV-vis Spectrophotometer v 3.8.1 (Nano Drop Technologies Inc, DE).

growth_protocol: Young (3 months old, 301±20 gm), middle-aged (12 months old, 423±18 gm) and aged (24 months old, 413±20 gm) male F344 rats were purchased from Charles River Laboratories (contracted with National Institute of Aging).  Rats received rat chow and water ad libitum, and were maintained in a 24°C room temperature on a 12:12 hr light-dark cycle.

extract_protocol: RNA from RVLM tissue punches was extracted and purified using RNeasy Lipid Tissue mini kit (Qiagen, CA) with QIAzol Lysis reagent (Qiagen, CA) according to the manufacturer’s protocol.  The quality and quantity of the RNA used for microarray were tested using the Agilent Bioanalyzer with RNA 6000 nano kit (Agilent Technologies, CA).  RNA samples RNA integrity number (RIN) was ≥7.  The purity of the RNA samples used for qPCR was estimated using Agilent High Sensitivity RNA ScreenTape System on Agilent TapeStation (Agilent Technologies, CA) and RNA samples with ≥7 RIN were used for qPCR.  The quantity of the RNA samples used for qPCR was estimated using Qubit RNA HS assay kit on Qubit Fluorometer (ThermoFisher Scientific, CA) following manufacturer’s instructions.  Extracted RNA samples were stored at -80°C until use.

treatment_protocol: Rats were deeply anesthetized with 5% Isoflurane followed by decapitation with a guillotine.  Brains were removed within 5 mins after decapitation and snap frozen with liquid nitrogen. All brains were stored at -80°C until use. RVLM brain tissue samples collected, by the modified Palkovit’s micro-punch technique.

value: Fisher 344 rat

tag: age

value: Aged (~24 months old)

tag: gender

value: male

tag: tissue

value: Micropunched Rostral ventral lateral medulla (RVLM)


title: Aged  RVLM biological replicate 3 technical replicate 1


title: Middle-aged  RVLM biological replicate 3 technical replicate 2

source_name: middle-aged RVLM

value: Middle-aged (~12 months old)


title: Aged RVLM biological replicate 1


title: N363S DEX-Rep1

description:
251485072641_1_4
Gene expression after 6 hours of glucocorticoid (dexamethasone,DEX) treatment


title: Middle-aged  RVLM biological replicate 3 technical replicate 1


title: Middle-aged  RVLM biological replicate 2


title: N363S DEX-Rep3

description:
251485072642_1_4
Gene expression after 6 hours of glucocorticoid (dexamethasone,DEX) treatment


title: Young RVLM biological replicate 3 technical replicate 2

source_name: young RVLM

value: Young (~3 months old)


title: Middle-aged RVLM biological replicate 1


title: Aged  RVLM biological replicate 2


title: Young RVLM biological replicate 2


title: Young RVLM biological replicate 3 technical replicate 1


title: Young RVLM biological replicate 1


title: PRIM_CD127+7+

city: PARIS

first: Bruno

last: CANQUE

address: 1 avenue Claude VELLEFAUX

department: INSERM U1126

country: France

institute: INSTITUT UNIVERSITAIRE D'HEMATOLOGIE

description: Cells were extracted from of 21-week-old fetal donor

hyb_protocol: Each sample was hybridized onto GeneChip human transcriptome array 2.0 (Affymetrix), washed, and stained with the Affymetrix® Fluidics Station 450

scan_protocol: Array Scanning was performed with the Affymetrix® GeneChip Scanner 3000 7G using the Command Console software (Affymetrix®)

data_processing: Array were analyzed using the Affymetrix® APT rma-sketch routine and gene-level analysis library files downloaded from the affymetrix web site.

source_name: Primary fetal donor (PRIM)

label_protocol: For each sample 1 ng of total RNA was amplified, labeled, and fragmented using GenChip WT Pico (Affymetrix)

growth_protocol: NSG mice were irradiated with 2.25 Gy 24 h before injection of 2.5 x 105 CD34+ HPCs in the caudal vein, and sacrificed 3 weeks later. Single-cell suspensions recovered from femura and tibias were depleted in mouse cells before being incubated with antibodies against CD45, CD34, CD38, CD117, CD45RA, CD7, CD2, CD115, CD116, CD123, CD127, ITGB7, CD10, CD19 and CD24. Gates were set on hu-CD45+ cells. Femura from a fetal donor (gestational ages 21 weeks) were sterilely excised. BM mononuclear cells were separated by Ficoll-Hypaque centrifugation.  Fetal BM cells were incubated with antibodies against CD45, CD34, CD38, CD117, CD45RA, CD7, CD2, CD115, CD116, CD123, CD127, ITGB7, CD10, CD19, CD3, CD14 and CD56. Gates were set on hu-CD45+ Lin- (Lin-: CD3-CD14-CD56-). For every population of interest, 5x103 cells were sorted and processed for trancriptome analyses. The CD127- and CD127+ ELPs have been shown to correspond to lymphoid founder populations. While CD127- ELPs generate ETPs as well as precursors of marginal-zone (MZ) B cells, conventional NK cells and ILC1s, the CD127+ ELPs generate precursors of follicular B lymphocytes and ILC3s. Within the CD127- ELPS, the CD7- and CD7+ cell populations correspond respectively to multi-lymphoid and T-NK/ILC polarized progenitors. Within the Within the CD127+ ELPS, the CD7- and CD7+ cell populations correspond respectively to and B polarized and multi-lymphoid progenitors.

extract_protocol: Cells were sorted in RLT Plus Buffer before total RNA purification using the Rneasy Plus Micro Kit (Qiagen). RNAs quantification and quality controls were performed using the HT RNA Pico sensitivity LabChip Kit and the Caliper LabChip Microfluidic System (Perkin Elmer)

value: Bone marrow

tag: cell type

value: Early Lymphoid Progenitors (ELPs)


title: PRIM_LMDP


title: PRIM_CD127+7-


title: B16F10atcc_CL

city: Cambridge

first: John

last: Prime

address: Aaron Klug Building

department: Oncology Research

country: United Kingdom

institute: Medimmune

hyb_protocol: Samples were hybridized to Mouse Exon 1.0 ST arrays (Affymetrix) according to NuGEN guidelines for Affymetrix GeneChip® arrays.

scan_protocol: Arrays were washed, stained and scanned in accordance with the Affymetrix GeneChip Whole Transcript (WT) Sense Target labelling Assay Manual.

data_processing: Raw microarray data for the in vitro and in vivo samples underwent Robust Multichip Algorithm (RMA) pre-processing/normalisation in Omicsoft ArrayStudio. 1192934 exon probes remained with a probe detection p value <= 0.05.

organism: Mus musculus

source_name: Melanoma cell line B16F10 ATCC grown in vitro

label_protocol: cDNA was fragmented and labelled using the FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies).

extract_protocol: RNA was extracted from the cell lines and from the tumor, spleen and lymph node tissues from each model using RNAStat 60 (Amsbio) and quality of total RNA was determined using a 2100 Bioanalyzer (Agilent).  Samples were amplified using the WT-Ovation Pico amplification kit (NuGEN Technologies).

value: B16F10 ATCC

tag: experimental group

value: Cell line

tag: mouse strain

tag: tissue of origin

value: Melanoma

tag: Sex

value: Female

tag: sample number


title: 4T1_CL

source_name: mammary tumour cell line 4T1 grown in vitro

value: Balb/C

value: Breast


title: NSG_LMDP, biological rep 2

description: Cells were extracted from the bone marrow of NSG mice were sacrificed three weeks post-graft with neonatal UCB CD34+ HPCs

source_name: NSG mice engrafted with neonatal UCB CD34+ HPCs (NSG)


title: TRAMPC2_CL

source_name: Prostate cancer cell line TRAMPC2 grown in vitro

value: Prostate

value: Male


title: NSG_CD127+7+, biological rep 1


title: NSG_CD127-7+


title: PRIM_CD127-7+


title: CT26_CL

source_name: Colon cancer cell line CT26 grown in vitro

value: Colon


title: NSG_CD127+7-, biological rep 2


title: MC38_CL

source_name: Colon cancer cell line MC38 grown in vitro


title: Hepa1-6_CL

source_name: Liver cancer cell line Hepa1-6 grown in vitro

value: Liver


title: ID8_CL

source_name: Ovarian cancer cell line ID8 grown in vitro

value: Ovary


title: TRAMPC1_CL

source_name: Prostate cancer cell line TRAMPC1 grown in vitro


title: EL4_CL

source_name: Blood cancer cell line EL4 grown in vitro

value: Blood


title: NSG_CD127-7-, biological rep 2


title: NSG_CD127+7-, biological rep 1


title: NSG_CD127+7+, biological rep 2


title: B16F0ecacc_CL

source_name: Melanoma cell line B16F0 ECACC grown in vitro

value: B16F0 ECACC


title: RENCA_CL

source_name: Renal cancer cell line Renca grown in vitro

value: Renca

value: Renal


title: NSG_CD127-7-, biological rep 1

value: Bone marrow


title: NSG_LMDP, biological rep 1.


title: PRIM_CD127-7-

value: Early Lymphoid Progenitors (ELPs)


title: B16F0atcc_CL

source_name: Melanoma cell line B16F0 ATCC grown in vitro

value: B16F0 ATCC


title: P815_CL

source_name: Mast cells cell line P815 grown in vitro

value: Cell line

value: Mast cells


title: PAN02_CL

source_name: Pancreatic cancer cell line PAN02 grown in vitro

value: Pancreas

value: Female


title: P815-Tumour-animal-27

source_name: Tumour from mouse with mast cell cancer cell line P815 grown in vivo subcutaneously on the back of DBA/2J mouse

value: tumour

tag: animal number


title: P815-Tumour-animal-30


title: LL2_CL

source_name: Lung cancer cell line LL2 grown in vitro

value: Lung


title: P815-Spleen-animal-30

source_name: Spleen from mouse with mast cell cancer cell line P815 grown in vivo subcutaneously on the back of DBA/2J mouse

value: Spleen


title: P815-Tumour-animal-29


title: P815-Tumour-animal-28


title: P815-Lymph-Node-animal-30

source_name: Tumour draining lymph node from mouse with mast cell cancer cell line P815 grown in vivo subcutaneously on the back of DBA/2J mouse

value: Lymph node


title: P815-Lymph-Node-animal-27


title: P815-Lymph-Node-animal-29


title: P815-Spleen-animal-29


title: P815-Spleen-animal-26


title: DBAFem-Spleen-animal-4

source_name: Spleen from non-tumour bearing female DBA/2J mouse

value: DBAfemSP


title: P815-Spleen-animal-28


title: P815-Lymph-Node-animal-28


title: P815-Tumour-animal-26


title: DBAFem-Spleen-animal-5


title: P815-Lymph-Node-animal-26


title: DBAFem-Lymph-Node-animal-4

source_name: Lymph node from non-tumour bearing female DBA/2J mouse

value: DBAfemLN


title: DBAFem-Spleen-animal-2


title: DBAFem-Spleen-animal-3


title: DBAFem-Lymph-Node-animal-5


title: DBAFem-Spleen-animal-1


title: DBAFem-Lymph-Node-animal-3


title: DBAFem-Lymph-Node-animal-2


title: P815-Spleen-animal-27


title: HTOXAR3_oxliplatin_onlya_repl3

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: Single treatment, derived oxaliplatin resistant HTOXAR3 colorectal cancer cell line, treated with oxaliplatin, biological replicate 3 of 3

hyb_protocol: For each sample, 825 ng of Cy3 labeled cRNA were hybridized in an Agilent Hyb Chamber for 17 h at 65ºC in a rotisserie oven with 10 rpm rotation speed in 0.5X fragmentation buffer, 1X Agilent Gene Expression hybridization buffer, 1X blocking agent. Each labeled sample was hybridized on a separate subarray of 8-plex in situ synthesized oligonucleotide probe microarray slides (SurePrint G3 HumanV2 GE 8x60K Microarrays, Agilent microarray design ID: 039494). The day after , slides were disassembled and washed first in Gene Expression Wash Buffer 1 with 0.005% Triton X102 for 1 minute at room temperature, followed by a second wash in Gene Expression Wash Buffer 2 with 0.05% Triton X102 for 1 minute at 37º C followed by scanning in an Agilent scanner.

scan_protocol: The Agilent Scan Control software was used to control de scanner and generate .tif images using default conditions for 8x60K G3 Microarray format (AgilentG3_GX_1Color: Green Dye channel, Scan Area 61 x 21.6 mm, Scan resolution 3 μm,  20 bit Tiff format (dynamic range of intensities from 1 to 1048576). The raw data as tabulated text files were obtained with Agilent Feature Extraction software version 10.7.3.1 with the following settings (annotation version: 039494_D_F_20140813, extraction protocol: GE1_107_Sep09).

data_processing: Raw data intensities were background corrected using normexp, and log2intensity distributions were made comparable between samples using quantile normalization. Values were collapsed using the aggregate function in R by common gene identifier and control probes were exluded from the statistical analysis. Differential gene expression was assessed by fitting to an empirical Bayesian linear model. Statistical significance in differential gene expression was determined by setting a false discovery rate applying the Benjamini and Yekutiely method for multiple testing adjustment correction. For analysis we used the Limma package and the R statistical programming environment (Smyth, 2005).

source_name: derived cell line

label_protocol: For each sample 100 ng of total RNA were reverse transcribed, amplified by in vitro transcription and labelled with Cy3-CTP using the One-color Microarray-Based Gene Expression Analysis  protocol (Version 6.6, September 2012, Agilent) with the low input quick Amp Labeling kit following the manufacturer's instructions. One-color RNA Spike (Agilent) was included for estimation of limit of detection and dynamic range (2 µl of 1:10,000 dilution per sample). After denaturation 10 minutes at 65ºC with oligonucleotide priomers reverse transcription into cDNA was perfomed by incubating for 2h at 40ºC, followed by heat inactivation 15 minutes at 70ºC, in vitro transcription into fluorescently tagged cRNA 2 hours at 40ºC, and cleanup of unincorporated label on RNAeasy columns (Qiagen). Labelled sample quality was assessed by spectrophotometry fullfilling manufacturer specifications (specific activity>6pmol/ug Cy3) .

growth_protocol: Cell lines were grown as monolayer in DMEM (Invitrogen, Life Technologies) medium supplemented with 10% of heat-inactivated FCS (Reactiva), 400 units/mL penicillin, 40 μg/mL gentamicin, 2 mmol/L L-glutamine (Sigma), and 10 mmol/L HEPES (Sigma). at 37°C in a humidified atmosphere of 5% CO2. Cells were periodically tested for Mycoplasma contaminationand were authenticated by short tandem repeat profiling.

extract_protocol: Total RNA was extracted using the EZNA total RNA kit I (Omega). RNA concentration was measured with a small volume spectrophotometer (Nanodrop). The quality of the RNA was analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay, with RIN ranging between 9.2 and 9.8.

treatment_protocol: HT29 and HTOXAR3 cells were treated with OXA or OXA plus Curcumin at IC50 doses for 24 h (10 uM OXA for HT29 or 30 uM OXA for HTOXAR3, alone or combined with 10 uM Curcumin) or left untreated

value: HTOXAR3 (HT29 derived cell line with acquired resistance to oxaliplatin)

tag: group

value: oxaliplatin resistant

tag: treatment

value: single treatment, oxaliplatin


title: HTOXAR3_oxaliplatin_only_repl2

description: Single treatment, derived oxaliplatin resistant HTOXAR3 colorectal cancer cell line, treated with oxaliplatin, biological replicate 2 of 3


title: TC1-Tumour-animal-20

source_name: Tumour from mouse with lung cancer cell line TC1 grown in vivo subcutaneously on the back of C57Bl6j mouse


title: HTOXAR3_oxaliplatin_plus_curcumin_repl1

description: Combined treatment, derived oxaliplatin resistant HTOXAR3 colorectal cancer cell line, treated with oxaliplatin and curcumin, biological replicate 1 of 3

value: combined treatment, oxaliplatin plus curcumin


title: HTOXAR3_oxaliplatin_plus_curcumin_repl2

description: Combined treatment, derived oxaliplatin resistant HTOXAR3 colorectal cancer cell line, treated with oxaliplatin and curcumin, biological replicate 2 of 3


title: TC1-Spleen-animal-24

source_name: Spleen from mouse with lung cancer cell line TC1 grown in vivo subcutaneously on the back of C57Bl6j mouse


title: TC1-Tumour-animal-24


title: TC1-Lymph-Node-animal-22

source_name: Tumour draining lymph node from mouse with lung cancer cell line TC1 grown in vivo subcutaneously on the back of C57Bl6j mouse


title: TC1-Spleen-animal-23


title: TC1-Lymph-Node-animal-23


title: HTOXAR3_oxaliplatin_only_repl1

description: Single treatment, derived oxaliplatin resistant HTOXAR3 colorectal cancer cell line, treated with oxaliplatin, biological replicate 1 of 3


title: HTOXAR3_untreated_repl2

description: Baseline control, derived oxaliplatin resistant HTOXAR3 colorectal cancer cell line, untreated, biological replicate 2 of 3

value: basal condition, untreated


title: TC1-Spleen-animal-19


title: PAN02-Tumour-animal-4

source_name: Tumour from mouse with pancreatic cencer cell line PAN02 grown orthotopically in C57Bl6j mouse


title: TC1-Spleen-animal-22


title: DBAFem-Lymph-Node-animal-1


title: TC1-Spleen-animal-20


title: PAN02-Tumour-animal-3


title: HTOXAR3_untreated_repl1

description: Baseline control, derived oxaliplatin resistant HTOXAR3 colorectal cancer cell line, untreated, biological replicate 1 of 3


title: TC1-Tumour-animal-23


title: TC1-Lymph-Node-animal-24


title: HT29_oxaliplatin_only_repl1

description: Single treatment, parental oxaliplatin sensitive HT29 colorectal cancer cell line, treated with oxaliplatin, biological replicate 1 of 3

source_name: parental cell line

value: HT29 (colorectal cancer cell line)

value: oxaliplatin sensitive


title: HTOXAR3_oxaliplatin_plus_curcumin_repl3

description: Combined treatment, derived oxaliplatin resistant HTOXAR3 colorectal cancer cell line, treated with oxaliplatin and curcumin, biological replicate 3 of 3


title: TC1-Tumour-animal-22


title: HT29_oxaliplatin_only_repl3

description: Single treatment, parental oxaliplatin sensitive HT29 colorectal cancer cell line, treated with oxaliplatin, biological replicate 3 of 3


title: HT29_oxaliplatin_only_repl2

description: Single treatment, parental oxaliplatin sensitive HT29 colorectal cancer cell line, treated with oxaliplatin, biological replicate 2 of 3


title: TC1-Lymph-Node-animal-19


title: TC1-Lymph-Node-animal-20


title: TC1-Tumour-animal-19


title: PAN02-Tumour-animal-6


title: PAN02-Spleen-animal-3

source_name: Spleen from mouse with pancreatic cencer cell line PAN02 grown orthotopically in C57Bl6j mouse


title: PAN02-Spleen-animal-6


title: PAN02-Spleen-animal-4


title: PAN02-Tumour-animal-1


title: HTOXAR3_untreated_repl3

description: Baseline control, derived oxaliplatin resistant HTOXAR3 colorectal cancer cell line, untreated, biological replicate 3 of 3


title: MC38-Tumour-animal-8

source_name: Tumour from mouse with colon cancer cell line MC38 grown in vivo subcutaneously on the back of C57Bl6j mouse

value: Colon


title: MC38-Tumour-animal-7


title: PAN02-Spleen-animal-5


title: HT29_untreated_repl2

description: Baseline control, parental oxaliplatin sensitive HT29 colorectal cancer cell line, untreated, biological replicate 2 of 3


title: HT29_oxaliplatin_plus_curcumin_repl2

description: Combined treatment, parental oxaliplatin sensitive HT29 colorectal cancer cell line, treated with oxaliplatin and curcumin, biological replicate 2 of 3


title: MC38-Tumour-animal-9


title: PAN02-Spleen-animal-1


title: MC38-Spleen-animal-8

source_name: Spleen from mouse with colon cancer cell line MC38 grown in vivo subcutaneously on the back of C57Bl6j mouse


title: MC38-Spleen-animal-9


title: HT29_oxaliplatin_plus_curcumin_repl3

description: Combined treatment, parental oxaliplatin sensitive HT29 colorectal cancer cell line, treated with oxaliplatin and curcumin, biological replicate 3 of 3


title: MC38-Tumour-animal-12


title: HT29_untreated_repl1

description: Baseline control, parental oxaliplatin sensitive HT29 colorectal cancer cell line, untreated, biological replicate 1 of 3


title: HT29_oxaliplatin_plus_curcumin_repl1

description: Combined treatment, parental oxaliplatin sensitive HT29 colorectal cancer cell line, treated with oxaliplatin and curcumin, biological replicate 1 of 3


title: MC38-Spleen-animal-7


title: B16F10nci_CL

source_name: Melanoma cell line B16f10 NCI grown in vitro

value: B16F10 NCI

value: Cell line

value: Melanoma


title: MC38-Lymph-Node-animal-9

source_name: Tumour draining lymph node from mouse with colon cancer cell line MC38 grown in vivo subcutaneously on the back of C57Bl6j mouse

value: Female


title: MC38-Tumour-animal-11

value: tumour


title: MC38-Spleen-animal-11

value: Spleen


title: HT29_untreated_repl3

description: Baseline control, parental oxaliplatin sensitive HT29 colorectal cancer cell line, untreated, biological replicate 3 of 3


title: MC38-Lymph-Node-animal-8

value: Lymph node


title: MC38-Lymph-Node-animal-11


title: EL4-Tumour-animal-18

source_name: Tumour from mouse with blood cancer cell line EL4 grown subcutaneously on the back of C57Bl6j mouse

value: Blood


title: MC38-Lymph-Node-animal-12


title: MC38-Lymph-Node-animal-7


title: EL4-Tumour-animal-13


title: MC38-Spleen-animal-12


title: EL4-Spleen-animal-18

source_name: Spleen from mouse with blood cancer cell line EL4 grown subcutaneously on the back of C57Bl6j mouse


title: EL4-Tumour-animal-15


title: EL4-Tumour-animal-14


title: EL4-Spleen-animal-17


title: EL4-Spleen-animal-14


title: EL4-Spleen-animal-15


title: EL4-Lymph-Node-animal-18

source_name: Tumour draining lymph node from mouse with blood cancer cell line EL4 grown subcutaneously on the back of C57Bl6j mouse


title: EL4-Lymph-Node-animal-15


title: EL4-Lymph-Node-animal-17


title: EL4-Spleen-animal-13


title: C57Male-Spleen-animal-1

source_name: Spleen from non-tumour bearing male C57BI6j mouse

value: Male


title: EL4-Lymph-Node-animal-13


title: C57Male-Spleen-animal-2


title: C57Male-Spleen-animal-3


title: C57Male-Lymph-Node-animal-5

source_name: Lymph node from non-tumour bearing male C57BI6j mouse


title: EL4-Tumour-animal-17


title: C57Male-Lymph-Node-animal-2


title: C57Male-Spleen-animal-4


title: C57Male-Lymph-Node-animal-4


title: C57Male-Lymph-Node-animal-1


title: C57Male-Lymph-Node-animal-3


title: TRAMPC2-Tumour-animal-35

source_name: Tumour from mouse with prostate cancer cell line TRAMPC2 grown in vivo subcutaneously on back of C57Bl6j mouse

value: Prostate


title: C57Male-Spleen-animal-5


title: TRAMPC2-Spleen-animal-35

source_name: Spleen from mouse with prostate cancer cell line TRAMPC2 grown in vivo subcutaneously on back of C57Bl6j mouse


title: TRAMPC2-Tumour-animal-32


title: EL4-Lymph-Node-animal-14


title: TRAMPC2-Spleen-animal-32


title: TRAMPC2-Spleen-animal-34


title: TRAMPC2-Spleen-animal-33


title: TRAMPC2-Tumour-animal-31


title: TRAMPC2-Tumour-animal-33


title: TRAMPC2-Lymph-Node-animal-35

source_name: Tumour draining lymph node from mouse with prostate cancer cell line TRAMPC2 grown in vivo subcutaneously on back of C57Bl6j mouse


title: TRAMPC2-Lymph-Node-animal-34


title: TRAMPC1-Tumour-animal-30

source_name: Tumour from mouse with prostate cancer cell line TRAMPC1 grown in vivo subcutaneously on back of C57Bl6j mouse


title: TRAMPC2-Lymph-Node-animal-33


title: TRAMPC1-Tumour-animal-29


title: TRAMPC1-Spleen-animal-29

source_name: Spleen from mouse with prostate cancer cell line TRAMPC1 grown in vivo subcutaneously on back of C57Bl6j mouse


title: TRAMPC2-Lymph-Node-animal-31


title: TRAMPC1-Spleen-animal-30


title: TRAMPC2-Spleen-animal-31


title: TRAMPC2-Lymph-Node-animal-32


title: TRAMPC1-Tumour-animal-25


title: TRAMPC1-Tumour-animal-28


title: TRAMPC1-Tumour-animal-26


title: TRAMPC1-Spleen-animal-28


title: TRAMPC1-Lymph-Node-animal-28

source_name: Tumour draining lymph node from mouse with prostate cancer cell line TRAMPC1 grown in vivo subcutaneously on back of C57Bl6j mouse


title: TRAMPC1-Lymph-Node-animal-26


title: TRAMPC1-Lymph-Node-animal-29


title: TRAMPC1-Spleen-animal-26


title: TRAMPC1-Lymph-Node-animal-30


title: TRAMPC1-Lymph-Node-animal-25


title: B16F0ecacc-Tumour-animal-6

source_name: Tumour from mouse with melanoma cell line B16F0 ECACC grown in vivo subcutaneously on the back of C57Bl6j mouse

value: B16F0 ECACC

value: B16F0 ECACC_T


title: B16F0ecacc-Tumour-animal-4


title: TRAMPC1-Spleen-animal-25


title: B16F0ecacc-Tumour-animal-2


title: B16F0ecacc-Spleen-animal-2

source_name: Spleen from mouse with melanoma cell line B16F0 ECACC grown in vivo subcutaneously on the back of C57Bl6j mouse

value: B16F0 ECACC_Sp


title: B16F0ecacc-Spleen-animal-3


title: B16F0ecacc-Tumour-animal-1


title: B16F0ecacc-Tumour-animal-3


title: B16F0ecacc-Lymph-Node-animal-6

source_name: Tumour draining lymph node from mouse with melanoma cell line B16F0 ECACC grown in vivo subcutaneously on the back of C57Bl6j mouse

value: B16F0 ECACC_LN


title: B16F0ecacc-Spleen-animal-1


title: B16F0ecacc-Lymph-Node-animal-4


title: B16F0ecacc-Lymph-Node-animal-3


title: B16F0ecacc-Lymph-Node-animal-2


title: B16F0ecacc-Lymph-Node-animal-1


title: B16F0ecacc-Spleen-animal-6


title: B16F0atcc-Spleen-animal-7

source_name: Spleen from mouse with melanoma cell line B16F0 ATCC grown in vivo subcutaneously on the back of C57Bl6j mouse

value: B16F0 ATCC

value: B16F0 ATCC_Sp


title: B16F0atcc-Tumour-animal-12

source_name: Tumour from mouse with melanoma cell line B16F0 ATCC grown in vivo subcutaneously on the back of C57Bl6j mouse

value: B16F0 ATCC_T


title: B16F0atcc-Spleen-animal-11


title: B16F0atcc-Tumour-animal-9


title: B16F0atcc-Spleen-animal-10


title: B16F0atcc-Tumour-animal-7


title: B16F0ecacc-Spleen-animal-4


title: B16F0atcc-Lymph-Node-animal-9

source_name: Tumour draining lymph node from mouse with melanoma cell line B16F0 ATCC grown in vivo subcutaneously on the back of C57Bl6j mouse

value: B16F0 ATCC_LN


title: B16F0atcc-Spleen-animal-9


title: B16F0atcc-Lymph-Node-animal-7


title: B16F0atcc-Tumour-animal-10


title: B16F0atcc-Spleen-animal-12


title: B16F0atcc-Lymph-Node-animal-11


title: B16F0atcc-Lymph-Node-animal-12


title: B16F0atcc-Lymph-Node-animal-10


title: RENCA-Tumour-animal-22

source_name: Tumour from mouse with renal cancer cell line Renca grown in vivo subcutaneously on the back of Balb/C mouse

value: Renca

value: Balb/C

value: Renal


title: RENCA-Tumour-animal-19

value: tumour

value: Female


title: RENCA-Tumour-animal-24


title: RENCA-Spleen-animal-23

source_name: Spleen from mouse with renal cancer cell line Renca grown in vivo subcutaneously on the back of Balb/C mouse

value: Spleen


title: RENCA-Spleen-animal-24


title: B16F0atcc-Tumour-animal-11

value: Melanoma


title: RENCA-Spleen-animal-22


title: RENCA-Spleen-animal-19


title: RENCA-Tumour-animal-21


title: RENCA-Spleen-animal-21


title: RENCA-Lymph-Node-animal-24

source_name: Tumour draining lymph node from mouse with renal cancer cell line Renca grown in vivo subcutaneously on the back of Balb/C mouse

value: Lymph node


title: RENCA-Lymph-Node-animal-21


title: RENCA-Lymph-Node-animal-23


title: RENCA-Tumour-animal-23


title: RENCA-Lymph-Node-animal-22


title: LL2-Tumour-animal-18

source_name: Tumour from mouse with lung cancer cell line LL2 grown in vivo subcutaneously on the back of C57Bl6j mouse

value: Lung


title: LL2-Spleen-animal-16

source_name: Spleen from mouse with lung cancer cell line LL2 grown in vivo subcutaneously on the back of C57Bl6j mouse


title: MC38-Tumour-animal-59

source_name: Tumour from mouse with colon cancer cell line MC38 grown in vivo subcutaneously on the back of C57Bl6j mouse

value: Colon


title: MC38-Lymph-Node-animal-58

source_name: Tumour draining lymph node from mouse with colon cancer cell line MC38 grown in vivo subcutaneously on the back of C57Bl6j mouse


title: LL2-Tumour-animal-14


title: LL2-Lymph-Node-animal-18

source_name: Tumour draining lymph node from mouse with lung cancer cell line LL2 grown in vivo subcutaneously on the back of C57Bl6j mouse


title: LL2-Spleen-animal-17


title: LL2-Spleen-animal-13


title: MC38-Spleen-animal-56

source_name: Spleen from mouse with colon cancer cell line MC38 grown in vivo subcutaneously on the back of C57Bl6j mouse


title: LL2-Tumour-animal-17


title: MC38-Tumour-animal-58


title: LL2-Spleen-animal-18


title: MC38-Lymph-Node-animal-59


title: LL2-Tumour-animal-13


title: LL2-Tumour-animal-16


title: LL2-Lymph-Node-animal-13


title: LL2-Lymph-Node-animal-14


title: CT26-Tumour-animal-29

source_name: Tumour from mouse with colon cancer cell line CT26 grown in vivo subcutaneously on the back of Balb/C mouse


title: MC38-Tumour-animal-56


title: MC38-Spleen-animal-59


title: LL2-Spleen-animal-14


title: MC38-Spleen-animal-58


title: RENCA-Lymph-Node-animal-19


title: LL2-Lymph-Node-animal-16


title: CT26-Tumour-animal-27


title: CT26-Tumour-animal-26


title: CT26-Tumour-animal-28


title: LL2-Lymph-Node-animal-17


title: CT26-Tumour-animal-25


title: CT26-Lymph-Node-animal-28

source_name: Tumour draining lymph node from mouse with colon cancer cell line CT26 grown in vivo subcutaneously on the back of Balb/C mouse


title: CT26-Lymph-Node-animal-29


title: CT26-Spleen-animal-28

source_name: Spleen from mouse with colon cancer cell line CT26 grown in vivo subcutaneously on the back of Balb/C mouse


title: CT26-Lymph-Node-animal-27


title: CT26-Spleen-animal-25


title: CT26-Spleen-animal-26


title: C57Bl6jFem-Lymph-Node-animal-4

source_name: Lymph Node from non-tumour bearing female C57BI6j mouse


title: CT26-Lymph-Node-animal-26


title: C57Bl6jFem-Lymph-Node-animal-2


title: CT26-Spleen-animal-29


title: C57Bl6jFem-Spleen-animal-4

source_name: Spleen from non-tumour bearing female C57BI6j mouse


title: CT26-Spleen-animal-27


title: C57Bl6jFem-Spleen-animal-1


title: C57Bl6jFem-Lymph-Node-animal-1


title: C57Bl6jFem-Lymph-Node-animal-3


title: C57Bl6jFem-Spleen-animal-5


title: CT26-Lymph-Node-animal-25


title: C57Bl6jFem-Spleen-animal-2


title: C57Bl6jFem-Spleen-animal-3


title: BALBFem-Spleen-animal-9

source_name: Spleen from non-tumour bearing female Balb/C mouse

value: BALBfemSP


title: VLX600

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

country: Sweden

institute: Uppsala university

description: Gene expression data from MCF7 cells treated with VLX600 for 6 hours.

hyb_protocol: Affymetrix GeneChip® expression arrays (Human Genome U133 Plus 2.0 Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.

scan_protocol: According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Breast cancer cell line MCF7

label_protocol: 2 micrograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA).

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions.

treatment_protocol: MCF7 cells treated with 10 microM VLX600 for 6 hours.

tag: perturbagen

value: small molecule

tag: sample type

value: treatment

tag: concentration

tag: vehicle

value: DMSO

tag: duration

value: 6 h


title: C57Bl6jFem-Lymph-Node-animal-5

tag: cell line


title: DMSO_control (VLX600)

description: Gene expression data from MCF7 cells treated 0.1% DMSO for 6 hours.

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions

treatment_protocol: MCF7 control cells treated with 0.1% DMSO for 6 hours.

value: control

value: DMSO control


title: Serum free medium

city: Taipei

first: Chen-Chi

last: Liu

address: No. 155, Sec. 2, Li-Nong Street

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang-Ming University School of Medicine

description: Gene expression data from Huh7 cells treated with PGG after 0 hour of treatment

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

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol by GeneChip® Scanner 3000 7G

data_processing: The data was pre-processed using the MAS5 method from the Affymetrix GeneChip® Operating Software (GCOS).

source_name: Human Lung Cancer Cell Line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Human lung cancer cells line A549 ells were grown in DMEM containing 10 units/ml penicillin, 10 μg/ml streptomycin, 2 mM glutamine, and 10% FBS, in a 37℃ humidified atmosphere with 5% CO2. Cells were harvested at day 12 of culture.

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

treatment_protocol: A549 cells were suspended in tumor sphere medium consisting of serum-free DMEM/F12, N2 supplement, human recombinant EGF (20 ng/ml) and bFGF (10 ng/ml). Spheres were formed at about day 5 of culture and grew slowly. Cells were harvested at day 12 of culture.


title: DMEM with 10% FBS


title: AGS miR-25-3p inhibitor treated biological replicate 2

city: Madurai

first: Kumaresan

last: Ganesan

state: Tamil Nadu

address: School of Biological Sciences,

department: Genetics

country: India

institute: Madurai Kamaraj University

description: mRNA profile of AGS cells treated with miR-25-3p inhibitor

hyb_protocol: The biotin labelled single stranded cDNA was hybridized with the probes on Human Gene 1.0 ST Array for 16 hrs at 45ºC  using GeneChip Hybridization Oven 640. GeneChips were stained with Phycoerythrin and washed using GeneChip Fluidics Station 450.

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

data_processing: The CEL files were subjected to RMA normalization at exon level using Expression Console (EC) software of Affymetrix. The CHP files were analysed for differential gene expression in Transcriptome Analysis Console (TAC) software of Affymetrix.

label: Biotin

source_name: AGS cell line (Gastric adenocarcinoma)_miR-25-3p inhibitor

label_protocol: Biotin was labelled to the single stranded cDNA fragments prepared from 500 ng of total RNA. The steps were followed as per the instructions in the user manuals of Ambion® WT Expression Kit, GeneChip® WT Terminal Labeling and Hybridization kit (Affymetrix).

growth_protocol: AGS cells were grown in DMEM (F12/HAM) media with 10% FBS and 2mM Glutamine. The cells were incubated at 37ºC with 5%CO2 and 95% humidity.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini Kit as per the instructions provided by the manufacturer.

treatment_protocol: In AGS cells, anti-miR miR-25-3p inhibitor or non targeting control RNA was transfected with oligofectamine transfection reagent (invitrogen). AGS cells were transfected with miRNA inhibitor at 70 % confluency. 24 hrs after transfection, cells were  transfected again with miRNA inhibitor or non targeting control RNA . After 48 hrs of first transfection, cells were harvested and total RNA was isolated.

value: AGS

value: Stomach

value: gastric cancer


title: AGS Non-Targeting Control RNA treated biological replicate 3

description: mRNA profile of AGS cells treated with non targeting control RNA

source_name: AGS cell line (Gastric adenocarcinoma)_control RNA


title: AGS miR-25-3p inhibitor treated biological replicate 3


title: AGS miR-25-3p inhibitor treated biological replicate 1


title: BALBFem-Spleen-animal-7

value: Balb/C


title: BALBFem-Spleen-animal-6

value: Female


title: B16F10nci-Tumour-animal-5

source_name: Tumour from mouse with melanoma cell line B16F10 NCI grown in vivo subcutaneously on the back of C57BI6j mouse

value: B16F10 NCI

value: B16F10 NCI_T

value: tumour


title: B16F10nci-Tumour-animal-3

value: Melanoma


title: BALBFem-Lymph-Node-animal-7

source_name: Lymph node from non-tumour bearing female Balb/C mouse

value: BALBfemLN

value: Lymph node


title: BALBFem-Lymph-Node-animal-6


title: BALBFem-Spleen-animal-10

value: BALBfemSP

value: Spleen


title: B16F10nci-Tumour-animal-2


title: BALBFem-Lymph-Node-animal-9


title: BALBFem-Spleen-animal-8


title: B16F10nci-Tumour-animal-1


title: BALBFem-Lymph-Node-animal-10


title: B16F10nci-Spleen-animal-6

source_name: Spleen from mouse with melanoma cell line B16F10 NCI grown in vivo subcutaneously on the back of C57BI6j mouse

value: B16F10 NCI_Sp


title: B16F10nci-Spleen-animal-2


title: AGS Non-Targeting Control RNA treated biological replicate 2


title: B16F10nci-Spleen-animal-5


title: 786O_WDR20cl3

city: Yufu

first: Mika

last: Takahashi

address: Idaigaoka 1-1

country: Japan

institute: Oita University

description: WDR20 B3

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing:
Feature Extraction software (Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis. Analysis of the raw data obtained from Feature Extraction software was performed with GeneSpring GX software(Aglrent).
For comparison among multiple arrays, probr set data were median-normalized per chip. The probes were filterd based on signal intensity and flagged velues. Genes showing more than 2 fold change between average expression level of 3 kinds of WDR20 expressing-cell clones (786O_WDR20cl1, 786O_WDR20cl2 and 786O_WDR20cl3) and two replicates of a vector transfected-cell clone (786O_vector) were screened.

source_name: cell line

label_protocol: Cy3-labeled cRNA targets were generated by use of Low input Quick Amp labeling Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from stable clones overexpressing WDR20 or the empty vector, using an RNeasy mini kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s instructions. As a normal control, the total RNAs were extracted from the empty vector.

tag: control or overexpression

value: WDR20 overexpression

value: kidney


title: BALBFem-Lymph-Node-animal-8

tag: tissue


title: 786O_vector (replicate of FLIG)

description:
Replicate sample of FLIG
FLIG B11

value: control


title: B16F10nci-Spleen-animal-3


title: 786O_WDR20cl2

description: WDR20 H7


title: 786O_WDR20cl1

description: WDR20 B5


title: AGS Non-Targeting Control RNA treated biological replicate 1

value: AGS

tag: cell type


title: B16F10nci-Spleen-animal-1

tag: experimental group


title: B16F10nci-Tumour-animal-6

tag: mouse strain


title: B16F10nci-Lymph-node-animal-3

source_name: Tumour draining lymph node from mouse with melanoma cell line B16F10 NCI grown in vivo subcutaneously on the back of C57BI6j mouse

value: B16F10 NCI_LN

tag: tissue of origin


title: B16F10nci-Lymph-node-animal-5

tag: Sex


title: B16F10nci-Lymph-node-animal-6

tag: sample number


title: 786O_vector (FLIG)

description: FLIG


title: B16F10atcc-Tumour-animal-9

source_name: Tumour from mouse with melanoma cell line B16F10atcc grown in vivo subcutaneously on back of C57BI6j mouse

value: B16F10 ATCC

value: B16F10 ATCC_T

tag: animal number


title: B16F10nci-Lymph-node-animal-2

value: Female


title: B16F10atcc-Tumour-animal-7


title: B16F10atcc-Tumour-animal-8


title: B16F10nci-Lymph-node-animal-1

value: B16F10 NCI


title: B16F10atcc-Spleen-animal-7

source_name: Spleen from mouse with melanoma cell line B16F10atcc grown in vivo subcutaneously on back of C57BI6j mouse

value: B16F10 ATCC_Sp


title: B16F10atcc-Spleen-animal-9


title: 4T1-Spleen-animal-34

source_name: Spleen from mouse with mammary tumour cell line 4T1 grown in vivo subcutaneously on back of BALB/c mouse

value: Balb/C

value: Breast


title: 4T1-Tumour-animal-32

source_name: Tumour from mouse with mammary tumour cell line 4T1 grown in vivo subcutaneously on back of BALB/c mouse

value: tumour


title: B16F10atcc-Spleen-animal-8

value: Melanoma


title: B16F10atcc-lymph-node-animal-12

source_name: Tumour draining lymph node from mouse with melanoma cell line B16F10atcc grown in vivo subcutaneously on back of C57BI6j mouse

value: B16F10 ATCC_LN

value: Lymph node


title: 4T1-Tumour-animal-33


title: 4T1-Tumour-animal-34


title: B16F10atcc-lymph-node-animal-11


title: B16F10atcc-lymph-node-animal-7


title: 4T1-Tumour-animal-36


title: B16F10atcc-lymph-node-animal-8


title: B16F10atcc-Tumour-animal-12


title: B16F10atcc-lymph-node-animal-9


title: 4T1-Tumour-animal-35


title: B16F10atcc-Tumour-animal-11


title: 4T1-Spleen-animal-36

value: Spleen


title: B16F10atcc-Spleen-animal-12


title: 4T1-Spleen-animal-35


title: B16F10atcc-Spleen-animal-11


title: 4T1-lymph-node-animal-36

source_name: Tumour draining lymph node from mouse with mammary tumour cell line 4T1 grown in vivo subcutaneously on back of BALB/c mouse


title: 4T1-Spleen-animal-33


title: 4T1-lymph-node-animal-34


title: 4T1-lymph-node-animal-32


title: 4T1-Spleen-animal-32


title: 4T1-lymph-node-animal-35


title: 4T1-lymph-node-animal-33


title: socci-00214: TCGA-13-0714-01A

type: genomic

scan_protocol: See mage-tab files linked to series entry for additional details

molecule: genomic DNA

source_name: solid tumor

tag: diseasestate

value: Serous cystadenocarcinoma

tag: organismpart

value: Ovary

tag: pathologic status

value: NOT SPECIFIED

source_name: Promega ref DNA

value: Promega ref DNA


title: socci-00214: TCGA-07-0227-20A

data_processing: See mage-tab files linked to series entry for additional details

source_name: cell


title: socci-00214: TCGA-01-0630-11A

source_name: normal tissue

label_protocol: See mage-tab files linked to series entry for additional details


title: socci-00214: TCGA-13-0802-01A

extract_protocol: See mage-tab files linked to series entry for additional details


title: socci-00214: TCGA-01-0638-11A


title: socci-00214: TCGA-09-0364-01A


title: socci-00214: TCGA-13-0751-01A


title: socci-00214: TCGA-13-0714-10B

source_name: normal Blood

value: Blood

value: NON-MALIGNANT


title: socci-00214: TCGA-01-0636-11A


title: socci-00214: TCGA-01-0629-11A


title: socci-00214: TCGA-13-0795-01A


title: ID8 (251469518775) vs Mouse genomic DNA Control

hyb_protocol: hybridised on Agilent Mouse genome CGH 1x224K oligo microarrays using the Oligo aCGH Hybridisation kit (Agilent)

scan_protocol: Arrays were scanned on an Agilent Microarray scanner

data_processing: images were processed using Agilent Feature Extraction software; .txt files were imported into ArrayStudio where the data was combined in 1 matrix, the log10ratios were converted to log2 and control probes excluded

source_name: syngeneic tumour cell line

label_protocol: Samples were 2 color labelled using the genomic DNA labelling kit PLUS (Agilent)

extract_protocol: Genomic DNA was extracted from one in vitro sample of each mouse tumor cell line using the DNeasy Blood and Tissue Kit (Qiagen) and quality controlled (OD A260/230 ratio ≥ 1.8) using a 2100 Bioanalyzer (Agilent).

tag: genetic background strain

source_name: mouse genomic DNA (Merck)

tag: sample type

value: reference


title: TRAMPC2 (251469518825) vs Mouse genomic DNA Control

value: Male

value: Prostate


title: socci-00214: TCGA-13-0764-01A


title: socci-00214: TCGA-13-0765-10A


title: B16F0 ATCC (251469518793) vs Mouse genomic DNA Control

value: B16F0 ATCC

value: Female


title: PAN02 (251469518794) vs Mouse genomic DNA Control

value: Pancreas


title: EL4 (251469518795) vs Mouse genomic DNA Control


title: P815 (251469518796) vs Mouse genomic DNA Control

value: Mast cells


title: Renca (251469518776) vs Mouse genomic DNA Control

value: Renca

value: Balb/C

value: Renal


title: Hepa1-6 (251469518774) vs Mouse genomic DNA Control

value: Liver


title: B16F0 ECAC (251469518797) vs Mouse genomic DNA Control

value: B16F0 ECAC

value: Melanoma


title: MC38 (251469518826) vs Mouse genomic DNA Control

value: Colorectal


title: socci-00214: TCGA-13-0793-10A

value: Serous cystadenocarcinoma

value: Promega ref DNA


title: B16F10 NCI (251469518762) vs Mouse genomic DNA Control

value: B16F10 NCI


title: TRAMPC1 (251469518823) vs Mouse genomic DNA Control

value: reference


title: LL2 (251469518824) vs Mouse genomic DNA Control

value: Lung


title: socci-00214: TCGA-09-0367-10A

value: Blood

value: NON-MALIGNANT


title: socci-00214: TCGA-13-0801-01A

value: Ovary

value: NOT SPECIFIED


title: socci-00214: TCGA-01-0639-11A


title: 4T1 (251469518777) vs Mouse genomic DNA Control

value: Female

value: Breast


title: socci-00214: TCGA-13-0805-10A


title: socci-00214: TCGA-13-0799-01A


title: socci-00214: TCGA-13-0726-10B


title: socci-00214: TCGA-13-0726-01A


title: socci-00214: TCGA-13-0755-10A


title: socci-00214: TCGA-09-0369-10C


title: socci-00214: TCGA-09-0364-10A


title: socci-00214: TCGA-13-0804-10A


title: socci-00214: TCGA-13-0803-01A


title: socci-00214: TCGA-09-0369-01A


title: socci-00214: TCGA-13-0725-10B


title: socci-00214: TCGA-13-0799-10A


title: socci-00214: TCGA-13-0793-01A


title: socci-00214: TCGA-13-0791-01A


title: socci-00214: TCGA-13-0758-10A


title: CT26 (251469518773) vs Mouse genomic DNA Control

value: Balb/C

value: Colon


title: socci-00214: TCGA-13-0768-01A


title: socci-00214: TCGA-01-0631-11A


title: B16F10 ATCC (251469518827) vs Mouse genomic DNA Control

value: B16F10 ATCC


title: socci-00214: TCGA-09-0366-10B


title: socci-00214: TCGA-13-0800-01A


title: socci-00214: TCGA-13-0717-01A


title: socci-00214: TCGA-01-0642-11A


title: socci-00214: TCGA-13-0724-01A


title: socci-00214: TCGA-13-0730-01A


title: socci-00214: TCGA-13-0805-01A


title: socci-00214: TCGA-13-0768-10A


title: socci-00214: TCGA-13-0717-10B


title: socci-00214: TCGA-13-0792-10A


title: socci-00214: TCGA-13-0794-10A


title: socci-00214: TCGA-13-0802-10A


title: socci-00214: TCGA-13-0792-01A


title: socci-00214: TCGA-13-0791-10A


title: socci-00214: TCGA-01-0633-11A


title: socci-00214: TCGA-09-0365-10A


title: socci-00214: TCGA-13-0727-01A


title: socci-00214: TCGA-13-0797-10A


title: socci-00214: TCGA-01-0628-11A


title: socci-00214: TCGA-13-0761-10A


title: socci-00214: TCGA-13-0720-10B


title: socci-00214: TCGA-13-0760-01A


title: socci-00214: TCGA-13-0720-01A


title: socci-00214: TCGA-13-0760-10A


title: socci-00214: TCGA-13-0794-01A


title: socci-00214: TCGA-13-0730-10B


title: socci-00214: TCGA-09-0367-01A


title: socci-00214: TCGA-09-0366-01A


title: Hypoxia2_053007

city: Kansas City

first: Michael

last: Soares

state: Kansas

address: 3901 Rainbow Blvd.,MS-3050

department: Pathology and Laboratory Medicine

institute: University of Kansas Medical Center

description: Gene Expression Data

hyb_protocol: RNA samples hybridized to rat 230.2 DNA microarray chip using gene ChIP Hybridization Oven 640 (Affymetrix).Washing was done using GeneChip fluidics station 450 (Affymetrics).

scan_protocol: Scanning was performed using Affymetrix Genechip Scanner 3000 with autoloader.

data_processing: Hybridization signals were normalized to internal controls using MAS5 algorithm in Expression Console (Affymetrix).Analysis was limited to probesets changing atleast 1.5 fold between groups with signal strengths ≥ 500 for the maximal value. Significant differences were determined by t-tests.

source_name: Rat metrial gland tissue in ambient (21% oxygen) and hypoxic (10.5% oxygen) conditions

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocol from 6ug of total RNA

growth_protocol: Pregnant animals were exposed to normoxic (21%) or hypoxic (10.5%) oxygen tensions from gestation day 6.5 to 13.5. Animals were sacrificed and metrial gland tissues were collected.

extract_protocol: Trizol based extraction of total RNA (manufacturer's protocol)

value: Rat Metrial Gland Tissue

tag: treatment

value: hypoxic (10.5% oxygen)


title: socci-00214: TCGA-13-0761-01A


title: socci-00214: TCGA-13-0762-01A


title: Hypoxia3_053007

description: Gene Expression Data

treatment_protocol: Pregnant animals were exposed to normoxic (21%) or hypoxic (10.5%) oxygen tensions from gestation day 6.5 to 13.5. Animals were sacrificed and metrial gland tissues were collected.


title: socci-00214: TCGA-13-0795-10A


title: socci-00214: TCGA-13-0765-01A


title: socci-00214: TCGA-13-0757-10A


title: socci-00214: TCGA-13-0764-10A


title: socci-00214: TCGA-09-0365-01A


title: socci-00214: TCGA-13-0797-01A


title: socci-00214: TCGA-13-0801-10A


title: socci-00214: TCGA-13-0766-01A


title: socci-00214: TCGA-13-0724-10B


title: Normoxia3_053007

description: Gene Expression Data

value: ambient (21% oxygen)


title: socci-00214: TCGA-13-0803-10A

value: Serous cystadenocarcinoma


title: Hypoxia1_053007

description: Gene Expression Data


title: socci-00214: TCGA-13-0766-10A

value: Promega ref DNA


title: rtsamb1_121710_(Rat230_2)

description: Gene Expression Data

source_name: Rat TS cell in amb oxygen

treatment_protocol: Cells were grown in RPMI based trophoblast stem cell media supplemented with 20% FBS, PEN STREP which consisted 30% of total media alongwith 70% of Rat Embryonic Fibroblast (REF) conditioned media in standard condions (37 degree centigrade, 5% CO2) and then exposed to 0.5% oxygen tension for 24 hours.

value: Trophoblast Stem Cells


title: rts0.5 3_121710_(Rat230_2)

description: Gene Expression Data

source_name: Rat TS cell in 0.5% oxygen

growth_protocol: Cells were grown in RPMI based trophoblast stem cell media supplemented with 20% FBS, PEN STREP which consisted 30% of total media alongwith 70% of Rat Embryonic Fibroblast (REF) conditioned media in standard condions (37 degree centigrade, 5% CO2)

value: hypoxic (0.5% oxygen)


title: Normoxia1_053007

description: Gene Expression Data


title: rts0.5 1_121710_(Rat230_2)

description: Gene Expression Data


title: rtsamb2_121710_(Rat230_2)

description: Gene Expression Data


title: socci-00214: TCGA-13-0751-10A


title: Normoxia2_053007

description: Gene Expression Data


title: rtsamb3_121710_(Rat230_2)

description: Gene Expression Data


title: socci-00214: TCGA-13-0757-01A


title: rts0.5 2_121710_(Rat230_2)

description: Gene Expression Data


title: socci-00214: TCGA-13-0723-01A


title: socci-00214: TCGA-13-0800-10A


title: socci-00214: TCGA-13-0804-01A


title: socci-00214: TCGA-13-0755-01A


title: socci-00214: TCGA-13-0758-01A


title: socci-00214: TCGA-13-0762-10A


title: socci-00214: TCGA-13-0725-01A


title: socci-00214: TCGA-13-0723-10B


title: socci-00214: TCGA-13-0727-10B


title: 7-day-old seedlings of HSFA6b-RD treated with 37℃ heat shock for 1h, biological rep2

first: Ya-Chen

last: Huang

address: No. 1, Sec. 4, Roosevelt Road

department: Institute of Plant Biology and Department of Life Science

institute: National Taiwan University

description:
7-day-old seedlings of HSFA6b-RD treated with 37℃ heat shock for 1hr
HS-RD-2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on the GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix® GeneChip® Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Seedlings were grown at 22℃ on 0.5X MS plates containing 1% sucrose for 7 days.

extract_protocol: Samples were collected for RNA extraction by use of the RNeasy RNA extraction kit (Qiagen)  according to the manufacturer's instructions.

treatment_protocol: 7-day-old seedlings were treated with 150mM NaCl for 6hr or 37℃ heat shock for 1hr, with 22℃ treatment as a control, then collected for RNA extracted.

tag: genotype

value: HSFA6b dominant-negative

value: seedling

tag: age

value: 37℃ heat shock for 1hr


title: 7-day-old seedlings of HSFA6b-OE treated with 37℃ heat shock for 1h, biological rep1

description:
7-day-old seedlings of HSFA6b-OE treated with 37℃ heat shock for 1hr
HS-OE-1


title: 7-day-old seedlings of Col-0 at control condition, biological rep2

description:
7-day-old seedling of Col-0 at control condition
CK-WT-2

tag: cultivar

value: wildtype


title: 7-day-old seedlings of HSFA6b-OE treated with 150mM NaCl for 6hr, biological rep2

description:
7-day-old seedlings of HSFA6b-OE treated with 150mM NaCl for 6hr
SALT-OE-2

tag: tissue

value: 150mM NaCl for 6hr


title: 7-day-old seedlings of Col-0 treated with 150mM NaCl for 6hr, biological rep1

description:
7-day-old seedlings of Col-0 treated with 150mM NaCl for 6hr
SAlT-WT-1


title: 7-day-old seedlings of HSFA6b-OE treated with 37℃ heat shock for 1h, biological rep2

description:
7-day-old seedlings of HSFA6b-OE treated with 37℃ heat shock for 1hr
HS-OE-2


title: 7-day-old seedlings of Col-0 treated with 37℃ heat shock for 1h, biological rep1

description:
7-day-old seedlings of Col-0 treated with 37℃ heat shock for 1hr
HS-WT-1


title: 7-day-old seedlings of HSFA6b-RD at control condition, biological rep2

description:
7-day-old seedling of HSFA6b-RD at control condition
CK-RD-2


title: Sample 39_Time Point 28d Dose 486ug [set 6]

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway, Building 22

country: Canada

institute: Health Canada

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (200ng) were co-hybridized to Agilent Sureprint Whole Mouse GE 4x44K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Time Point 28d Dose 486ug

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Five-to-seven week old female C57BL/6 mice (Jackson Laboratory, Bar Harbor, Maine) were housed in autoclaved cages, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine lung, liver, and heart were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.

treatment_protocol: Mice were dosed via single intratracheal instillation of 18 µg (very low), 54 µg (low dose), 162 µg (medium dose), or 486 µg (high dose) of TiO2NPs in a 40 µl suspension   Tissues were collected 24h and 28 days after instillation.

tag: strain

tag: gender

value: female

value: 5-7 weeks

tag: exposed to

value: anatase TiO2NPs of 8 nm diameter

tag: dosage

tag: time point

value: 28d post-exposure

value: lung

source_name: Universal Mouse Reference RNA

value: 11 mouse cell lines


title: 7-day-old seedlings of HSFA6b-RD treated with 150mM NaCl for 6hr, biological rep1

description:
7-day-old seedlings of HSFA6b-RD treated with 150mM NaCl for 6hr
SALT-RD-1


title: 7-day-old seedlings of Col-0 treated with 37℃ heat shock for 1h, biological rep2

description:
7-day-old seedlings of Col-0 treated with 37℃ heat shock for 1hr
HS-WT-2


title: Sample 40_Time Point 28d Dose 0ug [set 6]

source_name: Time Point 28d Dose 0ug


title: 7-day-old seedlings of HSFA6b-RD treated with 150mM NaCl for 6hr, biological rep2

description:
7-day-old seedlings of HSFA6b-RD treated with 150mM NaCl for 6h
SALT-RD-2


title: Sample 37_Time Point 28d Dose 162ug [set 6]

source_name: Time Point 28d Dose 162ug


title: 7-day-old seedlings of HSFA6b-OE treated with 150mM NaCl for 6hr, biological rep1

description:
7-day-old seedlings of HSFA6b-OE treated with 150mM NaCl for 6hr
SALT-OE-1


title: 7-day-old seedlings of HSFA6b-RD at control condition, biological rep1

description:
7-day-old seedling of HSFA6b-RD at control condition
CK-RD-1


title: 7-day-old seedlings of HSFA6b-OE at control condition, biological rep1

description:
7-day-old seedling of HSFA6b-OE at control condition
CK-OE-1


title: 7-day-old seedlings of Col-0 treated with 150mM NaCl for 6hr, biological rep2

description:
7-day-old seedlings of Col-0 treated with 150mM NaCl for 6hr
SAlT-WT-2


title: 7-day-old seedlings of HSFA6b-OE at control condition, biological rep2

description:
7-day-old seedling of HSFA6b-OE at control condition
CK-OE-2


title: 7-day-old seedlings of Col-0 at control condition, biological rep1

description:
7-day-old seedling of Col-0 at control condition
CK-WT-1


title: Sample 38_Time Point 28d Dose 54ug [set 6]

source_name: Time Point 28d Dose 54ug


title: Sample 33_Time Point 1d Dose 54ug [set 6]

source_name: Time Point 1d Dose 54ug

value: 1d post-exposure


title: Sample 35_Time Point 1d Dose 0ug [set 6]

source_name: Time Point 1d Dose 0ug


title: HPMSC_ET_1_BQ_123

city: Nanjing

first: Yue

last: Yu

state: Jiangsu

address: No. 300, Guangzhou Road

department: Department of Thoracic Surgery

country: China

institute: the First Affiliated Hospital of Nanjing Medical University

description: Gene expression in human pulmonary arterial smooth muscle cells treated by both endothelin (ET)-1 and BQ123

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 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 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: Feature Extraction software (version10.7.1.1, Agilent Technologies, USA) was used to analyze the acquired array images. Agilent GeneSpring GX software package (version 13.1, Agilent Technology, USA) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “P” were chosen for further data analysis. Differentially expressed genes or lncRNAs were then identified through fold change.

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: HPASMCs were obtained from KeyGEN BioTECH (Nanjing, China). Cells were routinely maintained in DMEM containing 10% FBS, 1% smooth muscle cell growth supplement (SMCGS) and 1% penicillin/streptomycin, and incubated in humidified air at 37˚C with 5% CO2. The purity of HPASMC cultures was confirmed by the positive staining for both smooth muscle specific α-actin (SMA) and heavy chain myosin (HCM).

extract_protocol: Total RNA was extracted from homogenized cell samples with TRIzol® reagent (Invitrogen Life Technologies, USA) according to the manufacturer’s protocol. Then the RNA was cleaned with a RNasey Mini Kit (Qiagen, USA). RNA quantity was measured using the NanoDrop ND-2000 spectrophotometer (Thermo Scientific, USA) measuring absorbance ratios of A260/A280 and A260/A230. RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies, USA).

treatment_protocol: The cells were randomly divided into four groups: control group, treated with culture medium alone; ET-1 group, treated with 1uM of ET-1 for 72 hours, a suitable concentration for ET-1 to trigger HPASMC proliferation as previously described (sunkai article); BQ123 group, treated with 0.2 uM of BQ-123, an ETA receptor blocker; BQ-123/ET-1 group, treated with 0.2uM of BQ-123 30min before 1uM of ET-1. Before treatment, cells were cultured in serum-free medium for 24 h to be synchronized.

tag: cell type

value: HPASMC

value: both endothelin (ET)-1 and BQ123


title: 7-day-old seedlings of HSFA6b-RD treated with 37℃ heat shock for 1h, biological rep1

description:
7-day-old seedlings of HSFA6b-RD treated with 37℃ heat shock for 1hr
HS-RD-1


title: Sample 34_Time Point 1d Dose 486ug [set 6]

source_name: Time Point 1d Dose 486ug


title: Sample 32_Time Point 28d Dose 162ug [set 6]


title: staud-00261: LYM439

source_name: diffuse large-B-cell lymphoma

tag: dlbcl sample (lym number)

tag: analysis set

value: Validation

tag: follow-up (years)

tag: status at follow-up

value: Dead

tag: subgroup

value: Type III

tag: ipi group

value: High

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature

tag: mhc class ii signature

tag: outcome predictor score


title: staud-00261: LYM435

value: GCB

value: Low


title: Sample 36_Time Point 1d Dose 162ug [set 6]

source_name: Time Point 1d Dose 162ug

tag: strain

tag: age

tag: tissue

tag: sample type


title: Sample 31_Time Point 28d Dose 486ug [set 6]

tag: gender

tag: exposed to

tag: dosage

tag: time point


title: HPMSC_BQ_123

description: Gene expression in human pulmonary arterial smooth muscle cells treated by BQ123

tag: cell type

tag: treatment


title: staud-00261: LYM418

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)

tag: status at follow-up

value: Alive

tag: subgroup

value: Medium


title: staud-00261: LYM400

value: ABC

tag: ipi group

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature

tag: mhc class ii signature


title: staud-00261: LYM399

tag: outcome predictor score


title: staud-00261: LYM396


title: staud-00261: LYM309


title: staud-00261: LYM411


title: staud-00261: LYM397


title: staud-00261: LYM304


title: Sample 30_Time Point 28d Dose 54ug [set 6]

tag: strain

tag: gender

value: female

tag: age

value: 5-7 weeks

tag: tissue

tag: sample type


title: staud-00261: LYM299


title: Sample 29_Time Point 28d Dose 0ug [set 6]

tag: exposed to

value: anatase TiO2NPs of 8 nm diameter

tag: dosage

tag: time point

value: 28d post-exposure


title: Sample 28_Time Point 1d Dose 162ug [set 6]

value: lung

value: 11 mouse cell lines


title: staud-00261: LYM303

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)


title: Sample 23_Time Point 28d Dose 162ug [set 6]


title: staud-00261: LYM284

tag: status at follow-up

tag: subgroup

tag: ipi group


title: Sample 26_Time Point 1d Dose 0ug [set 6]

value: 1d post-exposure


title: Sample 25_Time Point 1d Dose 486ug [set 6]


title: Sample 22_Time Point 28d Dose 54ug [set 6]


title: Sample 20_Time Point 1d Dose 54ug [set 6]


title: Sample 24_Time Point 28d Dose 486ug [set 6]


title: Sample 27_Time Point 1d Dose 54ug [set 6]


title: staud-00261: LYM272

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature


title: Sample 21_Time Point 28d Dose 0ug [set 6]

tag: strain


title: staud-00261: LYM266

tag: mhc class ii signature

tag: outcome predictor score


title: Sample 17_Time Point 1d Dose 0ug [set 6]

tag: gender

tag: age

tag: tissue


title: Sample 18_Time Point 1d Dose 486ug [set 6]

tag: exposed to

tag: dosage

tag: sample type


title: HPMSC_ET_1

description: Gene expression in human pulmonary arterial smooth muscle cells treated by endothelin (ET)-1

tag: cell type

value: HPASMC

tag: treatment

value: endothelin (ET)-1


title: staud-00261: LYM262

tag: dlbcl sample (lym number)

tag: analysis set

value: Validation

tag: follow-up (years)

tag: status at follow-up

value: Dead


title: HPMSC

description: Gene expression in human pulmonary arterial smooth muscle cells

value: untreated


title: Sample 16_Time Point 28d Dose 486ug [set 6]

tag: time point


title: staud-00261: LYM252

tag: subgroup

value: GCB

tag: ipi group

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature


title: Sample 15_Time Point 28d Dose 0ug [set 6]

tag: strain

tag: gender

tag: age


title: staud-00261: LYM249

value: High

tag: mhc class ii signature

tag: outcome predictor score


title: staud-00261: LYM248

value: Alive


title: socci-00214: TCGA-01-0637-11A

source_name: normal tissue

tag: diseasestate

value: Serous cystadenocarcinoma

tag: organismpart

value: Ovary

tag: pathologic status

value: NOT SPECIFIED

source_name: Promega ref DNA

tag: tissue

value: Promega ref DNA


title: staud-00261: LYM245

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)

value: Type III

value: Low


title: staud-00261: LYM234

tag: status at follow-up

tag: subgroup


title: staud-00261: LYM238

tag: ipi group

tag: germinal center b cell signature


title: staud-00261: LYM224

tag: lymph node signature

tag: proliferation signature


title: staud-00261: LYM222

value: Medium


title: staud-00261: LYM223


title: staud-00261: LYM221

value: ABC


title: staud-00261: LYM216


title: staud-00261: LYM211


title: staud-00261: LYM203


title: staud-00261: LYM199


title: Sample 14_Time Point 28d Dose 162ug [set 6]

tag: strain

tag: gender

value: female

value: 5-7 weeks

tag: exposed to

value: anatase TiO2NPs of 8 nm diameter

tag: dosage

tag: time point

value: 28d post-exposure

value: lung

tag: sample type

value: 11 mouse cell lines


title: staud-00261: LYM185

value: Validation

value: Dead

tag: mhc class ii signature

tag: outcome predictor score


title: Sample 19_Time Point 1d Dose 162ug [set 6]

tag: age

value: 1d post-exposure

tag: tissue


title: Sample 13_Time Point 28d Dose 54ug [set 6]


title: Sample 9_Time Point 1d Dose 0ug [set 6]


title: Sample 11_Time Point 1d Dose 162ug [set 6]


title: Sample 12_Time Point 1d Dose 54ug [set 6]


title: staud-00261: LYM183

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)

value: Alive

value: GCB


title: Sample 8_Time Point 28d Dose 0ug [set 6]


title: Sample 6_Time Point 28d Dose 162ug [set 6]


title: Sample 7_Time Point 28d Dose 54ug [set 6]


title: Sample 10_Time Point 1d Dose 486ug [set 6]


title: staud-00261: LYM182

tag: status at follow-up

tag: subgroup

tag: ipi group


title: staud-00261: LYM190

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature


title: staud-00261: LYM186


title: staud-00261: LYM181


title: Sample 3_Time Point 1d Dose 54ug [set 6]

tag: strain

tag: gender

tag: exposed to


title: Sample 4_Time Point 1d Dose 0ug [set 6]

tag: dosage

tag: time point

tag: sample type


title: Sample 39_Time Point 28d Dose 54ug [set 5]

tag: age

value: anatase TiO2NPs of 300 nm diameter


title: staud-00261: LYM169

tag: mhc class ii signature

tag: outcome predictor score


title: Sample 40_Time Point 28d Dose 486ug [set 5]

tag: tissue


title: Sample 36_Time Point 1d Dose 0ug [set 5]


title: Sample 2_Time Point 1d Dose 162ug [set 6]


title: Sample 1_Time Point 1d Dose 486ug [set 6]


title: staud-00261: LYM165

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)

value: High


title: Sample 35_Time Point 1d Dose 54ug [set 5]


title: Sample 37_Time Point 28d Dose 162ug [set 5]


title: Sample 38_Time Point 28d Dose 0ug [set 5]


title: Sample 5_Time Point 28d Dose 486ug [set 6]


title: staud-00261: LYM163

tag: status at follow-up

tag: subgroup

tag: ipi group


title: staud-00261: LYM146

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature


title: staud-00261: LYM145


title: staud-00261: LYM141

value: Type III


title: staud-00261: LYM139


title: staud-00261: LYM127

value: Low


title: staud-00261: LYM137

value: Medium


title: staud-00261: LYM112


title: staud-00261: LYM114

value: missing


title: Sample 33_Time Point 1d Dose 162ug [set 5]

tag: strain

tag: gender

value: female

tag: exposed to


title: Sample 34_Time Point 1d Dose 486ug [set 5]

value: 5-7 weeks

tag: dosage

tag: time point

tag: sample type


title: Sample 31_Time Point 28d Dose 162ug [set 5]

tag: age


title: staud-00261: LYM142

tag: mhc class ii signature

tag: outcome predictor score


title: staud-00261: LYM105

tag: dlbcl sample (lym number)

tag: analysis set


title: staud-00261: LYM103

tag: follow-up (years)

tag: status at follow-up


title: staud-00261: LYM102

tag: subgroup

tag: ipi group


title: Sample 30_Time Point 28d Dose 486ug [set 5]

tag: tissue


title: Sample 28_Time Point 1d Dose 486ug [set 5]


title: staud-00261: LYM107

value: ABC

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature


title: Sample 32_Time Point 28d Dose 0ug [set 5]

tag: strain

tag: gender

tag: exposed to

value: 28d post-exposure


title: Sample 26_Time Point 1d Dose 162ug [set 5]

tag: dosage

tag: time point

value: lung

tag: sample type


title: Sample 29_Time Point 28d Dose 54ug [set 5]

tag: age

value: 11 mouse cell lines


title: staud-00261: LYM097

tag: dlbcl sample (lym number)

value: Validation

tag: mhc class ii signature

tag: outcome predictor score


title: Sample 27_Time Point 1d Dose 0ug [set 5]


title: Sample 25_Time Point 1d Dose 54ug [set 5]


title: staud-00261: LYM095

tag: analysis set

tag: follow-up (years)

tag: status at follow-up


title: staud-00261: LYM094

tag: subgroup

tag: ipi group


title: staud-00261: LYM089

value: Dead

tag: germinal center b cell signature

tag: lymph node signature


title: staud-00261: LYM088

tag: proliferation signature


title: Sample 23_Time Point 28d Dose 486ug [set 5]

tag: strain

tag: gender

tag: tissue


title: Sample 24_Time Point 28d Dose 54ug [set 5]

tag: exposed to

tag: dosage

tag: time point


title: TRAMPC2-Tumour-animal-34

source_name: Tumour from mouse with prostate cancer cell line TRAMPC2 grown in vivo subcutaneously on back of C57Bl6j mouse

tag: cell line

tag: experimental group

value: tumour

tag: mouse strain

tag: tissue of origin

value: Prostate

tag: Sex

value: Male

tag: animal number

tag: sample number


title: Sample 22_Time Point 28d Dose 162ug [set 5]

tag: age

value: anatase TiO2NPs of 300 nm diameter

tag: sample type


title: staud-00261: LYM080

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)

tag: status at follow-up

value: Alive

tag: subgroup

tag: ipi group

tag: germinal center b cell signature

tag: lymph node signature

tag: mhc class ii signature

tag: outcome predictor score


title: staud-00261: LYM079

value: GCB

tag: proliferation signature


title: staud-00261: LYM078

value: Low


title: staud-00261: LYM063


title: Sample 18_Time Point 1d Dose 162ug [set 5]

tag: strain

tag: gender

tag: exposed to

tag: dosage

tag: time point

value: 1d post-exposure

tag: tissue


title: Sample 17_Time Point 1d Dose 0ug [set 5]

tag: age

tag: sample type


title: Sample 19_Time Point 1d Dose 486ug [set 5]


title: Sample 20_Time Point 1d Dose 54ug [set 5]


title: Sample 21_Time Point 28d Dose 0ug [set 5]


title: staud-00261: LYM054

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)


title: staud-00261: LYM043

tag: status at follow-up

tag: subgroup

tag: ipi group

value: Medium


title: staud-00261: LYM057

tag: germinal center b cell signature

tag: lymph node signature

tag: mhc class ii signature


title: staud-00261: LYM086

tag: proliferation signature

tag: outcome predictor score


title: staud-00261: LYM064


title: staud-00261: LYM058


title: staud-00261: LYM038

value: Type III


title: Sample 12_Time Point 1d Dose 0ug [set 5]

tag: strain

tag: gender

value: female

value: 5-7 weeks

tag: exposed to


title: Sample 16_Time Point 28d Dose 0ug [set 5]

tag: dosage

tag: time point

value: 28d post-exposure

tag: tissue


title: Sample 11_Time Point 1d Dose 162ug [set 5]

tag: age

value: lung

tag: sample type


title: Sample 15_Time Point 28d Dose 54ug [set 5]

value: 11 mouse cell lines


title: Sample 14_Time Point 28d Dose 486ug [set 5]


title: staud-00261: LYM035

tag: dlbcl sample (lym number)

tag: analysis set

value: Validation

tag: follow-up (years)


title: Sample 13_Time Point 28d Dose 162ug [set 5]


title: Sample 9_Time Point 1d Dose 54ug [set 5]


title: staud-00261: LYM019

tag: status at follow-up

tag: subgroup

tag: ipi group


title: staud-00261: LYM032

value: Dead

value: ABC

tag: germinal center b cell signature

tag: lymph node signature

tag: mhc class ii signature


title: Sample 10_Time Point 1d Dose 486ug [set 5]

tag: strain


title: Sample 8_Time Point 28d Dose 162ug [set 5]

tag: gender


title: Sample 7_Time Point 28d Dose 486ug [set 5]

tag: exposed to


title: Sample 2_Time Point 1d Dose 54ug [set 5]

tag: dosage


title: Sample 5_Time Point 28d Dose 54ug [set 5]

tag: time point


title: Sample 4_Time Point 1d Dose 162ug [set 5]

tag: tissue


title: staud-00261: LYM040

tag: proliferation signature

tag: outcome predictor score


title: Sample 1_Time Point 1d Dose 0ug [set 5]

tag: age

tag: sample type


title: staud-00261: LYM017

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)

value: High


title: staud-00261: LYM016

tag: status at follow-up

tag: subgroup

tag: ipi group


title: staud-00261: LYM014

tag: germinal center b cell signature

tag: lymph node signature

tag: mhc class ii signature


title: staud-00261: LYM013


title: staud-00261: LYM009


title: Sample 3_Time Point 1d Dose 486ug [set 5]

tag: strain

tag: gender

tag: exposed to


title: staud-00261: LYM003


title: Sample 6_Time Point 28d Dose 0ug [set 5]

tag: dosage

tag: time point

tag: tissue


title: staud-00261: LYM001

tag: proliferation signature

tag: outcome predictor score


title: Sample 40_Time Point 28d Dose 54ug [set 4]

tag: age

value: mix rutile/anatase TiO2NPs of 20 nm diameter

tag: sample type


title: staud-00261: LYM432

tag: dlbcl sample (lym number)

tag: analysis set

value: Training

tag: follow-up (years)


title: staud-00261: LYM433

tag: status at follow-up

tag: subgroup

tag: ipi group


title: staud-00261: LYM431

tag: germinal center b cell signature

tag: lymph node signature

tag: mhc class ii signature


title: staud-00261: LYM430

value: Alive


title: staud-00261: LYM429


title: Sample 39_Time Point 28d Dose 162ug [set 4]

tag: strain

tag: gender

tag: exposed to


title: Sample 37_Time Point 28d Dose 0ug [set 4]

tag: dosage

tag: time point

tag: tissue


title: staud-00261: LYM428

value: GCB

tag: proliferation signature

tag: outcome predictor score


title: Sample 35_Time Point 1d Dose 162ug [set 4]

tag: age

tag: sample type


title: Sample 38_Time Point 28d Dose 486ug [set 4]


title: Sample 28_Time Point 1d Dose 486ug [set 4]


title: Sample 27_Time Point 1d Dose 0ug [set 4]


title: staud-00261: LYM005

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)


title: staud-00261: LYM427

tag: status at follow-up

tag: subgroup

tag: ipi group


title: Sample 36_Time Point 1d Dose 54ug [set 4]


title: Sample 24_Time Point 28d Dose 54ug [set 4]


title: staud-00261: LYM425

tag: germinal center b cell signature

tag: lymph node signature

tag: mhc class ii signature


title: Sample 34_Time Point 1d Dose 486ug [set 4]

tag: strain

tag: gender

tag: exposed to


title: Sample 30_Time Point 28d Dose 162ug [set 4]

tag: dosage

tag: time point

tag: tissue


title: Sample 26_Time Point 1d Dose 162ug [set 4]

tag: age


title: Sample 25_Time Point 1d Dose 54ug [set 4]

tag: sample type


title: Sample 31_Time Point 28d Dose 0ug [set 4]


title: Sample 29_Time Point 28d Dose 54ug [set 4]


title: staud-00261: LYM423

tag: dlbcl sample (lym number)

tag: proliferation signature

tag: outcome predictor score


title: Sample 32_Time Point 28d Dose 486ug [set 4]


title: staud-00261: LYM424

tag: analysis set

tag: follow-up (years)

tag: status at follow-up

value: Low


title: Sample 33_Time Point 1d Dose 0ug [set 4]

value: 1d post-exposure


title: staud-00261: LYM422

tag: subgroup

tag: ipi group

tag: germinal center b cell signature


title: staud-00261: LYM421

tag: lymph node signature

tag: mhc class ii signature


title: staud-00261: LYM419


title: staud-00261: LYM415

value: Medium


title: staud-00261: LYM413


title: staud-00261: LYM409


title: staud-00261: LYM407


title: staud-00261: LYM406


title: staud-00261: LYM404


title: staud-00261: LYM398


title: Sample 23_Time Point 28d Dose 486ug [set 4]

tag: strain

tag: gender

tag: exposed to


title: staud-00261: LYM394


title: staud-00261: LYM401


title: staud-00261: LYM325


title: staud-00261: LYM391

value: Type III


title: Sample 22_Time Point 28d Dose 0ug [set 4]

value: female

tag: dosage

tag: time point

tag: tissue


title: Sample 18_Time Point 1d Dose 486ug [set 4]

tag: age

value: 5-7 weeks

tag: sample type


title: staud-00261: LYM408

tag: dlbcl sample (lym number)

tag: proliferation signature

tag: outcome predictor score


title: staud-00261: LYM324

tag: analysis set

tag: follow-up (years)

tag: status at follow-up


title: Sample 20_Time Point 1d Dose 0ug [set 4]


title: Sample 16_Time Point 28d Dose 486ug [set 4]

value: 28d post-exposure


title: Sample 21_Time Point 28d Dose 162ug [set 4]

value: lung


title: Sample 19_Time Point 1d Dose 162ug [set 4]

value: 11 mouse cell lines


title: staud-00261: LYM323

tag: subgroup

tag: ipi group

tag: germinal center b cell signature


title: staud-00261: LYM322

tag: lymph node signature

tag: mhc class ii signature


title: staud-00261: LYM321


title: Sample 14_Time Point 28d Dose 162ug [set 4]

tag: strain

tag: gender

tag: exposed to


title: staud-00261: LYM320


title: staud-00261: LYM318


title: Sample 13_Time Point 28d Dose 54ug [set 4]

tag: dosage

tag: time point

tag: tissue


title: staud-00261: LYM317

tag: dlbcl sample (lym number)


title: Sample 10_Time Point 1d Dose 162ug [set 4]

tag: age

tag: sample type


title: Sample 15_Time Point 28d Dose 0ug [set 4]


title: Sample 12_Time Point 1d Dose 486ug [set 4]


title: Sample 7_Time Point 28d Dose 0ug [set 4]


title: Sample 11_Time Point 1d Dose 54ug [set 4]


title: Sample 17_Time Point 1d Dose 54ug [set 4]


title: staud-00261: LYM316

tag: analysis set

tag: proliferation signature

tag: outcome predictor score


title: staud-00261: LYM315

tag: follow-up (years)

tag: status at follow-up

tag: subgroup


title: Sample 6_Time Point 28d Dose 162ug [set 4]


title: staud-00261: LYM312

tag: ipi group

tag: germinal center b cell signature

tag: lymph node signature


title: staud-00261: LYM313

tag: mhc class ii signature


title: Sample 8_Time Point 28d Dose 486ug [set 4]

tag: strain

tag: gender

tag: exposed to


title: Sample 4_Time Point 1d Dose 162ug [set 4]

tag: dosage

tag: time point

tag: tissue


title: Sample 5_Time Point 28d Dose 54ug [set 4]

tag: age

tag: sample type


title: Sample 3_Time Point 1d Dose 486ug [set 4]


title: Sample 9_Time Point 1d Dose 0ug [set 4]


title: staud-00261: LYM311

tag: dlbcl sample (lym number)

tag: analysis set

tag: proliferation signature


title: staud-00261: LYM308

tag: follow-up (years)

tag: status at follow-up

tag: outcome predictor score


title: Sample 2_Time Point 1d Dose 54ug [set 4]


title: Sample 1_Time Point 1d Dose 0ug [set 4]


title: Sample 37_Time Point 28d Dose 162ug [set 3]

source_name: Time Point 28d Dose 162ug [set 3]

value: rutile hydrophobic TiO2NPs of 20 nm diameter


title: staud-00261: LYM306

tag: subgroup

tag: ipi group

tag: germinal center b cell signature


title: staud-00261: LYM307

tag: lymph node signature

tag: mhc class ii signature


title: staud-00261: LYM305


title: staud-00261: LYM301

value: Dead


title: Sample 36_Time Point 28d Dose 54ug [set 3]

source_name: Time Point 28d Dose 54ug [set 3]

tag: strain

tag: gender

tag: exposed to


title: Sample 33_Time Point 28d Dose 162ug [set 3]

tag: dosage

tag: time point

tag: tissue


title: Sample 32_Time Point 1d Dose 54ug [set 3]

source_name: Time Point 1d Dose 54ug [set 3]

tag: age

tag: sample type


title: Sample 34_Time Point 1d Dose 486ug [set 3]

source_name: Time Point 1d Dose 486ug [set 3]


title: Sample 35_Time Point 28d Dose 0 [set 3]

source_name: Time Point 28d Dose 0 [set 3]


title: Sample 31_Time Point 1d Dose 486ug [set 3]

source_name: Universal Mouse Reference RNA


title: Sample 30_Time Point 28d Dose 0 [set 3]


title: staud-00261: LYM300

tag: dlbcl sample (lym number)

tag: analysis set

tag: proliferation signature


title: staud-00261: LYM298

tag: follow-up (years)

tag: status at follow-up

tag: outcome predictor score


title: staud-00261: LYM297

tag: subgroup

tag: ipi group

tag: germinal center b cell signature


title: staud-00261: LYM294

tag: lymph node signature

tag: mhc class ii signature


title: staud-00261: LYM286


title: staud-00261: LYM285


title: staud-00261: LYM281

value: ABC


title: staud-00261: LYM279


title: staud-00261: LYM263


title: staud-00261: LYM275


title: staud-00261: LYM267


title: staud-00261: LYM277


title: staud-00261: LYM255


title: Sample 29_Time Point 28d Dose 486ug [set 3]

source_name: Time Point 28d Dose 486ug [set 3]

tag: strain

tag: gender

tag: exposed to


title: Sample 25_Time Point 1d Dose 0 [set 3]

source_name: Time Point 1d Dose 0 [set 3]

tag: dosage

tag: time point

tag: tissue


title: Sample 27_Time Point 28d Dose 0 [set 3]

tag: age

tag: sample type


title: Sample 20_Time Point 28d Dose 0 [set 3]


title: Sample 22_Time Point 1d Dose 486ug [set 3]


title: Sample 24_Time Point 1d Dose 162ug [set 3]

source_name: Time Point 1d Dose 162ug [set 3]


title: Sample 23_Time Point 1d Dose 54ug [set 3]


title: staud-00261: LYM247

tag: dlbcl sample (lym number)

tag: analysis set

tag: proliferation signature


title: Sample 21_Time Point 28d Dose 486ug [set 3]


title: Sample 28_Time Point 28d Dose 54ug [set 3]


title: Sample 19_Time Point 1d Dose 162ug [set 3]


title: staud-00261: LYM244

tag: follow-up (years)

tag: status at follow-up

tag: outcome predictor score


title: Sample 26_Time Point 28d Dose 162ug [set 3]


title: Sample 13_Time Point 28d Dose 162ug [set 3]


title: Sample 18_Time Point 1d Dose control [set 3]

source_name: Time Point 1d Dose control [set 3]

value: control


title: Sample 17_Time Point 1d Dose 54ug [set 3]


title: Sample 12_Time Point 28d Dose 0 [set 3]


title: Sample 15_Time Point 28d Dose 54ug [set 3]


title: Sample 11_Time Point 1d Dose 162ug [set 3]


title: staud-00261: LYM237

tag: subgroup

tag: ipi group

tag: germinal center b cell signature


title: staud-00261: LYM233

tag: lymph node signature

tag: mhc class ii signature


title: staud-00261: LYM231


title: staud-00261: LYM230


title: staud-00261: LYM229


title: staud-00261: LYM227


title: staud-00261: LYM228


title: staud-00261: LYM219


title: staud-00261: LYM241


title: staud-00261: LYM213


title: staud-00261: LYM208


title: staud-00261: LYM212


title: Sample 10_Time Point 1d Dose 54ug [set 3]

tag: strain

tag: gender

tag: exposed to


title: staud-00261: LYM207

value: High


title: staud-00261: LYM205

value: Training


title: Sample 16_Time Point 1d Dose 0 [set 3]

tag: dosage

tag: time point

tag: tissue


title: Sample 14_Time Point 28d Dose 486ug [set 3]

tag: age

tag: sample type


title: Sample 8_Time Point 1d Dose 486ug [set 3]


title: staud-00261: LYM204

tag: dlbcl sample (lym number)

tag: analysis set

tag: proliferation signature


title: Sample 9_Time Point 1d Dose 0 [set 3]


title: Sample 5_Time Point 28d Dose 54ug [set 3]


title: Sample 2_Time Point 1d Dose 162ug [set 3]


title: staud-00261: LYM202

tag: follow-up (years)

tag: status at follow-up

tag: outcome predictor score


title: Sample 3_Time Point 1d Dose 54ug [set 3]


title: staud-00261: LYM198

tag: subgroup

tag: ipi group

tag: germinal center b cell signature


title: staud-00261: LYM200

tag: lymph node signature

tag: mhc class ii signature


title: Sample 1_Time Point 1d Dose 486ug [set 3]

tag: strain

tag: gender

tag: exposed to


title: Sample 7_Time Point 28d Dose 162ug [set 3]

tag: dosage

tag: time point

tag: tissue


title: Sample 38_Time Point 1d Dose 486ug [set 2]

tag: age

value: rutile hydrophilic TiO2NPs of 20 nm diameter

tag: sample type


title: Sample 39_Time Point 28d Dose 54ug [set 2]

source_name: Time Point 28d Dose 54ug


title: staud-00261: LYM197

tag: dlbcl sample (lym number)

tag: analysis set

value: GCB

tag: proliferation signature


title: Sample 37_Time Point 1d Dose 162ug [set 2]


title: Sample 4_Time Point 1d Dose 0 [set 3]


title: Sample 6_Time Point 28d Dose 486ug [set 3]


title: staud-00261: LYM195

tag: follow-up (years)

tag: status at follow-up

tag: outcome predictor score


title: staud-00261: LYM191

tag: subgroup

tag: ipi group

tag: germinal center b cell signature


title: staud-00261: LYM194

tag: lymph node signature

tag: mhc class ii signature


title: staud-00261: LYM184


title: Sample 35_Time Point 28d Dose 162ug [set 2]

source_name: Time Point 28d Dose 162ug

tag: strain

tag: gender

tag: exposed to


title: staud-00261: LYM180

source_name: diffuse large-B-cell lymphoma

value: Alive

value: Low


title: staud-00261: LYM179

value: Medium


title: Sample 34_Time Point 28d Dose 486ug [set 2]

source_name: Time Point 28d Dose 486ug

tag: dosage

tag: time point

tag: tissue


title: Sample 32_Time Point 28d Dose 54ug [set 2]

tag: age

tag: sample type


title: Sample 36_Time Point 1d Dose 0ug [set 2]

source_name: Time Point 1d Dose 0ug

value: 1d post-exposure


title: Sample 29_Time Point 1d Dose 486ug [set 2]

source_name: Time Point 1d Dose 486ug

value: female


title: Sample 27_Time Point 28d Dose 162ug [set 2]

value: 5-7 weeks


title: Sample 33_Time Point 28d Dose 0ug [set 2]

source_name: Time Point 28d Dose 0ug

value: 28d post-exposure


title: Sample 30_Time Point 1d Dose 162ug [set 2]

source_name: Time Point 1d Dose 162ug

value: lung


title: Sample 31_Time Point 1d Dose 0ug [set 2]

value: 11 mouse cell lines


title: staud-00261: LYM176

tag: dlbcl sample (lym number)

tag: analysis set

tag: proliferation signature


title: staud-00261: LYM173

tag: follow-up (years)

tag: status at follow-up

tag: outcome predictor score


title: staud-00261: LYM178

tag: subgroup

tag: ipi group

tag: germinal center b cell signature


title: staud-00261: LYM177

tag: lymph node signature

tag: mhc class ii signature


title: staud-00261: LYM172


title: staud-00261: LYM189


title: staud-00261: LYM166