title: 16h_LPS_donor2

description: Human monocytes_16h_5

tag: donor status/id

tag: stimulated with

value: 100 ng/ml E.coli O111:B4 LPS for 16hrs


title: Huh7,CD13+CD133+

status: Public on Mar 05 2015

type: RNA

city: Beijing

first: Yanying

last: Wang

address: 15 Datun Road, Chaoyang District,Beijing 100101, China

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

description: Gene expression data from CSCs of Huh7

hyb_protocol: Following labeling, 5.5 ug of cDNA was hybridized for 16 hr at 45 ℃ on GeneChip Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by using Affymetrix® GeneChip Command Console (AGCC) that installed in GeneChip® Scanner 3000 7G.

data_processing: Data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings. Values presented are log2 RMA signal intensity.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit.

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 100 μg/ml penicillin G, and 100 U/ml streptomycin (Invitrogen, NY, USA) at 37℃ with 5% CO2.

extract_protocol: Total RNA was isolated with Trizol from cells according to the manufacturer's instructions.

treatment_protocol: Cells were incubated with the following commercial antibodies: phycoerythrin (PE)-anti-human CD133 (Miltenyi Biotec) and fluorescein isothiocyanate (FITC)- anti-human CD13 (eBioscience) on ice for 30 minutes. Then, cells were washed with phosphate buffered saline (PBS) for three times, followed by sorting with FACS Aria III (BD Immunocytometry Systems, San Jose, CA, USA).

tag: cell line

tag: sorted cells


description: Gene expression data from control of HCC clinical sample

source_name: Hepatocellular carcinoma clinical sample, control cancer stem cells

growth_protocol: Cells were seeded on ultra-low attachment culture dishes (Corning) in serum-free medium. DMEM/F12 serum-free medium (Invitrogen) contained 2 mM L-glutamine, 1% sodium pyruvate (Invitrogen), 100 μg/ml penicillin G, and 100 U/ml streptomycin supplemented with 20 ng/ml epithelial growth factor (Invitrogen), 10 ng/ml fibroblast growth factor-2 (Invitrogen), N2 (Invitrogen), and B27 (Invitrogen). HCC Cells were incubated in a CO2 incubator for one to two weeks.

treatment_protocol: Cells were transfected with lentiviral constructs expressing shRNA or shCtrl as described above for 24 hr. Positive cells were selected with puromycin for 5 days. Then, cells were collected for protein and RNA analysis.

tag: genotype/variation

value: control

tag: disease state

value: HCC


title: PLC,CD13+CD133+

description: Gene expression data from CSCs of PLC

value: PLC


title: knee articular cartilage at T4, biological rep3

city: Taiyuan City

first: Xiao Chun

last: Wei

state: Shanxi Shanxi

address: No.382, Wuyi Road,Taiyuan City.

department: Department of Orthopaedics

institute: the Second Hospital of Shanxi Medical University

description:
Rattus norvegicus_T4-3
L85_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in latter-stage elderly

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA 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: Rattus norvegicus

source_name: Rattus norvegicus knee articular cartilage in latter-stage elderly

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: The cartilage that was harvested individually from the right knee joint were stored at liquid nitrogen temperatures at once with protected by Rnasin inhibitor.

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

treatment_protocol: After grinded under the ice, cartilage tissue were collected for further total RNA extraction.

tag: strain

value: Sprague-Dawley

tag: tissue

value: knee articular cartilage

tag: developmental stage

value: latter-stage elderly


title: Hep3B,CD13+CD133+

description: Gene expression data from CSCs of Hep3B


title: genomic DNA from Donor 1 CD3-CD56+CD57dim canonical NK cells

status: Public on Mar 06 2015

type: genomic

city: Stockholm

first: Yenan

last: Bryceson

state: Sweden

address: Karolinska University Hospital Huddinge

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

description:
Healthy blood donor
SAMPLE_1

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2; the non_normalized.txt contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: CD3-CD56+CD57dim canonical NK cells

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from sorted lymphocytes using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: No treatments were tested - genomic DNA was extracted directly from sorted cells

tag: donor status

value: CMV seropositive donor

tag: donor id

value: donor 1

value: Peripheral Blood

tag: cell type

value: CD3-CD56+CD57dim canonical NK cells


title: Control mammospheres, biological rep2

city: Berlin

first: Linxiang

last: Lan

address: Robert-Roessle-Str. 10

department: Cancer Research Program

country: Germany

institute: Max-Delbrueck-Center for Molecular Medicine

description:
LLX--02-Control-430A-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres infected with control retrovirus.

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized for 16 hr at 45C on Mouse Genome 430A 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The chips were scanned on an Affymetrix GeneChip Scanner.

data_processing: Array data were analyzed using Expression Console and were normalized with MAS5.0. Normalized data were used for calculating fold changes of deregulated genes using Student's test. Only genes with a false discovery rate (FDR) adjusted p-value <0.05 and at least 1.5 fold differential expression were included in the analysis.

label: Biotin

organism: Mus musculus

source_name: mammospheres, control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit, Affymetrix).

growth_protocol: Primary mammary tumor cells were cultured as mammospheres under the serum-free, non-attached conditions containing EGF, FGF and B27.

extract_protocol: Trizol extraction of total RNA and subsequent purification by QIAGEN RNeasy Kits was performed according to the manufacturer's instructions.

treatment_protocol: Mammospheres were treated with 50 nM 4-OHT for 2 hours and collected for RNA isolation 5 days later.

tag: strain/background

value: FVB/N

value: primary mammary tumor cells

tag: treatment

value: control retrovirus infection


title: Huh7,CD13-CD133-

description: Gene expression data from non-CSCs of Huh7


title: Control mammospheres, biological rep3

description:
LLX--03-Control-430A-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres infected with control retrovirus.


title: P4-011A

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

country: USA

institute: Washington University School of Medicine

description: Gene expression data from human knee artcular cartilage

hyb_protocol: cDNA hybridized into the GeneChip Hybridization Oven 640 for 18 hours on Gene 2.0 ST array. Then Affymetrix Gene 2.0 microarrays were washed and processed in the Affymetrix Fluidics Station 450.

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

data_processing: The data were normalized using quantile normalization with Partek Genomic Suite.

source_name: Articular cartilage from patient undergoing partial meniscectomy

label_protocol: Total RNA was amplified by Ovation Pico WTA Amplification System (NuGen, Inc., San Carlos, CA) and biotinylated cDNA synthesis was undertaken according to the standard NuGen Ovation Pico WTA System Amplification system using 50 ng total RNA. NuGen Encore Biotin Module kits were then used to fragment and label 5 μg of cDNA.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: patient id

tag: age

tag: bmi

tag: gender

value: Male

tag: procedure

value: knee undergoing partial meniscectomy

value: normal articular cartilage


title: Hep3B,CD13-CD133-

description: Gene expression data from non-CSCs of Hep3B

tag: cell line


title: PLC,CD13-CD133-

description: Gene expression data from non-CSCs of PLC

tag: sorted cells


title: P4-004A

value: Female


title: Bsub_LSB002_LPDM_T2_rep3

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
merged and smoothed log2 (ChIP/Input) ratio

organism: Bacillus subtilis

source_name: ChIP_DNA from Bsub strain expressing PhoP-SPA protein, T2 phase

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.ChIP DNA is labelled with Cy5 and CONTROL DNA with Cy3. See www.nimblegen.com.

growth_protocol: Cells of strain LSB002 were grown in LPDM with the addition of 1 µg ml-1 erythromycin plus 25 µg ml-1 lincomycin (MLS) and 100 mM IPTG with vigorous shaking at 37oC. Two hours after the onset of phosphate starvation state (T2), 50 ml were treated with formaldehyde.

extract_protocol: Crosslinking was performed by the addition of formaldehyde to a final concentration of 1% followed by 20 min incubation at room temperature with slow shaking. The cultures were then quenched with Glycine (0.36M final concentration) for 5 min at room temperature. Cells were collected by centrifugation at 4oC and the pellets were washed twice with 50 ml ice-cold Buffer A (10 mM Tris-HCl pH 7.5, 150 mM NaCl) before being snap frozen in a dry ice / ethanol bath.   Pellets were thawed at 37oC and resuspended in 0.5ml buffer B (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.2 mM EDTA, 0.1% Triton X-100) supplemented with 3 mg ml-1 lysozyme and 0.1 mg ml-1 RNaseA (final concentrations) and incubated for 30 min at 37oC, then the sample volume was adjusted to 1 ml with buffer B and samples placed on ice for 10 min. Genomic DNA was sheared by sonication (Diagenode Bioruptor Twin sonicator) into fragments between 0.2 and 1 kb. Sonicated samples were centrifuged for 10 min at 20 000 g (4oC) to remove insoluble debris. Fifty microliteres of the cleared lysates was removed to serve as the CONTROL sample, to which 50 microliters of 10X buffer C (10 mM Tris-HCl pH 8, 10% SDS, 10 mM EDTA) and 400 microliters buffer B were added and the sample was stored on ice. The remaining cleared lysates were each added to 40 microliters anti-FLAG M2-agarose resin (Sigma-Aldrich; A2220) equilibrated with ice-cold buffer B (according to manufacturers’ instructions) and incubated for two hours at 4oC with mild agitation. Beads were then collected by centrifugation for 1 min at 5000 g (4oC) and washed three times with 0.5 ml ice-cold buffer B. To reverse the crosslinking beads were transferred to new 1.5 ml eppendorf tubes, resuspended in 0.5 ml 1X buffer C and incubated along with the CONTROL samples for ~20 hours at 65oC with shaking (950 rpm). ChIP samples were collected by centrifugation for 1 min at 13 300 rpm (4oC).  DNA from both ChIP and CONTROL samples was purified using the QIAquick PCR purification kit (Qiagen, 28106), eluted in 50 microliters H2O and treated with 0.02 mg ml-1 RNaseA (Roche, 11119915001) for 30 min at 37oC. RNase was eliminated using the QIAquick PCR purification kit and samples were eluted in 30 microliters H2O.  Equal concentrations of ChIP DNA and CONTROL samples were amplified using the GenomePlex complete Whole Genome Amplification (WGA) kit (Sigma-Aldrich; WGA2-50RXN) as per manufacturers’ instructions and purified using the QIAquick PCR purification kit and eluted in 30 microliters H2O. Ten microliters of each of the purified amplified samples was subjected to a second round of amplification using the WGA kit as per manufacturer’s instructions, purified using the QIAquick PCR purification kit and eluted in 30 microliters H2O.  3.5-4  micrograms of twice-amplified ChIP DNA and CONTROL samples (of both tagged and mock precipitation experiments) at a concentration of ~250 ng per microliter (A260/A280 ≥1.7 and A260/A230 ≥ 1.6) from three separate ChIP experiments were submitted TO NimbleGen.  Crosslinking was performed by the addition of formaldehyde to a final concentration of 1% followed by 20 min incubation at room temperature with slow shaking. The cultures were then quenched with Glycine (0.36M final concentration) for 5 min at room temperature. Cells were collected by centrifugation at 4oC and the pellets were washed twice with 50 ml ice-cold Buffer A (10 mM Tris-HCl pH 7.5, 150 mM NaCl) before being snap frozen in a dry ice / ethanol bath.

tag: growth phase

tag: chip antibody

value: mouse anti-FLAG M2 (Sigma)

source_name: Control_DNA from Bsub strain expressing PhoP-SPA protein, T2 phase


title: Anti-BPTF B16 cells Replicate 3

city: San Francisoc

first: Mehdi

last: Nosrati

state: California

address: 475 Brannan, Suite 220

department: Research Institute

institute: California Pacific Medical Center

description:
M-IMCH-P4-232
The Universal Mouse Reference RNA is composed of total RNA from 11 mouse cell lines, to compensate for differential abundance of RNA species between cell lines.

hyb_protocol: Labeled cDNA was hybridized to a microarray slide at 63° C for 12-16 h.

scan_protocol: Slides were then washed and immediately scanned with Axon Imager 4000b (Axon Instruments, Foster City, Ca), using GenePixPro3 software.

data_processing: printTipLoess normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. SAM (Significance Analysis of Microarrays) was used to determine differntially expressed genes.

source_name: B16 murine melanoma cell line transfected with anti-BPTF shRNA-10

label_protocol: 10 microgram of total target RNA, side by side with 1 µg of universal mouse reference RNA (Stratagene #740100), was linearly amplified through two rounds of modified in vitro transcription. Randomized amplified RNAs were converted to aminoallyl-modified cDNA and coupled to N-hydroxysuccinimidyl esters of Cy3 or Cy5 (Amersham Biosciences, Piscataway, NJ),

growth_protocol: Cells were cultured in RPMI medium 1640 with 5% FBS and 800 g/ml Geneticin (37°C, 5% CO2) at less than 80% confluency.

extract_protocol: Cells were trypsinized and were spun down to form a pellet. Cell pellets were then homogenized [Polytron 1200C, Brinkmann, Westbury, NY, at setting 4 for 30 sec] with 600µl of RNA lysis buffer plus 1% 2-mercaptoethanol, and RNA was isolated using RNEasy columns (Qiagen, Valencia, Ca).

value: B16 murine melanoma cell line

tag: transfection

value: anti-BPTF shRNA-10

source_name: Stratagene Universal Mouse Reference RNA

tag: reference composition

value: embryo, fibroblast, kidney, liver, lung, B-lymphocyte, T-lymphocyte, mammary gland, muscle myoblast, skin, testis


title: Anti-BPTF B16 cells Replicate 2

description:
M-IMCH-P4-231
The Universal Mouse Reference RNA is composed of total RNA from 11 mouse cell lines, to compensate for differential abundance of RNA species between cell lines.


title: knee articular cartilage at T4, biological rep2

description:
Rattus norvegicus_T4-2
L83_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in latter-stage elderly

tag: strain

value: Sprague-Dawley

tag: tissue

value: knee articular cartilage

tag: developmental stage


title: Anti-BPTF B16 cells Replicate 1

description:
M-IMCH-P4-230
The Universal Mouse Reference RNA is composed of total RNA from 11 mouse cell lines, to compensate for differential abundance of RNA species between cell lines.


description: Gene expression data from lncTCF7 depletion of HCC clinical sample

source_name: Hepatocellular carcinoma clinical sample, lncTCF7 depletion in cancer stem cells

tag: genotype/variation

value: lncTCF7 depletion

tag: disease state

value: HCC


title: knee articular cartilage at T3, biological rep2

description:
Rattus norvegicus_T3-2
L72_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in early-stage elderly

source_name: Rattus norvegicus knee articular cartilage in early-stage elderly

value: early-stage elderly


title: knee articular cartilage at T4, biological rep1

description:
Rattus norvegicus_T4-1
L82_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in latter-stage elderly

value: latter-stage elderly


title: knee articular cartilage at T3, biological rep3

description:
Rattus norvegicus_T3-3
L75_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in early-stage elderly


title: Anti-BPTF B16 cells Replicate 5

description:
M-IMCH-P4-234
The Universal Mouse Reference RNA is composed of total RNA from 11 mouse cell lines, to compensate for differential abundance of RNA species between cell lines.


title: Control B16 cells Replicate 5

description:
M-IMCH-P4-229
The Universal Mouse Reference RNA is composed of total RNA from 11 mouse cell lines, to compensate for differential abundance of RNA species between cell lines.

source_name: B16 murine melanoma cell line transfected with control shRNA-203

value: control shRNA-203


title: knee articular cartilage at T2, biological rep2

description:
Rattus norvegicus_T2-2
L53_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in adult

source_name: Rattus norvegicus knee articular cartilage in adult

value: adult


title: 16h_LPS_donor1

city: Muenster

first: Nadine

last: Nippe

address: Roentgenstr. 21

department: Institute of Immunology

institute: University of Muenster

description: Human monocytes_16h_4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16h at 45°C on to Affymetrix Human Genome 133 A Gene Chip arrays. Gene Chip Arrays were washed and stained using the Gene Chip Fluidics Station 400.

scan_protocol: Fluorescent signals were detected by the HP G2500A Gene Array Scanner.

data_processing: The data were analyzed with MicroArray Suite (MAS) Software 5.0 (Affymetrix). Signals were scaled to a target intensity of each array was arbitrarily set to 100 and log transformed. The algorithm applied in the MAS 5.0 software assigned individual average background values to each cell intensity and subtracted it from single raw cell intensities.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Manual Target Preparation for GeneChip® 3' Expression Arrays, Affymetrix).

growth_protocol: Human monocytes were obtained from buffy coats from healthy individual donors.

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

treatment_protocol: Human monocytes were exposed for 4 and 16 hours with 100 ng/ml E.coli O111:B4 LPS (Sigma-Aldrich) or solvent as control.

tag: donor status/id

value: healthy donor 1

value: blood monocytes

tag: stimulated with

value: 100 ng/ml E.coli O111:B4 LPS for 16hrs


title: knee articular cartilage at T2, biological rep1

description:
Rattus norvegicus_T2-1
L52_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in adult


title: Bsub_LSB002_LPDM_T2_rep2


title: Bsub_LSB002_LPDM_T2_rep1


title: knee articular cartilage at T3, biological rep1

description:
Rattus norvegicus_T3-1
L71_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in early-stage elderly


title: Bsub_LSB002_LPDM_exp_rep2

source_name: ChIP_DNA from Bsub strain expressing PhoP-SPA protein, exponential phase

growth_protocol: Cells of strain LSB002 were grown in LPDM with the addition of 1 µg ml-1 erythromycin plus 25 µg ml-1 lincomycin (MLS) and 100 mM IPTG with vigorous shaking at 37oC. At early exponential growth phase (OD600nm~0.2), 200 ml were treated with formaldehyde.

value: exponential

source_name: Control_DNA from Bsub strain expressing PhoP-SPA protein, exponential phase


title: Bsub_LSB002_LPDM_exp_rep1


title: knee articular cartilage at T2, biological rep3

description:
Rattus norvegicus_T2-3
L54_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in adult


title: Control B16 cells Replicate 4

description:
M-IMCH-P4-228
The Universal Mouse Reference RNA is composed of total RNA from 11 mouse cell lines, to compensate for differential abundance of RNA species between cell lines.


title: Control B16 cells Replicate 3

description:
M-IMCH-P4-227
The Universal Mouse Reference RNA is composed of total RNA from 11 mouse cell lines, to compensate for differential abundance of RNA species between cell lines.


title: Bsub_LSB002_LPDM_exp_rep3

growth_protocol: Cells of strain LSB002were grown in LPDM with the addition of 1 µg ml-1 erythromycin plus 25 µg ml-1 lincomycin (MLS) and 100 mM IPTG with vigorous shaking at 37oC. At early exponential growth phase (OD600nm~0.2), 200 ml were treated with formaldehyde.


title: Control B16 cells Replicate 2

description:
M-IMCH-P4-226
The Universal Mouse Reference RNA is composed of total RNA from 11 mouse cell lines, to compensate for differential abundance of RNA species between cell lines.


title: knee articular cartilage at T1, biological rep1

description:
Rattus norvegicus_T1-1
L41_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in youth

source_name: Rattus norvegicus knee articular cartilage in youth

value: youth


title: knee articular cartilage at T0, biological rep3

description:
Rattus norvegicus_T0-3
L24_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in newborn

source_name: Rattus norvegicus knee articular cartilage in newborn

value: newborn


title: knee articular cartilage at T1, biological rep3

description:
Rattus norvegicus_T1-3
L43_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in youth


title: BEAS2B_SWCNT_6month_rep3

city: Morgantown

first: Todd

middle: A

last: Stueckle

state: WV

address: 1095 Willowdale Road

department: Health Effects Laboratory Division

institute: National Institute for Occupational Safety and Health

description: Genome expression after 6 month dispersed single wall carbon nanotube in vitro exposure

hyb_protocol: Microarray hybridization was performed at 65°C for 17 hours on NimbleGen 12x135k Whole Human Genome Oligonucleotide Microarray (HG18) in NimbleGen Hybridization System.

scan_protocol: After being washed in an ozone-free environment, image capture was performed with Axon GenePix 4000B (Molecular Devices) and uploaded into NimbleScan (v2.5), and Cy3 label intensities determined.

data_processing: GenePix data were uploaded into NimbleScan for Cy3 label intensity determination.  Intensities were quantile normalized using Robust Multichip Average method included in NimbleScan. Only genes expressing ≥50.0 normalized intensity in all 6 samples were subjected to further analysis. Gene expression text files were imported into GeneSpring GX (ver. 10.0) for further analysis.

source_name: BEAS2B immortalized human bronchial epithelial cell, dispersed SWCNT, 6 month exposed (24 passages), replicate 3

label_protocol: cDNA samples were amplified, Cy3-labeled with NimbleGen one-color DNA labeling kit following manufacturer’s protocol. Microarray hybridization was performed at 65°C for 17 hours to NimbleGen whole human genome 12x135K microarrays in NimbleGen Hybridization System.

growth_protocol: Cells were maintained in DMEM medium supplemented with 5% fetal bovine serum (FBS), 2 mM L-glutamine and 100 U/mL penicillin and streptomycin.  Cell cultures were held in a humid, 37o C and 5% CO2 cell culture incubator.

extract_protocol: At 3 passages post-exposure, cells (1E6) from each treatment were seeded in 60-mm dishes in triplicate.  At 24 h post-seeding, RNA samples (n=3) were collected with TRIzol (Invitrogen) using manufacturer’s protocol.  RNA quality was assessed in house using gel electrophoresis and 260/280 nm absorbance ratio.  Samples stored at -80o C were shipped to ArrayStar (Rockville, MD).  At ArrayStar, samples were treated with DNase digestion and analyzed for RNA quality using Nanodrop ND-100 and Bioanalyser 2100.

treatment_protocol: 0.1 mg/mL stock solutions of SWCNT (HipCo; Carbon Nanotechnology, Houston TX) were prepared in sterile MilliQ water containing 150 microliters/mL of the lung surfactant Survanta®.  Each stock solution was sonicated for 20 seconds using a small sonication horn and then diluted in fresh culture medium and added to culture plates.  Diluted dispersant only containing medium served as negative passage control.  Unexposed low passage BEAS-2B cells (5E4 cells/well) were seeded to 6-well plates per treatment.  After 24 hours, cell cultures were either exposed to 0.02 micrograms/sq. cm of each particle or Survanta-dispersant only for the following 6 months.  Cells were passage matched for a total of 24 passages.  Exposed media was changed every 3 to 4 days while cells were split once every 7 days.

tag: cell type

value: immortalized bronchial epithelial cell

tag: treatment

value: SWCNT


title: Dg_KO_mock_rep2_hyb3 reanalysis ControlvsmiR-126

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

department: Urology

institute: University of California, San Francisco

description: Dgcr8 KO + Mock

hyb_protocol: Standard Illumina protocol - the arrays are split up into 3 different hybridizations.

scan_protocol: Standard Illumina protocol

data_processing: All data was quantile normalized. Differential expression for data from hyb1 was performed using the limma package with a cutoff of adjusted p-value < 0.05. For the let-7, miR-125 comparisons, due to let-7 rep1 being performed at a different time, the RankProd package was used to determine rank based differental expression with a cutoff of adjusted p-value < 0.01.

source_name: ESC-derived GPCs

label_protocol: Standard Illumina protocol

growth_protocol: All cells were grown in N2 media + EGF and FGF. For differentiation, growth factors (EGF & FGF) were removed and 1% FBS and B27 were added

extract_protocol: RNA was extracted with the standard Trizol protocol

treatment_protocol: Tamoxifen was added at 1uM for 16 hours and 100 nM for 16 hours. Rep1, 2, and 3 for let7/miR-125 represent three separate tamoxifen treatments.

value: Tamoxifen

tag: hyb number

tag: genotype

value: Dgcr8 KO

value: ESC-derived GPCs


title: Dg_fd_undiff_rep3_hyb1 reanalysis Dgcr8_flox_delta_vs_KO

description: Dgcr8 flox/delta, Undiff


title: Dg_fd_undiff_rep2_hyb1 reanalysis Dgcr8_flox_delta_vs_KO

description: Dgcr8 flox/delta, Undiff


title: Dg_fd_undiff_rep1_hyb1 reanalysis Dgcr8_flox_delta_vs_KO

description: Dgcr8 flox/delta, Undiff


title: BEAS2B_SWCNT_6month_rep1

source_name: BEAS2B immortalized human bronchial epithelial cell, dispersed SWCNT, 6 month exposed (24 passages), replicate 1

tag: cell line


title: BEAS2B_dispersant_6month_rep3

description: Genome expression after 6 month dispersant-only in vitro exposure

source_name: BEAS2B immortalized human bronchial epithelial cell, dispersant only, 6 month exposed (24 passages), replicate 3

value: control


title: BEAS2B_SWCNT_6month_rep2

source_name: BEAS2B immortalized human bronchial epithelial cell, dispersed SWCNT, 6 month exposed (24 passages), replicate 2


title: Control B16 cells Replicate 1

description:
M-IMCH-P4-225
The Universal Mouse Reference RNA is composed of total RNA from 11 mouse cell lines, to compensate for differential abundance of RNA species between cell lines.

value: B16 murine melanoma cell line

value: embryo, fibroblast, kidney, liver, lung, B-lymphocyte, T-lymphocyte, mammary gland, muscle myoblast, skin, testis


title: knee articular cartilage at T1, biological rep2

description:
Rattus norvegicus_T1-2
L42_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in youth

value: Sprague-Dawley

value: knee articular cartilage


title: knee articular cartilage at T0, biological rep2

description:
Rattus norvegicus_T0-2
L23_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in newborn


title: BEAS2B_dispersant_6month_rep1

source_name: BEAS2B immortalized human bronchial epithelial cell, dispersant only, 6 month exposed (24 passages), replicate 1


title: liver Wrn mutant #3 / liver WT #3

city: Quebec

first: Michel

last: Lebel

state: Qc

address: 2705 Laurier Blvd, Local T-2-04

department: Centre Hospitalier de l’Université Laval (CHUL)

country: Canada

institute: Centre de Recherche du CHU de Québec

description: Biological Wrn replicate 3 of 4. Biological WT replicate 3 of 4.

hyb_protocol: Hybridization and washing was performed using the in situ Hybridization Plus kit (Agilent) and following the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Axon GenePix® 4000B. Data were extracted from images using GenePix® version 6.0 with local background estimation.

data_processing: Data were processed using limma in BioConductor (www.bioconductor.org). The data were background subtracted using normexp and also normalized using the loess method.

source_name: mutant liver tissue

label_protocol: Protocol from Agilent

growth_protocol: Mice were maintained on a reversed 12:12-h light-dark cycle with controlled temperature (21 ± 1°C) and humidity. Food and water were provided ad libitum.

extract_protocol: Extraction of total RNA protocol described in Sambrook et al., 1989. Molecular cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press.

treatment_protocol: No special treatment

tag: gender

value: male

value: Wrn mutant

tag: age

value: 3 months old

value: liver

source_name: WT liver tissue

value: wild type


title: liver Wrn mutant #4 / liver WT #4

description: Biological Wrn replicate 4 of 4. Biological WT replicate 4 of 4.


title: knee articular cartilage at T0, biological rep1

description:
Rattus norvegicus_T0-1
L21_(RaGene-2_0-st).rma-gene-full-Signal
Gene expression data from the rat knee articular cartilage in newborn


title: Dg_KO_let7_rep3_hyb3 ControlvsLet12

description: Dgcr8 KO + Let7

tag: expression


title: liver Wrn mutant #1 / liver WT #1

description: Biological Wrn replicate 1 of 4. Biological WT replicate 1 of 4.


title: liver Wrn mutant #2 / liver WT #2

description: Biological Wrn replicate 2 of 4. Biological WT replicate 2 of 4.


title: Dg_KO_mock_rep3_hyb3 reanalysis ControlvsmiR-127

description: Dgcr8 KO + Mock


title: BEAS2B_dispersant_6month_rep2

source_name: BEAS2B immortalized human bronchial epithelial cell, dispersant only, 6 month exposed (24 passages), replicate 2


title: HEK293 expressing GFP-TIAR REP1

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: human embryonic kidney cells (HEK293) expressing GFP-TIAR REP1

hyb_protocol: The samples were placed on ice and quickly loaded onto arrays, hybridized at 65ºC for 17 hours in a Hybridization oven rotator and then washed in GE wash buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at 37ºC (1 minute).

scan_protocol: Images were captured with an Agilent Microarray Scanner and spots quantified using Feature Extraction Software (Agilent Technologies).

data_processing: Raw intensities were background-corrected by normexp method with an offset of 50. Background-corrected signals were log2 transformed and normalized by quantile adjustment as described in limma package of bioconductor.

source_name: HEK293 cells expressing GFP-TIAR

label_protocol: Total RNA (200 ng) was amplified using One Color Low Input Quick Amp Labeling Kit (Agilent Technologies) and purified with RNeasy Mini Kit (Qiagen). Preparation of probes and hybridization was performed as described One-Color Microarray Based Gene Expression Analysis Manual Ver. 6.5, Agilent Technologies, using Rat Gene Expression Microarray v3 Agilent 4x44K. Briefly, for each hybridization 600 ng of Cy3 probes were mixed and added to 5 ul of 10x Blocking Agent, 1 ul of 25x Fragmentation Buffer and Nuclease free water in a 25 ul reaction, incubated at 60ºC for 30 minutes to fragment RNA and stopped with  25 ul of 2x Hybridization Buffer.

growth_protocol: For generating stable, isogenic and inducible mammalian expression cell line HEK293 was used the Flp recombinase-mediated integration method (Flp-InTM T-RExTM System from Invitrogen, USA), according to the manufacture's protocol. This system allows the generation of stable mammalian cell lines exhibiting tetracycline-inducible expression of a gene of interest at a site-specific genomic locus. By using this technology we have generated cell lines HEK293 expressing GFP, GFP-TIA1, GFP-TIAR and GFP-HuR proteins, respectively.

extract_protocol: RNA isolation and purification was performed using TRIZOL reagent (Invitrogen, USA)

value: expressing GFP-TIAR


title: HEK293 expressing GFP-TIAR REP2

description: human embryonic kidney cells (HEK293) expressing GFP-TIAR REP2


title: Dg_KO_mir125_rep1_hyb3 ControlvsmiR-128

description: Dgcr8 KO + miR125


title: HEK293 expressing GFP-TIA1 REP1

description: human embryonic kidney cells (HEK293) expressing GFP-TIA1 REP1

source_name: HEK293 cells expressing GFP-TIA1

value: expressing GFP-TIA1


title: Dg_KO_let7_rep2_hyb3 ControlvsLet11

description: Dgcr8 KO + Let7


title: Dg_KO_mir125_rep2_hyb3 ControlvsmiR-129

description: Dgcr8 KO + miR125


title: HEK293 expressing GFP REP1

description: human embryonic kidney cells (HEK293) expressing GFP REP1

source_name: HEK293 cells expressing GFP

value: expressing GFP


title: Dg_KO_mock_rep3_hyb3 ControlvsLet9

description: Dgcr8 KO + Mock


title: Dg_KO_mock_rep1_hyb3 ControlvsmiR-125

description: Dgcr8 KO + Mock


title: HEK293 expressing GFP-HuR REP2

description: human embryonic kidney cells (HEK293) expressing GFP-HuR REP2

source_name: HEK293 cells expressing GFP-HuR

value: expressing GFP-HuR


title: HEK293 expressing GFP-TIA1 REP2

description: human embryonic kidney cells (HEK293) expressing GFP-TIA1 REP2

source_name: HEK293 cells expressing GFP-TIA2


title: Dg_KO_undiff_rep3_hyb1 Dgcr8_flox_delta_vs_KO

description: Dgcr8 delta/delta, undiff, mock

value: Tamoxifen


title: Dg_KO_mir125_rep3_hyb3 ControlvsmiR-130

description: Dgcr8 KO + miR125

value: Dgcr8 KO


title: normal vein5

city: Saint Louis

first: Gwendalyn

last: Randolph

address: 425 S Euclid Ave

department: Pathology and Immunology

description:
14343
Gene expression in mesenteric arteries and veins

hyb_protocol: The balanced aRNAs were suspended in Agilent 2X Gene Expression buffer,Agilent 10X Blocking agent and Kreablock. The hybridization solutions were applied to Agilent Human v1 4x44K microarrays (G2519F-014850).Hybridization was carried out at 65C for 20 hours.  Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.

data_processing: Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies).

source_name: vein from nonIBD mesenteric fat

label_protocol: cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics).Labeled cDNA was purified with Quaigen PCR purification columns according to manufacturer’s protocol..  cDNAs were quantitated on a Nanodrop spectrophotometer.

extract_protocol: RNA was prepared using Acrtrus PicoPure RNA isolation kit (cat# 12204-01, Applied Biosystems) following manufacturer's recommended protocol. Total RNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm. DNAse treatment was performed using Ambion DNAse kit ( Cat# AM1906, Applied Biosystems) to remove contaminating DNA from RNA preparations Total RNA quality was then determined by Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer’s recommendations. RNA transcripts were amplified by WTA2 kit (Sigma Aldrich) according to manufacturer’s protocol.

treatment_protocol: Surgical tissues were immediately fixed in Carnoy's solution and later embedded in paraffin wax. Sections were cut and adhered to PEN membrane slides, deparaffinized, vessels were selected and removed using laser-capture microdissection and the captured material was immediately placed into Arcturus PicoPure RNA extraction buffer

value: mesenteric fat

tag: sample type

value: vein

value: nonIBD


title: Dg_KO_let7_rep1_hyb2 ControlvsLet10

description: Dgcr8 KO + Let7

value: ESC-derived GPCs


title: Dg_KO_mock_rep2_hyb3 ControlvsLet8

description: Dgcr8 KO + Mock


title: HEK293 expressing GFP-HuR REP1

description: human embryonic kidney cells (HEK293) expressing GFP-HuR REP1


title: Dg_KO_undiff_rep2_hyb1 Dgcr8_flox_delta_vs_KO

description: Dgcr8 delta/delta, undiff, mock


title: crohn's vein9

description:
14335
Gene expression in mesenteric arteries and veins

source_name: vein from Crohn's mesenteric fat

value: Crohn's


title: Dg_fd_diff_rep2_hyb1 UndiffvsDiff

description: Dgcr8 flox/delta, Diff


title: Dg_KO_undiff_rep1_hyb1 Dgcr8_flox_delta_vs_KO

description: Dgcr8 delta/delta, undiff, mock


title: Dg_fd_undiff_rep3_hyb1 UndiffvsDiff

description: Dgcr8 flox/delta, Undiff


title: normal vein6

description:
14341
Gene expression in mesenteric arteries and veins


title: crohn's vein8

description:
14338
Gene expression in mesenteric arteries and veins


title: Dg_KO_mock_rep1_hyb2 ControlvsLet7

description: Dgcr8 KO + Mock


title: HEK293 expressing GFP REP2

description: human embryonic kidney cells (HEK293) expressing GFP REP2


title: Dg_fd_diff_rep1_hyb1 UndiffvsDiff

description: Dgcr8 flox/delta, Diff


title: Dg_fd_undiff_rep1_hyb1 UndiffvsDiff

description: Dgcr8 flox/delta, Undiff


title: normal artery4

description:
14342
Gene expression in mesenteric arteries and veins

source_name: artery from nonIBD mesenteric fat

value: artery


title: crohn's artery6

description:
14337
Gene expression in mesenteric arteries and veins

source_name: artery from Crohn's mesenteric fat


title: Dg_fd_diff_rep3_hyb1 UndiffvsDiff

description: Dgcr8 flox/delta, Diff

source_name: ESC-derived GPCs


title: Dg_fd_undiff_rep2_hyb1 UndiffvsDiff

description: Dgcr8 flox/delta, Undiff


title: crohn's vein3

description:
13430
Gene expression in mesenteric arteries and veins


title: normal vein4

description:
14345
Gene expression in mesenteric arteries and veins


title: normal artery2

description:
13497
Gene expression in mesenteric arteries and veins


title: normal artery3

description:
14344
Gene expression in mesenteric arteries and veins


title: crohn's vein2

description:
13432
Gene expression in mesenteric arteries and veins


title: crohn's vein5

description:
14339
Gene expression in mesenteric arteries and veins


title: crohn's artery4

description:
13427
Gene expression in mesenteric arteries and veins


title: normal artery5

description:
14340
Gene expression in mesenteric arteries and veins


title: normal vein3


title: crohn's vein6

description:
12695
Gene expression in mesenteric arteries and veins


title: crohn's artery5

description:
14334
Gene expression in mesenteric arteries and veins


title: crohn's artery3

description:
13429
Gene expression in mesenteric arteries and veins


title: normal artery1

description:
13422
Gene expression in mesenteric arteries and veins


title: crohn's vein7

description:
14335
Gene expression in mesenteric arteries and veins


title: normal vein2

description:
13423
Gene expression in mesenteric arteries and veins


title: crohn's artery2

description:
13426
Gene expression in mesenteric arteries and veins


title: crohn's artery1

description:
13431
Gene expression in mesenteric arteries and veins


title: normal vein1

description:
13498
Gene expression in mesenteric arteries and veins


title: 3134Tet_+dnSnf2h_48hrs_rep2

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

description: Gene expression data from 3134 cells in the presence of tetracycline transactivator and Snf2h.

hyb_protocol: Biotin-labeled cDNAs were hybridized overnight to Mouse Gene 1.0 ST arrays. Wash and stain of these GeneChip microarrays was carried out under strictly controlled conditions with the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned with the Affymetrix Scanner.

data_processing: The data were analyzed with Affymetrix® Expression Console™ software version 1.1 using Affymetrix default analysis settings with quantile normalization and general background correction.

source_name: 3134Tet-dnSnf2h cell line with dnSnf2h expression, 48 hrs

label_protocol: Approximately 100 ng of total RNA were reverse transcribed and labeled by biotin (biotin-labeled cDNA) according to standard Affymetrix protocols used by NCI core facility (LMT/Affymetrix Group, Frederick National Laboratory for Cancer Research, http://atp.ncifcrf.gov/genetics-and-genomics/laboratory-of-molecular-technology/lmt-protocols-and-resources/microarray/service-details/).

growth_protocol: Cells were grown in 10%FBS Dulbecco's Modified Eagle's medium (DMEM) supplemented with L-glutamine in a 37 °C incubator with 5% CO2. All tetracycline-regulated cell lines (cells used here) were maintained in media additionally containing 5µg/ml tetracycline to repress expression of the tetracycline transactivator and dominant negative proteins.

extract_protocol: Total RNA were extracted from cells using Trizol according to the manufacturer's instructions (Invitrogen).

treatment_protocol: For experiments, cells were plated and grown in the above DMEM supplemented with 10% charcoal-dextran-treated FBS and L-glutamine with or without tetracycline for 48 hrs to induce expression of the tetracycline transactivator and dominant negative proteins.

value: 3134  mouse mammary epithelial cell line


title: crohn's vein1

description:
13425
Gene expression in mesenteric arteries and veins


title: 3134Tet_-dnSnf2h_48hrs_rep2

description: Gene expression data from 3134 cells in the absence of tetracycline transactivator and Snf2h.

source_name: 3134Tet-Snf2h cell line minus dnSnf2h expression, 48 hrs


title: 3134Tet_+dnChd4_48hrs_rep2

description: Gene expression data from 3134 cells in the presence of tetracycline transactivator and Chd4.

source_name: 3134Tet-Chd4 cell line with dnChd4 expression, 48 hrs


title: 3134Tet_+dnSnf2h_48hrs_rep1


title: 3134Tet_-dnSnf2h_48hrs_rep1


title: crohn's vein4

description:
13428
Gene expression in mesenteric arteries and veins


title: 3134Tet_+dnBrg1_48hrs_rep2

description: Gene expression data from 3134 cells in the presence of tetracycline transactivator and dnBrg1.

source_name: 3134Tet-dnBrg1 cell line with dnBrg1 expression, 48 hrs


title: 3134Tet_+dnChd4_48hrs_rep1


title: 3134Tet_-dnBrg1_48hrs_rep1

description: Gene expression data from 3134 cells in the absence of tetracycline transactivator and dnBrg1.

source_name: 3134Tet-dnBrg1 cell line minus dnBrg1 expression, 48 hrs


title: 3134Tet_-dnChd4_48hrs_rep2

description: Gene expression data from 3134 cells in the absence of tetracycline transactivator and Chd4.

source_name: 3134Tet-Chd4 cell line minus Chd4 expression, 48 hrs


title: 3134Tet_-dnBrg1_48hrs_rep2


title: 3134Tet_-TetActivator_48hrs_rep2

description: Gene expression data from 3134 cells in the absence of tetracycline transactivator.

source_name: 3134Tet cell line minus tetracycline transactivator expression, 48 hrs


title: 3134Tet_+TetActivator_48hrs_rep2

description: Gene expression data from 3134 cells in the presence of tetracycline transactivator.

source_name: 3134Tet cell line with tetracycline transactivator expression, 48 hrs


title: 3134Tet_-dnChd4_48hrs_rep1


title: Fast fibre 2-AAVshMCU-14days

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description:
Transfection with AAVshMCU to silence MCU after 14 days after transfection
Fast skeletal muscle fibre, derived from mouse with silenced MCU obtained with AAV injection and sacrification after 14 days after injection

hyb_protocol: Microarray experiments were performed using SurePrint G3 Mouse Gene Expression 8x60K microarrays (AgilentTechnologies). 800 ng of labeled cDNA target were mixed with 5 µl of 10X Blocking Agent (AgilentTechnologies) and water to a final volume of 25 µl. Samples were denaturated at 95°C for 2 min. and added to 25 µl of 2X GEx Hybridization Buffer HI-RPM (AgilentTechnologies). 40 µl mix was dispensed onto the array. Slides were loaded into the Agilent SureHyb chambers and hybridization was performed in a hybridization oven at 65°C for 17 hours with 10 rpm rotation. After hybridization, slides were washed using Wash Buffer Kit (Agilent Technologies) and dried at room temperature.

scan_protocol: Microarray slides were scanned using G2505C scanner (Agilent Technologies) at 3 µm resolution. Probes features were extracted using the Feature Extraction Software v. 10.7.3.1 with GE_1_Sep09 protocol (Agilent Technologies).

data_processing: Intra-array normalizations were directly performed by the Feature Extraction Software. Inter-array normalization of expression levels was performed with quantile method (Bolstad BM et al., 2003) and the values for within-arrays replicate spots were then averaged. Feature Extraction Software, which provided spot quality measures, was used to evaluate the quality and reliability of the hybridization. In particular, the flag “glsFound” (set to 1 if the spot had an intensity value significantly different from the local background and to 0 when otherwise) was used to filter out unreliable probes: the flag equal to 0 was to be noted as “not available (NA).” Probes with a high proportion of NA values were removed from the dataset in order to carry out a more solid and unbiased statistical analyses. Forty-five percent of NA was used as the threshold in the filtering process, and a total of 30,073 of 39,570 probes were obtained. To identify differentially expressed probes in at least one condition one way ANOVA analysis was performed using a threshold p-value ≤ 0.01. Significant diferentially expressed probes were used to search specific expression clusters according to Self Organizing Tree Algorithm (SOTA) (Herrero JA et al., 2001) as implemented in MultiExperiment Viewer version 4.8.1 (tMev) of the TM4 Microarray Software Suite (Saeed AI et al., 2006). Gene ontology analysis was performed using DAVID web tool (Huang DW et al., 2009), while pathway analysis was performed applying Gene Set Enrichment Analysis (GSEA) as implemented in Graphite web tool (Sales G et al., 2013). KEGG pathway database was used and only pathways that presented at least 10 mapped genes in common with our gene expression matrix were considered in the analysis.

source_name: fast skeletal muscle fibre_AAVshMCU-14days

label_protocol: Before preforming microarray experiments about 1/5 of the purified RNA was used to test, by qRT-PCR, the MCU overexpression or downregulation in the selected myofibers. RNA was retrotranscibed using the SuperScript III Reverse Transcriptase (Life Technologies) according to the manufacturer’s specifications. Gene-specific primers for exogenous MCU (AAV MCU), endogenous MCU, and ZsGreen were selected with Primer3Plus (http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi) and the specificity of each primer set was monitored by dissociation curve analysis. Tioredoxin 1 was chosen as reference gene. qRT-PCR experiments were performed in a 7500 Real-Time PCR System (Life Technologies) using the SYBR Green technology of GoTaq qPCR Master Mix (Promega).  The remaining purified RNA from myofibers demonstrating MCU reduction or overexpression was exponentially amplified using the TransPlex WholeTranscriptome Amplification 2 Kit (Sigma-Aldrich) according to Chemello F. et al., PlosOne 2011 to obtain a sufficient amount of cDNA for microarray experiments. Briefly, RNA was reverse transcribed in a cDNA library, and then library was exponentially amplified for 18 cycles, few cycles below the amplification “plateau” observed in a PCR test reaction. To remove the residual primers and nucleotides, amplification product was purified with the GenElute PCR Clean-up columns (Sigma-Aldrich). Resulting cDNA has been quantified with Nanodrop ND-1000 spectrophotometer (Thermo Scientific). 2 µg of amplified-purified cDNA were direct labeled using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies) as described in the manual. The kit uses random primers and the exo-Klenow fragment to directly label cDNA samples with Cy3-dUTP nucleotides. Labeled cDNA was purified using the Amicon 30kDa filters (Millipore) and quantified using NanoDrop ND-1000 spectrophotometer (Thermo Scientific). On average, cDNA yield was about 4 µg and the specific activity of 30 pmol Cy3 per µg of cDNA.

growth_protocol: Male CD1 mice were fed ad libitum (two mice per cage). Eight weeks old mice were used for EDL infection with AAVs.

extract_protocol: Mice were sacrificed by rapid cervical dislocation and wild-type or AAV injected EDL muscles were collected. Muscles were incubated for 45 min. at 37°C in 1 ml high-glucose Dulbecco’s modified Eagle medium (DMEM; Life Technologies) containing 10 mg type I collagenase (220 U mg-1; Sigma-Aldrich). Collagenase-treated muscles were sequentially rinsed for 2 min. in DMEM, DMEM supplemented with 10% fetal bovine serum (FBS), and transferred in DMEM again. Single myofibers were liberated by gentle physical trituration with a wide-mouth plastic Pasteur pipette, and the triturating process was repeated several times until the mayor part of myofibers were dissociated. Intact, no contracted and well-isolated myofibers were picked under stereo-microscope and washed in phosphate buffer saline (PBS). ZsGreen-expressing myofibers of AAV injected EDL muscles were selected using an inverted microscope (DMI4000, Leica). All myofibers were collected within 45 min. from the last trituration step.  Each single isolated myofiber was lysed in 250 µl of TRIzol Reagent (Life Technologies) and RNA was extracted in the aqueous phase following the manufacturer’s instructions. To purify RNA, spin-columns of the RNeasy Micro Kit (Qiagen) were used, adding 70% ethanol to the aqueous phase and following the Qiagen protocol.

treatment_protocol: EDL muscles were isolated  through a small hindlimb incision and 10^11 AAVs particles were injected along the muscle length. Muscles were analyzed 7 and 14 days post-injection.

value: adult; 8weeks

value: male

value: extensor digitorum longus (EDL) muscle

tag: transfected with

value: AAVshMCU to silence MCU

tag: tissue subtype

value: single skeletal muscle fibre

tag: time point

value: 14 days after transfection

tag: molecule subtype

value: long RNA (>200 bp)


title: 3134Tet_-TetActivator_48hrs_rep1


title: 3134Tet_+TetActivator_48hrs_rep1


title: Fast fibre 2-AAVshMCU-7days

description:
Transfection with AAVshMCU to silence MCU after 7 days after transfection
Fast skeletal muscle fibre, derived from mouse with silenced MCU obtained with AAV injection and sacrification after 7 days after injection

source_name: fast skeletal muscle fibre_AAVshMCU-7days

tag: strain

tag: tissue

value: 7 days after transfection


title: 3134Tet_+TetActivator_48hrs_rep3


title: 3134Tet_+dnBrg1_48hrs_rep1


title: Fast fibre 3-AAVshMCU-14days


title: Fast fibre 4-AAVshMCU-14days


title: UCC2003 -nanR versus UCC2003

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

institute: University College Cork

description: gene expression array

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003-nanR grown in mMRS supplemented with 0.05% cysteine and 0.5% ribose

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003  or Bifidobacterium breve UCC2003-nanR was grown in modified de Man, Rogosa and Sharpe (MRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), ,supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and containing  0.5% ribose  The strains were grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) to an optical density OD600 of 0.5

extract_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

value: nanR mutant

source_name: Bifidobacterium breve UCC200 grown in mMRS supplemented with 0.05% cysteine and 0.5% ribose

value: wild type


title: Fast fibre 3-AAVshMCU-7days


title: Fast fibre 1-AAVshMCU-14days


title: Fast fibre 4-AAVMCU-14days

description:
Transfection with AAVMCU to overexpress MCU 14 days after transfection
Fast skeletal muscle fibre, derived from mouse with overexpressed MCU obtained with AAV injection and sacrification after 14 days after injection

source_name: fast skeletal muscle fibre_AAVMCU-14days

value: AAVMCU to overexpress MCU


title: Fast fibre 1-AAVshMCU-7days


title: UCC2003 versus UCC2003 -nanR

description: gene expression array


title: Fast fibre 3-AAVMCU-14days


title: Fast fibre 3-AAVMCU-7days

description:
Transfection with AAVMCU to overexpress MCU 7 days after transfection
Fast skeletal muscle fibre, derived from mouse with overexpressed MCU obtained with AAV injection and sacrification after 7 days after injection

source_name: fast skeletal muscle fibre_AAVMCU-7days


title: Fast fibre 2-AAVMCU-14days


title: HUVEC-puro control cells

city: Wuhan

first: Junjie

last: Zhang

state: Hubei

address: Donghu Road, No. 115

department: Medical Research Institute

institute: Wuhan University

description: Gene expression data from KHSV-Vector control HUVEC stable cells

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

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

data_processing: The data were analyzed with 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.

source_name: HUVEC cells stably expressing vector control

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were purchase from Lifeline Cell Technology and maintained in human endothelial culture medium according to the instructions.

extract_protocol: RNeasy Mini Kit (Qiagen) was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: To establish stable cell lines, HUVECs were infected with lentivirus containing indicated genes (kGPCR or vector control) and selected with puromycin (1 μg/ml).

tag: transfection

value: Vector control

value: primary endothelial cells


title: cisplatin treated cells 24h rep2

city: Strasbourg

first: Christian

last: Gaiddon

address: 3 av. Moliere

country: France

institute: INSERM

description: Gene expression data of cisplatin treated cancer cells 24h rep2

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

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

data_processing: The data were analyzed with Microarray Suite version 4.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: cisplatin treated cancer cells 24h rep2

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

growth_protocol: Cells were grown in DMEM with 10% fœtal bovine serum

extract_protocol: RNA were extracted with Quiagen RNAeasy kit

treatment_protocol: Cells were treated for 6h or 24h.

tag: agent

value: cisplatin


title: Fast fibre 2-AAVMCU-7days


title: Fast fibre 1-AAVMCU-14days


title: cisplatin treated cells 24h rep3

description: Gene expression data of cisplatin treated cancer cells 24h rep3

source_name: cisplatin treated cancer cells 24h rep3


title: HUVEC-vGPCR stable cells

description: Gene expression data from KHSV-kGPCR expressed HUVEC stable cells

source_name: HUVEC cells stably expressing KSHV kGPCR

value: KSHV kGPCR

tag: cell type


title: cisplatin treated cells 24h rep1

description: Gene expression data of cisplatin treated cancer cells 24h rep1

source_name: cisplatin treated cancer cells 24h rep1


title: cisplatin treated cells 6h rep3

description: Gene expression data of cisplatin treated cancer cells 6h rep3

source_name: cisplatin treated cancer cells 6h rep3


title: XRL_38 mouse xenograft of human leukemia

city: Albuquerque

first: Richard

last: Harvey

state: NM

department: Pathology

institute: University of New Mexico

hyb_protocol: Following fragmentation, 12.5 µg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning of the microarrays was performed according to Affymetrix's recommended protocol  (GeneChip Expression Analysis Technical Manual).

data_processing: Data were masked according to the method outlined in Harvey et al, Blood 116:4874-4884, (2010) in order to remove uninformative probe pairs.  Default MAS 5.0 normalization was performed on the masked data using Expression Console software (Affymetrix).

source_name: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The leukemic cells were obtained from spleens of the xenograft mice and then cryopreserved.  The cryopreserved cells were the source of the isolated RNA.

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

treatment_protocol: Cryopreserved samples were shipped to the isolation laboratory.  After thawing the cells were gently pelleted and the supernatant was removed.  The loose cell pellet was dispersed and lysed with 1 mL Trizol/10 million cells.

value: mouse xenograft of human leukemia


title: Fast fibre 4-AAVshLuc-14days

description:
Transfection with AAV with no cloned insert (control for transfection 14 days after transfection)
Fast skeletal muscle fibre, derived from mouse with the same age of the one where MCU was silenced or overexpressed with AAV injection and sacrification after 7 or 14 days after injection, wild type transfected with control plasmid

source_name: fast skeletal muscle fibre_AAVshLuc-14days

value: AAV with no cloned insert


title: cisplatin treated cells 6h rep1

description: Gene expression data of cisplatin treatedcancer cells 6h rep1

source_name: cisplatin treatedcancer cells 6h rep1


title: XRL_37 mouse xenograft of human leukemia


title: XRL_35 mouse xenograft of human leukemia


title: Fast fibre 3-AAVshLuc-14days

value: adult; 8weeks


title: RDC treated cells 24h rep3

description: Gene expression data of RDC treated cancer cells 24h rep3

source_name: RDC treated cancer cells 24h rep3

value: RDC


title: RDC treated cells 6h rep3

description: Gene expression data of RDC treated cancer cells 6h rep3

source_name: RDC treated cancer cells 6h rep3


title: RDC treated cells 24h rep2

description: Gene expression data of RDC treated cancer cells 24h rep2

source_name: RDC treated cancer cells 24h rep2


title: cisplatin treated cells 6h rep2

description: Gene expression data of cisplatin treated cancer cells 6h rep2

source_name: cisplatin treated cancer cells 6h rep2


title: RDC treated cells 24h rep1

description: Gene expression data of RDC treated cancer cells 24h rep1

source_name: RDC treated cancer cells 24h rep1


title: Fast fibre 2-AAVshLuc-14days

value: male

value: extensor digitorum longus (EDL) muscle


title: XRL_36 mouse xenograft of human leukemia


title: Fast fibre 1-AAVMCU-7days

value: single skeletal muscle fibre


title: Fast fibre 1-AAVshLuc-14days

value: 14 days after transfection


title: RDC treated cells 6h rep2

description: Gene expression data of RDC treated cancer cells 6h rep2

source_name: RDC treated cancer cells 6h rep2


title: Fast fibre 2-AAVshLuc-7days

description:
Transfection with AAV with no cloned insert (control for transfection 7 days after transfection)
Fast skeletal muscle fibre, derived from mouse with the same age of the one where MCU was silenced or overexpressed with AAV injection and sacrification after 7 or 14 days after injection, wild type transfected with control plasmid

source_name: fast skeletal muscle fibre_AAVshLuc-7days

value: long RNA (>200 bp)


title: XRL_33 mouse xenograft of human leukemia


title: Fast fibre 3-AAVshLuc-7days

value: 7 days after transfection


title: XRL_32 mouse xenograft of human leukemia


title: Fast fibre 4-AAVshLuc-7days


title: RDC treated cells 6h rep1

description: Gene expression data of RDC treated cancer cells 6h rep1

source_name: RDC treated cancer cells 6h rep1


title: XRL_34 mouse xenograft of human leukemia


title: XRL_30 mouse xenograft of human leukemia


title: Control cells rep3

description: Gene expression data of Control cancer cells rep3

source_name: Control cancer cells rep3


title: Fast fibre 4-Wild type-14days

description:
Wild type control matching with 14 days of AAVshluc, AAVshMCU and AAVMCU transfections
Fast skeletal muscle fibre, derived from mouse with the same age of the one where MCU was silenced or overexpressed with AAV injection and sacrification after 7 or 14 days after injection, wild type

source_name: fast skeletal muscle fibre_Wild type-14days

value: none (control)


title: Control cells rep1

description: Gene expression data of Control cancer cells rep1

source_name: Control cancer cells rep1


title: Fast fibre 1-Wild type-7days

description:
Wild type control matching with 7 days of AAVshluc, AAVshMCU and AAVMCU transfections
Fast skeletal muscle fibre, derived from mouse with the same age of the one where MCU was silenced or overexpressed with AAV injection and sacrification after 7 or 14 days after injection, wild type

source_name: fast skeletal muscle fibre_Wild type-7days


title: XRL_27 mouse xenograft of human leukemia


title: Fast fibre 1-AAVshLuc-7days


title: Fast fibre 4-Wild type-7days


title: XRL_28 mouse xenograft of human leukemia


title: Fast fibre 2-Wild type-14days


title: Fast fibre 2-Wild type-7days


title: Fast fibre 1-Wild type-14days


title: Cells 2b

city: Utrecht

first: Jacco

last: Van Rheenen

address: Uppsalalaan 8,

department: Cancer Genomics Netherlands

country: Netherlands

institute: Hubrecht Institute-KNAW & University Medical Center Utrecht

description:
Biological replicate: 2
Technical replicate: 2

hyb_protocol: Per sample, 750 ng of the obtained biotinylated cRNA samples was hybridized onto the Illumina HumanHT-12 v4 (Illumina, Inc., San Diego, CA, U.S.A.). Each BeadChip contains twelve arrays. Hybridization and washing were performed according to the Illumina Manual “Direct Hybridization Assay Guide”

scan_protocol: Scanning was performed on the Illumina iScan (Illumina, Inc., San Diego, CA, U.S.A.).

data_processing: The data was quantile normalized using the R/Bioconductor package limma (Wang et al., 2013)

source_name: mammary gland orthotopic MDA-MB-231 tumors

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin, TX, U.S.A.) according to the manufacturer’s specifications with an input of 200 ng total RNA.

extract_protocol: Total RNA was isolated from cells and EVs using the TRIZOL reagent (Invitrogen, Carlsbad, CA). The RNA quality and integrity was determined using Lab-on-Chip analysis on the Agilent 2100 Bioanalyzer  (Agilent Technologies, Inc., Santa Clara, CA, U.S.A.)

tag: rna source type

value: Cellular RNA

tag: host

value: Mus musculus


title: XRL_26 mouse xenograft of human leukemia


title: Microvesicles 3b

description:
Biological replicate: 3
Technical replicate: 2

value: Extracellular vesicle RNA


title: XRL_23 mouse xenograft of human leukemia


title: Control cells rep2

description: Gene expression data of Control cancer cells rep2

source_name: Control cancer cells rep2


title: Fast fibre 3-Wild type-14days


title: XRL_24 mouse xenograft of human leukemia

source_name: Homo sapiens


title: Fast fibre 3-Wild type-7days


title: Microvesicles 2b


title: XRL_31 mouse xenograft of human leukemia


title: XRL_22 mouse xenograft of human leukemia


title: Cells 1b

description:
Biological replicate: 1
Technical replicate: 2


title: Cells 3b


title: XRL_21 mouse xenograft of human leukemia


title: Microvesicles 1b


title: XRL_25 mouse xenograft of human leukemia


title: XRL_20 mouse xenograft of human leukemia


title: Med23 KO ES cell, biological rep3

city: Shanghai

first: Gang

last: Wang

address: Yueyang Road 320

department: Institute of Biochemistry and Cell Biology, State Key Laboratory of Cell Biology,

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: Gene expression data from Med23 KO cells

hyb_protocol: The Affymetrix GeneChip arrays were hybridized and washed using the manufacturer's protocol.

scan_protocol: Affymetrix GeneChip arrays were scanned using the Affymetrix GeneArray scanner.

data_processing: The microarray data were normalized using the Robust Multichip Average (RMA) method. We discarded probe sets that did not have signals above background in more than 75% of the arrays for all samples using the Affymetrix MAS5 present/absent calls.

source_name: ES cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Regular ES cell culture as described in MATERIALS AND METHODS.

treatment_protocol: Culture with fresh complete ESC medium for 24 hours and then harvest samples with Trizol.

tag: genotype/variation

value: MED23 knockout


title: XRL_19 mouse xenograft of human leukemia


title: Med23 KO ES cell, biological rep2


title: Med23 KO ES cell, biological rep1


title: XRL_16 mouse xenograft of human leukemia


title: Microvesicles 1a

description:
Biological replicate: 1
Technical replicate: 1

tag: cell line


title: XRL_18 mouse xenograft of human leukemia


title: Microvesicles 2a

description:
Biological replicate: 2
Technical replicate: 1


title: XRL_15 mouse xenograft of human leukemia


title: Cells 2a


title: XRL_17 mouse xenograft of human leukemia


title: Cells 3a

description:
Biological replicate: 3
Technical replicate: 1


title: XRL_14 mouse xenograft of human leukemia


title: Mouse lung  at 7 months, DD-3

city: Haining

first: Jian

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

description: Gene expression data from the extracted total RNA

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C, 60 RPM on GeneChip Mouse Expression 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 and the Affymetrix Command Console v3.0 (AGCC) software.

data_processing: A DNA-Chip analyzer dChIP version 1.3 was utilized to adjust arrays to a common baseline using invariant set normalization. The lung tumor part was normalized to 12-month-old wildype part. The 7-month-old mouse lungs was normalized to 7-month-old wildtype mouse lungs.

source_name: part of mouse whole lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Affymetrix 3'IVT Express Manual, 2008-2010, RevB, Affymetrix).

growth_protocol: normal feed condition

extract_protocol: TRIzol reagent puls QIAGEN RNeasy total RNA isolation kit to clean up.

treatment_protocol: no treatment

tag: genotype

value: lung

value: 7 month

value: mixed background


title: Mouse lung  at 7 months, DD-2

tag: age


title: Head kidney+spleen_wt_VHSV_infected fish_biological replicate1

city: Madrid

first: Julio

middle: M

last: Coll

address: crt Coruna km7

department: Biotechnology

institute: INIA

description: 1.4 wt Biological Replicate 1

hyb_protocol: The slides were pre-treated with 1% BSA fraction V, 5 X SSC, 0.1% SDS for 30 min. at 50 ºC and washed with 2 X SSC (3 min) and 0.2 X SSC (3 min) and hybridized overnight in cocktail containing 1.3 X Denhardt's, 3 X SSC, 0.3% SDS, 2.1 ug/ul polyadenylate and 1 ug/ul yeast tRNA.

scan_protocol: Signal was captured and processed using an Agilent scanner (G2565B, Agilent Technologies). The scanner images were segmented by the Agilent Feature Extraction Software (v9.5) with the protocol GE1-v5_95.

data_processing: The gProccesedSignal was chosen for statistical analysis. Normalization within each microarray was carried out by using the sum of all the signals. Data was first filtered by non-uniform pixel distributed outliers and other replicate outliers (glsFeatNonUnifOL, glsBGNonUnifOL, glsFeatPopnOL and glsBGPopnOL) according to the default Agilent Feature Extraction criteria; ratio between processed signal and its error <2; differentiation from background signal; linear relationship between concentration and intensity below limits according to Spike-In information.

organism: Oncorhynchus mykiss

source_name: Head kidney+spleen of intraperitoneally injected trout 2 days post infection with wt VHSV

label_protocol: RNA were labeled with Cy3 (Amersham Pharmacia) by using SuperScript III reverse transcriptase (InVitroGen) and oligo(dT) primer, and the resulting cDNA was purified with Microcon YM30 (Millipore).

growth_protocol: Fingerling rainbow trout (Oncorhynchus mykiss) of 6-12 g (10 cm in length) were obtained from a local fish farm free of IPNV (Los Molinos, Madrid). Fingerling trout were maintained at 14-15 ºC in 200 l aquaria with tap-dechlorinated carbon-filtered water provided with biological filters and fed with a commercial feed diet.

extract_protocol: Spleen and head kidney from each individual trout were collected and preserved in RNAlater (Ambion, Austin, USA) until RNA extraction. For this purpose, the RNeasy Plus kit (Qiagen, Hilden, Germany) was used following the manufacturer's instructions.

treatment_protocol: After 2 weeks of acclimatization, each trout was intraperiotoneally injected with 100000 pfu of deleted NV (dNV) or wt VHSV 23.75. Trouts were anaesthetized by immersion in 50mg/l buffered tricaine ethanesulfonate (MS-222, Sigma, Madrid) prior to handling.

value: head kidney+spleen

tag: treatment

value: WT viral hemorrhagic septicemia virus (VHSV) infection

value: 2 days post infection

tag: number of trouts per group

value: one


title: wild type ES cell, biological rep2

description: Gene expression data from wild type ES cells

value: wildtype


title: Head kidney+spleen_wt_VHSV_infected fish_biological replicate2

description: 2.1 wt Biological Replicate 2


title: XRL_12 mouse xenograft of human leukemia

value: mouse xenograft of human leukemia


title: Mouse lung  at 7 months, DD-1


title: XRL_13 mouse xenograft of human leukemia


title: wild type ES cell, biological rep3


title: Mouse lung  at 7 months, pD-3

value: Ptend/d


title: Head kidney+spleen_wt_VHSV_infected fish_biological replicate3

description: 2.2 wt Biological Replicate 3


title: XRL_11 mouse xenograft of human leukemia


title: Cells 1a


title: wild type ES cell, biological rep1


title: Head kidney+spleen_dNV_VHSV_infected fish_biological replicate2

description: 1.2 dNV Biological Replicate 2

source_name: Head kidney+spleen of intraperitoneally injected trout 2 days post infection with deleted Nv gene VHSV

value: dNV viral hemorrhagic septicemia virus (VHSV) infection


title: Head kidney+spleen_dNV_VHSV_infected fish_biological replicate3

description: 1.3 dNV Biological Replicate 3


title: XRL_10 mouse xenograft of human leukemia


title: Mouse lung  at 7 months, pD-1


title: XRL_09 mouse xenograft of human leukemia


title: Head kidney+spleen_dNV_VHSV_infected fish_biological replicate1

description: 1.1 dNV Biological Replicate 1


title: Mouse lung  at 7 months, pD-2


title: Mouse lung  at 7 months, FF-2


title: Mouse lung  at 7 months, FF-3


title: XRL_08 mouse xenograft of human leukemia


title: XRL_07 mouse xenograft of human leukemia


title: Mouse lung tumor at 12 months (48345)

source_name: part of one single mouse lung tumor

value: lung tumor

value: 12 month


title: Mouse lung tumor at 12 months (49420)


title: Mouse lung tumor at 12 months


title: XRL_06 mouse xenograft of human leukemia


title: XRL_05 mouse xenograft of human leukemia


title: Mouse lung at 12 months (44322)


title: XRL_02 mouse xenograft of human leukemia


title: XRL_03 mouse xenograft of human leukemia


title: Mouse lung at 12 months (49424)


title: XRL_01 mouse xenograft of human leukemia


title: XRL_29 mouse xenograft of human leukemia


title: Mouse lung at 12 months (48343)


title: XRL_04 mouse xenograft of human leukemia


title: Mouse lung  at 7 months, FF-1


title: O4-/CD140a+ (F)

status: Public on Mar 04 2015

city: Buffalo

first: Fraser

middle: James

last: Sim

state: NY

address: 3435 Main Street

department: Pharmacology

institute: University at Buffalo

description: Sample name: 133

hyb_protocol: Standard Illumina hybridization protocol @ 48 deg Hyb

scan_protocol: Standard Illumina scanning protocol

data_processing: analysis performed in R. background adjustment was performed using 'bgAdjust.affy' algorithm, expression values were normalized using 'vsn', poor-quality data was removed using lumi detectionCall function, such that probes were retained if there were at least 2 P present cells among the samples in any cell type group

source_name: fetal brain

label_protocol: cDNA was amplified using NuGEN WTA Pico amplification kit and labeled using NuGen/UNG enzyme protocol (per manufacturer's instructions).

growth_protocol: cells were extracted immediately following FACS sorting

extract_protocol: total RNA extraction was performed using Omega-Bio RNA Mini Extraction Kit (per manufacturer's instructions).

tag: developmental stage

value: fetus

value: brain

tag: facs-sorted cell population

tag: sampleID

value: F


title: O4+/CD140a+ (E)

description: Sample name: 126

value: E


title: O4+/CD140a+ (F)

description: Sample name: 132


title: CL1-5_pcDNA3.1

city: Taipei

first: Kuo-Tai

last: Hua

address: No. 1, Sec. 1, Jen-Ai Rd.

country: Taiwan

institute: National Taiwan University

description: Gene expression data from CL1-5 cells with vector control

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with G418 or puromycin for two weeks.  Stably transduced cells were used for this experiment.

value: lung cancer

value: CL1-5 cells expressing pcDNA3.1


title: CL1-5_Luc shRNA

description: Gene expression data from CL1-5 cells with luciferase shRNA

value: CL1-5 cells expressing luciferase shRNA


title: O4-/CD140a- (F)

description: Sample name: 135


title: O4+/CD140a+ (C)

description: Sample name: 67

value: C


title: O4-/CD140a+ (C)

description: Sample name: 68


title: O4-/CD140a- (C)

description: Sample name: 70


title: CL1-5_pcDNA3.1/KEAP1

description: Gene expression data from CL1-5 cells with KEAP1 overexpression

value: CL1-5 cells expressing pcDNA3.1/KEAP1


title: O4+/CD140a- (E)

description: Sample name: 128


title: CL1-5_NRF2 shRNA

description: Gene expression data from CL1-5 cells with NRF2 shRNA

value: CL1-5 cells expressing NRF2 shRNA


title: O4+/CD140a+ (B)

description: Sample name: 32

value: B


title: O4-/CD140a- (B)

description: Sample name: 35


title: O4+/CD140a- (F)

description: Sample name: 134


title: O4-/CD140a- (D)

description: Sample name: 111

value: D


title: O4-/CD140a+ (E)

description: Sample name: 127


title: O4+/CD140a- (D)

description: Sample name: 110


title: O4+/CD140a+ (D)

description: Sample name: 108


title: O4-/CD140a+ (A)

description: Sample name: 29

value: A


title: O4-/CD140a+ (D)

description: Sample name: 109


title: O4-/CD140a- (A)

description: Sample name: 31


title: O4+/CD140a+ (A)

description: Sample name: 28


title: Spheres derived from CaSki cells rep1

city: Sapporo

first: Takuya

last: Asano

address: South 1 West 16, Chuo-ku

country: Japan

institute: Sapporo Medical University School of Medicine

description: no description

hyb_protocol: Cy3-labeled cRNA and Cy5-labeled cRNA were combined and then fragmented in a gene expression hybridization kit (Agilint Technologies).  Then the labeled cRNAs were hybridized to a 60-mer probe oligonucleotide microarray (G4845A human GE 4x44K V2 Microarray kit) and incubated for 20 hours at 50 °C.

scan_protocol: The fluorescent intensities were determined by an Agilent Technologies Scanner G2505C.

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and Linear and LOWESS normalization.

source_name: Spheres derived from CaSki cells: test

label_protocol: Purified total RNA (3 µg) was reverse-transcribed to generate double-stranded cDNA using an oligo dT T7 promoter primer and reverse transcriptase. Then, cRNA was synthesized using T7 RNA polymerase, which simultaneously incorporated Cy3- or Cy5-labeled cytidine triphosphate.

growth_protocol: CaSki were cultured in RPMI-1640 added 10% fetal bovine serum (FBS). Sphere cells were cultured in 6-well ultra-low attachment surface dishes (Corning, Tewksbury, MA, USA) for 5 to 14 days. The sphere culture medium was serum-free DMEM/F12 (Life Technologies, Carlsbad, CA, USA) supplemented with N-2 supplement (Wako, Osaka, Japan), 20 mg/ml recombinant human epithelial growth factor, 10 mg/ml human basic fibroblast growth factor (R&D Systems, Minneapolis, MN, USA), 4 µg/ml heparin (AY pharma, Tokyo, JAPAN) and 1% penicillin and streptomycin.

extract_protocol: Total RNA was isolated from each collected cells using RNeasy Mini Kit (QIAGEN, Valencia, CA, USA) following manufacturer’s protocol.

value: CaSki (CRL-1550)

tag: gender

value: female

value: 40 years old

value: cervix

source_name: adherent cultured CaSki cells: reference


title: HpSCs derived humanized liver_1

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

institute: Yokohama City University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarray 4x44K v2 for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner using one color scan setting for 4x44k v2 array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

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

value: HpSCs-derived humanized liver tissue


title: CD13+CD133+ HPCs 1

city: Isehara

first: Akihide

last: Kamiya

address: 143 Shimokasuya

institute: Tokai University

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the Agilent instructions. After hybridization, microarrays were washed and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software according to the Agilent instructions.

source_name: human iPS cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from total RNA according to the Agilent instructions.

growth_protocol: human iPS cells were culture with activin, fibroblast growth factor, and hepatocyte growth factor.

extract_protocol: RNA was extracted using RNeasy Micro Kit (Qiagen; Venlo, The Netherlands).

treatment_protocol: CD13+CD133+ cells derived from human iPS cell culture were sorted using flowcytometry.

value: liver

tag: Stage

value: human iPS cell culture


title: human adult hepatocyte(AH)_1

tag: tissue

value: Adult Hepatocyte


title: FLCs derived humanized liver_1

value: FLCs-derived humanized liver tissue


title: Human primary fetal liver cells(FLCs)_1

value: Human primary fetal liver cells


title: CD13+CD133+ HPCs 2


title: HpSCs derived humanized liver_2


title: Spheres derived from CaSki cells rep2

description: no description


title: human adult hepatocyte(AH)_2


title: Human hepatic stem cells(HpSCs)_1

value: Human Hepatic Stem Cells isolated from fetal liver cells


title: Human hepatic stem cells(HpSCs)_2


title: Head and neck Squamous cell carcinomas_HYPOPHARYNX_132

city: chicago

first: Tanguy

last: Seiwert

state: IL

address: 900 E. 57th street

institute: University of Chicago

hyb_protocol: Expression arrays were performed at the Argonne National Laboratory in an ozone-controlled atmosphere.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1. Raw data were background corrected, quantile normalized and log2 transformed.

source_name: Head and neck Squamous cell carcinomas_HYPOPHARYNX_pretreatmeant_132

label_protocol: Labeling for Agilent 4x44K v2 expression arrays was done using a Quick Amp Labeling Kit one-color according to the manufacturer’s protocol using 200ng of starting material.

extract_protocol: Guided by H&E stained slides, the region with the highest tumor content was cut from OCT blocks, pulverized using CryoPrep (Covaris, Woburn, MA) and homogenized in a lysis buffer from an AllPrepRNA/DNA/Protein Mini kit (Qiagen, Valencia, CA) or from a RNA/DNA/Protein Purification Kit (Norgen Biotek, Thorold, Canada) using an Ultrasonicator (Covaris, Woburn, MA). DNA, RNA and protein were isolated from each sample using the respective kit and following manufacturer’s protocol. RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). If DNA contamination was seen, RNAs were treated with TURBO DNA-free (Ambion, CA) to remove genomic DNA, and subsequently quantitated using a spectrophotometer. Only RNAs with integrity number (RIN) ≥7.5, a 260/280 ratio ≥1.8 and a 260/230 ratio ≥1.8 (≥1.1 for a few RNAs) were labeled for expression arrays.

treatment_protocol: All the patients were treated with concurrent chemoradiotherapy. Samples with microscopic tumor or tumor content <60% were excluded from further analysis.

tag: tissue type

value: head and neck squamous cell carcinoma (HNSCC)

tag: anatomic site

value: HYPOPHARYNX

value: M

tag: hpv status

value: neg


title: Microvesicles 3a

tag: rna source type

value: Extracellular vesicle RNA

value: Mus musculus


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_126

scan_protocol: Expression arrays were performed at the Argonne National Laboratory in an ozone-controlled atmosphere.

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_126

value: ORAL CAVITY


title: Head and neck Squamous cell carcinomas_HYPOPHARYNX_125

source_name: Head and neck Squamous cell carcinomas_HYPOPHARYNX_pretreatmeant_125


title: Head and neck Squamous cell carcinomas_OROPHARYNX_134

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_134

value: OROPHARYNX


title: Head and neck Squamous cell carcinomas_OROPHARYNX_130

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_130

value: pos


title: Head and neck Squamous cell carcinomas_OROPHARYNX_131

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_131


title: Head and neck Squamous cell carcinomas_HYPOPHARYNX_123

source_name: Head and neck Squamous cell carcinomas_HYPOPHARYNX_pretreatmeant_123


title: Head and neck Squamous cell carcinomas_OROPHARYNX_133

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_133

value: F


title: Head and neck Squamous cell carcinomas_OROPHARYNX_128

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_128


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_124

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_124

value: SUPRAGLOTTIC


title: Head and neck Squamous cell carcinomas_OROPHARYNX_120

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_120


title: Head and neck Squamous cell carcinomas_OROPHARYNX_122

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_122


title: Head and neck Squamous cell carcinomas_OROPHARYNX_129

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_129


title: Head and neck Squamous cell carcinomas_OROPHARYNX_118

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_118


title: Head and neck Squamous cell carcinomas_OROPHARYNX_127

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_127


title: Head and neck Squamous cell carcinomas_OROPHARYNX_117

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_117


title: Head and neck Squamous cell carcinomas_OROPHARYNX_119

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_119


title: Head and neck Squamous cell carcinomas_HYPOPHARYNX_121

source_name: Head and neck Squamous cell carcinomas_HYPOPHARYNX_pretreatmeant_121


title: Head and neck Squamous cell carcinomas_SUBGLOTTIC LARYNX_111

source_name: Head and neck Squamous cell carcinomas_SUBGLOTTIC LARYNX_pretreatmeant_111

value: SUBGLOTTIC LARYNX


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_115

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_115


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_116

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_116


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_114

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_114


title: Head and neck Squamous cell carcinomas_OROPHARYNX_112

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_112


title: Head and neck Squamous cell carcinomas_OROPHARYNX_113

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_113


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_108

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_108


title: Head and neck Squamous cell carcinomas_OROPHARYNX_107

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_107


title: Head and neck Squamous cell carcinomas_OROPHARYNX_110

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_110


title: Head and neck Squamous cell carcinomas_OROPHARYNX_105

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_105


title: Head and neck Squamous cell carcinomas_OROPHARYNX_109

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_109


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_106

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_106


title: Head and neck Squamous cell carcinomas_GLOTTIC LARYNX_104

source_name: Head and neck Squamous cell carcinomas_GLOTTIC LARYNX_pretreatmeant_104

value: GLOTTIC LARYNX


title: Head and neck Squamous cell carcinomas_OROPHARYNX_101

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_101


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_100

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_100


title: Head and neck Squamous cell carcinomas_OROPHARYNX_103

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_103


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_102

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_102


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_99

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_99


title: Head and neck Squamous cell carcinomas_OROPHARYNX_98

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_98


title: Head and neck Squamous cell carcinomas_OROPHARYNX_92

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_92


title: Head and neck Squamous cell carcinomas_OROPHARYNX_91

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_91


title: Head and neck Squamous cell carcinomas_OROPHARYNX_96

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_96


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_93

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_93


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_94

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_94


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_95

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_95


title: Head and neck Squamous cell carcinomas_OROPHARYNX_88

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_88


title: Head and neck Squamous cell carcinomas_OROPHARYNX_90

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_90


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_87

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_87


title: Head and neck Squamous cell carcinomas_OROPHARYNX_84

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_84


title: Head and neck Squamous cell carcinomas_OROPHARYNX_97

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_97


title: Head and neck Squamous cell carcinomas_OROPHARYNX_85

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_85


title: Head and neck Squamous cell carcinomas_OROPHARYNX_82

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_82


title: Head and neck Squamous cell carcinomas_OROPHARYNX_81

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_81


title: Head and neck Squamous cell carcinomas_OROPHARYNX_86

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_86


title: Head and neck Squamous cell carcinomas_OROPHARYNX_83

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_83


title: Head and neck Squamous cell carcinomas_OROPHARYNX_77

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_77


title: Head and neck Squamous cell carcinomas_OROPHARYNX_76

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_76


title: Head and neck Squamous cell carcinomas_OROPHARYNX_79

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_79


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_75

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_75


title: Head and neck Squamous cell carcinomas_OROPHARYNX_80

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_80


title: Head and neck Squamous cell carcinomas_OROPHARYNX_71

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_71


title: Head and neck Squamous cell carcinomas_OROPHARYNX_89

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_89


title: O4-/CD140a+ (B)

description: Sample name: 33

source_name: fetal brain

value: fetus

value: brain

value: B


title: Head and neck Squamous cell carcinomas_OROPHARYNX_78

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_78


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_74

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_74


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_73

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_73