title: MDAMB231-inhibitor BB94-biological rep 2

description:
BB2
Gene expression data from 90% confluent cell culture, 24hr after application of fresh full serum media + 10uM BB94


title: tb6884_Tcells

status: Public on Mar 21 2016

type: genomic

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

country: USA

institute: HUMC

description: Normal T cells, peripheral blood

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Data was extracted using GenomeStudio v2011.1. Background correction, normalization to Illumina internal control probes, and quantile normalization were performed. All probes mapping to the X or Y chromosome were removed, along with probes that queried CpGs overlapping the positions of known common DNA variants as reported in dbSNP build 138 (allele frequency>1 percent). As recommended by Illumina, fractional methylation (AVG_Beta) values with a detection p-value>0.05 were excluded from the analysis and replaced by missing values. In each tissue, probes with more than 20 percent missing values were excluded.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Sample tb6884, normal T cells, peripheral blood

label_protocol: According to manufacturers instructions.

extract_protocol: Genomic DNA samples were isolated using Phenol-chloroform extraction protocol. Genomic DNA (500 ng) was then bisulfite-converted using the EpiTect Bisulfite Kit (Qiagen)

tag: tissue

value: T cells, peripheral blood

tag: diagnosis

value: Normal


title: tb6663_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6663, normal T cells, peripheral blood


title: tb6650_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6650, normal T cells, peripheral blood


title: tb6664_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6664, normal T cells, peripheral blood


title: tb6665_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6665, normal T cells, peripheral blood


title: MMP-9, biological replicate3

type: RNA

city: MADRID

first: M Ángeles

last: García-Pardo

state: MADRID

address: RAMIRO DE MAEZTU, 9

country: Spain

institute: CENTRO DE INVESTIGACIONES BIOLÓGICAS, CSIC

description: Gene expression data from MEC-1 cells overexpressing MMP-9

hyb_protocol: Following fragmentation, cRNAs were hybridized to an Affymetrix GeneChip® Human Gene 1.0 ST Array on a GeneChip Hybridation Oven 640. GeneChips were washed and stained in a GeneChip Fluidics Station 450.

scan_protocol: Hybridized Affymetrix arrays were scanned using an Affymetrix Gene Array Scanner 3000 7G.

data_processing: The Robust Multi-array Analysis (RMA) was used for background correction, intra- and inter-microarray normalization, and calculation of the absolute expression signal for each gene. Significance Analysis of Microarray (SAM) was applied to calculate significant differential expression and find the gene probe sets differentially expressed in MMP-9 cells respect to Mock cells. The method uses permutations to provide robust statistical inference of the most significant genes and, by using a false discovery rate (FDR), adjust the raw p-values to take multiple testing into account. An FDR cut-off of = 0.1 was used for all the differential expression calculations.

label: Biotin

molecule: total RNA

source_name: MEC-1 cells overexpressing MMP-9

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 200 ng total RNA.

growth_protocol: 3 x 106 MEC-1 cells were cultured in IMDM/0.1% FBS at a final density of 2 x 106 cells/ml

extract_protocol: Total RNA was extracted and purified using the AllPrep® DNA/RNA/Protein Mini kit (Qiagen) following the manufacturer's instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: MEC-1 cells were genetically modified using a GFP lentiviral vector with (MMP-9 cells) or without (Mock cells) a proMMP-9 DNA construct.

tag: cell type

value: Chronic lymphocytic leukemia cell line MEC-1


title: MDAMB231-control-biological rep 4

city: Boston

first: Miles

last: Miller

state: MA

address: 185 Cambridge St

institute: Massachusetts General Hospital

description:
C4
Gene expression data from 90% confluent cell culture, 24hr after application of fresh full serum media + 0.1% DMSO

hyb_protocol: cRNA was hybridized using manufacturer's guidelines on Affymetrix Human Genome PrimeView Array. Arrays were washed and stained in the Affymetrix Fluidics Station 450. Performed at Massachusetts Institute of Technology BioMicroCenter Core Service

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G. Performed at Massachusetts Institute of Technology BioMicroCenter Core Service

data_processing: Data were preprocessed using the R/Bioconductor package “affy” and the RMA normalization routine using expresso.

label: biotin

source_name: MDAMB231_control_24hr post-treatment

label_protocol: Biotinylated cRNA were prepared according to the manufacturer's protocol using the NuGEN Applause system using the Massachusetts Institute of Technology BioMicroCenter Core Service

growth_protocol: MDA-MB231 cells were plated overnight in 10cm tissue culture plates at 70% confluency, in DMEM + 10% FBS.  Treatments were performed with fresh media change the following day.

extract_protocol: Total RNA was extracted following manufacturer's guidelines using Qiagen Rneasy Mini Kit.  RNA QC was performed using Agilent Bioanalyzer.

treatment_protocol: From 10mM DMSO stock diluted into fresh DMEM+10% FBS, cells were treated with either 10uM BB94 (batimastat metalloproteinase inhibitor) or 3uM PD325901 (MEK inhibitor) or DMSO vehicle control for 24h.

tag: cell line

value: human breast cancer cell line

tag: treated with

value: 0.1% DMSO vehicle control


title: tb6351_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6351, normal T cells, peripheral blood


title: MDAMB231-control-biological rep 3

description:
C3
Gene expression data from 90% confluent cell culture, 24hr after application of fresh full serum media + 0.1% DMSO


title: BFTC905_M10_0kPa_rep2.

city: New Taipei

first: Chih-Cheng

last: Chien

address: No 2, Ln 59, Jian-Cheng Rd, Sijhih Dist

country: Taiwan

institute: Sijhih Cathay General Hospital

description: 10 ug/ml of MMC

hyb_protocol: 0.6 μg of Cy3-labeled cRNA was fragmented to an average size of approximately 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes, and then differently fragmented cRNA was independently hybridized with Agilent SurePrint G3 Human GE 8x60K oligonucleotide microarray (Agilent Technologies) at 65°C for 17 hours

scan_protocol: After washing and drying by nitrogen gun blowing, the microarrays were scanned with an Agilent microarray scanner (Agilent Technologies) at 535 nm, according to Agilent’s standard protocols.

data_processing: The scanned images were analyzed with Agilent Feature Extraction software (Agilent Technologies), version 10.5.1.1. Image analysis and normalization software were used to quantify the signal and background intensity for each feature, substantially normalizing the data using the rank-consistency-filtering LOWESS method 19. After global normalization, probes with intensity <70 were filtered out.

source_name: BFTC905, M10, 0kPa, replicate 2

label_protocol: 0.2 μg of total RNA (two samples from UC cells treated with MMC and hydrostatic pressure and two samples from controls) was amplified into cRNA using a Low Input Quick-Amp Labeling kit (Agilent Technologies) and was labeled with Cy3-deoxycytidine triphosphate during the in vitro transcription process.

extract_protocol: Total RNA from each culture was independently extracted using the RNeasy Mini Kit, according to the manufacturer’s instructions (Qiagen, Valencia, CA, USA). Before microarray hybridization, each extract of total RNA was quantified using a NanoDrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE, USA) and a Bioanalyzer RNA Nano 6000 chip (Agilent Technologies, Palo Alto, CA, USA).

tag: treatment

value: 10 ug/ml of MMC


title: BFTC905_M10_10kPa_rep2.

description: 10 ug/ml of MMC and 10 kPa pressure treatment

source_name: BFTC905, M10, 10kPa, replicate 2


title: tb6598_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6598, normal T cells, peripheral blood


title: MEC1, ATO, biological rep1

description: Gene expression data from MEC-1 cells cultured with ATO for 24h

data_processing: The Robust Multi-array Analysis (RMA) was used for background correction, intra- and inter-microarray normalization, and  calculation of the absolute expression signal for each gene.

source_name: MEC-1 cells cultured with 5 µM ATO for 24 h

growth_protocol: 5 x 106 MEC-1 cells were cultured in IMDM/0.1% FBS at a final density of 2 x 106 cells/ml

extract_protocol: Total RNA was extracted and purified using the Qiagen AllPrep® DNA/RNA/Protein Mini kit following the manufacturer's instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer.

treatment_protocol: MEC-1 cells were incubated with or without 5 μM ATO for 24 hours at 37ºC, 5% CO2.

value: chronic lymphocytic leukemia cell line MEC-1


title: tb6865_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6865, normal T cells, peripheral blood


title: MDAMB231-control-biological rep 2

description:
C2
Gene expression data from 90% confluent cell culture, 24hr after application of fresh full serum media + 0.1% DMSO


title: BFTC905_M10_0kPa_rep1.

description: 10 ug/ml of MMC

source_name: BFTC905, M10, 0kPa, replicate 1


title: Control, biological replicate2

description: Gene expression data from MEC-1 cells with basal MMP-9 expression

source_name: MEC-1 cells with basal MMP-9 expression


title: MMP-9, biological replicate2


title: BT147 Control in vivo

city: calgary

first: Xueqing

last: Lun

state: Alberta

address: 3330 hospital drive nw

department: oncology

country: Canada

institute: University of calgary

description:
BT147 Ctrl at 2 week oral administration
Gene Expression data from tumor tissue exposed to Oral Plus (Control Vehicle) .

hyb_protocol: 12ug cRNA was fragmented and hybridized to Affymetrix GeneChip Human PrimeView Arrays at 45°C for 16h.

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

data_processing: Array raw data files were generated with GeneChip® Command Console® Software.  Array analysis was performed with Partek Genomic Suites 6.0. The Fold Change between treatment and control was calculated based on ANOVA file.

source_name: BT147 Human BTICS

label_protocol: 100ng of RNA of each sample with RIN higher than 9 was labelled with 3' IVT Express Kit (Ambion)

growth_protocol: patient derived BTICs grown in brain tumor stem cell medium with EGF and FGF

extract_protocol: Total RNA was isolated with Trizol according to the manufacturer's instructions. Before labeling, total RNA was purified with RNeasy Plus Micro Kit (Qiagen, Valencia, USA) to remove genomic DNA.

treatment_protocol: patient derived BTICs grown in brain tumor stem cells medium (with EGF and FGF) were treated with DSF (50nM) and Cu (1uM) for 12 hours. Cells were then collectedand prepared for gene expression analysis.  For the in vivo study, BT147 was implanted into the left brain hemisphere of CB17 SCID mice. 4 wks following implantation animals were treated with control vehicle (oral-plus) or DSF (100mg/kg) daily via oral administration for two weeks (5 days on, 2 days off) and Copper (2mg/kg ) daily via oral administartion for two weeks. Animals were sacrificed and brain tumor tissue was excised and used for gene expression analysis.

value: Brain Tumor Initiating Cells (BTICs)

value: Brain tumor from CB17SCID mouse

tag: genotype

value: Wild type

tag: age

value: 6-8 weeks


title: BT147 Dilsulfiram & Copper in vivo

description:
BT147 DSF/Cu at 2 week oral administration
Gene Expression data from tumor tissue exposed to DSF and Copper.


title: BT147 Dilsulfiram in vitro

description:
BT147 DSF at 12h
Gene Expression data from BTICS exposed to media containing DSF for 12h.

value: BTICs exposed to media containing DSF.


title: Control, biological replicate4


title: Control, biological replicate3


title: BT147 Copper in vitro

description:
BT147 Cu at 12h
Gene Expression data from BTICS exposed to media containing copper for 12h.

value: BTICs exposed to control media


title: MDAMB231-control-biological rep 1

description:
C1
Gene expression data from 90% confluent cell culture, 24hr after application of fresh full serum media + 0.1% DMSO


title: MMP-9, biological replicate1


title: FTC236 Notch1_48hr_1ugDox_rep3

city: Madison

first: Brian

middle: P

last: Johnson

state: WI

address: 1400 University Ave

department: Oncology

institute: UW-Madison

hyb_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis 17hrs 65 deg celcius Surehyb chamber

scan_protocol: Agilent Technologies Scanner G2505B US22502567 3um 16bit

data_processing: Agilent Feature extraction version 10.7.3.1 for background subtraction - Background and Multiplicitive detrending. Data analyzed in R using Limma.  Threshold: 1.0   Logbase: 2   Technology: Agilent.SingleColor.28005  Normalization: Quantile

source_name: FTC236-Notch1 cell line, 48hr, 1ug/ml Dox, replicate 3

label_protocol: Total RNA was amplified and labeled according to manufactures instructions. Agilent One Color Microarray-Based Gene Expression Analysis Agilent low RNA input linear amplification kit, PLUS

growth_protocol: FTC236-Notch1 cells were maintained in DMEM/Ham’s F-12 (1:1; Invitrogen) medium supplemented with 10% FBS, 0.01 U/mL of thyroid-stimulating hormone (TSH) and 10 µg/mL of insulin (Sigma-Aldrich) and were under dual antibiotic selection (G418 and hygromycin)

extract_protocol: Processed with an Qiagen Rneasy Mini kit

treatment_protocol: FTC236-Notch1 cells were treated with doxycycline at 1 µg/mL or without doxycycline.

tag: type of cancer

value: follicular cancer

tag: target gene turned on

value: Yes

value: thyroid


title: BFTC905_M10_10kPa_rep1.

source_name: BFTC905, M10, 10kPa, replicate 1

value: 10 ug/ml of MMC and 10 kPa pressure treatment


title: BT134 Dilsulfiram in vitro

description:
BT134 DSF at 12h
Gene Expression data from BTICS exposed to media containing DSF for 12h.

source_name: BT134 Human BTICS

value: BTICs exposed to medium with DSF


title: MEC1, Control, biological rep3

description: Gene expression data from MEC-1 cells cultured without ATO for 24h

source_name: MEC-1 cells cultured without ATO for 24 h


title: BT147 Control in vitro

description:
BT147 Ctrl at 12h
Gene Expression data from BTICS exposed to control media for 12h.


title: BT147 Dilsulfiram and Copper in vitro

description:
BT147 DSF/Cu at 12h
Gene Expression data from BTICS exposed to DSF and copper containing media for 12h.


title: Control, biological replicate1


title: SKOV3ip1 miR-192-3

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Probe group profile option of Illumina BeadStudio software.

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

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

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

source_name: Ovarian cancer cells

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

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

value: SKOV3.ip1 ovarian carcinoma cell line


title: MMP-9, biological replicate4

description: Gene expression data from MEC-1 cells overexpressing MMP-9

value: Chronic lymphocytic leukemia cell line MEC-1


title: SKOV3ip1 miR-192-2


title: FTC236 Notch1_48hr_0ugDox_rep1

source_name: FTC236-Notch1 cell line, 48hr, 0ug/ml Dox, replicate 1

value: No


title: tb6599_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6599, normal T cells, peripheral blood

value: T cells, peripheral blood

value: Normal


title: BT134 Copper in vitro

description:
BT134 Cu at 12h
Gene Expression data from BTICS exposed to media containing copper for 12h.

value: BTICs exposed to media containing copper


title: BT134 Dilsulfiram and Copper in vitro

description:
BT134 DSF/Cu at 12h
Gene Expression data from BTICS exposed to DSF and copper containing media for 12h.

value: Brain Tumor Initiating Cells (BTICs)

value: BTICs exposed to DSF and copper media


title: Pseudomonas aeruginosa_CDA_treated (Array_block_3)

city: Kermanshah

first: Hossein

last: Fallahi

state: Kermanshah

address: Bagh-e-Abrisham

department: Biology

country: Iran

institute: Razi University

description: Gene expression in 5 days old culture of P. aeruginosa were analyzed in presence and absent of CDA

hyb_protocol: Samples were hybridized using hybridization station TrayMix S4 (Biotray)

scan_protocol: P. aeruginosa PAO1 glass slide arrays (Mycroarray Inc.) were scanned using a ScanArray Express scanner (Perkin-Elmer).

data_processing: Raw data (spots intensity) were obtained by image processing through ProScanArray Express (Version 4.0) software. Data normalization and calibration was conducted by applying Robust Multichip Averaging (RMA) algorithm in R package. Identification of differentially expressed genes conducted using Flexarray software.

organism: Pseudomonas aeruginosa

source_name: 0 nmol CDA, P_aeruginosa,5 days culture

label_protocol: cDNA was synthesized and aminoallyl labeled using Aminoallyl labeling kit for DNA microarrays (Arrayit). After cDNA purification, labeling was performed using CyDye post-labeling reactive dye pack (Amersham, GE Healthcare). Labeling efficiency was then assessed using a NanoDrop ND1000 spectrophotometer (NanoDrop Technologies, Wilmington)

growth_protocol: P. aeruginosa PAO1 biofilms were cultivated on the interior surfaces of tubing of a once-through continuous-flow-reactor system at room temperature with a flow rate of 280 µl.min-1.

extract_protocol: After 1 h, the biofilms remaining on the walls of the tubing were washed by a gentle bath of PBS to remove planktonic bacteria and biofilm cells were immediately re-suspended in RNAprotect Bacteria Reagent (Qiagen) and harvested from the interior surface of the tubing. Total RNA was extracted using RNeasy mini kit (Qiagen). Purified total RNA was treated with deoxyribonuclease I (Thermo scientific). RNA preparations were checked for DNA contamination by PCR and quantified spectrometrically at 260 nm and 280 nm. RNA quality was further checked by formaldehyde agarose gel electrophoresis.

treatment_protocol: After 5 days, established biofilms were exposed to 100 nM CDA or left untreated (as a control).

tag: sample type

value: 5 days old, biofilms, planktonic cells

value: 0 nmol CDA

source_name: 100 nmol CDA, P_aeruginosa,5 days culture

value: 100 nmol CDA


title: SKOV3ip1 Control miR-2

value: Control miR


title: SKOV3ip1 Control miR-1


title: Pseudomonas aeruginosa_CDA_treated (Array_block_1)


title: BT134 Control in vitro

description:
BT134 Ctrl at 12h
Gene Expression data from BTICS exposed to control media for 12h.

value: BTICs exposed to control media

value: Wild type


title: Pseudomonas aeruginosa_CDA_treated (Array_block_2)


title: Grade1 (Cy5) x Grade3 (Cy3)

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

description: Dye-swap (Cy5/Cy3) of Grade1 vs Grade3

hyb_protocol: Agilent: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505B

data_processing: Software: Feature Extraction ver 9.5.3.1; Normalization is performed by LOWESS (locally weighted linear regression) which calculates the log ratio of dye-normalized Cy3- and Cy5-signals, as well as the final error of log ratio. The statistical significance of the log ratio values obtained for individual microarray probes is calculated using the “most conservative error model” default function of the Feature Extraction software, by which both a propagated and a universal error model are evaluated, and the higher (more conservative estimate of error) p-value of two error models is reported (Agilent Technologies).

organism: Oryza sativa

source_name: Y3-Grade3 (out of grade)

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Japonica-type rice (Oryza sativa L.) cv. Koshihikari was used as the test material. The commercially available rice as dry mature seeds were obtained from Japan Agriculture (JA Zen-Noh, Japan; http//www.zennoh.or.jp/) branch in Ami-town of Ibaraki prefecture (Kanto region), Japan, in September 2010.

extract_protocol: Kit: QIAGEN, Rneasy Mini

treatment_protocol: The JA Zen-Noh, Japan (http//www.zennoh.or.jp) classifies seeds based on quality control standards for rice seed in Japan as Grade 1 (labeled in this study as Y1) and 2 (labeled in this study as Y2) and out of grade (labeled in this study as Y3). The seed quality was also investigated using a commercial analysis laboratory (SATAKE CORPORATION; http://www.satake-japan.co.jp/).

tag: cultivar

value: Koshihikari

tag: grade

value: mature seed


title: Grade1 (Cy3) x Grade3 (Cy5)

description: Dye-swap (Cy3/Cy5) of Grade1 vs Grade3


title: SKOV3ip1 miR-192-1


title: SKOV3ip1 Control miR-3


title: N2 wild-type, biological rep3

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: Gene expression data from wild-type

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C.elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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 100.

organism: Caenorhabditis elegans

source_name: wild-type worms

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: Wild-type and atfs-1(et18) worms were synchronized by bleaching and raised on solid media

extract_protocol: Total RNA was isolated using the RNA STAT reagent (Tel-Test Inc) according to the manufacturer's instructions.

treatment_protocol: Worms were fed E. coli OP50 and harvested at L4 stage

value: whole organism

value: wild-type


title: N2 wild-type, biological rep2

description: Gene expression data from wild-type


title: atfs-1(et18), biological rep3

description: Gene expression data from atfs-1(et18)

source_name: atfs-1(et18) worms


title: N2 wild-type, biological rep1

description: Gene expression data from wild-type


title: Grade1 (Cy5) x Grade2 (Cy3)

description: Dye-swap (Cy5/Cy3) of Grade1 vs Grade2


title: FTC236 Notch1_48hr_1ugDox_rep2

source_name: FTC236-Notch1 cell line, 48hr, 1ug/ml Dox, replicate 2

value: follicular cancer

value: Yes

value: thyroid


title: Grade1 (Cy3) x Grade2 (Cy5)

description: Dye-swap (Cy3/Cy5) of Grade1 vs Grade2


title: Arabidopsis bMCE3

city: Davis

first: John

middle: J

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California, Davis

description: Laser capture microdissected (LCM) micropylar endosperm at the bending-cotyledon stage, biological replicate 3.  Micropylar endosperm collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined using the LEICA LMD6000 system for microdissection.

hyb_protocol: Following fragmentation, five micrograms of cDNA was hybridized for 18 hr at 45°C with the GeneChip ATH1 Arabidopsis Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating system 1.4 (GCOS) using default analysis settings and global scaling as a normalization method. The mean target intensity of each array was set to 500.

organism: Arabidopsis thaliana

source_name: Arabidopsis bending-cotyledon stage micropylar endosperm captured by LCM

label_protocol: 2 to 5 ng of total RNA was amplified using the WT-Ovation Pico RNA Amplification System (NuGEN, San Carlos, CA). cDNAs were fragmented and labeled with NuGEN FL-Ovation™ cDNA Biotin Module V2.

growth_protocol: Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20°C and 50% - 70% relative humidity.

extract_protocol: Total RNA was extracted using the RNaqueous Micro-Kit (Ambion, Austin, TX) using a modified protocol incorporating an on-column DNase treatment (Qiagen RNase-Free DNase Set) during column washes.

treatment_protocol: Siliques containing bending cotyledon stage seeds were collected from 38-46 day old plants. Siliques were sub-divided and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin. Microdissection of compartments was carried out on sections using a Leica LMD6000 system.

value: embryo proper

tag: developmental stage

value: bending-cotyledon stage


title: atfs-1(et18), biological rep2

description: Gene expression data from atfs-1(et18)


title: Arabidopsis bMCE1

description: Laser capture microdissected (LCM) micropylar endosperm at the bending-cotyledon stage, biological replicate 1.  Micropylar endosperm collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined using the LEICA LMD6000 system for microdissection.


title: white adipose tissue control 4

status: Public on Mar 20 2016

city: Lund

first: Maria

last: Björkqvist

state: Skåne

address: Sölvegatan 17

department: Experimental Medical Sciences

country: Sweden

institute: Lund University

description: Gene expression data from control subject

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed using expression console software version 1.1.2 using default analysis settings and RMA as normalization method.

source_name: subcutaneous adipose tissue control 4

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

growth_protocol: Subcutaneous adipose tissue biospies were obtained from premanifest HD gene carriers, stage II/III HD patients and healthy control subjects by needle aspiration from the buttock under local topical anaesthetic.

extract_protocol: Frozen tissues were homogenized using a Fastprep-24 homogenizer (MP Biomedicals) at 4m/s for 40 sec prior to RNA extraction using the Rneasy Lipid Tissue Mini Kit (Qiagen) following manufacturer's protocol.

treatment_protocol: The biopsies were then immediately snap frozen in liquid nitrogen and stored at -80°C prior to total RNA extraction.

tag: gender

value: Female

tag: cag

tag: bmi


title: white adipose tissue control 5

source_name: subcutaneous adipose tissue control 5


title: white adipose tissue premanifest HD 5

description: Gene expression data from premanifest HD subject

source_name: subcutaneous adipose tissue premanifest HD 5


title: white adipose tissue premanifest HD 7

source_name: subcutaneous adipose tissue premanifest HD 7

value: Male


title: atfs-1(et18), biological rep1

description: Gene expression data from atfs-1(et18)

tag: tissue


title: white adipose tissue premanifest HD 6

source_name: subcutaneous adipose tissue premanifest HD 6


title: white adipose tissue control 7

source_name: subcutaneous adipose tissue control 7


title: white adipose tissue premanifest HD 8

source_name: subcutaneous adipose tissue premanifest HD 8


title: white adipose tissue control 6

source_name: subcutaneous adipose tissue control 6


title: Strain_adenocarcinoma_partial-EMT_suc-treated_D545_UC-Denver

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: Mouse Transgenic Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a Agilent fluorescent scanner and image intensity data were extracted and analyzed with Agilent analysis software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

organism: Mus musculus

source_name: Mouse Reference

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

extract_protocol: Qiagen Rneasy Kit

tag: reference

value: Whole mouse total RNA

tag: sample

value: Mouse Transgenic Tumor


title: white adipose tissue stage II/III HD 2

description: Gene expression data from stage II/III HD subject

source_name: subcutaneous adipose tissue stage II/III HD 2


title: Strain_plemorphic_ spindle-cell_papillary_full-EMT_suc-treated_D568_UC-Denver

description: Mouse Transgenic Tumor

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: Strain_papillary_partial-EMT_suc-treated_A747_UC-Denver

description: Mouse Transgenic Tumor


title: white adipose tissue premanifest HD 4

source_name: subcutaneous adipose tissue premanifest HD 4


title: white adipose tissue stage II/III HD 3

source_name: subcutaneous adipose tissue stage II/III HD 3


title: Strain_adenosquamous_secretory_partial-EMT_dox-treated_D729_UC-Denver

description: Mouse Transgenic Tumor


title: white adipose tissue premanifest HD 2

source_name: subcutaneous adipose tissue premanifest HD 2


title: Strain_adenosquamous_partial-EMT_dox-treated_D723_UC-Denver

description: Mouse Transgenic Tumor


title: white adipose tissue premanifest HD 3

source_name: subcutaneous adipose tissue premanifest HD 3


title: white adipose tissue stage II/III HD 5

source_name: subcutaneous adipose tissue stage II/III HD 5


title: white adipose tissue control 2

source_name: subcutaneous adipose tissue control 2


title: white adipose tissue stage II/III HD 4

source_name: subcutaneous adipose tissue stage II/III HD 4


title: Strain_plemorphic_undifferentiated_sarcomatoid_full-EMT_dox-treated_A336_UC-Denver

description: Mouse Transgenic Tumor


title: UT-SCC-8-[6 hours after 4 Gy]

status: Public on Mar 19 2016

city: Amsterdam

first: Monique

middle: C.

last: de Jong

address: Plesmanlaan 121

department: Dept of Biological Stress Response and Dept. of Radiation Oncology

country: Netherlands

institute: Netherlands Cancer Institute

hyb_protocol: The cRNA (1,500 ng per array) was hybridized to v3 Illumina bead arrays according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

scan_protocol: Standard Illumina scanning protocol

data_processing: Background adjustment was done using the method from the affy package, after which data were log2 transformed and robust spline normalized.

source_name: HNSCC cell line derived from supraglottic larynx

label_protocol: Biotin-labeled cRNA was generated using the Illumina® TotalPrep RNA Amplification kit (AMIL1791, Ambion Inc., Austin, TX). Briefly, to synthesize biotin-labeled cRNA, 350 ng of total RNA was reversed transcribed and subsequently amplified and labeled with biotin (in vitro transcription).

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s medium, supplemented with 1% L-glutamine, 1% nonessential amino acids, 10% fetal bovine serum and antibiotics. Cells were incubated in humidified air with 5% CO2 at 37°C. Depending on the doubling time, cells were subcultured every 3-14 days to ensure exponential growth. Cells were used for experiments when they were around 60-70% confluent. Preferably low passages (10-20) were used.

extract_protocol: Mock-irradiated cells were harvested for all cell lines, as well as cells at 2 and 6 hours after 4 Gy. At the given time points cells were rinsed with ice-cold PBS twice and then collected in RNA-Bee (Campro Scientific). Cells in RNA-Bee were used to extract total RNA. Messenger RNAs were further purified using the Rneasy Mini Kit and the RNase-Free DNase Set from Qiagen. The RNA was isolated and DNAse treated using the spin columns according to the manufacturer’s instructions. The Agilent 2100 bioanalyzer was used to confirm the presence of intact RNA.

treatment_protocol: Cells were irradiated using a 137Cs irradiation unit with a dose rate of  0.662 Gy/min.

tag: cell line

tag: cell type

value: Head and neck squamous cell carcinoma (HNSCC) cell line

tag: source subsite

value: supraglottic larynx

tag: time from (mock) irradiation to harvest of rna

tag: irradiation dose (gy)

tag: radiosensitivity (auc)

tag: radiosensitivity (auc) binary

tag: passage tested

tag: source gender

value: M


title: Strain_adenosquamous_partial-EMT_suc-treated_D538_UC-Denver

description: Mouse Transgenic Tumor


title: UT-SCC-6A-[6 hours after 4 Gy]

value: F


title: Strain_adenocarcinoma-secretory-papillary_no-EMT_dox-treated_A284_UC-Denver

description: Mouse Transgenic Tumor


title: UT-SCC-7-[6 hours after 4 Gy]

source_name: HNSCC cell line derived from cutis regio temporalis

value: cutis regio temporalis


title: white adipose tissue premanifest HD 1

source_name: subcutaneous adipose tissue premanifest HD 1

tag: age


title: Strain_adenosquamous_no-EMT_suc-treated_A588_UC-Denver

description: Mouse Transgenic Tumor


title: FaDu_EMT-induced

description: FaDu-HIF-ΔODD

source_name: HNSCC cell line

extract_protocol: Cells were harvested for all cell lines in confulent growth phase. Cells were rinsed with ice-cold PBS twice and then collected in RNA-Bee (Campro Scientific). Cells in RNA-Bee were used to extract total RNA. Messenger RNAs were further purified using the Rneasy Mini Kit and the RNase-Free DNase Set from Qiagen. The RNA was isolated and DNAse treated using the spin columns according to the manufacturer’s instructions. The Agilent 2100 bioanalyzer was used to confirm the presence of intact RNA.

treatment_protocol: Radiosensitivity of all cell lines was tested with a 96-well plate clonogenic assay, developed by Grénman et al. The radiosensitivity of a cell line was defined as the area under the survival curve, with measurements of the survival fraction at 6 different doses, each repeated at least 3 times.

tag: radiosensitivity (area under survival curve)


title: UT-SCC-9-[6 hours after 4 Gy]

source_name: HNSCC cell line derived from glottic larynx

value: glottic larynx


title: white adipose tissue control 1

source_name: subcutaneous adipose tissue control 1

tag: gender


title: UT-SCC-90-[6 hours after 4 Gy]

source_name: HNSCC cell line derived from tongue

value: tongue


title: white adipose tissue stage II/III HD 1

source_name: subcutaneous adipose tissue stage II/III HD 1

tag: cag


title: UT-SCC-60B-[6 hours after 4 Gy]

source_name: HNSCC cell line derived from tonsil

value: tonsil


title: UT-SCC-79A-[6 hours after 4 Gy]

source_name: HNSCC cell line derived from parotid gland

value: parotid gland


title: Strain_adenosquamous_partial-EMT_suc-treated_D630_UC-Denver

description: Mouse Transgenic Tumor

source_name: Mouse Reference


title: UT-SCC-54C-[6 hours after 4 Gy]

source_name: HNSCC cell line derived from buccal mucosa

value: buccal mucosa


title: FaDu_control


title: UT-SCC-5-[6 hours after 4 Gy]


title: UT-SCC-76A-[6 hours after 4 Gy]


title: UT-SCC-45-[6 hours after 4 Gy]

source_name: HNSCC cell line derived from floor of mouth

value: floor of mouth


title: UT-SCC-32-[6 hours after 4 Gy]


title: UT-SCC-47-[6 hours after 4 Gy]


title: white adipose tissue control 3

source_name: subcutaneous adipose tissue control 3

tag: bmi


title: UT-SCC-48-[6 hours after 4 Gy]


title: UT-SCC-77-[6 hours after 4 Gy]


title: UT-SCC-4-[6 hours after 4 Gy]


title: UT-SCC-20A-[6 hours after 4 Gy]


title: UT-SCC-19B-[6 hours after 4 Gy]


title: UT-SCC-90-[2 hours after 4 Gy]


title: UT-SCC-16A-[6 hours after 4 Gy]


title: UT-SCC-8-[2 hours after 4 Gy]


title: UT-SCC-23-[6 hours after 4 Gy]


title: UT-SCC-24A-[6 hours after 4 Gy]


title: UT-SCC-36-[6 hours after 4 Gy]


title: UT-SCC-2-[6 hours after 4 Gy]


title: UT-SCC-19A-[6 hours after 4 Gy]


title: UT-SCC-1A-[6 hours after 4 Gy]

source_name: HNSCC cell line derived from gingiva mandibulae

value: gingiva mandibulae


title: UT-SCC-15-[6 hours after 4 Gy]


title: UT-SCC-27-[6 hours after 4 Gy]


title: UT-SCC-9-[2 hours after 4 Gy]


title: UT-SCC-60B-[2 hours after 4 Gy]


title: UT-SCC-25-[6 hours after 4 Gy]


title: UT-SCC-5-[2 hours after 4 Gy]


title: UT-SCC-7-[2 hours after 4 Gy]


title: UT-SCC-77-[2 hours after 4 Gy]


title: UT-SCC-79A-[2 hours after 4 Gy]


title: UT-SCC-54C-[2 hours after 4 Gy]


title: UT-SCC-12-[6 hours after 4 Gy]

source_name: HNSCC cell line derived from cutis nasi

value: cutis nasi


title: UT-SCC-76A-[2 hours after 4 Gy]


title: UT-SCC-47-[2 hours after 4 Gy]


title: UT-SCC-48-[2 hours after 4 Gy]


title: UT-SCC-6A-[2 hours after 4 Gy]


title: UT-SCC-22-[6 hours after 4 Gy]


title: UT-SCC-42A-[2 hours after 4 Gy]


title: UT-SCC-46A-[2 hours after 4 Gy]

source_name: HNSCC cell line derived from gingiva maxillae

value: gingiva maxillae


title: UT-SCC-45-[2 hours after 4 Gy]


title: UT-SCC-4-[2 hours after 4 Gy]

source_name: HNSCC cell line derived from supraglottic larynx


title: UT-SCC-46A-[6 hours after 4 Gy]


title: UT-SCC-24A-[2 hours after 4 Gy]


title: UT-SCC-32-[2 hours after 4 Gy]


title: UT-SCC-27-[2 hours after 4 Gy]


title: UT-SCC-25-[2 hours after 4 Gy]


title: UT-SCC-23-[2 hours after 4 Gy]


title: UT-SCC-20A-[2 hours after 4 Gy]


title: UT-SCC-22-[2 hours after 4 Gy]


title: UT-SCC-2-[2 hours after 4 Gy]


title: UT-SCC-19B-[2 hours after 4 Gy]


title: UT-SCC-19A-[2 hours after 4 Gy]


title: UT-SCC-1A-[2 hours after 4 Gy]


title: UT-SCC-77-[Mock irradiated]


title: UT-SCC-79A-[Mock irradiated]


title: UT-SCC-6A-[Mock irradiated]


title: UT-SCC-15-[2 hours after 4 Gy]


title: UT-SCC-12-[2 hours after 4 Gy]


title: UT-SCC-60B-[Mock irradiated]


title: UT-SCC-54C-[Mock irradiated]


title: UT-SCC-16A-[2 hours after 4 Gy]


title: UT-SCC-90-[Mock irradiated]


title: UT-SCC-42A-[6 hours after 4 Gy]


title: UT-SCC-7-[Mock irradiated]

source_name: HNSCC cell line derived from cutis regio temporalis


title: UT-SCC-9-[Mock irradiated]


title: UT-SCC-76A-[Mock irradiated]


title: UT-SCC-8-[Mock irradiated]


title: UT-SCC-5-[Mock irradiated]


title: UT-SCC-25-[Mock irradiated]


title: UT-SCC-23-[Mock irradiated]


title: UT-SCC-24A-[Mock irradiated]


title: UT-SCC-48-[Mock irradiated]


title: UT-SCC-32-[Mock irradiated]


title: UT-SCC-27-[Mock irradiated]


title: UT-SCC-46A-[Mock irradiated]


title: UT-SCC-22-[Mock irradiated]


title: UT-SCC-42A-[Mock irradiated]


title: UT-SCC-47-[Mock irradiated]


title: UT-SCC-36-[Mock irradiated]


title: UT-SCC-1A-[Mock irradiated]


title: Skin of uninfected salmon fed with feed with low dose of the GLs-containing ingredient_3

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays

scan_protocol: Arrays were scanned with GenePix 4100A DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1 and GenePix Pro 6.0. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Skin of uninfected salmon fed with feed with 15% GLs-containing ingredient

label_protocol: Amplified and labeled according to Agilent Two-Color Quick Amp labelling kits (Agilent).

growth_protocol: Salmon (initial average weight (377 ± 16g) was kep in 500 L tanks with sea water

extract_protocol: RNA was isolated using TRIzol® (Invitrogen), and purified with Qiagen RNeasy mini kits

treatment_protocol: The fish were fed diets enriched in the plant derived phytochemical called Glucosinolates or standard control diet

tag: tissue

value: skin

source_name: Pooled skin samples

tag: sample type

value: reference


title: UT-SCC-16A-[Mock irradiated]


title: UT-SCC-4-[Mock irradiated]


title: Skin of uninfected salmon fed with feed with low dose of the GLs-containing ingredient_4


title: UT-SCC-15-[Mock irradiated]


title: UT-SCC-20A-[Mock irradiated]


title: Sample 6 Near-infrared treatment 10 rounds

city: Matsumoto

first: Yohei

last: Tanaka

state: Nagano

department: Plastic Surgery

institute: Clinica Tanaka

description: Gene expression after 10 rounds of near-infrared treatment

hyb_protocol: Hybridization mixtures were prepared by adding 2x Hybridization Buffer and mixing well by pipetting. Hybridization was carried out at 65°C for 17 hours. Washing was performed using the Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned using an Agilent Technologies Microarray Scanner (Agilent Technologies), and images were processed by Agilent Feature Extraction software (Agilent Technologies) with background correction.

data_processing: Data were imported into GeneSpring and normalization was performed 75 percentile shift. After normalization and data filtering of the raw date output files, log-fold changes in gene expression in NIR irradiated group compared with control were analyzed to determine up-regulated and down-regulated genes, using a 2-fold change as the cut-off using GeneSpring GX 11.0 software (Agilent Technologies). Up-regulated and down-regulated genes were further clustered into functional gene groups using ontology analysis with GeneSpring GX 11.0 software.

source_name: human epidermal cell

label_protocol: Cy3-labeled cRNA samples were synthesized using an Agilent Low Input Quick Amp Labeling kit, according to the manufacturer's instructions (Agilent Technologies). For each time point, 50 ng of total RNA was used to generate first-strand cDNA. After the denaturation step (10 min at 65°C) and cRNA synthesis step (2 hr at 40°C), the reactions were incubated at 70°C for 15 minutes to inactivate the AffinityScript enzyme. For the labeling reactions, cRNA samples were each mixed with 6 μL of Transcription Master Mix cocktail containing Cy3-CTP, and incubated at 40°C for 2 hours. Purification was performed using Qiagen RNeasy mini spin columns (Qiagen). Labeled cRNA were quantified on a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE) and quality was also checked by Agilent 2100 bioAnalyzer series II (Agilent Technologies).

growth_protocol: Human epidermal cells were prepared from normal human epidermal keratinocytes. The medium was changed every 2 days until the cultures became subconfluented. The subconfluented cells were subcultured with trypsin and seeded on a cell culture insert containing a microporous membrane with 0.4 μm pore size. Cells were cultivated between an air and liquid interface to form a multilayered, highly skin-like structure. All cells were grown at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNAs were extracted in QIAzol reagent (Qiagen, Hilden, Germany) and spin-column purified using RNeasy Mini spin column (Qiagen). The RNA was extracted from control and irradiated group, which consists of 8 whole individual 3-dimensional reconstructed human epidermal models. Quantity and quality of RNA samples were then measured using UV absorbance (NanoDrop Technologies, Wilmington, DE) and quality was also assessed using an Agilent 2100 bioAnalyzer series II (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: The NIR device emits an NIR spectrum between 1100 and 1800 nm, with water filtering to remove wavelengths between 1400 and 1500 nm. To avoid thermal effects, the sapphire contact cooling tip was set to a fixed temperature of 20°C. We performed 5 and 10 rounds of NIR irradiation at 10 J ⁄cm2.

value: human epidermal tissue culture model

tag: treatment

value: 10 rounds of near-infrared irradiation at 10 J /cm2


title: UT-SCC-12-[Mock irradiated]

tag: cell line

value: Head and neck squamous cell carcinoma (HNSCC) cell line


title: UT-SCC-45-[Mock irradiated]

tag: cell type

value: M


title: UT-SCC-19B-[Mock irradiated]

source_name: HNSCC cell line derived from glottic larynx

tag: source subsite


title: UT-SCC-2-[Mock irradiated]

tag: time from (mock) irradiation to harvest of rna


title: UT-SCC-19A-[Mock irradiated]

tag: irradiation dose (gy)


title: Skin of uninfected salmon fed with feed with low dose of the GLs-containing ingredient_2


title: Skin of uninfected salmon fed with feed with low dose of the GLs-containing ingredient_1


title: Skin of uninfected salmon fed with control feed_5


title: Skin of uninfected salmon fed with control feed_3


title: Skin of uninfected salmon fed with control feed_4


title: Skin of lice infected salmon fed with feed with high dose of the GLs-containing ingredient_4

source_name: Skin of lice infected salmon fed with feed with 15% GLs-containing ingredient


title: Skin of lice infected salmon fed with feed with high dose of the GLs-containing ingredient_3


title: Sample 2 No treatment

description: Gene expression of no treatment control

value: no treatment


title: Sample 4 Near-infrared treatment 5 rounds

description: Gene expression after 5 rounds of near-infrared treatment

value: 5 rounds of near-infrared irradiation at 10 J /cm2


title: Sample 5 Near-infrared treatment 10 rounds


title: UT-SCC-36-[2 hours after 4 Gy]

tag: radiosensitivity (auc)


title: Skin of lice infected salmon fed with feed with low dose of the GLs-containing ingredient_4

source_name: Skin of lice infected salmon fed with feed with 3.75% GLs-containing ingredient


title: Skin of lice infected salmon fed with feed with low dose of the GLs-containing ingredient_1


title: Skin of lice infected salmon fed with feed with low dose of the GLs-containing ingredient_3


title: Skin of uninfected salmon fed with control feed_1


title: Skin of lice infected salmon fed with feed with high dose of the GLs-containing ingredient_2


title: Skin of lice infected salmon fed with control feed_5


title: Skin of lice infected salmon fed with feed with low dose of the GLs-containing ingredient_5


title: UT-SCC-9_6 hours after 4 Gy [miRNA]

hyb_protocol: hybridized in a TECAN HS4800 Hybridization Station

scan_protocol: The slides were scanned in a DNA Microarray Scanner (Model G250B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11).

data_processing: After subtraction of the mean background signal, arrays were log2 transformed and normalized using the lowess method (using Imagene 6.0 software). Probes with missing data for more than 1 sample were removed. Data from spots for the same reporter were averaged. Annotations were updated (data in matrix norm used for analyses).

label_protocol: Using the Exiqon miRCURY LNA microRNA Array kit (5th generation),  1ug total RNA was labeled with Hy3 and a reference pool of all samples with Hy5.

extract_protocol: Mock-irradiated cells were harvested for all cell lines, as well as cells at 6 hours after 4 Gy. At the given time points cells were rinsed with ice-cold PBS twice and then collected in RNA-Bee (Campro Scientific). Cells in RNA-Bee were used to extract total RNA. Messenger RNAs were further purified using the Rneasy Mini Kit and the RNase-Free DNase Set from Qiagen. The RNA was isolated and DNAse treated using the spin columns according to the manufacturer’s instructions. The Agilent 2100 bioanalyzer was used to confirm the presence of intact RNA.

value: glottic larynx

tag: radiosensitivity (auc) binary

source_name: Pool of all HNSCC cell line samples


title: Skin of lice infected salmon fed with feed with low dose of the GLs-containing ingredient_2


title: Sample 3 Near-infrared treatment 5 rounds


title: Skin of lice infected salmon fed with feed with high dose of the GLs-containing ingredient_1


title: Skin of lice infected salmon fed with control feed_2


title: Skin of lice infected salmon fed with feed with high dose of the GLs-containing ingredient_5


title: UT-SCC-90_6 hours after 4 Gy [miRNA]

source_name: HNSCC cell line derived from tongue

value: tongue

tag: passage tested


title: Skin of lice infected salmon fed with control feed_1


title: Skin of lice infected salmon fed with control feed_3


title: Sample 1 No treatment

description: Gene expression of no treatment control


title: LSCCLY28

city: Beijing

first: Run

last: Tong

address: 17# Pan Jia Yuan Nan Li, Chao Yang District, P.O. Box 2258

department: Department of Etiology and Carcinogenesis

country: China

institute: Cancer Hospital and Institute, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Gene expression of human lung squamous cell carcinoma tissue

hyb_protocol: For human airway epithelium cells from nonsmokers, 600 ng of Cy3-labelled cRNA (specific activity >=8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer’s specifications. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and 40 ml hybridization sample each was hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarray (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.    For immortalized human bronchial epithelial cell lines and lung squamous cell carcinoma tissues, 1.65 μg of Cy3-labelled cRNA (specific activity >=8.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer’s specifications. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and 100 mL hybridization sample each was hybridized to Agilent Whole Human Genome Microarray 4x44K (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash buffer 2 (Agilent). Then put the slides in a slide holder and scanned slides immediately.

scan_protocol: For human airway epithelium cells from nonsmokers, slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60K array slides. For immortalized human bronchial epithelial cell lines and lung squamous cell carcinoma tissues, slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K array slides.

data_processing: For human airway epithelium cells from nonsmokers, the scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. For immortalized human bronchial epithelial cell lines and lung squamous cell carcinoma tissues, the scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: lung squamous cell carcinoma tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.05 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer’s specifications, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: For human airway epithelium cells from nonsmokers, total RNA was isolated with RNeasy Micro kit (Qiagen, MD, USA). For immortalized human bronchial epithelial cell lines and lung squamous cell carcinoma tissues, total RNA was isolated with RNeasy Mini kit (Qiagen, MD, USA). RNA was quantitated with ND-1000 UV-VIS Spectrophotometer (NanoDrop Technologies, DE, USA) and the integrity of RNA was assessed using the RNA 6000 Labchip kit in combination with the Agilent 2100 Bioanalyzer (Agilent, CA, US).

treatment_protocol: For human airway epithelium cells from nonsmokers, samples were treated with RNAlater TM (Ambion, Austin, TX, USA) overnight and stored at -80°C before RNA preparation and microarray examination. No additional treatment was applied. For immortalized human bronchial epithelial cell lines, no additional treatment was applied. For lung squamous cell carcinoma tissues, samples were snap-frozen in liquid nitrogen and stored at -80°C before RNA preparation and microarray examination. No additional treatment was applied.

tag: sample id

value: sample LY28

value: Male

tag: histology

value: lung squamous cell carcinoma

tag: Stage

value: IIB

tag: n stage


title: LSCCLY25

value: sample LY25

value: human lung squamous cell carcinoma tissue

tag: gender

tag: age


title: LSCCLY27

value: sample LY27

tag: tissue

value: IB


title: Skin of lice infected salmon fed with control feed_4

value: skin

tag: sample type

value: reference


title: Skin of uninfected salmon fed with control feed_2


title: UT-SCC-77_6 hours after 4 Gy [miRNA]


title: LSCCLY21

value: sample LY21

value: IIIA


title: LSCCLY22

value: sample LY22


title: UT-SCC-79A_6 hours after 4 Gy [miRNA]

source_name: HNSCC cell line derived from parotid gland

value: Head and neck squamous cell carcinoma (HNSCC) cell line

value: parotid gland

value: F


title: LSCCLY29

value: sample LY29


title: UT-SCC-76A_6 hours after 4 Gy [miRNA]

value: tongue

value: M


title: LSCCLY20

value: sample LY20

value: Male

value: lung squamous cell carcinoma


title: UT-SCC-7_6 hours after 4 Gy [miRNA]

value: cutis regio temporalis


title: UT-SCC-8_6 hours after 4 Gy [miRNA]

value: supraglottic larynx


title: UT-SCC-60B_6 hours after 4 Gy [miRNA]

source_name: HNSCC cell line derived from tonsil

value: tonsil


title: UT-SCC-6A_6 hours after 4 Gy [miRNA]


title: UT-SCC-54C_6 hours after 4 Gy [miRNA]

source_name: HNSCC cell line derived from buccal mucosa

value: buccal mucosa


title: UT-SCC-5_6 hours after 4 Gy [miRNA]


title: LSCCLY24

value: sample LY24

value: human lung squamous cell carcinoma tissue


title: LSCCLY15

value: sample LY15

value: IB


title: UT-SCC-48_6 hours after 4 Gy [miRNA]

value: Head and neck squamous cell carcinoma (HNSCC) cell line


title: LSCCLY16

value: sample LY16

value: IIIA


title: LSCCLY19

value: sample LY19


title: RAW 8B_BSO+LPS_2h_rep4

city: Brighton

first: Pietro

last: Ghezzi

address: BSMS Teaching Building

country: United Kingdom

institute: Brighton & Sussex Medical School

description: Gene expression after 6h in GSH-depleted LPS-treated cells

hyb_protocol: Amplified labeled RNA was hybridised onto Single Colour SurePrint G3 Mouse GE 8x60K Microarrays (AMADID:046066; Agilent)

scan_protocol: Slides were scanned immediately after washing on the Agilent C microarray Scanner (G2505B) for G3 microarray format scan setting for 8 X 60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Red and Green PMT).

data_processing: The scanned images were analysed with Feature Extraction software v10.7.3.1 to generate the array data from the images

source_name: RAW cells, 6h, BSO+LPS, replicate 3

label_protocol: RNA was amplified and labeled with Cyanine-3 (Cy3)

growth_protocol: RAW 264.7 mouse macrophage-like cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum

extract_protocol: Cells were lysed with QIAzol (QIAGEN) and total RNA was extracted by using the miRNeasy system and protocol (QIAGEN)

treatment_protocol: Cells were incubated for 24 h with buthionine sulfoximine (BSO) to deplete glutathione (GSH) and then treated with LPS 10 ng/ml for 2 h or 6 h

value: macrophage-like cell line


title: UT-SCC-47_6 hours after 4 Gy [miRNA]

source_name: HNSCC cell line derived from floor of mouth

value: floor of mouth

value: M


title: UT-SCC-46A_6 hours after 4 Gy [miRNA]

source_name: HNSCC cell line derived from gingiva maxillae

value: gingiva maxillae


title: LSCCLY17

value: sample LY17

value: Male

value: lung squamous cell carcinoma


title: RAW 4B_BSO+LPS_2h_rep3

description: Gene expression after 2h in GSH-depleted LPS-treated cells

source_name: RAW cells, 2h, BSO+LPS, replicate 3


title: LSCCLY14

value: sample LY14


title: RAW 5B_ctr_2h_rep4

description: Gene expression after 6h in control cells

source_name: RAW cells, 6h, control, replicate 3


title: UT-SCC-45_6 hours after 4 Gy [miRNA]


title: LSCCLY09

value: sample LY09


title: LSCCLY02

value: sample LY02


title: LSCCLY03

value: sample LY03

value: human lung squamous cell carcinoma tissue

value: IIB


title: RAW 7B_BSO_2h_rep4

description: Gene expression after 6h in GSH-depleted cells

source_name: RAW cells, 6h, BSO, replicate 3


title: AEC130

description: Gene expression of human airway epithelium cells from nonsmokers

source_name: human airway epithelium cells from nonsmokers of malignant lung diseases

value: sample 130

value: Female

value: Malignant


title: LSCCLY12

value: sample LY12

value: IIIA


title: RAW 1B_ctr_2h_rep3

description: Gene expression after 2h in control cells

source_name: RAW cells, 2h, control, replicate 3

value: macrophage-like cell line


title: RAW 2B_LPS_2h_rep3

description: Gene expression after 2h in LPS-treated cells

source_name: RAW cells, 2h, LPS, replicate 3


title: UT-SCC-42A_6 hours after 4 Gy [miRNA]

source_name: HNSCC cell line derived from supraglottic larynx

value: Head and neck squamous cell carcinoma (HNSCC) cell line

value: supraglottic larynx

value: M


title: UT-SCC-32_6 hours after 4 Gy [miRNA]

value: tongue


title: RAW 6B_LPS_2h_rep4

description: Gene expression after 6h in LPS-treated cells

source_name: RAW cells, 6h, LPS, replicate 3


title: RAW 3B_BSO_2h_rep3

description: Gene expression after 2h in GSH-depleted cells

source_name: RAW cells, 2h, BSO, replicate 3


title: RAW 7A_BSO_2h_rep2

source_name: RAW cells, 6h, BSO, replicate 2


title: UT-SCC-27_6 hours after 4 Gy [miRNA]

source_name: HNSCC cell line derived from gingiva mandibulae

value: gingiva mandibulae

source_name: Pool of all HNSCC cell line samples


title: LSCCGZ31

source_name: lung squamous cell carcinoma tissue

value: sample GZ31

value: lung squamous cell carcinoma

value: IB


title: LSCCLY06

value: sample LY06


title: AEC126

value: sample 126

value: human airway epithelium cells from nonsmokers


title: UT-SCC-36_6 hours after 4 Gy [miRNA]

value: floor of mouth


title: RAW 8A_BSO+LPS_2h_rep2

source_name: RAW cells, 6h, BSO+LPS, replicate 2


title: AEC121

value: sample 121

value: Female


title: UT-SCC-25_6 hours after 4 Gy [miRNA]

source_name: HNSCC cell line derived from tongue


title: AEC124

value: sample 124

value: Malignant


title: LSCCGZ21

value: sample GZ21

value: human lung squamous cell carcinoma tissue

value: Male

value: IA


title: AEC117

value: sample 117


title: AEC111

value: sample 111


title: AEC116

value: sample 116


title: RAW 5A_ctr_6h_rep2

source_name: RAW cells, 6h, control, replicate 2

value: macrophage-like cell line


title: LSCCGZ26

value: sample GZ26

value: lung squamous cell carcinoma

value: IIB


title: UT-SCC-24A_6 hours after 4 Gy [miRNA]

value: Head and neck squamous cell carcinoma (HNSCC) cell line

value: tongue

value: M


title: LSCCGZ18

value: sample GZ18


title: RAW 6A_LPS_6h_rep2

source_name: RAW cells, 6h, LPS, replicate 2


title: RAW 3A_BSO_2h_rep2

source_name: RAW cells, 2h, BSO, replicate 2


title: LSCCGZ24

value: sample GZ24

value: Female

value: IB


title: RAW 4A_BSO+LPS_2h_rep2

source_name: RAW cells, 2h, BSO+LPS, replicate 2


title: UT-SCC-23_6 hours after 4 Gy [miRNA]

source_name: HNSCC cell line derived from glottic larynx

value: glottic larynx


title: RAW 1A_ctr_2h_rep2

source_name: RAW cells, 2h, control, replicate 2


title: RAW 2A_LPS_2h_rep2

source_name: RAW cells, 2h, LPS, replicate 2


title: AEC107

source_name: human airway epithelium cells from nonsmokers of malignant lung diseases

value: sample 107

value: Malignant


title: AEC104

value: sample 104

value: human airway epithelium cells from nonsmokers


title: RAW 8C_BSO+LPS_6h_rep1

source_name: RAW cells, 6h, BSO+LPS, replicate 1


title: UT-SCC-22_6 hours after 4 Gy [miRNA]


title: RAW 7C_BSO_6h_rep1

source_name: RAW cells, 6h, BSO, replicate 1


title: UT-SCC-20A_6 hours after 4 Gy [miRNA]

source_name: HNSCC cell line derived from floor of mouth

value: floor of mouth

value: F


title: LSCCGZ15

value: sample GZ15

value: human lung squamous cell carcinoma tissue

value: Male


title: LSCCGZ10

value: sample GZ10

value: lung squamous cell carcinoma


title: LSCCGZ09

value: sample GZ09


title: UT-SCC-19A_6 hours after 4 Gy [miRNA]

value: Head and neck squamous cell carcinoma (HNSCC) cell line

value: M


title: UT-SCC-19B_6 hours after 4 Gy [miRNA]


title: UT-SCC-2_6 hours after 4 Gy [miRNA]


title: UT-SCC-1A_6 hours after 4 Gy [miRNA]

value: gingiva mandibulae


title: AEC095

value: sample 095


title: LSCCCC51

value: sample CC51

value: IIIA


title: RAW 5C_ctr_6h_rep1

source_name: RAW cells, 6h, control, replicate 1

value: macrophage-like cell line


title: AEC101

value: sample 101

value: Female

value: Malignant


title: LSCCCC71

value: sample CC71


title: UT-SCC-16A_6 hours after 4 Gy [miRNA]

value: tongue

value: F


title: AEC102

value: sample 102

value: human airway epithelium cells from nonsmokers

value: Male


title: LSCCCC14

value: sample CC14

value: human lung squamous cell carcinoma tissue

value: lung squamous cell carcinoma

value: IIB


title: RAW 3C_BSO_2h_rep1

source_name: RAW cells, 2h, BSO, replicate 1


title: RAW 6C_LPS_6h_rep1

source_name: RAW cells, 6h, LPS, replicate 1


title: AEC098

value: sample 098


title: AEC092

value: sample 092


title: LSCCCC27

source_name: lung squamous cell carcinoma tissue

value: sample CC27

value: IIIA


title: AEC091

source_name: human airway epithelium cells from nonsmokers of benign lung diseases

value: sample 091

value: Benign


title: LSCCCC09

value: sample CC09

value: IB


title: NPC_NDb_24H_+NeuroAid_Rep2

city: Singapore

first: Lawrence

middle: W

last: Stanton

address: 60 Biopolis Street, Genome

country: Singapore

institute: Genome Institute of Singapore

description: biological replicate 4

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data was extracted with Genome Studio with background subtraction and normalised using quantile normalisation with GeneSpring GX12.5

source_name: H9 human ESC

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep RNA Amplification kit (Ambion) according to the manufacturer's protocol for Illumina arrays.

extract_protocol: RNA was extracted with Invitrogen TRIzol® reagent followed by clean-up and DNase I treatment with QIAGEN RNeasy® micro kit in accordance to the prescribed protocol.

value: NPC derived from H9 hESC

tag: treatment

value: yes

tag: neural differentiation medium

value: without BDNF, GDNF and anti-oxidants


title: RAW 2C_LPS_2h_rep1

source_name: RAW cells, 2h, LPS, replicate 1

tag: cell line

tag: cell type

value: macrophage-like cell line


title: UT-SCC-15_6 hours after 4 Gy [miRNA]

source_name: HNSCC cell line derived from tongue

value: Head and neck squamous cell carcinoma (HNSCC) cell line

tag: source subsite

value: tongue

tag: time from (mock) irradiation to harvest of rna

value: M

source_name: Pool of all HNSCC cell line samples


title: LSCC98

value: sample 98

value: human lung squamous cell carcinoma tissue

value: Female

value: lung squamous cell carcinoma


title: UT-SCC-12_6 hours after 4 Gy [miRNA]

source_name: HNSCC cell line derived from cutis nasi

value: cutis nasi

tag: irradiation dose (gy)

tag: radiosensitivity (auc)

value: F


title: AEC090

value: sample 090

value: human airway epithelium cells from nonsmokers

value: Malignant


title: LSCCGZ16

value: sample GZ16

value: Male

value: IIB


title: AEC093

value: sample 093


title: UT-SCC-90_Mock irradiated [miRNA]

tag: radiosensitivity (auc) binary

tag: passage tested


title: RAW 1C_ctr_2h_rep1

source_name: RAW cells, 2h, control, replicate 1

value: macrophage-like cell line


title: UT-SCC-9_Mock irradiated [miRNA]

source_name: HNSCC cell line derived from glottic larynx

value: Head and neck squamous cell carcinoma (HNSCC) cell line

value: glottic larynx


title: UT-SCC-8_Mock irradiated [miRNA]

source_name: HNSCC cell line derived from supraglottic larynx

value: supraglottic larynx

value: M


title: UT-SCC-4_6 hours after 4 Gy [miRNA]


title: LSCC85

tag: sample id

value: sample 85

value: human lung squamous cell carcinoma tissue

tag: histology

value: IB


title: LSCC82

value: sample 82

value: lung squamous cell carcinoma

tag: Stage

tag: n stage


title: UT-SCC-77_Mock irradiated [miRNA]

value: tongue

tag: gender


title: NPC_NDb_24H_+NeuroAid_Rep1

description: biological replicate 3

value: NPC derived from H9 hESC

value: yes

value: without BDNF, GDNF and anti-oxidants


title: LSCC81

value: sample 81

tag: tissue

value: Male

tag: age


title: UT-SCC-76A_Mock irradiated [miRNA]


title: NPC_NDb_24H_-NeuroAid_Rep2

description: biological replicate 4

tag: treatment

value: no


title: UT-SCC-79A_Mock irradiated [miRNA]

source_name: HNSCC cell line derived from parotid gland

value: parotid gland

value: F


title: NPC_NDb_24H_-NeuroAid_Rep1

description: biological replicate 3

tag: neural differentiation medium


title: AEC086

source_name: human airway epithelium cells from nonsmokers of malignant lung diseases

value: sample 086

value: Female

value: Malignant


title: LSCC91

value: sample 91


title: AEC089

value: sample 089

value: human airway epithelium cells from nonsmokers

value: Benign


title: AEC084

value: sample 084


title: LSCC76

value: sample 76

value: human lung squamous cell carcinoma tissue

value: lung squamous cell carcinoma

value: IB


title: NPC_NDb_12H_+NeuroAid_Rep1

description: biological replicate 3

value: NPC derived from H9 hESC

value: yes

value: without BDNF, GDNF and anti-oxidants


title: AEC080

value: sample 080


title: AEC078

value: sample 078


title: AEC085

value: sample 085


title: AEC077

value: sample 077

value: Female


title: NPC_NDb_12H_+NeuroAid_Rep2

description: biological replicate 4


title: NPC_NDb_12H_-NeuroAid_Rep2

description: biological replicate 4

value: no


title: LSCC70

value: sample 70

value: Male

value: IIB


title: LSCC57

value: sample 57


title: AEC076

value: sample 076

value: human airway epithelium cells from nonsmokers

value: Benign


title: NPC_NDb_8H_+NeuroAid_Rep2

description: biological replicate 4


title: NPC_NDb_12H_-NeuroAid_Rep1

description: biological replicate 3


title: UT-SCC-7_Mock irradiated [miRNA]

source_name: HNSCC cell line derived from cutis regio temporalis

tag: cell line

value: Head and neck squamous cell carcinoma (HNSCC) cell line

value: cutis regio temporalis

value: M


title: LSCC58

value: sample 58

value: human lung squamous cell carcinoma tissue

value: lung squamous cell carcinoma

value: IIIA


title: LSCC5

value: sample 5


title: UT-SCC-60B_Mock irradiated [miRNA]

source_name: HNSCC cell line derived from tonsil

tag: cell type

value: tonsil


title: AEC074

value: sample 074

value: Malignant


title: LSCCL21

value: sample L21

value: Male


title: UT-SCC-6A_Mock irradiated [miRNA]

tag: source subsite

value: supraglottic larynx

value: F


title: NPC_NDb_8H_-NeuroAid_Rep2

description: biological replicate 4

value: NPC derived from H9 hESC

value: no

value: without BDNF, GDNF and anti-oxidants


title: NPC_NDb_8H_-NeuroAid_Rep1

description: biological replicate 3


title: LSCC46

value: sample 46


title: LSCC42

value: sample 42

value: IIB


title: AEC073

value: sample 073

value: human airway epithelium cells from nonsmokers

value: Female


title: UT-SCC-54C_Mock irradiated [miRNA]

source_name: HNSCC cell line derived from buccal mucosa

value: Head and neck squamous cell carcinoma (HNSCC) cell line

value: buccal mucosa

tag: time from (mock) irradiation to harvest of rna


title: NPC_NDb_8H_+NeuroAid_Rep1

description: biological replicate 3

value: yes


title: AEC072

value: sample 072

value: Benign


title: UT-SCC-5_Mock irradiated [miRNA]

value: tongue

tag: irradiation dose (gy)

value: M


title: UT-SCC-48_Mock irradiated [miRNA]

value: parotid gland

tag: radiosensitivity (auc)


title: LSCC45

value: sample 45

value: human lung squamous cell carcinoma tissue

value: Male

value: lung squamous cell carcinoma


title: NPC_NDb_4H_+NeuroAid_Rep1

description: biological replicate 3

value: NPC derived from H9 hESC

value: without BDNF, GDNF and anti-oxidants


title: NPC_NDb_4H_+NeuroAid_Rep2

description: biological replicate 4


title: AEC070

value: sample 070


title: UT-SCC-47_Mock irradiated [miRNA]

source_name: HNSCC cell line derived from floor of mouth

value: floor of mouth

tag: radiosensitivity (auc) binary


title: UT-SCC-46A_Mock irradiated [miRNA]

source_name: HNSCC cell line derived from gingiva maxillae

value: gingiva maxillae

tag: passage tested


title: UT-SCC-45_Mock irradiated [miRNA]

value: Head and neck squamous cell carcinoma (HNSCC) cell line


title: LSCC36

source_name: lung squamous cell carcinoma tissue

tag: sample id

value: sample 36

value: IB


title: UT-SCC-42A_Mock irradiated [miRNA]

value: supraglottic larynx


title: UT-SCC-4_Mock irradiated [miRNA]

value: F


title: AEC063

source_name: human airway epithelium cells from nonsmokers of benign lung diseases

value: sample 063

value: Female

tag: histology

value: Benign


title: LSCC160

value: sample 160

tag: Stage

value: IIB


title: LSCC159

value: sample 159

value: human lung squamous cell carcinoma tissue

value: Male

tag: n stage


title: AEC064

value: sample 064

value: human airway epithelium cells from nonsmokers

tag: gender

value: Malignant


title: AEC061

value: sample 061

tag: tissue


title: NPC_NDb_4H_-NeuroAid_Rep2

description: biological replicate 4

source_name: H9 human ESC

value: NPC derived from H9 hESC

value: no

value: without BDNF, GDNF and anti-oxidants


title: UT-SCC-36_Mock irradiated [miRNA]

value: Head and neck squamous cell carcinoma (HNSCC) cell line

value: floor of mouth

value: M


title: NPC_ND2_24H_+NeuroAid_Rep1

description: biological replicate 1

value: yes

value: optimized


title: AEC062

value: sample 062

value: Female

tag: age


title: NPC_NDb_4H_-NeuroAid_Rep1

description: biological replicate 3

tag: treatment


title: LSCC156

value: sample 156

value: lung squamous cell carcinoma

value: IIB


title: UT-SCC-32_Mock irradiated [miRNA]

value: tongue


title: NPC_ND2_24H_+NeuroAid_Rep2

description: biological replicate 2

tag: neural differentiation medium


title: LSCC157

value: sample 157

value: human lung squamous cell carcinoma tissue

value: Male


title: LSCC20

value: sample 20

value: IB


title: AEC059

value: sample 059

value: human airway epithelium cells from nonsmokers

value: Malignant


title: NPC_ND2_24H_-NeuroAid_Rep1

description: biological replicate 1

value: NPC derived from H9 hESC

value: no


title: AEC041

value: sample 041

value: Benign


title: NPC_ND2_24H_-NeuroAid_Rep2

description: biological replicate 2

value: optimized


title: LSCC152

value: sample 152


title: NPC_ND2_12H_+NeuroAid_Rep2

description: biological replicate 2

value: yes


title: UT-SCC-27_Mock irradiated [miRNA]

source_name: HNSCC cell line derived from gingiva mandibulae

tag: cell line

value: Head and neck squamous cell carcinoma (HNSCC) cell line

value: gingiva mandibulae

value: M


title: AEC047

value: sample 047

value: Female


title: LSCC155

value: sample 155

value: human lung squamous cell carcinoma tissue

value: Male

value: lung squamous cell carcinoma

value: IIB


title: RAW 4C_BSO+LPS_2h_rep1

source_name: RAW cells, 2h, BSO+LPS, replicate 1

tag: cell type

value: macrophage-like cell line


title: AEC067

value: sample 067

value: human airway epithelium cells from nonsmokers

value: Malignant


title: UT-SCC-22_Mock irradiated [miRNA]

tag: source subsite

value: glottic larynx

source_name: Pool of all HNSCC cell line samples


title: NPC_ND2_12H_+NeuroAid_Rep1

description: biological replicate 1

value: NPC derived from H9 hESC

value: optimized


title: AEC036

value: sample 036


title: AEC035

value: sample 035


title: LSCC153

value: sample 153


title: NPC_ND2_8H_+NeuroAid_Rep2

description: biological replicate 2

value: yes


title: AEC034

value: sample 034

value: Female


title: LSCC149

value: sample 149

value: human lung squamous cell carcinoma tissue

value: IB


title: UT-SCC-20A_Mock irradiated [miRNA]

value: Head and neck squamous cell carcinoma (HNSCC) cell line

value: floor of mouth

tag: time from (mock) irradiation to harvest of rna

value: F


title: UT-SCC-24A_Mock irradiated [miRNA]

source_name: HNSCC cell line derived from tongue

value: tongue

tag: irradiation dose (gy)

value: M


title: UT-SCC-2_Mock irradiated [miRNA]

tag: radiosensitivity (auc)


title: NPC_ND2_12H_-NeuroAid_Rep2

description: biological replicate 2

value: no


title: AEC044

value: sample 044

value: human airway epithelium cells from nonsmokers

value: Male

value: Malignant


title: AEC032

value: sample 032


title: LSCC127

value: sample 127

value: lung squamous cell carcinoma


title: NPC_ND2_8H_+NeuroAid_Rep1

description: biological replicate 1

value: NPC derived from H9 hESC

value: yes

value: optimized


title: AEC033

value: sample 033

value: Female


title: LSCC136

value: sample 136

value: human lung squamous cell carcinoma tissue

value: IIIB


title: LSCC150

value: sample 150


title: AEC031

value: sample 031

value: Benign


title: AEC029

value: sample 029

value: human airway epithelium cells from nonsmokers


title: UT-SCC-23_Mock irradiated [miRNA]

value: Head and neck squamous cell carcinoma (HNSCC) cell line

value: glottic larynx

tag: radiosensitivity (auc) binary

value: M


title: NPC_ND2_4H_+NeuroAid_Rep2

description: biological replicate 2


title: NPC_ND2_8H_-NeuroAid_Rep2

description: biological replicate 2

value: no


title: LSCC126

value: sample 126

value: Male

value: lung squamous cell carcinoma

value: IIIA


title: NPC_ND2_8H_-NeuroAid_Rep1

description: biological replicate 1

value: NPC derived from H9 hESC

value: optimized


title: UT-SCC-19B_Mock irradiated [miRNA]

tag: passage tested


title: UT-SCC-19A_Mock irradiated [miRNA]


title: LSCC123

tag: sample id

value: sample 123

value: human lung squamous cell carcinoma tissue

value: IIB


title: UT-SCC-16A_Mock irradiated [miRNA]

value: tongue

value: F


title: AEC025

value: sample 025

value: Female

tag: histology

value: Malignant


title: NPC_ND2_4H_+NeuroAid_Rep1

description: biological replicate 1

value: yes


title: UT-SCC-15_Mock irradiated [miRNA]

value: Head and neck squamous cell carcinoma (HNSCC) cell line

value: M


title: AEC023

value: sample 023

value: human airway epithelium cells from nonsmokers


title: UT-SCC-12_Mock irradiated [miRNA]

source_name: HNSCC cell line derived from cutis nasi

value: cutis nasi


title: LSCC121

value: sample 121

value: Male

value: lung squamous cell carcinoma

tag: Stage


title: LSCC12

value: sample 12

value: IA

tag: n stage


title: NPC_ND2_4H_-NeuroAid_Rep2

description: biological replicate 2

value: NPC derived from H9 hESC

value: no

value: optimized


title: LSCC11

value: sample 11

value: human lung squamous cell carcinoma tissue

tag: gender

value: IIIA


title: NPC_ND2_4H_-NeuroAid_Rep1

description: biological replicate 1


title: AEC022

value: sample 022

tag: tissue

value: Female

value: Malignant


title: LSCC106

value: sample 106

tag: age

value: IIB


title: NPC_ND2_0H_+NeuroAid_Rep2

description: biological replicate 2

tag: treatment

value: yes


title: NPC_ND2_0H_+NeuroAid_Rep1

description: biological replicate 1

tag: neural differentiation medium


title: AEC018

value: sample 018

value: human airway epithelium cells from nonsmokers


title: AEC017

value: sample 017


title: LSCC103

value: sample 103

value: Male

value: lung squamous cell carcinoma


title: NPC_ND2_0H_-NeuroAid_Rep1

description: biological replicate 1

value: NPC derived from H9 hESC

value: no


title: LSCC15

value: sample 15


title: NPC_ND2_0H_-NeuroAid_Rep2

description: biological replicate 2

value: optimized


title: AEC014

value: sample 014

value: Benign


title: Y-BE25-3

source_name: immortalized human bronchial epithelial cell lines of passage 25

value: sample Y25-3

value: immortalized normal


title: Y-BE25-4

value: sample Y25-4

value: immortalized human bronchial epithelial cell lines


title: AEC016

value: sample 016

value: Malignant


title: NPC_ND1_24H_+NeuroAid_Rep2

description: technical replicate 2

value: yes


title: Y-BE25-2

value: sample Y25-2


title: AEC011

value: sample 011

value: human airway epithelium cells from nonsmokers

value: Female


title: LSCC101

value: sample 101

value: human lung squamous cell carcinoma tissue

value: Male

value: lung squamous cell carcinoma

value: IA


title: NPC_ND1_24H_+NeuroAid_Rep1

description: technical replicate 1

value: NPC derived from H9 hESC

value: optimized


title: NPC_ND1_24H_-NeuroAid_Rep2

description: technical replicate 2

value: no


title: AEC010

value: sample 010

value: Benign


title: NPC_ND1_24H_-NeuroAid_Rep1

description: technical replicate 1


title: Y-BE115-4

source_name: immortalized human bronchial epithelial cell lines of passage 115

value: sample Y115-4

value: immortalized normal


title: AEC013

value: sample 013


title: Y-BE25-1

value: sample Y25-1

value: immortalized human bronchial epithelial cell lines


title: NPC_ND1_12H_+NeuroAid_Rep2

description: technical replicate 2

value: yes


title: AEC008-2

value: sample 008-2

value: human airway epithelium cells from nonsmokers

value: Female

value: Malignant


title: Y-BE115-3

value: sample Y115-3


title: Y-BE115-2

value: sample Y115-2


title: NPC_ND1_12H_-NeuroAid_Rep2

description: technical replicate 2

value: NPC derived from H9 hESC


title: AEC005

value: sample 005


title: NPC_ND1_12H_+NeuroAid_Rep1

description: technical replicate 1

value: optimized


title: AEC006

value: sample 006


title: NPC_ND1_12H_-NeuroAid_Rep1

description: technical replicate 1

value: no


title: AEC004

value: sample 004


title: Y-BE115-1

value: sample Y115-1

value: immortalized normal


title: NPC_ND1_8H_+NeuroAid_Rep2

description: technical replicate 2


title: 8 month rd/rd central retina replicate 3

city: Parkville

first: Robb

last: de Iongh

state: VIC

address: Grattan Street

department: Anatomy & Neuroscience

country: Australia

institute: University of Melbourne

description: 8 mo replicate 3 (#10)

hyb_protocol: Standard illumina hybridization protocol

scan_protocol: Standard illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Mouse retina

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy kit in accordance with on-column DNase1 digest as per the prescribed protocol provided with the kit. Quality control was performed with an Agilent Bioanalyser.

treatment_protocol: No treatement; comparison is between different age animals of the same strain.

tag: strain

value: retina


title: AEC003

source_name: human airway epithelium cells from nonsmokers of malignant lung diseases

value: sample 003


title: 2 month rd/rd central retina replicate 3

description: 2 mo replicate 2 (#9)


title: NPC_ND1_8H_-NeuroAid_Rep2

description: technical replicate 2

tag: cell type


title: Rbsh_IgG_3

city: Tokyo

first: Shunsuke

last: Kitajima

address: 3-8-31 Ariake, Koto

institute: Japanese Foundation for Cancer Research

description:
Sample name: MCF7 RB shRNA with IgG 3
Gene expression of RB-depleted MCF7 cells in the presence of IgG

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >7.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Whole Genome Microarray 4x44K (G4122F) 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 by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing: These Raw data were analyzed further with GeneSpring 12-6-1 GX PA software (Agilent Technologies Inc.). Normalization was performed as follows: 1. We used the linear data summarized over probes; 2. Thresholod raw signals to 1.0; 3. Log transfomration is done on the dataset; 4. 75th percentile methods were used to normalize each array; 5. Entities having Detected flag across all samples were extracted.

source_name: MCF7, Rbsh, IgG

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions with some changes. 3rd Spike mix was made by diluted 2nd Spike-Mix 10 times, and 1.8 ul of 3rd Spike-Mix was added to samples. Cy3 labeled cRNA was synthesized at 40°C for 20 hours and purified by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MCF7 cells were cultured in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (#74106, Qiagen) according to the manufacturer’s instruction. RNA was quantified, and quality was monitored by the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: MCF7 cells were transduced with RB shRNA (TRCN0000040163, sigma) or control shRNA (SHC002, Sigma), selected by 2 ug/ml puromycin, and cultured in the presence of 2 ug/ml anti-IL-6 antibody (#554541, BD Biosciences) or control IgG (#009-000-003, Jackson ImmunoResearch) for 24 hours.

tag: cell line

value: Rb shRNA

tag: agent

value: IgG antibody


title: 2 month rd/rd central retina replicate 2

description: 2 mo replicate 1 (#8)


title: AEC001

value: sample 001

value: human airway epithelium cells from nonsmokers

value: Male


title: AEC002

value: sample 002

value: Female

value: Malignant


title: 2 month rd/rd central retina replicate 1

description: 2 mo replicate 1 (#7)


title: 8 month rd/rd central retina replicate 2

description: 8 mo replicate 2 (#2)


title: Rbsh_IgG_1

description:
Sample name: MCF7 RB shRNA with IgG 1
Gene expression of RB-depleted MCF7 cells in the presence of IgG


title: AECB20

value: sample B20

value: Benign


title: NPC_ND1_4H_+NeuroAid_Rep2

description: technical replicate 2

value: NPC derived from H9 hESC

value: yes

value: optimized


title: AECB18

value: sample B18


title: NPC_ND1_8H_+NeuroAid_Rep1

description: technical replicate 1


title: 8 month rd/rd central retina replicate 1

description: 8 mo replicate 1 (#1)


title: Rbsh_antiIL6_2

description:
Sample name: MCF7 RB shRNA with anti-IL6 2
Gene expression of RB-depleted MCF7 cells in the presence of anti-IL6

source_name: MCF7, Rbsh, anti-IL6

value: anti-IL6 antibody


title: NPC_ND1_8H_-NeuroAid_Rep1

description: technical replicate 1

value: no


title: Rbsh_antiIL6_1

description:
Sample name: MCF7 RB shRNA with anti-IL6 1
Gene expression of RB-depleted MCF7 cells in the presence of anti-IL6


title: NPC_ND1_4H_-NeuroAid_Rep2

description: technical replicate 2


title: Rbsh_antiIL6_3

description:
Sample name: MCF7 RB shRNA with anti-IL6 3
Gene expression of RB-depleted MCF7 cells in the presence of anti-IL6


title: NPC_ND1_4H_-NeuroAid_Rep1

description: technical replicate 1


title: NPC_ND1_4H_+NeuroAid_Rep1

description: technical replicate 1


title: UT-SCC-43A_EMT-induced

hyb_protocol: The cRNA (1,500 ng per array) was hybridized to Illumina bead arrays according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

source_name: HNSCC cell line

treatment_protocol: Radiosensitivity of all cell lines was tested with a 96-well plate clonogenic assay, developed by Grénman et al (23,24). The radiosensitivity of a cell line was defined as the area under the survival curve, with measurements of the survival fraction at 6 different doses, each repeated at least 3 times.

value: Head and neck squamous cell carcinoma (HNSCC) cell line

tag: radiosensitivity (area under survival curve)


title: AECB15

value: sample B15


title: AECB17

value: sample B17


title: Rbsh_IgG_2

description:
Sample name: MCF7 RB shRNA with IgG 2
Gene expression of RB-depleted MCF7 cells in the presence of IgG

value: Rb shRNA

value: IgG antibody


title: AECB14

value: sample B14

value: human airway epithelium cells from nonsmokers

value: Male


title: Non_IgG_3

description:
Sample name: MCF7 Non-target with IgG 3
Gene expression of control MCF7 cells in the presence of IgG

source_name: MCF7, Non, IgG

value: control shRNA


title: UT-SCC-43A_control


title: Non_IgG_2

description:
Sample name: MCF7 Non-target with IgG 2
Gene expression of control MCF7 cells in the presence of IgG


title: AECB13

value: sample B13

value: Female

value: Malignant


title: NPC_ND1_0H_+NeuroAid_Rep2

description: technical replicate 2

value: NPC derived from H9 hESC

value: yes


title: NPC_ND2_12H_-NeuroAid_Rep1

description: biological replicate 1

value: optimized


title: NPC_ND1_0H_+NeuroAid_Rep1

description: technical replicate 1


title: Non_antiIL6_3

description:
Sample name: MCF7 Non-target with anti-IL6 3
Gene expression of control MCF7 cells in the presence of anti-IL6

source_name: MCF7, Non, anti-IL6

value: anti-IL6 antibody


title: AECB09

value: sample B09


title: Non_IgG_1

description:
Sample name: MCF7 Non-target with IgG 1
Gene expression of control MCF7 cells in the presence of IgG


title: A375P-2, poorly aggressive cell line, biological replicate 3

status: Public on Mar 18 2016

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

country: Italy

institute: University of Padova

description: miRNA expression profiling of A375P cell line (A375P-2)

hyb_protocol: Labeled RNA was hybridized to Agilent miRNA arrays for 22 hours at 55°C using the Agilent's Hybridization Oven that is suited for bubble-mixing and microarray hybridization processes. Washing was performed using the Gene Expression Wash Buffer kit (Agilent Technologies) following the manufacturer's instructions.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 5% sensitivity settings. Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing: Only spots with signal minus background flagged as positive and significant (flag=1) were used in the following analysis as “detected” spot while probes with flag equal to 0 were noted as “null”. Probes with less than 50% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were and inter-array normalized with cyclic Lowess (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) and then log2-transformed.

source_name: A375P cell line

label_protocol: We performed miRNA expression profiling from 200 ng of total RNA and following the miRNA Microarray System protocol v. 1.5 (Agilent Technologies). Total RNA was dephosphorylated and ligated with pCp-Cy3. Unincorporated dyes were removed with MicroBioSpin6 columns (BioRad) . Labeled RNA was hybridized to Agilent miRNA arrays for 22 hours at 55°C using the Agilent's Hybridization Oven that is suited for bubble-mixing and microarray hybridization processes.

growth_protocol: For proliferation and anchorage independent growth assays, cells were plated in 96-well plates or in 6 cm bacterial dishes (mixed with agar) and growth was followed up to 5 or 21 days, respectively.

extract_protocol: Total RNA was isolated from 107 cells by using Trizol® Reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop), while RNA integrity and content of microRNAs (%) in each samples were assessed by capillary electrophoresis using the RNA 6000 Nano LabChip and the Small RNA Nano LabChip respectively using the Agilent Bioanalyzer 2100 (Agilent Technologies). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 6, or higher, and the percentage of miRNA < 20% were used for microarray analysis.

value: A375P (poorly aggressive B-RAF V600E-mutated parental cell line)


title: Non_antiIL6_2

description:
Sample name: MCF7 Non-target with anti-IL6 2
Gene expression of control MCF7 cells in the presence of anti-IL6


title: NPC_ND1_0H_-NeuroAid_Rep2

description: technical replicate 2

value: no


title: Non_antiIL6_1

description:
Sample name: MCF7 Non-target with anti-IL6 1
Gene expression of control MCF7 cells in the presence of anti-IL6


title: A375P, poorly aggressive cell line, biological replicate 1

description: miRNA expression profiling of A375P cell line (A375P)


title: AECB06

description: Gene expression of human airway epithelium cells from nonsmokers

value: sample B06


title: NPC_ND1_0H_-NeuroAid_Rep1

description: technical replicate 1


title: A375P-3, poorly aggressive cell line, biological replicate 4

description: miRNA expression profiling of A375P cell line (A375P-3)


title: MC2, metastatic cell line, two rounds of injections in mice

description: miRNA expression profiling of MC2 cell line (MC2)

source_name: MC2 cell line

value: MC2 (MA2 (variant of A375P cell line derived from two subsequent rounds of injections in mice)


title: MC1, metastatic cell line, one round of injections in mice

description: miRNA expression profiling of MC1 cell line (MC1)

source_name: MC1 cell line

value: MC1 (variant of A375P cell line derived from one round of injections in mice)


title: MA1, metastatic cell line, one round of injections in mice

description: miRNA expression profiling of MA1 cell line (MA1)

source_name: MA1 cell line

value: MA1 (variant of A375P cell line derived from one round of injections in mice)


title: A375P-1, poorly aggressive cell line, biological replicate 2

description: miRNA expression profiling of A375P cell line (A375P-1)


title: 5W P2 E3

first: Shamit

last: Soneji

address: Solvegatan 19

institute: BMC

description: H2B-mCherry labeling was induced in Col1a1-tetO-H2B-mCherry mice - 5 weeks after labeling HSCs were isolated. After fluidigm run RT-PCR data was correlated to proliferation history.

data_processing: Ct values calculated and exported using Fluidigm Biomark software. Data normalised by subtraction of the median Ct per cell followed by z-score scaling.

label: EvaGreen

source_name: Bone marrow HSC

label_protocol: For cDNA synthesis, qScript cDNA supermix (Quanta Bioscience, Carlsbad, CA) was used. Specific target amplification (STA) of genes of interest were performed in multiplex using 96 Delta Gene assays and TATAA preAmp GrandMaster Mix (Tataa Biocenter, Gothenburg, Sweden) using cycling conditions of 95°C for 10 minutes followed by 22 x (96°C for 15 seconds, 60°C for 6 minutes). After STA, samples were treated with Exonuclease I (New England Biolabs, Ipswich, MA) at 37°C for 30 minutes to remove excess primers. Thereafter, inactivation of the enzyme was performed at 80°C for 15 minutes. The cDNA was diluted 5 times with TE low buffer (10mM TrisHCl pH 8.0, 0.1 mM EDTA) prior to qPCR on the BioMark HD (Fluidigm Corporation, San Francisco, CA). All primers were used at 500 nM in the final reaction and EvaGreen Supermix with Low ROX (Bio-Rad, Hercules, CA) was used for detection of the qPCR products. The qPCR was performed using the 96.96 Dynamic Array Integrated Fluidic Circuits (IFC) (Fluidigm Corporation, San Francisco, CA) chip in combination with the BioMark HD with the following thermal cycler program: thermal mix 70°C for 4 minutes followed by 60°C for 30 seconds, hot start 95°C for 60 seconds, PCR cycle 30x (96°C 5 seconds, 60°C for 20 seconds), followed by melting curve analysis.

extract_protocol: Cells were sorted into 96 well plates with 5µl lysis buffer (10mM TrisHCl pH 8.0, 0,1 mM EDTA, 0.1 units/µl SUPERase-In™ (Life Technologies, Carlsbad, CA), 0.5% NP40)  and immediately frozen at -80°C.

treatment_protocol: Single cell suspension of BM cells were FACS sorted to obtain HSC cells

value: bone marrow

value: hematopoietic stem cells

tag: genotype

tag: cell subtype


title: 5W P2 D9


title: LSCC146

description: Gene expression of human lung squamous cell carcinoma tissue

source_name: lung squamous cell carcinoma tissue

value: sample 146

value: Male

value: lung squamous cell carcinoma

value: IIIB


title: AEC021

value: sample 021

value: human airway epithelium cells from nonsmokers

value: Female

value: Malignant


title: AECB05

value: sample B05


title: MA2, metastatic cell line, two rounds of injections in mice

description: miRNA expression profiling of MA2 cell line (MA2)

source_name: MA2 cell line

value: MA2 (variant of A375P cell line derived from two subsequent rounds of injections in mice)


title: 5W P2 D7


title: 5W P2 D10


title: AECB08

value: sample B08


title: 5W P2 D11


title: 5W P2 E1


title: UT-SCC-1A_Mock irradiated [miRNA]

source_name: HNSCC cell line derived from gingiva mandibulae

value: Head and neck squamous cell carcinoma (HNSCC) cell line

tag: source subsite

value: gingiva mandibulae

tag: time from (mock) irradiation to harvest of rna

tag: irradiation dose (gy)

tag: radiosensitivity (auc)

tag: radiosensitivity (auc) binary

tag: passage tested

value: F

source_name: Pool of all HNSCC cell line samples


title: 5W P2 E2

tag: tissue


title: 5W P2 D8


title: 5W P2 E5


title: 5W P2 D2


title: 5W P2 D12


title: 5W P2 E9


title: 5W P2 D1


title: 5W P2 E8


title: 5W P2 E6


title: 5W P2 E10


title: 5W P2 D4


title: 5W P2 E11


title: 5W P2 E12


title: 5W P2 C7


title: 5W P2 F1


title: 5W P2 C11


title: 5W P2 E4


title: 5W P2 F2


title: 5W P2 C8


title: 5W P2 C9


title: 5W P2 C10


title: 5W P2 F3


title: 5W P2 F5


title: 5W P2 C1


title: 5W P2 F6


title: 5W P2 C12


title: 5W P2 E7


title: 5W P2 D6


title: 5W P2 C2


title: 5W P2 F8


title: 5W P2F7


title: 5W P2 D5


title: 5W P2 C5


title: 5W P2 C6


title: 5W P2 F9


title: 5W P2 C4


title: 5W P2 F12


title: 5W P2 F4


title: 5W P2 B8


title: 5W P2 G3


title: 5W P2 C3


title: 5W P2 G2


title: 5W P2 F10


title: 5W P2 B10


title: 5W P2 B12


title: 5W P2 G4


title: 5W P2 G5


title: 5W P2 G7


title: 5W P2 G6


title: 5W P2 F11


title: 5W P2 G1


title: 5W P2 B1


title: 5W P2 B3


title: 5W P2 G8


title: 5W P2 G9


title: 5W P2 G10


title: 5W P2 B11


title: 5W P2 B4


title: 5W P2 B2


title: 5W P2 B7


title: 5W P2 B5


title: 5W P2 B6


title: 5W P2 G12


title: 5W P2 G11


title: 5W P2 B9


title: 5W P2 A7


title: 5W P2 A10


title: 5W P2 A9


title: 5W P2 A8


title: 5W P2 A11


title: 5W P2 A2


title: 5W P2 A12


title: 5W P1 D7


title: 5W P2 A5


title: 5W P1 D8


title: 5W P1 E1


title: 5W P1 E2


title: 5W P1 E3


title: 5W P2 A6


title: 5W P2 A4


title: 5W P1 E5


title: 5W P2 A3


title: 5W P1 D11


title: 5W P1 D9


title: 5W P1 D12