title: 621-SZ-L5-R1

description:
pair 30, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 30, layer L5, diagnosis Schiz, replicate R1


title: 700-CR-L5-R1

status: Public on Jul 23 2017

type: RNA

city: Pittsburgh

first: David

last: Lewis

state: PA

address: 3811 O'Hara St

department: Psychiatry and Neuroscience

country: USA

institute: University of Pittsburgh

description:
pair 29, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 29, layer L5, diagnosis Control, replicate R1

hyb_protocol: cDNA was synthesized and amplified using the Ovation Pico WTA System

scan_protocol: loaded on an Affymetrix GeneChip® HT HG-U133+ PM Array Plate

data_processing: Expression intensities were extracted from Affymetrix Expression Console and normalized using Robust Multi-array Average Express.

label: Encore Biotin module (Nugen)

molecule: total RNA

organism: Homo sapiens

source_name: dorsolateral prefrontal cortex

label_protocol: Labeled using the Encore Biotin module (Nugen).

growth_protocol: Tissue sections (12 μm) containing DLPFC area 9 were cut on a cryostat, mounted on glass polyethylene naphthalate membrane slides (Leica Microsystems, Bannockburn, IL) which were blinded as to diagnosis, and stained with thionin for Nissl substance.

extract_protocol: For each sample, RNA was extracted using the QIAGEN® RNeasy Plus Micro kit (QIAGEN, Valencia).

treatment_protocol: An independent committee of experienced research clinicians made consensus DSM-IV diagnoses for all 72 subjects on the basis of medical records and structured diagnostic interviews conducted with the decedent’s family members.

tag: tissue

value: dorsolateral prefrontal cortex

tag: cell type

value: pyramidal neuron cell

tag: dsm-iv diagnoses

value: Unaffected Comparison


title: 567-CR-L3-R1

description:
pair 19, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 19, layer L3, diagnosis Control, replicate R1


title: 727-CR-L3-R1

description:
pair 27, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 27, layer L3, diagnosis Control, replicate R1


title: 546-CR-L3-R1

description:
pair 22, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 22, layer L3, diagnosis Control, replicate R1


title: 533-SZ-L3-R1

description:
pair 18, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 18, layer L3, diagnosis Schiz, replicate R1

value: Chronic undifferentiated schizophrenia


title: 787-SZ-L3-R1

description:
pair 26, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 26, layer L3, diagnosis Schiz, replicate R1

value: Schizoaffective disorder; ODC


title: 634-CR-L5-R1

description:
pair 32, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 32, layer L5, diagnosis Control, replicate R1


title: 933-SZ-L5-R1

description:
pair 36, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 36, layer L5, diagnosis Schiz, replicate R1

value: Disorganized schizophrenia


title: 722-SZ-L3-R1

description:
pair 32, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 32, layer L3, diagnosis Schiz, replicate R1

value: Chronic undifferentiated schizophrenia; ODR; OAR


title: 681-CR-L5-R1

description:
pair 24, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 24, layer L5, diagnosis Control, replicate R1


title: 857-CR-L5-R1

description:
pair 35, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 35, layer L5, diagnosis Control, replicate R1


title: 656-SZ-L5-R1

description:
pair 31, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 31, layer L5, diagnosis Schiz, replicate R1

value: Schizoaffective disorder; ADC


title: 537-SZ-L3-R1

description:
pair 19, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 19, layer L3, diagnosis Schiz, replicate R1

value: Schizoaffective disorder


title: 727-CR-L5-R1

description:
pair 27, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 27, layer L5, diagnosis Control, replicate R1


title: 871-CR-L3-R1

description:
pair 28, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 28, layer L3, diagnosis Control, replicate R1


title: 551-CR-L5-R1

description:
pair 23, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 23, layer L5, diagnosis Control, replicate R1


title: 537-SZ-L5-R1

description:
pair 19, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 19, layer L5, diagnosis Schiz, replicate R1


title: 686-CR-L5-R1

description:
pair 31, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 31, layer L5, diagnosis Control, replicate R1


title: 592-CR-L5-R1

description:
pair 18, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 18, layer L5, diagnosis Control, replicate R1


title: H. thermophilus anaerobic mix #1

city: Tokyo

first: Masafumi

last: Kameya

state: No U.S. state/territory

address: 2-12-1, Ookayama, Meguro-ku

department: Earth-Life Science Institute

country: Japan

institute: Tokyo Institute of Technology

description: This sample is of H. thermophilus TK-6 anaerobically grown on ammonium and nitrate. It is the first of two biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed with Hybridization System 4 according to the NimbleGen Arrays User´s Guide for Gene Expression Analysis (Roche NimbleGen).

scan_protocol: Array scanning was performed with MS200 Microarray Scanner according to the NimbleGen Arrays User´s Guide for Gene Expression Analysis (Roche NimbleGen).

data_processing: The raw data (.pair file) was subjected to RMA, quantile normalization, and background correction as implemented in the NimbleScan software 2.5 (Roche NimbleGen).

organism: Hydrogenobacter thermophilus TK-6

source_name: Hydrogenobacter thermophilus TK-6 wild type

label_protocol: Labeling of double stranded cDNA synthesized with the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) was performed according to the instructions for NimbleGen Arrays User’s Guide for Gene Expression Analysis by Roche NimbleGen using One-Color DNA Labeling Kit (Roche NimbleGen).

growth_protocol: H. thermophilus TK-6 was grown at 70°C to mid-log phase (OD 0.4-0.5) anaerobically (85% H2, 15% CO2) in the presence of 3 g/l ammonium sulfate and 4 g/l sodium nitrate as nitrogen sources.

extract_protocol: Total RNA was extracted by a hot-phenol method. After contaminated DNA was eliminated by RQ1 DNase (Promega) treatment, RNA was purified by RNeasy mini columns (Qiagen).

treatment_protocol: The culture was mixed with equal volumes of RNAprotect Bacterial Reagent (Qiagen) before RNA purification.

tag: nitrogen source

value: Ammonium and nitrate

tag: aerobic/anaerobic condition

value: Anaerobic


title: H. thermophilus anaerobic mix #2

description: This sample is of H. thermophilus TK-6 anaerobically grown on ammonium and nitrate. It is the second of two biological replicates used in this experiment, each from separate cultures.


title: H. thermophilus aerobic ammonium #2

description: This sample is of H. thermophilus TK-6 aerobically grown on ammonium. It is the second of two biological replicates used in this experiment, each from separate cultures.

growth_protocol: H. thermophilus TK-6 was grown at 70°C to mid-log phase (OD 0.4-0.5) aerobically (75% H2, 10% O2, 15% CO2) in the presence of 3 g/l ammonium sulfate as the sole nitrogen source.

value: Ammonium

value: Aerobic


title: H. thermophilus aerobic ammonium #1

description: This sample is of H. thermophilus TK-6 aerobically grown on ammonium. It is the first of two biological replicates used in this experiment, each from separate cultures.


title: H. thermophilus aerobic nitrate #2

description: This sample is of H. thermophilus TK-6 aerobically grown on nitrate. It is the second of two biological replicates used in this experiment, each from separate cultures.

growth_protocol: H. thermophilus TK-6 was grown at 70°C to mid-log phase (OD 0.4-0.5) aerobically (75% H2, 10% O2, 15% CO2) in the presence of 4 g/l sodium nitrate as the sole nitrogen source.

value: Nitrate


title: H. thermophilus aerobic nitrate #1

description: This sample is of H. thermophilus TK-6 aerobically grown on nitrate It is the first of two biological replicates used in this experiment, each from separate cultures.


title: ΔJ_#11

city: Yokohama

first: Junji

last: Hirota

address: 4259-B63 Nagatsuta-cho

department: Center for Biological Resources and Informatics

hyb_protocol: Biotinylated cRNA were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) using GeneChip Hybridization Oven-640 (Affymetrix). GeneChips were washed and stained in the Fluidics Station-450 (Affymetrix).

scan_protocol: Array scanning was performed by GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Affymetrix Gene Expression Console sofware using default analysis settings and global scaling as normalization method.

label: biotin

organism: Mus musculus

source_name: J-knockout MOE (n#2)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using WT PLUS Reagent Kit (Affymetrix).

extract_protocol: Total RNA was extracted from the main olfactory epihelium using QIAGEN RNeasy Mini Kit  according to the manufacturer's instructions. The quality of extracted total RNA was checked by Agilent 2100 Bioanalyzer.

value: Main olfactory epithelium

tag: Sex

value: Male

tag: age

tag: strain


title: ΔJ_#22

source_name: J-knockout MOE (n#4)

value: Female


title: ΔJ_#14

source_name: J-knockout MOE (n#3)


title: Wild-type_#19

source_name: Wild-type control MOE (n#3)


title: Wild-type_#39

source_name: Wild-type control MOE (n#6)


title: hasmc_tp2hr_biological rep1

status: Public on Jul 22 2017

city: Philadelphia

first: Emanuela

last: Ricciotti

address: 3400 Civic Center Blvd.

department: Department of Pharmacology/Institute for Translational Medicine and Therapeutics

institute: University of Pennsylvania

hyb_protocol: Hybridization was carried out at the Penn Microarray Facility. Affymetrix Human Genome U133A v2 was used.

scan_protocol: Data were collected at the Penn Microarray Facility.

data_processing: RMA was used for background correction, normalization and summarization based on a custom CDF: HGU133A2_Hs_ENTREZG_16.0.0

source_name: human aortic smc, 2hr IL-1beta exposure

label_protocol: Labeling was carried out at the Penn Microarray Facility.

growth_protocol: Primary human aortic smooth muscle cells (3F1243) from Lonza were cultured using standard cell culture. Cells were harvested from culture after 0 or 2 hours incubation with interleukin-1beta (10 ng/mL).

extract_protocol: Qiagen kit was used to isolate total RNA.

treatment_protocol: Cells were incubated with DMSO (vehicle) for 2 hours. Subsequently, cells were stimulated with interleukin-1beta (10 ng/mL). The start of incubation with interleukin-1beta is taken to be time zero.

tag: gender

value: male

tag: race

value: white

value: heart

value: aortic smooth muscle cell

tag: material type

value: primary cell

tag: time point

tag: cell line


title: Wild-type_#14

source_name: Wild-type control MOE (n#4)


title: hasmc_tp0hr_biological rep1

source_name: human aortic smc, control 0hr timepoint, no IL-1beta


title: ΔJ_#23

source_name: J-knockout MOE (n#5)


title: Wild-type_#12

source_name: Wild-type control MOE (n#1)


title: hasmc_tp2hr_biological rep4


title: Wild-type_#15

source_name: Wild-type control MOE (n#2)


title: Wild-type_#38

source_name: Wild-type control MOE (n#5)


title: ΔJ_#36

source_name: J-knockout MOE (n#6)


title: hasmc_tp0hr_biological rep3


title: hasmc_tp2hr_biological rep2


title: hasmc_tp0hr_biological rep2


title: ΔJ_#10

source_name: J-knockout MOE (n#1)


title: hasmc_tp2hr_biological rep3


title: Cells_ANGPTL4-knockdown_4-OHT treatment_4days

city: Singapore

first: Zi Qiang

last: Teo

state: Singapore

address: School of Biological Sciences,

department: SBS

country: Singapore

institute: NTU

description: Cell Culture

hyb_protocol: 2 ug of cDNA were hybridized for 18hrs at 45C on GeneChip Human Gene 1.0ST Array inside genechip hybridization oven 640. Genechip fluidics station 450 was used for the washing and staining of the chips.

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

data_processing: Partek genomic suite 6.6 with RMA was used to analyse samples

source_name: MKN28snai1ER gastric cancer cells, ANGPTL4-knockdown, 4-OHT treatment, 4days

label_protocol: Further sample processing of the RNA was carried out using Applause® WT-Amp ST System (NuGEN), followed by the NuGEN Encore biotin label kit

growth_protocol: MKN28 cells were grown in RPMI with 10%FBS and seeded at 5.25×102 cell/cm2 to allow the formation of individual colonies before indicated treatments

extract_protocol: RNA was extracted from the respective treatments with Trizol following the manufacturer’s protocol.

treatment_protocol: Hypoxia treatments were performed  in hypoxic chamber (Stem cell Technology, USA) purged with 5% CO2 and 95% N2 to obtain O2 concentration at 1% as determined by an O2 sensor. For TGF-β-induced EMT, cells were treated with 10 ng/mL of TGF-β for 2 days. For Snai1-mediated EMT, MKN28Snai1ER/shANGPTL4 and MKN28Snai1ER cells were exposed to 20 ng/mL of 4-hydroxytamoxifen (4-OHT) for 4 days.


title: hasmc_tp0hr_biological rep4


title: Cells_4-OHT treatment_2days

description: Cell Culture

source_name: MKN28snai1ER gastric cancer cells, 4-OHT treatment, 2day


title: Cells_ANGPTL4-knockdown_4-OHT treatment_2days

description: Cell Culture

source_name: MKN28snai1ER gastric cancer cells, ANGPTL4-knockdown, 4-OHT treatment, 2days


title: Cells_4-OHT treatment_4days

description: Cell Culture

source_name: MKN28snai1ER gastric cancer cells, 4-OHT treatment, 4days


title: Cells_ANGPTL4-knockdown_TGFb treatment_1day

description: Cell Culture

source_name: MKN28 gastric cancer cells,ANGPTL4-knockdown, TGFb treatment, 1day


title: 802-SZ-L5-R1

description:
pair 34, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 34, layer L5, diagnosis Schiz, replicate R1

source_name: dorsolateral prefrontal cortex

value: dorsolateral prefrontal cortex

value: pyramidal neuron cell

value: Schizoaffective disorder; ADC; ODR


title: Cells_no 4-OHT treatment_4days

description: Cell Culture

source_name: MKN28snai1ER gastric cancer cells, no 4-OHT treatment, 4days


title: Cells_TGFb treatment_2days

description: Cell Culture

source_name: MKN28 gastric cancer cells, TGFb treatment, 2day


title: Cells_ANGPTL4-knockdown_TGFb treatment_2days

description: Cell Culture

source_name: MKN28 gastric cancer cells,ANGPTL4-knockdown, TGFb treatment, 2days


title: Cells_ANGPTL4-knockdown_hypoxia treatment_1day

description: Cell Culture

source_name: MKN28 gastric cancer cells,ANGPTL4-knockdown, hypoxia treatment, 1day


title: Cells_hypoxia treatment_2days

description: Cell Culture

source_name: MKN28 gastric cancer cells, hypoxia treatment, 2day


title: Cells_ANGPTL4-knockdown_hypoxia treatment_2days

description: Cell Culture

source_name: MKN28 gastric cancer cells,ANGPTL4-knockdown, hypoxia treatment, 2days


title: Cells_hypoxia treatment_1day

description: Cell Culture

source_name: MKN28 gastric cancer cells, hypoxia treatment, 1day


title: HSC3-GFP

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: human  tongue cancer cell line with GFP transfection

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: human  tongue cancer cell line

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) supplemented by 10% FB

extract_protocol: RNA samples were extracted from cells after 24 hours from transfection, by Nucleospin RNA (Macherey-Nagel).

treatment_protocol: Full length DKK3-HA-Tag expression plasmid or GFP expression plasmid were transfected into HSC-3 cells. Transfected C2C12 cells were cultured in DMEM containing 10% FBS.

tag: tag


title: HSC3

description: human  tongue cancer cell line


title: Cells_TGFb treatment_1day

description: Cell Culture

source_name: MKN28 gastric cancer cells, TGFb treatment, 1day


title: 546-CR-L5-R1

description:
pair 22, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 22, layer L5, diagnosis Control, replicate R1

value: Unaffected Comparison


title: 581-SZ-L3-R1

description:
pair 21, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 21, layer L3, diagnosis Schiz, replicate R1

value: Chronic paranoid schizophrenia; ADC; OAC


title: HepaRG_week3_C

type: genomic

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

description: barcode: 9611518141_R06C02

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan  with standard recommended Illumina scanner settings

data_processing:
GenomeStudio v2011.1 and R/Bioconductor packages
BMIQ (beta-mixture quantile normalization) normalized Average Beta. Probes with detection P Values > 0.01 were filtered out.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: HepaRG

label_protocol: Standard Illumina Protocol

growth_protocol: HepaRG were kept in culture 5 weeks, until full hepatocyte differentiation.

extract_protocol: genomic DNA was extracted and purified from HepaRG samples by desalting, proteinase K digestion, and ammonium acetate precipitation

treatment_protocol: DNA was extracted from triplicate wells at every week during the differentiation process.

value: HepaRG


title: HSC3-DKK3

description: human  tongue cancer cell line with DKK3 transfection

value: HA


title: HepaRG_week2_C

description: barcode: 9611518141_R06C01


title: HepaRG_week1_C

description: barcode: 9611518141_R04C02


title: Cells_no hypoxia treatment_2days

description: Cell Culture

source_name: MKN28 gastric cancer cells, no hypoxia treatment, 2 days


title: HepaRG_week4_C

description: barcode: 9611518141_R04C01


title: Borderline NASH Rep5

status: Public on Jul 21 2017

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description:
Liver biopsy from male adolescent diagnosed with Borderline NASH
NAS_42

hyb_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocol.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing:
.CEL files were directly imported into GeneSpringv12.6.1, where data log-transformed and underwent quantile normalization and baselining to the median of all samples.
probe group file: HuGene-1_0-st-v1.na34.1.hg19.probeset.csv
meta-probeset file: HuGene-1_0-st-v1.na34.1.hg19.transcript.csv

source_name: Liver biopsy_male adolescent diagnosed with Borderline NASH

label_protocol: standard Affymetrix protocol

growth_protocol: Left or right liver lobe obtained intra-operatively from an obese adolescent undergoing bariatric surgery.

extract_protocol: mRNeasy Mini Kit

treatment_protocol: Immediate submersion into RNAlater for stabilization

tag: sample type

value: Liver wedge biopsy

tag: histology

value: Borderline NASH

tag: age (yrs)

tag: bmi

tag: cholesterol

tag: hdl

tag: ldl

tag: triglycerides


title: Definite NASH Rep1

description:
Liver biopsy from female adolescent diagnosed with Definite NASH
NAS_28

source_name: Liver biopsy_female adolescent diagnosed with Definite NASH

value: female

value: Definite NASH


title: Borderline NASH Rep3

description:
Liver biopsy from female adolescent diagnosed with Borderline NASH
NAS_34

source_name: Liver biopsy_female adolescent diagnosed with Borderline NASH


title: NAFLD not NASH Rep24

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_91

source_name: Liver biopsy_female adolescent diagnosed with NAFLD not NASH

value: NAFLD not NASH


title: Borderline NASH Rep2

description:
Liver biopsy from male adolescent diagnosed with Borderline NASH
NAS_33

value: male


title: Borderline NASH Rep1

description:
Liver biopsy from female adolescent diagnosed with Borderline NASH
NAS_15


title: NAFLD not NASH Rep20

description:
Liver biopsy from male adolescent diagnosed with NAFLD not NASH
NAS_81

source_name: Liver biopsy_male adolescent diagnosed with NAFLD not NASH


title: Borderline NASH Rep4

description:
Liver biopsy from female adolescent diagnosed with Borderline NASH
NAS_35


title: NAFLD not NASH Rep23

description:
Liver biopsy from male adolescent diagnosed with NAFLD not NASH
NAS_88


title: NAFLD not NASH Rep25

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_94


title: NAFLD not NASH Rep22

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_84


title: NAFLD not NASH Rep18

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_8


title: NAFLD not NASH Rep26

description:
Liver biopsy from male adolescent diagnosed with NAFLD not NASH
NAS_98R


title: NAFLD not NASH Rep21

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_82


title: HepaRG_week0_C

description: barcode: 9611518141_R05C02


title: NAFLD not NASH Rep19

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_80


title: Definite NASH Rep2

description:
Liver biopsy from male adolescent diagnosed with Definite NASH
NAS_54

source_name: Liver biopsy_male adolescent diagnosed with Definite NASH


title: HepaRG_week1_B

description: barcode: 9611518141_R03C01


title: HepaRG_week0_B

description: barcode: 9611518141_R01C01


title: NAFLD not NASH Rep17

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_76


title: HepaRG_week3_A

description: barcode: 9611518091_R03C01


title: HepaRG_week3_B

description: barcode: 9611518141_R02C01


title: NAFLD not NASH Rep14

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_69


title: NAFLD not NASH Rep15

description:
Liver biopsy from male adolescent diagnosed with NAFLD not NASH
NAS_73


title: NAFLD not NASH Rep13

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_68


title: NAFLD not NASH Rep16

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_75


title: HepaRG_week4_B

description: barcode: 9611518141_R01C02


title: HepaRG_week2_B

description: barcode: 9611518141_R02C02


title: HepaRG_week4_A

description: barcode: 9611518091_R04C02


title: HepaRG_week2_A

description: barcode: 9611518091_R02C02


title: NAFLD not NASH Rep11

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_57


title: HepaRG_week0_A

description: barcode: 9611518091_R01C01


title: NAFLD not NASH Rep9

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_39


title: NAFLD not NASH Rep6

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_17


title: NAFLD not NASH Rep7

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_18


title: NAFLD not NASH Rep8

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_29


title: NAFLD not NASH Rep3

description:
Liver biopsy from male adolescent diagnosed with NAFLD not NASH
NAS_13


title: NAFLD not NASH Rep10

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_56


title: NAFLD not NASH Rep2

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_105


title: NAFLD not NASH Rep4

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_14


title: HepaRG_week1_A

description: barcode: 9611518091_R06C02


title: NAFLD not NASH Rep12

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_66


title: NAFLD not NASH Rep5

description:
Liver biopsy from female adolescent diagnosed with NAFLD not NASH
NAS_16


title: No NAFLD Rep34

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_97

source_name: Liver biopsy_female adolescent diagnosed with No NAFLD

value: No NAFLD


title: No NAFLD Rep33

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_96


title: NAFLD not NASH Rep1

description:
Liver biopsy from male adolescent diagnosed with NAFLD not NASH
NAS_104


title: No NAFLD Rep31

description:
Liver biopsy from male adolescent diagnosed with No NAFLD
NAS_89

source_name: Liver biopsy_male adolescent diagnosed with No NAFLD


title: No NAFLD Rep30

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_87


title: No NAFLD Rep32

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_92


title: No NAFLD Rep29

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_86


title: No NAFLD Rep27

description:
Liver biopsy from male adolescent diagnosed with No NAFLD
NAS_83


title: No NAFLD Rep28

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_85R


title: No NAFLD Rep24

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_74R


title: No NAFLD Rep23

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_72


title: No NAFLD Rep26

description:
Liver biopsy from male adolescent diagnosed with No NAFLD
NAS_79


title: No NAFLD Rep25

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_77


title: No NAFLD Rep20

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_60


title: No NAFLD Rep21

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_62


title: No NAFLD Rep19

description:
Liver biopsy from male adolescent diagnosed with No NAFLD
NAS_6


title: No NAFLD Rep22

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_71R


title: No NAFLD Rep18

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_55


title: No NAFLD Rep16

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_48


title: No NAFLD Rep13

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_45


title: No NAFLD Rep10

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_36


title: No NAFLD Rep15

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_47


title: No NAFLD Rep17

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_49


title: No NAFLD Rep11

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_37


title: No NAFLD Rep12

description:
Liver biopsy from male adolescent diagnosed with No NAFLD
NAS_38


title: No NAFLD Rep8

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_26


title: No NAFLD Rep14

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_46


title: No NAFLD Rep2

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_101


title: No NAFLD Rep3

description:
Liver biopsy from male adolescent diagnosed with No NAFLD
NAS_106


title: No NAFLD Rep7

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_21


title: No NAFLD Rep9

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_27


title: No NAFLD Rep6

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_19


title: No NAFLD Rep4

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_107


title: 300 µM propofol rep2

city: Houston

first: Ying

last: Liu

address: 1825 Pressler

institute: UTHealth

description: NES-GFP 300-2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Variance-stabilizing transformation and normalization with Robust Spline Normalization method in the package lumi of R

source_name: neural progenitors

label_protocol: Beadarray data was annotated with GenomeStudio.

growth_protocol: The NPCs were cultured and expanded in neural stem cell medium and passaged every 4-5 days with Accutase.

extract_protocol: Total RNA was isolated with RNAeasy mini kit (Qiagen)

treatment_protocol: Zero µM, 20 µM and 300 µM of propofol treatment in human Nestin reporter iPSC-derived NPCs for 6 hours

tag: treatment

value: 300 uM propofol


title: No NAFLD Rep5

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_12


title: HN137-Pri 2

first: Shumei

last: Chia

institute: Genome Institute of Singapore

description: replicate 2

hyb_protocol: Standard Agilient hybridization protocol

scan_protocol: Standard Agilient scanning protocol

data_processing: Data was g-process

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

extract_protocol: RNA was extracted with Qiazol reagent, followed by  purification using RNeasy Mini Kit in accordance with the prescribed protocol provided with the kit.

tag: patient id

tag: tissue

value: primary cancer cells

tag: passage number


title: 20 µM propofol rep1

description: NES-GFP 20-1

value: 20 uM propofol


title: untreated rep2

description: NES-GFP 0-2

value: untreated


title: HN137-Met 2

description: replicate 2

value: metastatic cancer cells


title: 300 µM propofol rep1

description: NES-GFP 300-1


title: No NAFLD Rep1

description:
Liver biopsy from female adolescent diagnosed with No NAFLD
NAS_100

tag: gender


title: renal tissue 20 min warm ischemia 4h perfusion 4°C Belzer solution additioned with MSC replicate 1

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

description: gene expression after 4h perfusion at 4°C with Belzer Solution supplemented with 3 milions MSC

hyb_protocol: Fluorescent dye-labeled cRNA was hybridized to SurePrint G3 Rat Gene Expression 8x60K arrays (Agilent); hybridization and washing were performed on Agilent’s microarray platform, according to standard protocols.

scan_protocol: Microarray images were acquired using an Agilent DNA microarray scanner.

data_processing: Raw data were generated using Agilent Feature Extraction software. Raw median spot intensities were pre-processed using the limma package of the R/Bioconductor project. Briefly, raw data were log2-transformed and normalized using loess normalization implemented in the normalizeBetweenArrays function.

organism: Rattus norvegicus

source_name: renal tissue

label_protocol: Total RNA was amplified using the Low Input Quick Amp WT Labeling kit, according to the manufacturer’s instructions (Agilent Technologies, Santa Clara, USA). 100 ng of total RNA was reverse-transcribed into double-stranded cDNA, which was translated into cRNA in the presence of Cy3-dCTP and amplified by T7 RNA polymerase.

growth_protocol: Rats were maintained at the animal facility of Università degli Studi di Pavia. Animal experiments were authorized by the Italian Health Ministry (n° 339/2016-PR), and performed in accordance to institutional guidelines.

extract_protocol: Total RNA was extracted from rat kidney samples using RNeasy Midi Kit (Qiagen), purified with RNeasy MinElute Cleanup (Qiagen), and quantified by spectrophotometry (ND-1000 spectrophotometer, NanoDrop, Wilmington, DE, USA). RNA integrity was verified using the RNA 6000 Nano Assay Kit (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Rats were anesthetized using Isoflurane 2-5% (Baxter, Como, Italy) and after 20 min of warm ischemia obtained by abdominal aorta clamping, nephrectomy was performed. Kidneys were then perfused with Belzer solution (BS), or  BS supplemented with 3 millions of MSC (MSC), or BS supplemented with MV derived from 3 millions of MSC (MV). Kidney continuous perfusion was performed for 4 h at 4°C.

value: kidney

value: MSC-perfused


title: 20 µM propofol rep2

description: NES-GFP 20-2


title: HN137-Met 1

description: replicate 1


title: untreated rep1

description: NES-GFP 0-1


title: renal tissue 20 min warm ischemia 4h perfusion 4°C Belzer solution additioned with MSC replicate 4


title: renal tissue 20 min warm ischemia 4h perfusion 4°C Belzer solution additioned with MSC replicate 2


title: HN137-Pri 1

description: replicate 1


title: renal tissue 20 min warm ischemia 4h perfusion 4°C Belzer solution additioned with MSC replicate 3


title: renal tissue 20 min warm ischemia 4h perfusion 4°C Belzer solution replicate 3

description: gene expression after 4h perfusion at 4°C with Belzer Solution

value: Not perfused


title: renal tissue 20 min warm ischemia 4h perfusion 4°C Belzer solution replicate 2


title: renal tissue 20 min warm ischemia 4h perfusion 4°C Belzer solution replicate 4


title: renal tissue 20 min warm ischemia 4h perfusion 4°C Belzer solution replicate 5


title: Young normal diet liver, ZT 0, replicate 4

city: College Station

first: Shogo

last: Sato

state: Texas

address: 3258 TAMU, Biological Science Building West (BSBW) 309

department: Biology

institute: Texas A&M University

description: Gene expression data from mouse liver at indicated ZT

hyb_protocol: Hybridisation mixture was prepared according to the Gene Atlas protocol (Affymetrix). Each sample target was hybridised to a Mouse Genome 430 PM array. After hybridisation for 16 hours at 45°C, washing and staining was performed in the GeneAtlas Fluidics Station (Affymetrix).

scan_protocol: The arrays were scanned in a GeneAtlas Imaging Station (Affymetrix). All processing was performed according to manufacturer’s recommendations.

data_processing: Overall array intensity was normalised between arrays and the probe intensity of all probes in a probe set summarised to a single value using RMA (Robust Multichip Average). By selecting the probe that has the highest interquantile range per gene, we reduce the probeset to one probe per gene.

label_protocol: cDNA library preparation and amplification were performed from 25ng total RNA using WTA2 (Sigma-Aldrich) with 17 cycles of amplification. 8µg cDNA were subsequently fragmented by DNAseI and biotinylated by terminal transferase obtained from GeneChip Mapping 10Kv2 Assay Kit (Affymetrix).

growth_protocol: Animals were housed in 12 hour Light/Dark conditions and harvested livers every 4 hours over the circadian cycle

extract_protocol: RNA was extracted using TRizol (Life Technologies)

treatment_protocol: Mice were fed either a normal diet or calorie-restricted diet for 25 weeks

value: Male

tag: strain

tag: age

value: 48 weeks

tag: diet

value: Normal diet

tag: zt


title: renal tissue 20 min warm ischemia 4h perfusion 4°C Belzer solution replicate 1


title: Young calorie-restricted diet liver, ZT 20, replicate 1

value: 51 weeks

value: Calorie-restricted diet


title: Young calorie-restricted diet liver, ZT 20, replicate 3

value: Female

value: 52 weeks


title: Old calorie-restricted diet liver, ZT 20, replicate 4

value: 83 weeks


title: Old normal diet liver, ZT 0, replicate 1

value: 91 weeks


title: Old normal diet liver, ZT 20, replicate 3

value: 88 weeks


title: Young normal diet liver, ZT 20, replicate 2


title: Old normal diet liver, ZT 0, replicate 2

value: 87 weeks


title: Old calorie-restricted diet liver, ZT 0, replicate 3


title: Young normal diet liver, ZT 0, replicate 3


title: Old normal diet liver, ZT 16, replicate 3

value: 90 weeks


title: Old calorie-restricted diet liver, ZT 20, replicate 2


title: Young calorie-restricted diet liver, ZT 0, replicate 1

value: 47 weeks


title: Old calorie-restricted diet liver, ZT 0, replicate 2


title: Young calorie-restricted diet liver, ZT 16, replicate 4

value: 49 weeks


title: Young calorie-restricted diet liver, ZT 20, replicate 5


title: Old calorie-restricted diet liver, ZT 16, replicate 3

value: 89 weeks


title: Young calorie-restricted diet liver, ZT 20, replicate 2

value: 53 weeks


title: Young normal diet liver, ZT 20, replicate 4


title: Young calorie-restricted diet liver, ZT 16, replicate 2


title: Young calorie-restricted diet liver, ZT 0, replicate 5


title: Young normal diet liver, ZT 16, replicate 4

value: 54 weeks


title: Young calorie-restricted diet liver, ZT 8, replicate 2

value: Male


title: Old normal diet liver, ZT 12, replicate 2


title: Old normal diet liver, ZT 20, replicate 1

value: 86 weeks


title: Old calorie-restricted diet liver, ZT 16, replicate 1


title: Young normal diet liver, ZT 20, replicate 1

value: Normal diet


title: Old normal diet liver, ZT 20, replicate 2


title: Young normal diet liver, ZT 20, replicate 3


title: Old normal diet liver, ZT 8, replicate 2


title: Young calorie-restricted diet liver, ZT 12, replicate 5

value: 51 weeks


title: Young normal diet liver, ZT 8, replicate 3


title: Old calorie-restricted diet liver, ZT 8, replicate 1

value: Calorie-restricted diet


title: Old normal diet liver, ZT 12, replicate 1


title: Young calorie-restricted diet liver, ZT 12, replicate 1


title: Old calorie-restricted diet liver, ZT 12, replicate 3


title: Young calorie-restricted diet liver, ZT 8, replicate 3

value: Female


title: Old calorie-restricted diet liver, ZT 8, replicate 2


title: Young normal diet liver, ZT 8, replicate 1

value: 55 weeks


title: Young normal diet liver, ZT 16, replicate 2


title: Young normal diet liver, ZT 12, replicate 3


title: Young calorie-restricted diet liver, ZT 0, replicate 3


title: Old calorie-restricted diet liver, ZT 20, replicate 3


title: Young calorie-restricted diet liver, ZT 16, replicate 5


title: Old calorie-restricted diet liver, ZT 12, replicate 4

value: 92 weeks


title: Young normal diet liver, ZT 12, replicate 4

value: 52 weeks


title: Young calorie-restricted diet liver, ZT 12, replicate 6

value: 48 weeks


title: Old normal diet liver, ZT 16, replicate 1

value: 93 weeks


title: Old calorie-restricted diet liver, ZT 0, replicate 4


title: Young calorie-restricted diet liver, ZT 12, replicate 4


title: Old calorie-restricted diet liver, ZT 12, replicate 2

value: 91 weeks


title: Old calorie-restricted diet liver, ZT 20, replicate 1

value: 85 weeks


title: Young calorie-restricted diet liver, ZT 20, replicate 4


title: Young calorie-restricted diet liver, ZT 4, replicate 5


title: Young calorie-restricted diet liver, ZT 4, replicate 3


title: Young calorie-restricted diet liver, ZT 8, replicate 4

value: 50 weeks


title: Young normal diet liver, ZT 4, replicate 1


title: Young normal diet liver, ZT 4, replicate 2


title: Old normal diet liver, ZT 4, replicate 2


title: Young normal diet liver, ZT 4, replicate 3

value: 57 weeks


title: Young calorie-restricted diet liver, ZT 4, replicate 6

value: 49 weeks


title: Young calorie-restricted diet liver, ZT 4, replicate 2

value: 53 weeks


title: Old normal diet liver, ZT 0, replicate 4

value: Male


title: Old calorie-restricted diet liver, ZT 4, replicate 2

value: 97 weeks


title: Old normal diet liver, ZT 4, replicate 3

value: 88 weeks

value: Normal diet


title: Young calorie-restricted diet liver, ZT 0, replicate 2

value: Calorie-restricted diet


title: Old normal diet liver, ZT 0, replicate 3

value: Female


title: Young normal diet liver, ZT 0, replicate 1

value: 55 weeks


title: Old calorie-restricted diet liver, ZT 0, replicate 1


title: Young calorie-restricted diet liver, ZT 0, replicate 4

value: 51 weeks


title: Young normal diet liver, ZT 0, replicate 2


title: Old normal diet liver, ZT 16, replicate 4

value: 90 weeks


title: Young calorie-restricted diet liver, ZT 12, replicate 3


title: Old normal diet liver, ZT 4, replicate 1

value: 89 weeks


title: Old normal diet liver, ZT 12, replicate 3


title: Old calorie-restricted diet liver, ZT 12, replicate 5


title: Old calorie-restricted diet liver, ZT 12, replicate 1

value: 86 weeks


title: 2 Tumour

city: Cambridge

first: Muhammad

middle: Abdullah

last: Alvi

address: Addenbrooke's site

country: United Kingdom

institute: University of Cambridge

description: FFPE tissue

hyb_protocol: Standard Illumina whole genome DASL HT Protocol

scan_protocol: iScan default settings

data_processing: Normalised to average (no background subtraction) using genomestudio v1.9. Missing data imputed.

source_name: Colon/rectum

growth_protocol: Surgical resections from colorectal cancers patients

extract_protocol: RNeasy FFPE Kit (Qiagen, UK)  FFPE Kit (Qiagen, UK)

treatment_protocol: Formal fixed paraffin embedded

value: tumour


title: 27 Tumour

description: FFPE tissue

label_protocol: Standard Illumina whole genome DASL HT Protocol


title: 28 Tumour

description: FFPE tissue


title: Old normal diet liver, ZT 12, replicate 4

value: 91 weeks


title: 6 Tumour

description: FFPE tissue


title: 3 Tumour

description: FFPE tissue


title: Young normal diet liver, ZT 12, replicate 1


title: Old calorie-restricted diet liver, ZT 16, replicate 2


title: 19 Tumour

description: FFPE tissue


title: 16 Tumour

description: FFPE tissue


title: Young calorie-restricted diet liver, ZT 16, replicate 3


title: 26 Tumour

description: FFPE tissue


title: 24 Tumour

description: FFPE tissue


title: 1 Tumour

description: FFPE tissue


title: 23 Tumour

description: FFPE tissue


title: 18 Tumour

description: FFPE tissue


title: 13 Tumour

description: FFPE tissue


title: Old normal diet liver, ZT 16, replicate 2

value: 85 weeks


title: Young normal diet liver, ZT 16, replicate 3

value: 56 weeks


title: 15 Tumour

description: FFPE tissue


title: 22 Tumour

description: FFPE tissue


title: 14 Tumour

description: FFPE tissue


title: Young calorie-restricted diet liver, ZT 16, replicate 1


title: 12 Tumour

description: FFPE tissue


title: Young calorie-restricted diet liver, ZT 12, replicate 2

value: 54 weeks


title: 11 Tumour

description: FFPE tissue


title: Old calorie-restricted diet liver, ZT 16, replicate 4


title: 9 Tumour

description: FFPE tissue


title: Young normal diet liver, ZT16, replicate 1


title: 7 Tumour

description: FFPE tissue


title: 10 Tumour

description: FFPE tissue


title: 5 Tumour

description: FFPE tissue


title: 17 Tumour

description: FFPE tissue


title: 7 Normal

description: FFPE tissue

value: normal


title: 12 Normal

description: FFPE tissue


title: 4 Tumour

description: FFPE tissue


title: 11 Normal

description: FFPE tissue


title: 13 Normal

description: FFPE tissue


title: 16 Normal

description: FFPE tissue


title: Old calorie-restricted diet liver, ZT 8, replicate 3

value: 87 weeks


title: Old calorie-restricted diet liver, ZT 4, replicate 3


title: Young calorie-restricted diet liver, ZT 4, replicate 4

value: 50 weeks


title: Young normal diet liver, ZT 8, replicate 4

value: Male


title: Old normal diet liver, ZT 4, replicate 4

value: 88 weeks

value: Normal diet


title: Young calorie-restricted diet liver, ZT 8, replicate 1

value: 53 weeks

value: Calorie-restricted diet


title: Young calorie-restricted diet liver, ZT 4, replicate 1


title: 2 Normal

description: FFPE tissue


title: Young normal diet liver, ZT 4, replicate 5


title: Young normal diet liver, ZT 8, replicate 2

value: Female

value: 52 weeks


title: 3 Normal

description: FFPE tissue


title: Old calorie-restricted diet liver, ZT 4, replicate 1


title: Old normal diet liver, ZT 8, replicate 3


title: Old calorie-restricted diet liver, ZT 8, replicate 4


title: 5 Normal

description: FFPE tissue


title: 4 Normal

description: FFPE tissue


title: Young calorie-restricted diet liver, ZT 8, replicate 5


title: 15 Normal

description: FFPE tissue


title: Old normal diet liver, ZT 8, replicate 1

value: 84 weeks


title: Young normal diet liver, ZT 12, replicate 2

value: 57 weeks


title: Young normal diet liver, ZT 4, replicate 4

value: 23 weeks


title: 30 Tumour

description: FFPE tissue

value: tumour


title: 8 Tumour

description: FFPE tissue


title: S16 Tumor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450 Beadchip using standard Illumina protocol

data_processing: Genome studio methylation module v19

source_name: Colon/Rectum

extract_protocol: Maxwell 16 FFPE Plus LEV DNA Purification Kit (Promega, UK)

tag: disease state

tag: sample type

value: validation cohort


title: S17 Tumor


title: S13 Tumor


title: S12 Tumor


title: S10 Tumor


title: S8 Tumor


title: S6 Tumor


title: 28 Tumor

value: test cohort


title: S7 Tumor


title: S18 Tumor


title: S11 Tumor


title: S2 Tumor


title: S5 Tumor


title: S4 Tumor


title: S15 Tumor


title: S14 Tumor


title: 30 Tumor


title: 4 Tumor


title: 5 Tumor


title: S3 Tumor


title: 9 Tumor


title: 27 Tumor


title: S9 Tumor


title: 7 Tumor


title: 3 Tumor


title: 2 Tumor


title: 22 Tumor


title: S1 Tumor


title: 8 Tumor


title: 6 Tumor


title: 1 Tumor


title: 26 Tumor


title: Retina Male Aged3

city: Hershey

first: Penn State

last: COM

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description:
Replicate 3
8129677029_H

data_processing: The data were normalized using average normalization

source_name: Retina

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

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 Bioanalyser.

treatment_protocol: Mice were aged without any genetic or pharmacological intervention

value: male

value: 24 months


title: Retina Male Aged1

description:
Replicate 1
7469531035_D

value: 12 months


title: Retina Male Aged4

description:
Replicate 4
8129677038_A


title: Retina Male Aged2

description:
Replicate 2
8129677029_B


title: 7 Normal

value: normal


title: 12 Tumor


title: Retina Male Young4

description:
Replicate 4
8129677029_F

value: 3 months


title: 5 Normal


title: Retina Male Young3

description:
Replicate 3
8129677029_D


title: 23 Tumor


title: Retina Male Young2

description:
Replicate 2
8129677027_B


title: 18 Tumor


title: 17 Tumor


title: 10 Tumor


title: 19 Tumor


title: 24 Tumor


title: Retina Female Aged4

description:
Replicate 4
8129677038_D

value: female


title: Retina Female Young4

description:
Replicate 4
8129677049_H


title: Retina Female Aged1

description:
Replicate 1
7469531035_B


title: Retina Male Young1

description:
Replicate 1
7469531035_C


title: Retina Female Aged3

description:
Replicate 3
8129677027_E


title: Retina Female Aged2

description:
Replicate 2
7469531035_H


title: Retina Female Young3

description:
Replicate 3
8129677038_F


title: 15 Normal


title: 2 Normal


title: 15 Tumor


title: 16 Tumor


title: Retina Female Young2

description:
Replicate 2
8129677029_E


title: EV replicate 2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: gene expression data with EV control

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 18 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: EV-transfected SW480 cell line

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

growth_protocol: Human colorectal cancer cell line SW480 (from ATCC) was grown in DMEM supplemented with 10% (v/v) FCS, 20 mM glutamine and penicillin/streptomycin (1000 U/ml; Thermo Fisher Scientific)

extract_protocol: Total RNA was extracted using RNeasy Total RNA Mini Kit (from Qiagen)

treatment_protocol: Cells were transiently transfected using liposomes (Turbofect, Thermo Fisher Scientific) in triplicates of either TUSC3-pTarget expression plasmid  or pTarget (Promega) empty vector (EV) control

value: EV


title: 13 Normal


title: EV replicate 1

description: gene expression data with EV control


title: 14 Tumor


title: HN137_Pri_CL_BW

description:
Biological replicate 1 of 1. Cancer cell line derived from lymph node metastatic tumor of patient HN137
Identification of primary tumor specific genomic alteration

hyb_protocol: Agilient insitu hybridisation kit (cat. No. 5188-6420)

scan_protocol: Scanned on a G2600D Sure Scan microarray scanner

data_processing: At least 3 consecutive probe sets were used to call a CNV. Abberent intervals were identified using the Aberation Detection Algorithms (ADM-2) with a threshold of 6.0, a minimum absolute average log2 ratio per region of 0.25, and nesting filter of 100

source_name: HN137 primary cancer cells

label_protocol: Agilent Sure Tag Genomic DNA labelling kit (Agilient cat. No. 5190-3399).  Random primer labeling using Exo-Klenow to label restriction digested DNA samples.

growth_protocol: Cell lines were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum

extract_protocol: Total DNA extracted using Qiagen DNeasy blood & tissue kit following manufacturer's instructions

tag: cell line

value: primary cancer cells

source_name: DNA from HN137 blood

value: blood


title: HN137_Met_CL_BW

description:
Biological replicate 1 of 1. Cancer cell line derived from primary tumor of patient HN137
Identification of metastatic tumor specific genomic alteration

source_name: HN137 metastatic cancer cells

value: metastatic cancercells


title: 11 Tumor


title: TUSC3 replicate 3

description: gene expression data with TUSC3 overexpression

source_name: TUSC3-transfected SW480 cell line


title: 4 Normal


title: 13 Tumor


title: 11 Normal


title: 3 Normal


title: 12 Normal


title: 16 Normal


title: Retina Female Young1

description:
Replicate 1
8129677027_F


title: TUSC3 replicate 1


title: Individual 20_B

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

institute: INSERM

hyb_protocol: 825 ng of Cy5 labelled probe was cohybridized the same amount of Cy3 labelled control probe. We used the Whole Human Genome Microarray Kit, 4x44K from Agilent with the gene expression hybridization kit according to the manufacturer’s protocol

scan_protocol: Micro-arrays were scanned on a InnoScan 710A scanner (Innopsys, Carbonne, France, EU) and data were extracted with Mapix software version 6.5.0 (Innopsys).

data_processing: Features with a signal to background ratio strictly below 2 in both color as well as control spots were discarded. The data without background subtraction were normalized with the Lowess procedure and quantiles method by use of R.

source_name: Subcutaneous adipose tissue from obese individual;  after dietary intervention

label_protocol: Total RNA quality was checked by capillary electrophoresis (Experion, BioRad) and quantified using Nanodrop ND-1000 Spectrophotometer (Labtech). Only good quality RNA extracts only were used for microarray hybridization. Fluorescent probes were obtained by amplifying and labelling 200ng of RNA with the low RNA input linear amplification kit (Agilent).

extract_protocol: Adipose tissue was crushed in QIAzol (Qiagen) and total RNA was extracted with the RNeasy mini kit (Qiagen) according to manufacturer instructions.

treatment_protocol: individuals followed a low-calorie (800-1000 kcal/day) diet for 8 weeks; those that lost at least 8% of their baseline weight were randomized to one of four ad libitum follow-up diets or a control diet for 6 months

tag: Sex

value: mix of male and female

value: mix of liver, adipose tissue and skeletal muscle

source_name: Subcutaneous adipose tissue

value: Female

value: Subcutaneous adipose tissue

tag: group

value: Poor-controller


title: EV replicate 3

description: gene expression data with EV control


title: Individual 20_A

source_name: Subcutaneous adipose tissue from obese individual;  baseline


title: TUSC3 replicate 2


title: Individual 18_A


title: Individual 19_A


title: Individual 21_B


title: Individual 19_B


title: Individual 21_A


title: Individual 18_B


title: Individual 16_A

value: Male


title: Individual 15_B


title: Individual 15_A


title: Individual 16_B


title: Individual 17_B


title: Individual 14_A


title: Individual 14_B


title: Individual 17_A


title: Individual 12_B


title: Individual 13_B


title: Individual 13_A


title: Individual 11_A

value: Good-controller


title: Individual 9_A


title: Individual 11_B


title: Individual 10_B


title: Individual 10_A


title: Individual 9_B


title: Individual 12_A


title: Individual 8_B


title: Individual 6_B


title: Individual 7_A


title: Individual 4_B


title: Individual 6_A


title: Individual 8_A


title: Individual 7_B


title: Individual 5_A


title: Individual 5_B


title: Individual 2_B


title: Individual 1_A


title: Individual 1_B


title: Individual 2_A


title: Individual 3_A


title: Individual 4_A


title: 9237300012_E

status: Public on Jul 20 2017

city: Frankfurt

first: Andreas

last: Weigert

address: Theodor-Sern-Kai 7

department: Medicine

institute: Goethe-University

description: WT MCA_replicate 1

data_processing: The data were normalised using quantile normalisation with R and the Bioconductor package 'preprocessCore'

source_name: Mouse MCA fibrosarcoma

label_protocol: The NuGEN Ovation Pico WTA System (linear isothermal DNA amplification process) was used to generate single-stranded cDNA from small input amounts of 2,5ng RNA Labeled cRNA were prepared according to Nugene Encore® BiotinIL Module.

extract_protocol: RNA from pooled FACS-sorted CD11b-high macrophages was isolated using the RNEasy micro kit (Quiagen), quality controlled using the Agilent 2100 Bioanalyzer and pico RNA chips (Agilent) and amplified using the µMACS SuperAmp Kit (Miltenyi)

value: male

tag: tumor type

value: MCA fibrosarcoma


title: 9237300012_C

description: internal control mixed MCA macrophages_replicate 1


title: 9237300012_D

description: internal control mixed MCA macrophages_replicate 2


title: 9237300012_A

description: S1PR1 KO MCA_replicate 1


title: 9237299028_F

description: internal control for array reproducibility - identical to 9237300012_A


title: 9237300012_B

description: S1PR1 KO MCA_replicate 2


title: 9237300012_F

description: WT MCA_replicate 2


title: 9237299028_C

description: S1PR1 KO PyMT_replicate 2

source_name: Mouse PyMT breast tumor

value: PyMT breast tumor


title: 9237299028_E

description: WT PyMT_replicate 2


title: 9237299028_B

description: S1PR1 KO PyMT_replicate 1


title: juvenile-GCT tumour 5

city: Auckland

first: Wei-Tzu

last: Cheng

address: 85 Park Road

department: Obstetrics and Gynaecology

country: New Zealand

institute: The University of Auckland

description: MicroRNA expression data from juvenile-GCT FFPE tumour 5

hyb_protocol: Biotin labelled sample was hybridized for 16 hr at 48C on MiRNA v3 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: MicroRNAChips were scanned using the Affymetrix MicroRNAChip Scanner 7G.

data_processing: Quality assessment of the raw array data was performed using the Affymetrix Expression Console software (Affymetrix), and arrays were normalised using the Detection Above Background (DABG) algorithm for background correction using the Affymetrix Transcriptomic Analysis Console 2.0 software (Affymetrix, USA).

source_name: juvenile-GCT tumour 5

label_protocol: Biotinylated RNA were prepared using 8 µl input (FlashTag™ Biotin HSR RNA Labeling Kit, Affymetrix)

extract_protocol: Total RNA was extracted from four 20micron FFPE sections using RecoverAll Total Nucleic Acid Isolation Kit for FFPE according to manufacturer's instructions.

tag: tissue preparation

tag: histological subtype

value: juvenile-GCT

value: ovary

tag: cell type

value: granulosa cell tumor


title: juvenile-GCT tumour 4

description: MicroRNA expression data from juvenile-GCT FFPE tumour 4

source_name: juvenile-GCT tumour 4


title: adult-GCT tumour 3

description: MicroRNA expression data from adult-GCT FFPE tumour 3

source_name: adult-GCT tumour 3

value: adult-GCT


title: juvenile-GCT tumour 1

description: MicroRNA expression data from juvenile-GCT FFPE tumour 1

source_name: juvenile-GCT tumour 1


title: adult-GCT tumour 4

description: MicroRNA expression data from adult-GCT FFPE tumour 4

source_name: adult-GCT tumour 4


title: adult-GCT tumour 2

description: MicroRNA expression data from adult-GCT FFPE tumour 2

source_name: adult-GCT tumour 2


title: 9237299028_A

description: internal control mixed PyMT macrophages

value: female


title: juvenile-GCT tumour 2

description: MicroRNA expression data from juvenile-GCT FFPE tumour 2

source_name: juvenile-GCT tumour 2


title: adult-GCT tumour 5

description: MicroRNA expression data from adult-GCT FFPE tumour 5

source_name: adult-GCT tumour 5


title: juvenile-GCT tumour 3

description: MicroRNA expression data from juvenile-GCT FFPE tumour 3

source_name: juvenile-GCT tumour 3


title: adult-GCT tumour 1

description: MicroRNA expression data from adult-GCT FFPE tumour 1

source_name: adult-GCT tumour 1


title: 9237299028_D

description: WT PyMT_replicate 1


title: Individual 3_B


title: mouse corpus callosum microglia P3_3

status: Public on Jul 19 2017

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

description:
P083_03_MG.CC3.P3
mouse brain P3

hyb_protocol: Biotinylated cRNA was hybridized on GeneChip® Mouse Gene 2.0 ST Arrays , that were stained, washed and scanned following standard procedures.

data_processing: Background correction and normalization was performed using RMA as implemented in BRB-Tools

source_name: corpus callosum microglia P3

label_protocol: Total RNA was amplified using the Ovation PicoSL WTA System V2 and further processed using the Encore Biotin Module according to the instructions supplied by the manufacturer (NuGen).

growth_protocol: SPF housed mice

extract_protocol: Microglia from the mouse brain were isolated preparing single cells by a percoll gradient followed by sorting cells by the surface marker CD45, CD11b positive, Gr1 negative.

treatment_protocol: no treatment prior to cell isolation

value: brain

tag: tissue region

value: corpus callosum

value: microglia

tag: developmental stage

value: postnatal day 3


title: mouse corpus callosum microglia adult_3

description:
A992d_12_aCC3
mouse brain adult

scan_protocol: Biotinylated cRNA was hybridized on GeneChip® Mouse Gene 2.0 ST Arrays , that were stained, washed and scanned following standard procedures.

source_name: corpus callosum microglia adult

tag: tissue

value: adult


title: mouse cortex microglia P3_2

description:
P083_05_MG.Cx2.P3
mouse brain P3

source_name: cortex microglia P3

value: cortex


title: mouse cortex microglia adult_3

description:
A992d_09_aCx3
mouse brain adult

source_name: cortex microglia adult


title: mouse corpus callosum microglia P3_2

description:
P083_02_MG.CC2.P3
mouse brain P3


title: mouse cortex microglia adult_2

description:
A992d_08_aCx2
mouse brain adult


title: mouse cortex microglia adult_1

description:
A992d_07_aCx1
mouse brain adult


title: mouse corpus callosum microglia P3_1

description:
P083_01_MG.CC1.P3
mouse brain P3


title: mouse cortex microglia P3_3

description:
P083_06_MG.Cx3.P3
mouse brain P3


title: mouse corpus callosum microglia adult_2

description:
A992d_11_aCC2
mouse brain adult


title: mouse corpus callosum microglia P7_2

description:
A992d_05_P7.CC2
mouse brain P7

source_name: corpus callosum microglia P7

value: postnatal day 7


title: mouse cortex microglia P3_1

description:
P083_04_MG.Cx1.P3
mouse brain P3


title: mouse corpus callosum microglia adult_1

description:
A992d_10_aCC1
mouse brain adult


title: mouse corpus callosum microglia P7_1

description:
A992d_04_P7.CC1
mouse brain P7


title: mouse cortex microglia P7_3

description:
A992d_03_P7.Cx3
mouse brain P7

source_name: cortex microglia P7


title: mouse cortex microglia P7_2

description:
A992d_02_P7.Cx2
mouse brain P7


title: mouse cortex microglia P7_1

description:
A992d_01_P7.Cx1
mouse brain P7


title: mouse corpus callosum microglia P7_3

description:
A992d_06_P7.CC3
mouse brain P7


title: Bone met sample 46

city: UMEÅ

first: Pernilla

last: Wikström

address: Department of Medical biosciences, Buildning 6M, 2nd floor

department: Medical biosciences, Pathology

country: Sweden

institute: Umeå University

description: SAMPLE 46

data_processing: The data were normalized using the cubic spline algorithm (GenomeStudio software, version 2011.1) and probes with all signals lower than two-times the mean background were excluded.

label: Biotin

source_name: Patient 46

label_protocol: Biotinylated cRNA were prepared with Ambions Illumina TotalPrep RNA Amplification Kit. Quality control was performed with Agilent Bioanalyzer.

extract_protocol: RNA was extracted with Trizol reagent or QIAGEN Allprep DNA/RNA/Protein Mini Kit. Quality control was performed with Agilent Bioanalyzer.

value: Untreated sarcoma

value: Bone metastases


title: Bone met sample 48

description: SAMPLE 48

source_name: Patient 48

value: Untreated kidney cancer


title: Bone met sample 49

description: SAMPLE 49

source_name: Patient 49

value: Untreated unknown adenocarcinoma


title: Bone met sample 47

description: SAMPLE 47

source_name: Patient 47

value: Untreated lung squamous cell carcinoma


title: Bone met sample 44

description: SAMPLE 44

source_name: Patient 44

value: Untreated liver cancer


title: Bone met sample 57

description: SAMPLE 57

source_name: Patient 57

value: Untreated prostate cancer


title: Bone met sample 43

description: SAMPLE 43

source_name: Patient 43

value: Untreated colon cancer


title: Bone met sample 58

description: SAMPLE 58

source_name: Patient 58


title: Bone met sample 53

description: SAMPLE 53

source_name: Patient 53

value: Untreated myeloma


title: Bone met sample 59

description: SAMPLE 59

source_name: Patient 59


title: Bone met sample 39

description: SAMPLE 39

source_name: Patient 39

value: Castration-resistant prostate cancer

tag: crpc subgroup according to ar activity

value: AR driven


title: Bone met sample 52

description: SAMPLE 52

source_name: Patient 52


title: Bone met sample 50

description: SAMPLE 50

source_name: Patient 50


title: Bone met sample 51

description: SAMPLE 51

source_name: Patient 51


title: Bone met sample 56

description: SAMPLE 56

source_name: Patient 56


title: Bone met sample 60

description: SAMPLE 60

source_name: Patient 60


title: Bone met sample 40

description: SAMPLE 40

source_name: Patient 40


title: Bone met sample 55

description: SAMPLE 55

source_name: Patient 55


title: Bone met sample 54

description: SAMPLE 54

source_name: Patient 54


title: Bone met sample 41

description: SAMPLE 41

source_name: Patient 41


title: Bone met sample 45

description: SAMPLE 45

source_name: Patient 45

value: Untreated lymphoma


title: Bone met sample 37

description: SAMPLE 37

source_name: Patient 37


title: Bone met sample 35

description: SAMPLE 35

source_name: Patient 35

value: non-AR driven


title: Bone met sample 36

description: SAMPLE 36

source_name: Patient 36


title: Bone met sample 42

description: SAMPLE 42

source_name: Patient 42


title: Bone met sample 34

description: SAMPLE 34

source_name: Patient 34


title: Bone met sample 38

description: SAMPLE 38

source_name: Patient 38


title: Bone met sample 31

description: SAMPLE 31

source_name: Patient 31


title: Bone met sample 33

description: SAMPLE 33

source_name: Patient 33


title: Bone met sample 32

description: SAMPLE 32

source_name: Patient 32


title: Bone met sample 24

description: SAMPLE 24

source_name: Patient 24


title: Bone met sample 21

description: SAMPLE 21

source_name: Patient 21


title: Bone met sample 19

description: SAMPLE 19

source_name: Patient 19


title: Bone met sample 15

description: SAMPLE 15

source_name: Patient 15


title: Bone met sample 12

description: SAMPLE 12

source_name: Patient 12


title: Bone met sample 14

description: SAMPLE 14

source_name: Patient 14


title: Bone met sample 29

description: SAMPLE 29

source_name: Patient 29


title: Bone met sample 27

description: SAMPLE 27

source_name: Patient 27


title: Bone met sample 18

description: SAMPLE 18

source_name: Patient 18


title: Bone met sample 23

description: SAMPLE 23

source_name: Patient 23


title: Bone met sample 26

description: SAMPLE 26

source_name: Patient 26


title: Bone met sample 30

description: SAMPLE 30

source_name: Patient 30


title: Bone met sample 16

description: SAMPLE 16

source_name: Patient 16


title: Bone met sample 7

description: SAMPLE 7

source_name: Patient 7


title: Bone met sample 11

description: SAMPLE 11

source_name: Patient 11


title: Bone met sample 17

description: SAMPLE 17

source_name: Patient 17


title: Bone met sample 6

description: SAMPLE 6

source_name: Patient 6


title: Bone met sample 8

description: SAMPLE 8

source_name: Patient 8


title: Bone met sample 20

description: SAMPLE 20

source_name: Patient 20


title: Bone met sample 25

description: SAMPLE 25

source_name: Patient 25


title: Bone met sample 9

description: SAMPLE 9

source_name: Patient 9


title: Bone met sample 22

description: SAMPLE 22

source_name: Patient 22


title: Bone met sample 13

description: SAMPLE 13

source_name: Patient 13


title: Bone met sample 4

description: SAMPLE 4

source_name: Patient 4


title: Bone met sample 3

description: SAMPLE 3

source_name: Patient 3


title: Bone met sample 10

description: SAMPLE 10

source_name: Patient 10


title: Bone met sample 2

description: SAMPLE 2

source_name: Patient 2


title: Bone met sample 5

description: SAMPLE 5

source_name: Patient 5


title: Bone met sample 1

description: SAMPLE 1

source_name: Patient 1


title: Patient 37 Border

city: Mainz

first: Jens

last: Marquardt

address: Langenbeckstraße 1

department: Department of Medicine I

institute: Johannes Gutenberg University Mainz

description: Sample name: HCC-37-B

hyb_protocol: Standard Illumina pipeline.

scan_protocol: Iscan pipeline

data_processing: Illumina pipeline background subtraction quantile normalization.

source_name: liver tissue, border

label_protocol: Standard Illumina pipeline.

extract_protocol: Standard Illumina pipeline.

tag: disease status

value: hepatocellular carcinoma (HCC)

value: invasive border region of liver tumor

tag: patient identifier


title: Patient 36 Border

description: Sample name: HCC-36-B


title: Patient 37 Normal

description: Sample name: HCC-37-N

source_name: liver tissue, normal

value: normal liver surrounding tumor


title: Patient 36 Tumor

description: Sample name: HCC-36-T

source_name: liver tissue, tumor

value: liver tumor


title: Patient 29 Border

description: Sample name: HCC-29-B


title: CNS xenograft sample, biological rep6

city: Ulm

first: Hans

middle: A

last: Kestler

address: Albert-Einstein-Allee 11

department: Research Group Bioinformatics and Systems Biology

institute: University of Ulm

description: Gene expression data from human leukemic cells isolated from CNS of xenografted CNS-positive NOD/SCID mice

hyb_protocol: After aRNA purification, quality and quantity evaluation, and fragmentation of 15µg aRNA according to the manuals' instructions, 12.5µg aRNA was hybridzed for 16h at 45°C on HG-U133 Plus2.0 Affymetrix microarray gene chips following the manufacturer's instructions. Cartridges were washed and stained using the Affymetrix Fluidics Station 450DX

scan_protocol: Cartridge arrays were scanned using the Scan GCS3000Dx and were analysed using Afymetrix' GCOS software 1.2 or 1.4

data_processing: Expression data were analyzed using R/Bioconductor. Arrays were normalized and log2 transformed using robust multiple-array average (RMA) with default parameters (Bioconductor package affy). Differentially expressed genes were calculated by the shrinkage T-statistic (package st) and controlled for multiple comparison by FDR.

source_name: human leukemia cells isolated from CNS of a CNS-positive sample

label_protocol: 100ng total RNA was biotin-labeled according to Affymetrix' recommendations (Affymetrix User Manual P/N 702646 Rev. 8)

growth_protocol: Primograft human leukemic cells were intravenously xenotransplanted into NOD/SCID mice. Mice were monitored biweekly for the appearance of human leukemic cells in peripheral blood. When moribund mice were sacrificed and human leukemia was validated in CNS and BM. Cells isolated from CNS and BM were subjected for RNA preparation.

extract_protocol: Trizol preparation following the manufacturer's instructions

tag: tissue/xenotransplantation model

value: human leukemia cells isolated from CNS of NOD/SCID mice


title: Patient 33 Normal

description: Sample name: HCC-33-N


title: Patient 37 Tumor

description: Sample name: HCC-37-T


title: Patient 32 Normal

description: Sample name: HCC-32-N


title: Patient 31 Border

description: Sample name: HCC-31-B


title: Patient 36 Normal

description: Sample name: HCC-36-N


title: CNS xenograft sample, biological rep1


title: Patient 30 Normal

description: Sample name: HCC-30-N


title: Patient 30 Border

description: Sample name: HCC-30-B


title: Patient 32 Border

description: Sample name: HCC-32-B


title: Patient 33 Border

description: Sample name: HCC-33-B


title: Patient 32 Tumor

description: Sample name: HCC-32-T


title: BM xenograft sample, biological rep1

description: Gene expression data from human leukemic cells isolated from BM of xenografted CNS-positive NOD/SCID mice

source_name: human leukemia cells isolated from BM of a CNS-positive sample

value: human leukemia cells isolated from BM of NOD/SCID mice


title: Patient 31 Tumor

description: Sample name: HCC-31-T


title: Patient 34 Normal

description: Sample name: HCC-34-N


title: Patient 27 Border

description: Sample name: HCC-27-B


title: Patient 31 Normal

description: Sample name: HCC-31-N


title: Patient 27 Tumor

description: Sample name: HCC-27-T


title: Patient 29 Tumor

description: Sample name: HCC-29-T


title: Patient 30 Tumor

description: Sample name: HCC-30-T


title: Patient 33 Tumor

description: Sample name: HCC-33-T


title: Patient 34 Border

description: Sample name: HCC-34-B


title: Patient 29 Normal

description: Sample name: HCC-29-N


title: Patient 34 Tumor

description: Sample name: HCC-34-T


title: Patient 26 Tumor

description: Sample name: HCC-26-T


title: BM xenograft sample, biological rep6


title: BM xenograft sample, biological rep8


title: Bone met sample 28

description: SAMPLE 28

source_name: Patient 28

value: Bone metastases


title: CNS xenograft sample, biological rep7


title: Patient 24 Border

description: Sample name: HCC-24-B


title: Patient 27 Normal

description: Sample name: HCC-27-N


title: CNS xenograft sample, biological rep8


title: Patient 26 Border

description: Sample name: HCC-26-B


title: BM xenograft sample, biological rep7


title: Patient 23 Border

description: Sample name: HCC-23-B


title: Patient 26 Normal

description: Sample name: HCC-26-N


title: Patient 23 Tumor

description: Sample name: HCC-23-T


title: Patient 24 Tumor

description: Sample name: HCC-24-T


title: Patient 22 Border

description: Sample name: HCC-22-B


title: Patient 21 Normal

description: Sample name: HCC-21-N


title: Patient 20 Tumor

description: Sample name: HCC-20-T


title: Patient 24 Normal

description: Sample name: HCC-24-N


title: Patient 21 Tumor

description: Sample name: HCC-21-T


title: BM xenograft sample, biological rep5


title: Patient 20 Border

description: Sample name: HCC-20-B


title: Patient 22 Tumor

description: Sample name: HCC-22-T


title: Patient 22 Normal

description: Sample name: HCC-22-N


title: CNS xenograft sample, biological rep5


title: Patient 21 Border

description: Sample name: HCC-21-B


title: Patient 23 Normal

description: Sample name: HCC-23-N


title: CNS xenograft sample, biological rep3


title: Patient 20 Normal

description: Sample name: HCC-20-N


title: SM16_4

city: Philadelphia

first: Louise

middle: C

last: Showe

address: 3601 Spruce St

institute: The Wistar Institute

description: clonal mouse

hyb_protocol: Hyb on Illumina Mouse Ref-8 v2 Expression BeadChip Kit using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina GenomeStudio software was used to export expression levels and detection p-values for each probe of each sample. Signal intensity data was quantile normalized and  genes that showed insignificant detection p-value (p>0.05) in all samples were removed from further analysis.

source_name: TANs following treatment with SM16

label_protocol: Biotin Labeling of RNA at 250ng with Ambion Illumina® TotalPrep RNA Amplification Kit (Cat #AMIL1791)

extract_protocol: Total RNA from formalin-fixed paraffin embedded tissues was isolated with High Pure RNA Paraffin Kit (Roche Applied Science, Branford, CT).

treatment_protocol: Ectocervical biopsies were placed in Safe Fix II All-Purpose Fixative (Fisher) for 4 hours at room temperature, and then washed twice in 80% ethanol (5 minutes) and then stored in 80% ethanol (room temperature) until embedded in paraffin.

value: tumor-associated neutrophils (TANs)


title: BM xenograft sample, biological rep2


title: SM16_5

description: clonal mouse


title: Patient 17 Tumor

description: Sample name: HCC-17-T


title: BM xenograft sample, biological rep3


title: SM16_3

description: clonal mouse


title: SM16_2

description: clonal mouse


title: Patient 17 Normal

description: Sample name: HCC-17-N


title: BM xenograft sample, biological rep9


title: Patient 17 Border

description: Sample name: HCC-17-B


title: Patient 11 Tumor

description: Sample name: HCC-11-T


title: SM16_1

description: clonal mouse


title: G-MDSC_4

description: clonal mouse

source_name: Splenic neut. of tumor-bearing mice

value: splenic neutrophils of tumor-bearing mice


title: CNS xenograft sample, biological rep4


title: CNS xenograft sample, biological rep9


title: G-MDSC_1

description: clonal mouse


title: G-MDSC_3

description: clonal mouse


title: BM xenograft sample, biological rep4


title: G-MDSC_2

description: clonal mouse


title: Patient 10 Border

description: Sample name: HCC-10-B


title: Patient 11 Normal

description: Sample name: HCC-11-N


title: Patient 8 Tumor

description: Sample name: HCC-8-T


title: TAN_1

description: clonal mouse

source_name: Neutrophils from tumor


title: Patient 10 Tumor

description: Sample name: HCC-10-T


title: Patient 11 Border

description: Sample name: HCC-11-B


title: Patient 8 Border

description: Sample name: HCC-8-B


title: Patient 10 Normal

description: Sample name: HCC-10-N


title: NN_6

description: clonal mouse

source_name: BM naïve neutrophils

value: BM naïve neutrophils


title: TAN_2

description: clonal mouse


title: Patient 8 Normal

description: Sample name: HCC-8-N


title: Patient 4 Tumor

description: Sample name: HCC-4-T


title: Patient 4 Border

description: Sample name: HCC-4-B


title: CNS xenograft sample, biological rep2


title: NN_7

description: clonal mouse


title: NN_2

description: clonal mouse


title: NN_1

description: clonal mouse


title: NN_5

description: clonal mouse


title: OC20_donor 2

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

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

country: Spain

institute: Josep Carreras Research Institute (IJC)

description: CD14 cells treated with M-CSF/RANKL for 20 days

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing:
Expression data has been normalized using functions from the R package limma. In detail the data was background corrected using the function "normexp" and then normalized between arrays using quantile normalization. Normalized array feature values were grouped by gene name and summarized by mean. The "patient effect" was substracted from the genewise data by a linear model using "patient" as predictor.
Given are the luminescense values (Cy3) from the Agilent array; as raw data for all array features and as normalized and summarized genewise expression values as described above.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human monocytes were isolated using MACS CD14 microbeads (Milteny) from peripheral blood mononuclear cells using the manufacturer's protocol

extract_protocol: Not provided

treatment_protocol: No treatment


title: Patient 1 Tumor

description: Sample name: HCC-1-T


title: Patient 3 Tumor

description: Sample name: HCC-3-T


title: Patient 1 Border

description: Sample name: HCC-1-B


title: OC20_donor 3

source_name: CD14 cells treated with M-CSF/RANKL for 20 days


title: MAC20_donor 3

description: CD14 cells treated with M-CSF for 20 days


title: OC20_donor 1

value: CD14 cells treated with M-CSF/RANKL for 20 days


title: NN_4

description: clonal mouse


title: Patient 3 Normal

description: Sample name: HCC-3-N


title: MAC20_donor 1

source_name: CD14 cells treated with M-CSF for 20 days


title: OC5_donor 2

description: CD14 cells treated with M-CSF/RANKL for 5 days


title: OC5_donor 3

source_name: CD14 cells treated with M-CSF/RANKL for 5 days


title: NN_3

description: clonal mouse


title: OC5_donor 1

value: CD14 cells treated with M-CSF/RANKL for 5 days


title: MAC20_donor 2

value: CD14 cells treated with M-CSF for 20 days


title: MAC5_donor 3

description: CD14 cells treated with M-CSF for 5 days


title: MAC5_donor 2

source_name: CD14 cells treated with M-CSF for 5 days


title: Patient 3 Border

description: Sample name: HCC-3-B


title: MAC5_donor 1

value: CD14 cells treated with M-CSF for 5 days


title: Patient 1 Normal

description: Sample name: HCC-1-N


title: CD14_monocyte_donor 1

description: peripheral blood isolated CD14+ cells (monocytes)


title: CD14_monocyte_donor 3

source_name: peripheral blood isolated CD14+ cells (monocytes)


title: Patient 4 Normal

description: Sample name: HCC-4-N


title: CD14_monocyte_donor 2

value: peripheral blood isolated CD14+ cells (monocytes)


title: oxBS-OC20 D1

description: CD14 cells treated with M-CSF/RANKL for 20 days (oxidative bisulfite-treated, oxBS)

hyb_protocol: BS or oxBS converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing: Regular BeadStudio processing

source_name: OC20_donor 1 (oxidative bisulfite-treated, oxBS)

label_protocol: Standard Illumina Protocol

treatment_protocol: Bisulfite (BS) samples obtained by standard bisulfite modification. Oxidative-bisulfite (oxBS)-derived samples were obtained after potassium perruthenate treatment and later bisulfite modification


title: oxBS-MAC20 D3

description: CD14 cells treated with M-CSF for 20 days (oxidative bisulfite-treated, oxBS)

source_name: MAC20_donor 3 (oxidative bisulfite-treated, oxBS)


title: oxBS-MAC5 D1

description: CD14 cells treated with M-CSF for 5 days (oxidative bisulfite-treated, oxBS)

source_name: MAC5_donor 1 (oxidative bisulfite-treated, oxBS)


title: oxBS-MO D1

description: peripheral blood isolated CD14+ cells (monocytes) (oxidative bisulfite-treated, oxBS)

source_name: CD14_monocyte_donor 1 (oxidative bisulfite-treated, oxBS)


title: oxBS-OC5 D1

description: CD14 cells treated with M-CSF/RANKL for 5 days (oxidative bisulfite-treated, oxBS)

source_name: OC5_donor 1 (oxidative bisulfite-treated, oxBS)


title: oxBS-MAC5 D2

source_name: MAC5_donor 2 (oxidative bisulfite-treated, oxBS)


title: oxBS-MAC20 D1

source_name: MAC20_donor 1 (oxidative bisulfite-treated, oxBS)


title: oxBS-OC20 D3

source_name: OC20_donor 3 (oxidative bisulfite-treated, oxBS)


title: TAN_4

description: clonal mouse


title: oxBS-MO D3

source_name: CD14_monocyte_donor 3 (oxidative bisulfite-treated, oxBS)


title: oxBS-MO D2

source_name: CD14_monocyte_donor 2 (oxidative bisulfite-treated, oxBS)


title: oxBS-OC20 D2

source_name: OC20_donor 2 (oxidative bisulfite-treated, oxBS)


title: oxBS-OC5 D2

source_name: OC5_donor 2 (oxidative bisulfite-treated, oxBS)


title: oxBS-OC5 D3

source_name: OC5_donor 3 (oxidative bisulfite-treated, oxBS)


title: oxBS-MAC20 D2

source_name: MAC20_donor 2 (oxidative bisulfite-treated, oxBS)


title: oxBS-MAC5 D3

source_name: MAC5_donor 3 (oxidative bisulfite-treated, oxBS)


title: BS-MAC20 D3

description: CD14 cells treated with M-CSF for 20 days (bisulfite-treated, BS)

source_name: MAC20_donor 3 (bisulfite-treated, BS)


title: DGM-01051_lg

status: Public on Jul 18 2017

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: large airway epithelium brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: nonsmoker

value: large airway epithelium


title: DGM-00897_Tr

source_name: Trachea epithelial brushing

value: Trachea epithelium


title: DGM-00926_Tr


title: DGM-00936_Tr


title: DGM-00765_Tr


title: DGM-00795_Tr


title: DGM-00906_Tr


title: DGM-00829_Tr


title: DGM-00553_Tr


title: BS-MAC20 D1

source_name: MAC20_donor 1 (bisulfite-treated, BS)


title: DGM-00084_Tr


title: DGM-00080_Tr


title: BS-OC5 D3

description: CD14 cells treated with M-CSF/RANKL for 5 days (bisulfite-treated, BS)

source_name: OC5_donor 3 (bisulfite-treated, BS)


title: DGM-00036_Tr


title: BS-OC20 D2

description: CD14 cells treated with M-CSF/RANKL for 20 days (bisulfite-treated, BS)

source_name: OC20_donor 2 (bisulfite-treated, BS)


title: BS-OC20 D3

source_name: OC20_donor 3 (bisulfite-treated, BS)


title: BS-MO D2

description: peripheral blood isolated CD14+ cells (monocytes) (bisulfite-treated, BS)

source_name: CD14_monocyte_donor 2 (bisulfite-treated, BS)


title: BS-MAC5 D3

description: CD14 cells treated with M-CSF for 5 days (bisulfite-treated, BS)

source_name: MAC5_donor 3 (bisulfite-treated, BS)


title: BS-MAC5 D2

source_name: MAC5_donor 2 (bisulfite-treated, BS)


title: BS-OC5 D1

source_name: OC5_donor 1 (bisulfite-treated, BS)


title: BS-MAC5 D1

source_name: MAC5_donor 1 (bisulfite-treated, BS)


title: BS-MO D3

source_name: CD14_monocyte_donor 3 (bisulfite-treated, BS)


title: DGM-00904_Tr


title: BS-MO D1

source_name: CD14_monocyte_donor 1 (bisulfite-treated, BS)


title: BS-OC5 D2

source_name: OC5_donor 2 (bisulfite-treated, BS)


title: DGM-00416_Tr


title: DGM-00123_Tr


title: DGM-00740_sm

source_name: small airway epithelium brushing

value: COPD

value: small airway epithelium


title: DGM-00977_sm

value: smoker


title: DGM-01002_sm


title: DGM-00433_Tr


title: DGM-00568_Tr

source_name: Trachea

value: NS


title: DGM-00696_Tr


title: DGM-00661_Tr


title: DGM-00685_Tr


title: DGM-00551_Tr


title: DGM-00465_Tr


title: DGM-00529_Tr


title: BS-MAC20 D2

source_name: MAC20_donor 2 (bisulfite-treated, BS)


title: BS-OC20 D1

source_name: OC20_donor 1 (bisulfite-treated, BS)


title: DGM-00073_Tr


title: negCont.6h.6

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: raw data file: 140122 252665222064  Area 17  Cy5 3A24h Cy3 6C6h 488 1B6h.gpr

hyb_protocol: labeled aRNA samples were hybridized onto Agilent Human GE 4x44K V2 microarray slides

scan_protocol: Slides were washed and scanned with GenePix 4200 AL (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
These arrays were triple-labeled but analyzed as single-channel arrays. All raw data files are available in a tar archive on the series record.
Image segmentation was done using GenePixPro 6.1 software (Molecular Devices). Spot intensities were calculated as the median intensity. Data were imported into R software v. 2.3, and analysed with the BioConductor package limma

source_name: differentiation of THP-1 monocytes into macrophages

label_protocol: T7 amplification method (Amino Allyl MessageAmp II aRNA AmplificationKit, Ambion, Carlsbad, CA, USA) was performed to synthetize antisense RNA copies (aRNA). aRNA samples were indirectly labelled either with monoreactive Cy3, Cy5 or Alexa 488.

growth_protocol: THP-1 cells (ATCC TIB-202) were grown in cell culturing flasks (75 cm2) in 30 ml of RPMI 1640 media (Gibco, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (PEST) antibiotics and 2mM Ultraglutamine. THP-1 cells (1.5 x 106 cells/well) were differentiated with 50nm PMA (phorbol-12-myristate-13-acetate) and exposed in six-well plates

extract_protocol: Cells were harvested, lysed and the total RNA was extracted and purified by Qiagen RNeasy Plus Mini Kit manual

treatment_protocol: Cells were exposed by replacing the old media by adding 100 µg of the CNM in 1 ml of fresh complete RPMI and incubated for 6 or 24 hours

tag: differentiation status

value: macrophages

tag: exposure

value: RPMI medium

tag: exposure method

value: differentiated THP-1 cells in culture

tag: time


title: DGM-00268_Tr


title: DGM-00041_Tr


title: Baytube.24h.3

description: raw data file: 140122 252665222063  Area 14  Cy5 5C24h Cy3 10A6h 488 7A24h.gpr

tag: cell line

value: 100 ug of CNM in 1ml of RPMI medium


title: rCNT.6h.3

description: raw data file: 140122 252665222064  Area 18  Cy5 2A6h Cy3 6B24h 488 2C6h.gpr


title: rCNT.24h.3

description: raw data file: 140122 252665222063  Area 16  Cy5 4C6h Cy3 1C24h 488 2B24h.gpr


title: Graphite.24h.3

description: raw data file: 140117 252665222066  Area 07  Cy5 1C6h Cy3 9C6h 488 8B24h.gpr


title: negCont.24h.6

description: raw data file: 140122 252665222063  Area 15  Cy5 9A24h Cy3 8B6h 488 1A24h.gpr


title: tCNT.24h.3

description: raw data file: 140117 252665222066  Area 08  Cy5 5A6h Cy3 2A24h 488 3C24h.gpr


title: Fullerene.6h.3

description: raw data file: 140122 252665222063  Area 13  Cy5 6B6h Cy3 3B24h 488 9A6h.gpr


title: t1_fluc_end_rep1

city: S. Michele all'Adige (TN)

first: Tobias

last: Weil

address: Via E. Mach, 1

institute: Fondazione Edmund Mach

hyb_protocol: Genomic DNA was digested with Alu I and RSA I, amplified, labelled and hybridized according to manufacturer’s instructions using the Agilent Genomic DNA enzymatic labelling Kit.

scan_protocol: Arrays were scanned on an Agilent G2565AA microarray scanner and microarray scan data was extracted using Agilent feature extraction software.

data_processing: Quality control was assessed with R/Bioconductor packages GLAD and arrayQualityMetrics. No significant bias was detected. The four samples presented statistically comparable distributions so no additional data processing was performed, taking the normalized LogRatio provided by Agilent feature extraction and processing software for the present values.

organism: Candida albicans

source_name: candida albicans, t1, fluconazole, replicate1

growth_protocol: Strains were grown in synthetic defined medium minus uracil (SD without uracil, 0.67% yeast nitrogen base, 2% glucose, 0,2% drop-out mix, with 2% agar for solid medium only) at 30°C.

extract_protocol: DNA was extracted using the Genomic-tip 100/G kit (Qiagen) according to manufacturer’s instructions. DNA was resuspended in EB-buffer and DNA quantity and integrity was assessed using the Quant-it™ Picogreen® ds DNA quantitation assay and by agarose gel electrophoresi.

treatment_protocol: Resistance to antifungal drugs was monitored using the E-test assay method (AB biodisk, Biomerieux). Therefore, cells were grown to mid-log phase, washed in 1xPBS, and diluted to an OD600 of 0.015. 150μl of cells were plated on SD minus uracil agar plates (pH7) using glass beads and allowed to dry for 15-30 minutes before applying a fluconazole E-test strip (0.016– 256 μg/ml, AB Biodisk). Plates were incubated at 30°C and the MIC was determined after 48 hours. To test for clone diversity of highly resistant strains (MIC=256μg/ml; T1FH a-c) were plated on SD minus uracil agar plates and 3 single colonies were picked for DNA extraction (T1FH a-c).

tag: strain

tag: treatment

value: Fluconazole

source_name: candida albicans, t0, none, replicate1


title: SES.6h.3

description: raw data file: 140117 252665222065  Area 09  Cy5 8A6h Cy3 4C24h 488 10B6h.gpr


title: t1_fluc_end_rep2

source_name: candida albicans, t1, fluconazole, replicate2

label_protocol: Genomic DNA was digested with Alu I and RSA I, amplified, labelled and hybridized according to manufacturer’s instructions using the Agilent Genomic DNA enzymatic labelling Kit.

source_name: candida albicans, t0, none, replicate2


title: Fullerene.24h.3

description: raw data file: 140117 252665222065  Area 12  Cy5 7B24h Cy3 2B6h 488 9C24h.gpr


title: negCont.24h.5

description: raw data file: 140117 252665222065  Area 10  Cy5 10C6h Cy3 3C6h 488 6C24h.gpr


title: negCont.6h.5

description: raw data file: 140114 252665222067  Area 04  Cy5 3B6h Cy3 7C24h 488 6A6h.gpr


title: SES.24h.3

description: raw data file: 140117 252665222066  Area 06  Cy5 7C6h Cy3 5B6h 488 10A24h.gpr


title: tCNT.6h.3

description: raw data file: 140114 252665222067  Area 03  Cy5 2C24h Cy3 9B24h 488 3A6h.gpr


title: t1_fluc_end_rep3

source_name: candida albicans, t1, fluconazole, replicate3

source_name: candida albicans, t0, none, replicate3


title: Graphite.6h.3

description: raw data file: 140114 252665222067  Area 02  Cy5 4B24h Cy3 5A24H 488 8C 6h.gpr


title: Baytube.6h.3

description: raw data file: 140114 252665222067  Area 01  Cy5 10B024h Cy3 1A6H 488 7B 6h.gpr


title: negCont.6h.4


title: Baytube.6h.2

description: raw data file: 140122 252665222064  Area 20  Cy5 8C24h Cy3 7A6h 488 4A24h.gpr


title: DGM-00082_Tr

source_name: Trachea epithelial brushing


title: negCont.24h.3


title: negCont.24h.4


title: SES.24h.2

description: raw data file: 140122 252665222064  Area 19  Cy5 9B6h Cy3 10C24h 488 5B24h.gpr


title: tCNT.24h.2


title: Fullerene.6h.2


title: Graphite.6h.2


title: Fullerene.6h.1


title: Baytube.24h.2


title: rCNT.24h.2


title: Graphite.24h.1


title: SES.6h.2

description: raw data file: 140122 252665222063  Area 14  Cy5 5C24h Cy3 10A6h 488 7A24h.gpr


title: tCNT.6h.2


title: Graphite.24h.2

description: raw data file: 140117 252665222066  Area 05  Cy5 6A24h Cy3 8A24h 488 4B6h.gpr


title: negCont.6h.3


title: Fullerene.24h.1


title: negCont.6h.2


title: rCNT.6h.1

description: raw data file: 140122 252665222064  Area 18  Cy5 2A6h Cy3 6B24h 488 2C6h.gpr


title: rCNT.6h.2


title: tCNT.24h.1

description: raw data file: 140122 252665222064  Area 17  Cy5 3A24h Cy3 6C6h 488 1B6h.gpr


title: Fullerene.24h.2


title: negCont.24h.2


title: DGM-00072_Tr


title: negCont.24h.1

description: raw data file: 140117 252665222065  Area 11  Cy5 1B24h Cy3 4A6h 488 5C6h.gpr


title: negCont.6h.1

description: raw data file: 140117 252665222066  Area 07  Cy5 1C6h Cy3 9C6h 488 8B24h.gpr


title: SES.6h.1


title: Baytube.24h.1


title: SES.24h.1


title: 13_id_Graphite

description: raw data file: US11263921_252800520994_S01_GE2_1105_Oct12_2_1.txt

hyb_protocol: Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays, , according to the manufacturer's recommendations.

scan_protocol: Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.

data_processing:
These are dual-channel arrays that have been analyzed as single-channel arrays. All raw data files are available in a tar archive on the series record.
Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and analyzed with BioConductor package Limma.

source_name: Graphite

label_protocol: Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.

growth_protocol: Female C57BL/6 mice (7-8 weeks old) were housed in groups of four in stainless steel cages, bedded with aspen chip and were provided with standard mouse chow diet and tab water ad lib. 12 h dark/light cycle was used in the animal room temperature being 20-21 degree celcius and humidity of 40-45 %.

extract_protocol: RNA isolation from the lung samples was done with TRIsure (phenol-chloroform extraction) and the quantity and purity was determined by NanoDrop spectrophotometer. Further quality check of the total RNA was performed with the Agilent BioAnalyzer, according to the manufacturer's recommendations.

treatment_protocol: mice lung tissue samples collected 24h after final exposure. Tissue samples stored in RNAlater in -80ºC

value: lung

tag: gender

value: female

value: 10 ug of CNM in 50 ul of PBS

value: oropharyngeal aspiration


title: Graphite.6h.1

description: raw data file: 140117 252665222065  Area 09  Cy5 8A6h Cy3 4C24h 488 10B6h.gpr


title: 21_id_fullerene

description: raw data file: US11263921_252800520995_S01_GE2_1105_Oct12_1_1.txt

source_name: fullerene


title: Baytube.6h.1


title: tCNT.6h.1


title: rCNT.24h.1


title: 9_id_tCNT

description: raw data file: US11263921_252800520995_S01_GE2_1105_Oct12_2_3.txt

source_name: tCNT


title: 6_id_rCNT

description: raw data file: US11263921_252800520994_S01_GE2_1105_Oct12_1_4.txt

source_name: rCNT


title: 22_id_fullerene

description: raw data file: US11263921_252800520994_S01_GE2_1105_Oct12_1_2.txt