title: S64_yko_trp_rep3

description: Normalization Batch 2

source_name: yko, sc-trp


title: S66_pb_arg_rep1

status: Public on Aug 11 2017

type: genomic

city: Vancouver

first: Erica

last: Acton

state: British Columbia

address: Pharmaceutical Sciences Building, Wesbrook Mall

department: Genome Science and Technology

country: Canada

institute: University of British Columbia

description: Normalization Batch 3

hyb_protocol: Each sample was hybridized for 16 hrs at 42 °C and 20 rpm with 60 uL of hybridization mix, as well as 30 uL of uptag and 30 uL of downtag PCR product. The hybridization mix consisted of 45uL 2x hybridization buffer, 0.3uL B213 control oligonucleotide (1fmol/uL), 7.2uL mixed oligonucleotide (12.5 pmol/uL), 1.8uL 50x Denhardt's. The 120uL sample/hyb mix was boiled for 2 minutes and iced for 2 minutes before loading onto a pre-treated Affymetrix chip.

scan_protocol: After the stain was removed and replaced with a wash buffer consisting of 6xSSPE, 0.01%Tween and H2O the chips were scanned immediately with the Affymetrix Scanner.

data_processing: The raw data for uptags and downtags were normalized separately to the median of all arrays within a set (9 sets as defined by pool, media (SC), drug (YPD), or no growth (t0). Estimates of the background thresholds were determined independently for the control arrays in each set using Gaussian mixture models initialized on the unassigned tags on the control arrays.

label: biotin

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: pb, sc-arg

label_protocol: A biotin-labelling mix was made using 180uL 20xSSPE, 12uL 50x Denhardt's, 6ul 1% Tween 20, 1ul of 1mg/mL streptavidin-R-phycoerythrin congugate and 401uL ddH2O per sample. After priming the fluidics station, chips were stained with the biotin-labelling mix for approximately 30 minutes.

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Arg (cat#1346-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.

extract_protocol: Genomic DNA was extracted from cell pellets using YeastStar Genomic DNA Kit (Zymo Research, #D2002) and quantified using the NanoDrop 2000. Uptags and downtags were then PCR amplified using separate primers and 160ng of diluted genomic DNA with Phusion Hotstart.

treatment_protocol: no drug

tag: collection

value: pb


title: T38

type: RNA

city: Milan

first: Paolo

last: Gandellini

address: Via Amadeo 42

department: Department of Applied Research and Technological Development

country: Italy

institute: Fondazione IRCCS Istituto Nazionale Tumori

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to the Illumina Sentrix BeadChip according to the protocols provided by the manufacturer.

scan_protocol: Standard Illumina scanning protocol

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3 (Gene Expression Module v3.3.8). Raw expression data were log2-transformed and normalized using the robust spline normalization method.

molecule: total RNA

organism: Homo sapiens

source_name: DMPM frozen tumor specimen

label_protocol: Biotinylated cDNA was prepared with the TotalPrep Amplification kit (Ambion) for Illumina arrays

extract_protocol: For total RNA extraction, approximately 100 mg of frozen tissue was homogenized using a bench-top homogenizer (MM200, Retsch, Germany) in 1 mL of TRIzol Reagent (Invitrogen).

tag: tissue

value: DMPM frozen tumor specimen

tag: telomerase activity


title: S65_pb_ade_rep1

description: Normalization Batch 3

source_name: pb, sc-ade

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Ade (cat#1302-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S60_yko_met_rep3

description: Normalization Batch 2

source_name: yko, sc-met

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Met (cat#1343-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.

value: yko


title: S63_yko_thr_rep3

description: Normalization Batch 2

source_name: yko, sc-thr

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Thr (cat#1354-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S67_pb_gln_rep1

description: Normalization Batch 3

source_name: pb, sc-gln

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Gln (cat#1355-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S62_yko_ser_rep3

description: Normalization Batch 2

source_name: yko, sc-ser

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Ser (cat#1366-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: T33


title: S61_yko_sc_rep3

description: Normalization Batch 2

source_name: yko, sc

growth_protocol:
Grown 5 generations in Sunrise Science Products SC (cat#1300-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: T34


title: T32


title: S59_yko_lys_rep3

description: Normalization Batch 2

source_name: yko, sc-lys

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Lys (cat#1307-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S55_yko_arg_rep3

description: Normalization Batch 2

source_name: yko, sc-arg


title: T31


title: S58_yko_gly_rep3

description: Normalization Batch 2

source_name: yko, sc-gly

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Gly (cat#1308-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S56_yko_gln_rep3

description: Normalization Batch 2

source_name: yko, sc-gln


title: S57_yko_gln_rep3

description: Normalization Batch 2


title: T35


title: C-012_Day0

city: Bethesda

first: Foo

last: Cheung

address: Bethesda

country: USA

institute: NIH

description: Gene expression data from PBMC extracted from control individual C-012 at Day0.

hyb_protocol: Biotin-labeled sample was well mixed with hybridization master mix, denatured and then hybridized onto Affymetrix Human Gene 1.0 ST Array at 48C and 60 rpm for 18 hours.

scan_protocol: Affymetrix scanner 3000.

data_processing: Expression Console 1.2 (RMA+DABG) software package was used for data summarization, normalization and quality control. Cel files are used for further analysis.

label: Biotin

source_name: Individual C-012 at Day0

label_protocol: Five hundred nanogram of total RNA was polyA tailed, then biotinylated using Affymetrix FlashTag Biotin HSR RNA Labeling kit (P/N 703095 v1).

extract_protocol: Total RNA including small RNA is isolated and purified using Qiagen miRNeasy mini kit (Cat #: 217004).

tag: disease state

value: healthy

tag: gender

value: female

tag: age (yr)

value: peripheral blood mononuclear cell (PBMC)

tag: time point post 2012-2013 seasonal influenza vaccine

value: Day 0

tag: individual id


title: C-010_Day0

description: Gene expression data from PBMC extracted from control individual C-010 at Day0.

source_name: Individual C-010 at Day0

value: male


title: T30


title: T29


title: T27


title: T28


title: C-011_Day0

description: Gene expression data from PBMC extracted from control individual C-011 at Day0.

source_name: Individual C-011 at Day0


title: T26


title: S50_yko_sc_rep2

description: Normalization Batch 2


title: S49_yko_met_rep2

description: Normalization Batch 2


title: T24


title: T25


title: MES-F

source_name: normal mesothelial cells

tag: cell line

value: normal mesothelial cell line (MES-F)


title: S53_yko_trp_rep2

description: Normalization Batch 2

source_name: yko, sc-trp

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Trp (cat#1305-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S51_yko_ser_rep2

description: Normalization Batch 2


title: S48_yko_lys_rep2

description: Normalization Batch 2


title: T23


title: C-006_Day0

description: Gene expression data from PBMC extracted from control individual C-006 at Day0.

source_name: Individual C-006 at Day0


title: S46_yko_arg_rep2

description: Normalization Batch 2


title: S54_yko_ade_rep3

description: Normalization Batch 2

source_name: yko, sc-ade


title: C-009_Day0

description: Gene expression data from PBMC extracted from control individual C-009 at Day0.

source_name: Individual C-009 at Day0


title: C-003_Day0

description: Gene expression data from PBMC extracted from control individual C-003 at Day0.

source_name: Individual C-003 at Day0


title: C-007_Day0

description: Gene expression data from PBMC extracted from control individual C-007 at Day0.

source_name: Individual C-007 at Day0


title: T22

source_name: DMPM frozen tumor specimen


title: S52_yko_thr_rep2

description: Normalization Batch 2

source_name: yko, sc-thr


title: S47_yko_gly_rep2

description: Normalization Batch 2


title: C-001_Day0

description: Gene expression data from PBMC extracted from control individual C-001 at Day0.

source_name: Individual C-001 at Day0


title: C-002_Day0

description: Gene expression data from PBMC extracted from control individual C-002 at Day0.

source_name: Individual C-002 at Day0


title: C-005_Day0

description: Gene expression data from PBMC extracted from control individual C-005 at Day0.

source_name: Individual C-005 at Day0


title: 010_Day30

description: Gene expression data from PBMC extracted from individual 010 at Day30.

source_name: Individual 010 at Day30

value: acute myeloid leukemia (AML) remission

value: Day 30


title: S45_yko_ade_rep2

description: Normalization Batch 2


title: 009_Day30

description: Gene expression data from PBMC extracted from individual 009 at Day30.

source_name: Individual 009 at Day30


title: T21


title: S44_yko_trp_rep1

description: Normalization Batch 2


title: T19


title: T18


title: S43_yko_thr_rep1

description: Normalization Batch 2


title: 007_Day30

description: Gene expression data from PBMC extracted from individual 007 at Day30.

source_name: Individual 007 at Day30


title: S40_yko_met_rep1

description: Normalization Batch 2

source_name: yko, sc-met


title: T17


title: T16


title: S41_yko_sc_rep1

description: Normalization Batch 2

source_name: yko, sc


title: T15


title: S39_yko_lys_rep1

description: Normalization Batch 2

source_name: yko, sc-lys


title: S38_yko_gly_rep1

description: Normalization Batch 2

source_name: yko, sc-gly


title: 006_Day30

description: Gene expression data from PBMC extracted from individual 006 at Day30.

source_name: Individual 006 at Day30


title: T20


title: T12


title: T14


title: S42_yko_ser_rep1

description: Normalization Batch 2

source_name: yko, sc-ser


title: 004_Day30

description: Gene expression data from PBMC extracted from individual 004 at Day30.

source_name: Individual 004 at Day30


title: 002_Day30

description: Gene expression data from PBMC extracted from individual 002 at Day30.

source_name: Individual 002 at Day30


title: S37_yko_gln_rep1

description: Normalization Batch 2

source_name: yko, sc-gln


title: 009_Day0

description: Gene expression data from PBMC extracted from individual 009 at Day0.

source_name: Individual 009 at Day0


title: 005_Day30

description: Gene expression data from PBMC extracted from individual 005 at Day30.

source_name: Individual 005 at Day30


title: 001_Day30

description: Gene expression data from PBMC extracted from individual 001 at Day30.

source_name: Individual 001 at Day30


title: 008_Day30

description: Gene expression data from PBMC extracted from individual 008 at Day30.

source_name: Individual 008 at Day30


title: 010_Day0

description: Gene expression data from PBMC extracted from individual 010 at Day0.

source_name: Individual 010 at Day0


title: S35_yko_ade_rep1

description: Normalization Batch 2

source_name: yko, sc-ade


title: 003_Day30

description: Gene expression data from PBMC extracted from individual 003 at Day30.

source_name: Individual 003 at Day30


title: T11

source_name: DMPM frozen tumor specimen


title: T13


title: S34_bc_ura_rep3

description: Normalization Batch 1

source_name: bc, sc-ura

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Ura (cat#1306-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.

value: bc


title: S36_yko_arg_rep1

description: Normalization Batch 2

source_name: yko, sc-arg


title: 007_Day0

description: Gene expression data from PBMC extracted from individual 007 at Day0.

source_name: Individual 007 at Day0


title: T10


title: T9


title: T8


title: 008_Day0

description: Gene expression data from PBMC extracted from individual 008 at Day0.

source_name: Individual 008 at Day0


title: T6


title: T7


title: S31_bc_thr_rep1

description: Normalization Batch 1

source_name: bc, sc-thr


title: T5


title: 006_Day0

description: Gene expression data from PBMC extracted from individual 006 at Day0.

source_name: Individual 006 at Day0


title: T4


title: S32_bc_thr_rep2

description: Normalization Batch 1


title: 005_Day0

description: Gene expression data from PBMC extracted from individual 005 at Day0.

source_name: Individual 005 at Day0


title: T2


title: T3


title: S30_bc_ser_rep2

description: Normalization Batch 1

source_name: bc, sc-ser


title: S29_bc_ser_rep1

description: Normalization Batch 1


title: 004_Day0

description: Gene expression data from PBMC extracted from individual 004 at Day0.

source_name: Individual 004 at Day0


title: S33_bc_trp_rep3

description: Normalization Batch 1

source_name: bc, sc-trp


title: S25_bc_leu_rep3

description: Normalization Batch 1

source_name: bc, sc-leu

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Leu (cat#1304-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: T1


title: 003_Day0

description: Gene expression data from PBMC extracted from individual 003 at Day0.

source_name: Individual 003 at Day0


title: 002_Day0

description: Gene expression data from PBMC extracted from individual 002 at Day0.

source_name: Individual 002 at Day0


title: S26_bc_lys_rep3

description: Normalization Batch 1

source_name: bc, sc-lys


title: S27_bc_met_rep3

description: Normalization Batch 1

source_name: bc, sc-met


title: S28_bc_sc_rep3

description: Normalization Batch 1

source_name: bc, sc


title: S23_bc_gly_rep2

description: Normalization Batch 1

source_name: bc, sc-gly


title: 001_Day0

description: Gene expression data from PBMC extracted from individual 001 at Day0.

source_name: Individual 001 at Day0


title: CL

source_name: DMPM cell line

value: cell line derived from the tumor of a DMPM patient


title: N5

source_name: normal peritoneum

value: normal peritoneum


title: N4


title: S24_bc_his_rep3

description: Normalization Batch 1

source_name: bc, sc-his

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-His (cat#1303-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S22_bc_gly_rep1

description: Normalization Batch 1


title: N3


title: N2


title: S20_bc_gln_rep1

description: Normalization Batch 1

source_name: bc, sc-gln


title: S21_bc_gln_rep2

description: Normalization Batch 1


title: S18_bc_ade_rep3

description: Normalization Batch 1

source_name: bc, sc-ade


title: S16_bc_trp_rep2

description: Normalization Batch 1


title: S19_bc_arg_rep3

description: Normalization Batch 1

source_name: bc, sc-arg


title: S17_bc_ura_rep2

description: Normalization Batch 1

source_name: bc, sc-ura


title: S15_bc_sc_rep2

description: Normalization Batch 1


title: S14_bc_met_rep2

description: Normalization Batch 1


title: S10_bc_ade_rep2

description: Normalization Batch 1


title: N1


title: S12_bc_his_rep2

description: Normalization Batch 1


title: S13_bc_leu_rep2

description: Normalization Batch 1


title: mouse label 12, diet HFD, tissue liver, time/age Week 18

city: Beijing

first: Lei

last: Li

address: No. 55 Zhongguancun East Road, 100190

country: China

institute: Academy of Mathematics and Systems Science

hyb_protocol: Following standard Affymetrix protocol

scan_protocol: Following standard Affymetrix protocol

data_processing: Each probe set of the Affymetrix mouse430 microarray contains 11 probes, and thus we need to summarize their information into one value for each sample. From the microarray data we seek for differentially expressed genes among the samples. However, the information of gene ex-pression differences is confounded with variations due to uncontrollable experiment factors. To reduce the unwanted variations, we need to normalize the data in a way or another.  The micro-array data in this study were preprocessed by several methods such as RMA and MAS 5.0 (http://www.affymetrix.com). It was shown that spatial variations of microarrays due to factors such as uneven hybridization and washing accounted for a large portion of unwanted variations. Thus we applied a more sophisticated preprocessing, namely, the sub-sub normalization fol-lowed by the probe-treatment-reference summarization, to the microarray data of each tis-sue. Specifically, this procedure normalized each target microarray against a reference as fol-lows. Each Mouse430-2.0 chip, consisting of 1002 by 1002 probes, was decomposed into subar-rays of 50 by 50 probes. For each corresponding pair of subarrays on the reference and target chip, a piecewise (with one knot)  linear relationship was estimated using least trimmed squares, and was used to adjust the target sub-array. We allowed adjacent subarrays to overlap by 25 probes both horizontally and vertically. Therefore a probe belonging to multiple subar-rays got multiple adjusted values, and we took their average. For each tissue, we selected sev-eral raw microarrays as references, and used the probe-treatment-reference model, to summa-rize the normalized microarrays.

organism: Mus musculus

source_name: diet HFD_tissue liver_time/age Week 18

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

growth_protocol: Male outbred CD-1 mice at 3 weeks of age were purchased from Charles River Laboratories via Vital River Laboratories (VRL, Beijing, China) and kept in a temperature-controlled environment. Food and water were available ad libitum unless otherwise indicated.

extract_protocol: The epididymal fat pads, the liver, and the pancreas were collected immediately and prepared for mRNA extraction to detect differential RNA expression.

treatment_protocol: They were used in this study at 4 week of age (weighing 15.3±0.6 g) and this time was set as week 0 of the experiment that was then carried out for 18 weeks in total. All mice were randomly assigned to a control group (n=28) fed on regular chow (RC; approximately 17% fat, 19% protein, and 64% carbohydrate) and a HFD group (n = 43) fed on the HFD (HFD; approximately 42% fat, 19% protein, and 38% carbohydrate). Fasting blood glucose (FBG) and body weight (BW) were measured weekly. Week 1, 9, and 18 were set as time points for performing glucose tolerance tests (GTT) and insulin tolerance tests (ITT). Then several mice from each group at the three time points were sacrificed after saline perfusion.

tag: strain background

value: outbred CD-1

tag: mouse id

value: mouse label 12

tag: diet

value: diet HFD

tag: age

value: Week 18

value: liver


title: S11_bc_arg_rep2

description: Normalization Batch 1


title: mouse label 7, diet RC, tissue pancreas, time/age Week 18

source_name: diet RC_tissue pancreas_time/age Week 18

value: mouse label 7

value: diet RC

value: pancreas


title: S8_bc_trp_rep1

description: Normalization Batch 1

source_name: bc, sc-trp


title: mouse label 12, diet HFD, tissue pancreas, time/age Week 18

source_name: diet HFD_tissue pancreas_time/age Week 18


title: mouse label 9, diet RC, tissue pancreas, time/age Week 18

value: mouse label 9


title: S9_bc_ura_rep1

description: Normalization Batch 1


title: mouse label 12, diet HFD, tissue adipose, time/age Week 18

source_name: diet HFD_tissue adipose_time/age Week 18

value: adipose


title: mouse label 9, diet RC, tissue adipose, time/age Week 18

source_name: diet RC_tissue adipose_time/age Week 18

value: male


title: mouse label 7, diet RC, tissue adipose, time/age Week 18


title: mouse label 7, diet RC, tissue liver, time/age Week 18

source_name: diet RC_tissue liver_time/age Week 18


title: mouse label 17, diet RC, tissue pancreas, time/age Week 9

source_name: diet RC_tissue pancreas_time/age Week 9

value: mouse label 17

value: Week 9


title: mouse label 9, diet RC, tissue liver, time/age Week 18


title: S4_bc_leu_rep1

description: Normalization Batch 1

source_name: bc, sc-leu


title: S6_bc_met_rep1

description: Normalization Batch 1

source_name: bc, sc-met


title: S5_bc_lys_rep1

description: Normalization Batch 1

source_name: bc, sc-lys


title: mouse label 17, diet RC, tissue liver, time/age Week 9

source_name: diet RC_tissue liver_time/age Week 9


title: mouse label 11, diet RC, tissue pancreas, time/age Week 18

value: mouse label 11


title: mouse label 17, diet RC, tissue adipose, time/age Week 9

source_name: diet RC_tissue adipose_time/age Week 9


title: S3_bc_his_rep1

description: Normalization Batch 1

source_name: bc, sc-his

value: bc


title: S2_bc_arg_rep1

description: Normalization Batch 1


title: S1_bc_ade_rep1

description: Normalization Batch 1

source_name: bc, sc-ade


title: mouse label 11, diet RC, tissue adipose, time/age Week 18


title: mouse label 4, diet HFD, tissue pancreas, time/age Week 18

value: mouse label 4


title: mouse label 11, diet RC, tissue liver, time/age Week 18


title: mouse label 4, diet HFD, tissue liver, time/age Week 18


title: mouse label 2, diet HFD, tissue liver, time/age Week 18

value: mouse label 2


title: mouse label 2, diet HFD, tissue pancreas, time/age Week 18

value: outbred CD-1


title: mouse label 4, diet HFD, tissue adipose, time/age Week 18


title: mouse label 2, diet HFD, tissue adipose, time/age Week 18


title: KHOS/NP transfected with Pccl vector and treated with Adriamycin

city: hangzhou

first: yangling

last: li

state: zhejiang

address: 866 Yuhangtang Road

department: College of Pharmaceutical Sciences

institute: zhejiang university

description: Gene expression data from KHOS transfected with Pccl vector and treated with Adriamycin

hyb_protocol: After fragmentation of these amplified RNA (aRNA), sample was hybridized to the Affymetrix PrimeViewTM Human Gene Expression Array for 16-18 h at 45°C.

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

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using default analysis settings and global scaling as normalization method by Partek® Genomics Suite 6.6.

source_name: osteosarcoma

label_protocol: a total of 500 ng RNA was used for a single round of amplification and simultaneously labeled with biotincongugated nucleotide.

growth_protocol: The KHOS/NP osteosarcoma cell line was seeded onto the 60mm cell culture plate

extract_protocol: Total RNA was extracted by Trizol/Chloroform, and then purified with magnetic beads of Agencourt Ampure (APN 000132, Beckman Coulter).

treatment_protocol: Cells were treated with pccl vector, Adriamycin(50nM) and pccl-klf-4, collected, and 0.5 million cells were homogenized in 1ml Trizol reagent.

value: KHOS/NP

tag: cell type

value: osteosarcoma

tag: transfection

value: pccl


title: mouse label 1, diet HFD, tissue pancreas, time/age Week 18

value: mouse label 1

value: diet HFD

value: Week 18


title: mouse label 26, diet HFD, tissue liver, time/age Week 18

value: mouse label 26

value: liver


title: KHOS/NP transfected with Pccl-klf-4

description: Gene expression data from KHOS transfected with Pccl-klf-4


title: Enterovirus A71 at 72 hours, biological rep1

city: wilayah persekutuan

first: THINESSHWARY

last: YOGARAJAH

address: kuala lumpur

department: PATHOLOGY

country: Malaysia

institute: university of malaya

description: Gene expression data from Enterovirus A71 infected SK-N-SH cell at 72 hours

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip® 3' IVT Express Array. GeneChips were washed and stained in the Affymetrix® GeneChip® Fluidics Station 450 User Guide (P/N 08-0092).

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: The data were analyzed with Expression console software, Affymetrix default analysis settings and the processing algorithm used is RMA. Statistical tests for gene level differential expression were performed using Transcriptome Analysis Console (TAC) v2.0 software.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from  100ng total RNA (GeneChip 3' IVT Express Array, 2008-2010, Affymetrix).

growth_protocol: SK-N-SH cells were grown in DMEM supplemented with 10% FBS and grown at 37°C in a CO2 incubator.

extract_protocol: Total RNA were extracted from infected cells using the RNeasy Plus Mini kit (Qiagen, Germany) according to manufactures instruction.

treatment_protocol: SK-N-SH cells were trypsinized and re-suspended in 2.0ml microcentrifuge tubes. EV-A71 and CV-A16, respectively, were added to cells at a multiplicity of infection (MOI) of 10 and incubated at 37°C for 2 hrs in suspension, in a shaking incubator at 100rpm. The cells were then centrifuged at 400 xg to remove supernatant and washed twice with phosphate-buffered saline (PBS) followed by re-suspension in 500μl of culture medium. Re-suspended cells were added into 24-well plates, 500μl per well and incubated at 37°C until the time of harvest.

value: SK-N-SH

value: Neuroblastoma

tag: pathogen

value: Enterovirus A71

tag: time point (hours)


title: mouse label 26, diet HFD, tissue pancreas, time/age Week 18

value: male

value: pancreas


title: Coxsackievirus A16 at 72 hours, biological rep3

description: Gene expression data from Coxsackievirus A16 infected SK-N-SH cell at 72 hours

value: Coxsackievirus A16


title: Coxsackievirus A16 at 72 hours, biological rep1

source_name: Coxsackievirus A16 infected SK-N-SH cell at 72 hours


title: KHOS/NP transfected with Pccl vector

description: Gene expression data from KHOS transfected with Pccl vector


title: SK-N-SH cells at 72 hours, biological rep3

description: Gene expression data from mock infected control of SK-N-SH cell at 72 hours

source_name: Mock infected control of SK-N-SH cell at 72 hours

value: none (mock infected)


title: Enterovirus A71 at 72 hours, biological rep2

source_name: Enterovirus A71 infected SK-N-SH cell at 72 hours


title: SK-N-SH cells at 72 hours, biological rep2


title: Coxsackievirus A16 at 72 hours, biological rep2


title: Enterovirus A71 at 72 hours, biological rep3


title: mouse label 26, diet HFD, tissue adipose, time/age Week 18

value: adipose


title: mouse label 17, diet HFD, tissue pancreas, time/age Week 18

value: outbred CD-1

value: mouse label 17


title: mouse label 11, diet HFD, tissue liver, time/age Week 18

source_name: diet HFD_tissue liver_time/age Week 18

value: mouse label 11


title: mouse label 5, diet RC, tissue adipose, time/age Week 9

value: mouse label 5

value: diet RC

value: Week 9


title: mouse label 11, diet HFD, tissue adipose, time/age Week 18

value: diet HFD

value: Week 18


title: mouse label 17, diet HFD, tissue liver, time/age Week 18

value: liver


title: mouse label 17, diet HFD, tissue adipose, time/age Week 18


title: SK-N-SH cells at 72 hours, biological rep1

value: SK-N-SH


title: Coxsackievirus A16 at 48 hours, biological rep3

description: Gene expression data from Coxsackievirus A16 infected SK-N-SH cell at 48 hours

value: Neuroblastoma


title: Enterovirus A71 at 48 hours, biological rep1

description: Gene expression data from Enterovirus A71 infected SK-N-SH cell at 48 hours

value: Enterovirus A71


title: mouse label 21, diet RC, tissue pancreas, time/age Week 1

source_name: diet RC_tissue pancreas_time/age Week 1

value: male

value: mouse label 21

value: Week 1


title: Enterovirus A71 at 48 hours, biological rep3

source_name: Enterovirus A71 infected SK-N-SH cell at 48 hours


title: SK-N-SH cells at 48 hours, biological rep3

description: Gene expression data from mock infected control of SK-N-SH cell at 48 hours

source_name: Mock infected control of SK-N-SH cell at 48 hours

value: none (mock infected)


title: mouse label 1, diet RC, tissue pancreas, time/age Week 9

value: mouse label 1

value: pancreas


title: mouse label 21, diet RC, tissue liver, time/age Week 1

source_name: diet RC_tissue liver_time/age Week 1

value: outbred CD-1


title: Enterovirus A71 at 48 hours, biological rep2


title: mouse label 5, diet RC, tissue pancreas, time/age Week 9

source_name: diet RC_tissue pancreas_time/age Week 9


title: mouse label 20, diet RC, tissue pancreas, time/age Week 1

value: mouse label 20


title: mouse label 1, diet RC, tissue liver, time/age Week 9


title: mouse label 5, diet RC, tissue liver, time/age  Week 9

value: mouse label 5


title: mouse label 19, diet RC, tissue liver, time/age Week 1

value: mouse label 19

value: diet RC


title: mouse label 1, diet RC, tissue adipose, time/age Week 9

value: Week 9

value: adipose


title: mouse label 21, diet RC, tissue adipose, time/age Week 1

source_name: diet RC_tissue adipose_time/age Week 1


title: Coxsackievirus A16 at 48 hours, biological rep1

source_name: Coxsackievirus A16 infected SK-N-SH cell at 48 hours

value: Coxsackievirus A16


title: mouse label 20, diet RC, tissue liver, time/age Week 1

value: liver


title: mouse label 40, diet HFD, tissue pancreas, time/age Week 1

source_name: diet HFD_tissue pancreas_time/age Week 1

value: mouse label 40

value: diet HFD


title: mouse label 19, diet RC, tissue adipose, time/age Week 1

value: male


title: Coxsackievirus A16 at 48 hours, biological rep2

value: SK-N-SH

value: Neuroblastoma


title: mouse label 7, diet HFD, tissue pancreas, time/age Week 9

source_name: diet HFD_tissue pancreas_time/age Week 9

value: mouse label 7


title: SK-N-SH cells at 48 hours, biological rep2

value: none (mock infected)


title: mouse label 40, diet HFD, tissue liver, time/age Week 1

source_name: diet HFD_tissue liver_time/age Week 1

value: Week 1


title: mouse label 7, diet HFD, tissue liver, time/age Week 9

source_name: diet HFD_tissue liver_time/age Week 9

value: outbred CD-1


title: mouse label 19, diet RC, tissue pancreas, time/age Week 1

value: pancreas


title: mouse label 20, diet RC, tissue adipose, time/age Week 1

value: mouse label 20


title: SK-N-SH cells at 48 hours, biological rep1


title: Hepatogenic differentiation, MSC cells

type: protein

city: Taipei

first: Chien-Wei

last: Lee

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang-Ming University

description: raw file: Ray biotech Mouse L308 Array(block1=HD28 block2=MSCs).xlsx

hyb_protocol: Protocol is following the manufacturer’s directions (Ray biotech Mouse L308 Array, Glass Slide Cat# AAM-BLG-1-4). See http://www.raybiotech.com/files/manual/Antibody-Array/AAM-BLG-1.pdf

data_processing: Fluorescence intensity data has obtained automatically by scanner software. Intensity of signal should subtract the background and normalize to the Positive Control signals before proceeding to analysis. If background is higher than signal, One-step Tukey’s BiWeight (TBW) mehod would be applied. For best results, it is recommended that comparing signal intensities representing the MEDIAN background signals minus local background.

label: Streptavidin-conjugated fluorescent dye (Cy3 equivalent)

molecule: protein

source_name: MSC

growth_protocol: Mouse MSCs were cultured in an mMSC-maintenance medium, low glucose DMEM supplemented with 10% FBS; mouse primary hepatocytes were cultured in Hep-maintenance medium, and DMEM/F12 supplemented with 10% FBS; HD 28 cells are differentiated from mMSCs by following methods. MSCs were treated with a Step-1 differentiation medium, consisting of IMDM supplemented with 20 ng/ml HGF and 10 ng/ml bFGF (R&D Systems), and nicotinamide 0.61 g/L (Sigma-Aldrich), for 7 days, then treated with a Step-2 differentiation medium, consisting of IMDM supplemented with 20 ng/ml oncostatin M (Invitrogen), 1 μmol/L dexamethasone (Sigma-Aldrich), and 50 mg/ml ITS+ premix (BD Biosciences). The medium was changed once per week to generate HD 28 cells. dHD 28 cells are derived from HD 28 cells by following methods. Hepatogenic de-differentiation was induced in HD 28 cells derived from MSCs by replacing the Step-2 medium with MSC-maintenance medium.

extract_protocol: Cell lysate were lysed in lysis buffer containing protease and phosphatase inhibitors (Sigma-Aldrich) according to the manufacturer’s directions.

treatment_protocol: See growth protocol

value: MSC

tag: strain

value: Balb/C

tag: Sex


title: Hepatogenic differentiation, dHD28 cells

description: raw file: Ray biotech Mouse L308 Array(block1=Heps block2=dHD28).xlsx

scan_protocol: Protocol is following the manufacturer’s directions (Ray biotech Mouse L308 Array, Glass Slide Cat# AAM-BLG-1-4). See http://www.raybiotech.com/files/manual/Antibody-Array/AAM-BLG-1.pdf

source_name: dHD 28 cels

value: dHD28 cells


title: Hepatogenic differentiation, HD28 cells

source_name: HD 28 cells

label_protocol: Protocol is following the manufacturer’s directions (Ray biotech Mouse L308 Array, Glass Slide Cat# AAM-BLG-1-4). See http://www.raybiotech.com/files/manual/Antibody-Array/AAM-BLG-1.pdf

value: HD28 cells


title: Hepatogenic differentiation, Hepatocyte

source_name: Hepatocytes

value: Hepatocytes


title: S7_bc_sc_rep1

description: Normalization Batch 1

source_name: bc, sc

tag: collection

value: bc


title: mouse label 40, diet HFD, tissue adipose, time/age Week 1

source_name: diet HFD_tissue adipose_time/age Week 1

value: mouse label 40

tag: tissue

value: adipose


title: mouse label 38, diet HFD, tissue adipose, time/age Week 1

tag: gender

value: male

value: mouse label 38

value: diet HFD


title: mouse label 35, diet HFD, tissue adipose, time/age  Week 9

source_name: diet HFD_tissue adipose_time/age Week 9

value: mouse label 35

value: Week 9


title: mouse label 38, diet HFD, tissue pancreas, time/age Week 1

value: Week 1


title: light.8h.replicate1

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to ATH lincRNA v1 array for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x15k array slides.

data_processing: Raw data of processed signal intensities are obtained by analysis using Feature Extraction Software (Agilent) with default parameters. Standard QC analysis, background normalization and quantile normalization were performed using GeneSpring GX Software (Agilent) with default parameters.

organism: Arabidopsis thaliana

label_protocol: We performed RNA labeling, hybridization and scaning using protocols according to the Agilent's instructions. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent).

growth_protocol: The Arabidopsis thaliana Columbia (Col-0) ecotype was used as wild type. Plants were grown in light (145 µmolm-2s-1), in a temperature (22ºC) and humidity (65%) controlled chambers under 8h light/16h dark photoperiods.Leaf samples were collected from 30 day-old plants.

extract_protocol: Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen).

tag: ecotype

value: Leaf


title: MPDC-exsomes

city: Hangzhou

first: Wang

last: Lantian

state: Zhejiang

address: 88 Jiefang Road

department: Department of Surgery

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

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

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

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

source_name: Cell culture supernatants

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

growth_protocol: The murine pancreatic cancer cell line, developed from tumor tissue obtained from KrasLSL-G12D/+, Trp53LSL-R172H/+, Pdx1-Cre(KPC) mice which can develop spontaneous pancreatic ductal adenocarcinoma (PDAC), was maintained in RPMI-1640 medium (Gibco, Shanghai, China), supplemented with 20% fetal bovine serum (FBS), 1% sodium pyruvate(100×), 1% MEM Non-Essential Amino Acids(NEAA 100×). The murine pancreatic ductal epithelial cell line (MPDC) was purchased from CELLBIO Company (CBR131654, Shanghai, China) and cultured in Dulbecco's modified Eagle's Medium containing L-Glutamine, 4.5g/L D-Glucose, 110mg/L sodium pyruvate (DMEM; Gibco, Shanghai, China), supplemented with 10% FBS.

extract_protocol: Exosomes were isolated by differential ultracentrifugation. Total RNA from exosomes was isolated  using the mirVanaTM RNA Isolation Kit (AM1561, AMBION, US.).

tag: sample type

value: exosomes derived from murine pancreatic ductal epithelial cells (MPDC)


title: dark.16h.replicate2


title: light.8h.replicate2


title: mouse label 36, diet HFD, tissue liver, time/age Week 1

value: outbred CD-1

value: mouse label 36

value: liver


title: dark.16h.replicate1


title: mouse label 38, diet HFD, tissue liver, time/age Week 1


title: mouse label 7, diet HFD, tissue adipose, time/age Week 9

value: mouse label 7


title: dark.12h.replicate2


title: light.4h.replicate2


title: mouse label 10, diet HFD, tissue adipose, time/age Week 9

value: mouse label 10


title: KPC-exosomes

value: exosomes derived from murine pancreatic cancer cells (KPC cells)


title: dark.12h.replicate1


title: dark.20h.replicate2


title: dark.20h.replicate1


title: mouse label 36, diet HFD, tissue adipose, time/age Week 1


title: mouse label 10, diet HFD, tissue liver, time/age Week 9


title: mouse label 35, diet HFD, tissue liver, time/age Week 9


title: light.4h.replicate1


title: light.0h.replicate2


title: EQ0057_110_b

city: Tokyo

first: Akira

last: Saito

address: 7-31-, Hongo, Bunkyo

country: Japan

institute: Tokyo University

description: assay_ID: EQ0057_10

scan_protocol: LightCycler® 480 Instrument II

data_processing: Exiqon GenEx software

label: SYBR® Green

source_name: gingival crevicular fluid

label_protocol: Single stranded cDNA was synthesized by reverse transcription of RNA using universal cDNA Synthesis Kit II (Exiqon). Quantitative PCR was performed for the cDNA using Human miRNome microRNA PCR Panel I+II (Exiqon), following the manufacturer's  protocol for Human miRCURY LNA™ Universal RT microRNA PCR System.

extract_protocol: GCF samples were collected by gently inserting paper strips (PerioPaper®) into the periodontal pocket

tag: group

value: periodontitis


title: mouse label 10, diet HFD, tissue pancreas, time/age Week 9

value: pancreas


title: EQ0057_109_b

description: assay_ID: EQ0057_09


title: mouse label 35, diet HFD, tissue pancreas, time/age Week 9


title: EQ0057_107_b

description: assay_ID: EQ0057_07


title: EQ0057_105_b

description: assay_ID: EQ0057_05

value: healthy


title: light.0h.replicate1


title: EQ0057_103_b

description: assay_ID: EQ0057_03


title: EQ0057_102_b

description: assay_ID: EQ0057_02


title: EQ0057_106_b

description: assay_ID: EQ0057_06


title: EQ0057_101_b

description: assay_ID: EQ0057_01


title: EQ0057_104_b

description: assay_ID: EQ0057_04


title: MSC_donor6_P2_FCS [Illumina]

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

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

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.

label: Cy5 and Cy3

source_name: mesenchymal stromal cells in FCS for 2 passages

growth_protocol: Cells were continuously cultured in parallel in basal medium with either 10% FCS or 10% HPL. Basal medium consisted of Dulbecco’s Modified Eagle Medium (DMEM, 1g/L glucose; PAA, Pasching, Austria) with 1% penicillin/streptomycin (PAA) and 1% L-glutamine

extract_protocol: Genomic DNA of MSCs was harvested with the NucleoSpin Tissue kit (Macherey-Nagel, Düren, Germany)

treatment_protocol: 10% FCS or 10% HPL

tag: donor

value: donor 6

value: female

value: FCS

value: mesenchymal stromal cells

tag: passage

value: passage 20


title: RA synovial macrophages, donor 1

status: Public on Aug 10 2017

city: New York

first: Lionel

middle: B.

last: Ivashkiv

state: NY

address: 535 East 70th Street

institute: Hospital for Special Surgery

description:
Gene expression data from fresh macrophages from RA synovial fluid
S11_121_RA_Signal

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 750.  After exporting the .chp files and before data analsysis, probesets that were flagged as Absent in all the samples were eliminated from further data analysis

source_name: RA synovial macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).

growth_protocol: For control macrophages, CD14+ monocytes were isolated from healthy donor blood samples and cultured cells in RPMI+10% FBS+1% Pencillin/Streptomycin/Glutamine with MCSF (20 ng/ml) for 3 days

extract_protocol: RNA was isolatedwith the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: subject status

value: rheumatoid arthritis patient

tag: subject id

value: donor 1

value: synovial fluid

value: macrophages

tag: cell status

value: freshly isolated cells


title: RA synovial macrophages, donor 5

description:
Gene expression data from fresh macrophages from RA synovial fluid
S15_134_RA_Signal

value: donor 5

tag: cell type


title: RA synovial macrophages, donor 7

description:
Gene expression data from fresh macrophages from RA synovial fluid
S17_137_RA_Signal

value: donor 7


title: RA synovial macrophages, donor 9

description:
Gene expression data from fresh macrophages from RA synovial fluid
S20_149_RA_Signal

value: donor 9


title: RA synovial macrophages, donor 8

description:
Gene expression data from fresh macrophages from RA synovial fluid
S19_142_RA_Signal

value: donor 8


title: MSC_donor2_P2_FCS [Illumina]

label_protocol: Standard Infinium HD Methylation Assay protocol

value: donor 2

value: male

tag: age


title: RA synovial macrophages, donor 2

description:
Gene expression data from fresh macrophages from RA synovial fluid
S12_123_RA_Signal


title: MSC_donor4_P2_HPL [Illumina]

source_name: mesenchymal stromal cells in HPL for 2 passages

value: donor 4

value: HPL


title: control macrophages, donor A

description:
Gene expression data from blood macrophages from healthy donor cultured for 3 days
S1_CtrlA_3d_Signal

source_name: control macrophages

value: healthy individual

value: donor A

value: peripheral blood

value: cultured for 3 days


title: MSC_donor2_P2_HPL [Illumina]

value: mesenchymal stromal cells

value: passage 20


title: control macrophages, donor B

description:
Gene expression data from blood macrophages from healthy donor cultured for 3 days
S2_CtrlB_3d_Signal

value: donor B


title: RA synovial macrophages, donor 3

description:
Gene expression data from fresh macrophages from RA synovial fluid
S13_125_RA_Signal

value: rheumatoid arthritis patient

value: donor 3

value: synovial fluid

value: macrophages


title: RA synovial macrophages, donor 4

description:
Gene expression data from fresh macrophages from RA synovial fluid
S14_126_RA_Signal

value: freshly isolated cells


title: control macrophages, donor C

description:
Gene expression data from blood macrophages from healthy donor cultured for 3 days
S3_CtrlC_3d_Signal

value: donor C


title: Placenta_nonLactating_16

city: Columbia

first: Matthew

last: Lucy

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri

hyb_protocol: 130 µl of hybridization solution containing 50 ng/µl of fragmented aRNA was hybridized to the Bovine Genome Array Genechip (Affymetrix, Santa Clara, CA) at 45° C for 20 h. After hybridization, the chips were washed and stained with R-phycoerythrin-streptavidin on Affymetrix fluidics station 450 using fluidics protocol Midi_euk2v3-450.

scan_protocol: The image data were acquired by Affymetrix Genechip scanner 3000.

data_processing: Differential expression analysis of the liver, intercaruncular endometrium, caruncular endometrium and placenta tissue microarray data was performed separately using the Bioconductor software package limma with the R statistical programming language (version 3.2.2). Background intensities in the array data were normalized to log-expression values. Array quality metrics were assessed using the arrayQualityMetrics package. The data were filtered to remove control probesets (n=112). For the differential expression analysis within tissue, a linear model was fitted to the expression data for each probe with lactation status (lactating, non-lactating), group (one, two), day of gestation (28, 35, 42), and their interactions included as fixed effects. For the differential expression analysis between caruncular and intercaruncular tissue, the linear model included tissue (caruncular endometrium, intercaruncular endometrium), day of gestation (28, 35, 42) and their interaction as fixed effects and cow as a random effect. For each analysis, the limma package applies empirical Bayes methods to compute moderated t-tests. Transcripts were deemed differentially expressed at P≤0.01 after adjustment for multiple testing using the Benjamini and Hochberg (BH) method.

organism: Bos taurus

label_protocol: 0.5 µg of total RNA was used to make the biotin-labeled antisense RNA (aRNA) target using the MessageAmpTM Premier RNA amplification kit (Ambion, Austin, TX) by following the manufacturer’s procedures. Briefly, the total RNA was reverse transcribed to first strand cDNA with an oligo(dT) primer bearing a 5’-T7 promoter using ArrayScript reverse transcriptase (Ambion). The first strand cDNA then underwent second-strand synthesis to convert into double stranded cDNA template for in vitro transcription. The biotin-labeled aRNA was synthesized using T7 RNA transcriptase with biotin-NTP mix. After purification, the aRNA was fragmented in fragmentation buffer at 94° C for 35 min.

extract_protocol: Cows were stunned by using a pneumatic captive bolt and then killed by exsanguination. The reproductive tracts and a liver sample were collected, placed on crushed ice and taken to the laboratory within 30 minutes of slaughter. The pregnancy (placental membranes encasing placental fluids and fetuses) was removed from the uterus. The placental fluids (mixture of both amniotic and allantoic fluids) were collected and a sample frozen at -80oC. Samples of placenta, caruncular endometrium and intercaruncular endometrium were frozen in liquid nitrogen so that they could be used for RNA analysis. For endometrial tissue collection (caruncular and intercaruncular endometrium), 5 to 10 representative 1 cm x 1 cm samples were collected from each region, frozen in liquid nitrogen, and stored at -80oC. The five to ten individual tissue samples within each tissue type from each cow were later combined and ground together under liquid nitrogen with a mortar and pestle. Total cellular RNA was isolated by using the TRIzol reagent (Invitrogen; Carlsbad, CA). Caruncular endometrium and intercaruncular endometrium samples were further purified by using the QIAmp Mini Spin Column (Qiagen, Valencia, CA). The integrity of RNA was determined by visual inspection of 28S and 18S RNA bands after agarose gel electrophoresis and by calculating the ratio of absorbance at 260 nm and 280 nm. The RNA that was used had intact 28S and 18S RNA bands and the 260:280 nm ratio was greater than 1.8. The RNA was diluted in water and stored at -80°C.

tag: breed

value: Holstein dairy cow

value: Placenta

tag: Stage

value: non-Lactating

tag: day of pregnancy


title: control macrophages, donor D

description:
Gene expression data from blood macrophages from healthy donor cultured for 3 days
S4_CtrlD_3d_Signal

value: donor D


title: RA synovial macrophages, donor 6

description:
Gene expression data from fresh macrophages from RA synovial fluid
S16_135_RA_Signal

value: donor 6


title: MSC_donor1_P2_FCS [Illumina]

value: donor 1

value: male

value: FCS


title: Placenta_nonLactating_18


title: control macrophages, donor E

description:
Gene expression data from blood macrophages from healthy donor cultured for 3 days
S5_CtrlE_3d_Signal

value: healthy individual

value: donor E

value: peripheral blood

value: cultured for 3 days


title: MSC_donor3_P2_HPL [Illumina]

value: donor 3

value: HPL

value: mesenchymal stromal cells

value: passage 20


title: MSC_donor1_P2_HPL [Illumina]


title: MSC_donor6_P2_HPL [Illumina]

value: female


title: MSC_donor3_P2_FCS [Illumina]


title: MSC_donor5_P2_HPL [Illumina]

value: donor 5


title: Placenta_nonLactating_17

value: Holstein dairy cow

value: Placenta


title: Placenta_nonLactating_8

value: non-Lactating


title: Placenta_nonLactating_13


title: Placenta_nonLactating_11


title: Placenta_Lactating_21

value: Lactating


title: EQ0057_108_b

description: assay_ID: EQ0057_08

value: periodontitis


title: Placenta_nonLactating_7


title: Placenta_nonLactating_5


title: Placenta_Lactating_18


title: Placenta_Lactating_22


title: Placenta_nonLactating_2


title: Placenta_Lactating_17


title: Placenta_nonLactating_12


title: Placenta_nonLactating_6


title: Placenta_nonLactating_10


title: Placenta_nonLactating_9


title: Placenta_Lactating_20


title: Placenta_nonLactating_1


title: Placenta_nonLactating_14


title: Placenta_nonLactating_4


title: Placenta_nonLactating_3


title: MSC_donor5_P2_FCS [Illumina]


title: Placenta_Lactating_16


title: Placenta_Lactating_19


title: Placenta_Lactating_15


title: Placenta_Lactating_11


title: Placenta_Lactating_13


title: Placenta_Lactating_14


title: Placenta_Lactating_12


title: MSC_donor4_P2_FCS [Illumina]

value: donor 4

value: male


title: Placenta_Lactating_6


title: Liver_nonLactating_17

value: Liver


title: Placenta_Lactating_7


title: Liver_nonLactating_13


title: Placenta_Lactating_8


title: Placenta_Lactating_3


title: Placenta_Lactating_10


title: Placenta_Lactating_9


title: Liver_nonLactating_12


title: Placenta_Lactating_2


title: Liver_nonLactating_9


title: Liver_nonLactating_14


title: Liver_nonLactating_7


title: Placenta_Lactating_1


title: Liver_nonLactating_18


title: Liver_nonLactating_16


title: Liver_nonLactating_10


title: Placenta_Lactating_4


title: Placenta_Lactating_5


title: Liver_nonLactating_8


title: Liver_nonLactating_11


title: Liver_nonLactating_6


title: Liver_nonLactating_2


title: Liver_nonLactating_4


title: Liver_nonLactating_5


title: Liver_nonLactating_3


title: Liver_nonLactating_1


title: Liver_Lactating_20


title: Liver_Lactating_10


title: Liver_Lactating_21


title: Liver_Lactating_14


title: Liver_Lactating_16


title: Liver_Lactating_18


title: Liver_Lactating_12


title: Liver_Lactating_15


title: Liver_Lactating_19


title: Liver_Lactating_8


title: Liver_Lactating_11


title: Liver_Lactating_22


title: Liver_Lactating_3


title: Liver_Lactating_6


title: Liver_Lactating_9


title: Liver_Lactating_4


title: Intercaruncular_nonLactating_15

value: InterCaruncular endometrium


title: Placenta_nonLactating_15


title: Liver_Lactating_13


title: Intercaruncular_nonLactating_19


title: Liver_Lactating_17


title: Intercaruncular_nonLactating_13


title: Liver_nonLactating_19


title: Liver_Lactating_2


title: Liver_nonLactating_15


title: Intercaruncular_nonLactating_14


title: Liver_Lactating_5


title: Liver_Lactating_1


title: Liver_Lactating_7


title: Intercaruncular_nonLactating_18


title: Intercaruncular_nonLactating_11


title: Intercaruncular_nonLactating_12


title: Intercaruncular_nonLactating_9


title: Intercaruncular_nonLactating_10


title: Intercaruncular_nonLactating_7


title: Intercaruncular_nonLactating_8


title: Intercaruncular_nonLactating_1


title: Intercaruncular_nonLactating_4


title: Intercaruncular_Lactating_20


title: Intercaruncular_nonLactating_3


title: Intercaruncular_Lactating_21


title: Intercaruncular_nonLactating_2


title: Intercaruncular_Lactating_19


title: Intercaruncular_nonLactating_6


title: Intercaruncular_Lactating_12


title: Intercaruncular_Lactating_14


title: Intercaruncular_Lactating_9


title: Intercaruncular_Lactating_16


title: Intercaruncular_Lactating_10


title: Intercaruncular_Lactating_5


title: Intercaruncular_Lactating_17


title: Intercaruncular_Lactating_13


title: Intercaruncular_Lactating_8


title: Intercaruncular_Lactating_7


title: Intercaruncular_Lactating_11


title: Intercaruncular_Lactating_6


title: Intercaruncular_nonLactating_5


title: Intercaruncular_Lactating_15


title: Intercaruncular_Lactating_18


title: Intercaruncular_Lactating_2


title: Caruncular_nonLactating_19

value: Caruncular endometrium


title: Caruncular_nonLactating_15


title: Caruncular_nonLactating_11


title: Intercaruncular_Lactating_1


title: Caruncular_nonLactating_18


title: Intercaruncular_Lactating_3


title: Caruncular_nonLactating_12


title: Intercaruncular_Lactating_4


title: Caruncular_nonLactating_16


title: Caruncular_nonLactating_10


title: Caruncular_nonLactating_3


title: Caruncular_nonLactating_6


title: Caruncular_nonLactating_2


title: Caruncular_nonLactating_17


title: Caruncular_nonLactating_4


title: Caruncular_nonLactating_9


title: Caruncular_Lactating_20


title: Caruncular_nonLactating_7


title: Caruncular_nonLactating_13


title: Caruncular_nonLactating_5


title: Caruncular_nonLactating_1


title: Caruncular_Lactating_21


title: Caruncular_Lactating_22


title: Caruncular_Lactating_17


title: Caruncular_Lactating_16


title: Caruncular_Lactating_18


title: Caruncular_Lactating_7


title: Caruncular_Lactating_14


title: Caruncular_Lactating_8


title: Caruncular_Lactating_12


title: Caruncular_Lactating_9


title: Caruncular_Lactating_10


title: Caruncular_Lactating_19


title: Caruncular_Lactating_13


title: Caruncular_Lactating_5


title: Caruncular_Lactating_3


title: Caruncular_Lactating_4


title: Caruncular_Lactating_15


title: Caruncular_Lactating_6


title: Caruncular_Lactating_2


title: Caruncular_Lactating_11


title: Caruncular_Lactating_1


title: satellite cells adult animal calorie restriction diet T8, biological replicate 3

city: Barcelona

first: Aikaterini

last: Symeonidi

state: Barcelona

address: Baldiri i Reixac, 10

department: Oncology

country: Spain

institute: Institut for Research in Biomedicine (IRB-Barcelona)

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)

source_name: muscle stem cells

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

extract_protocol: RNA was extracted using TRizol (Sigma-Aldrich).

treatment_protocol: Per-1 venus C57B6/J aged and adult mice were fed either ad libitum with control diet or a 30% food reduction compared to the ad libitum group intake of calorie restricted diet. The experiment was 25 week-long and started after an adaption period of 3 weeks, where calorie restricted animals were subjected to a 10% food reduction per week.

value: skeletal muscle

tag: time point

tag: diet

value: calorie restriction

tag: genotype/variation

value: Per1-Venus BAC transgenic mice with C57B6/J background

value: 47-57 week old


title: satellite cells adult animal calorie restriction diet T4, biological replicate 4

tag: tissue


title: satellite cells adult animal calorie restriction diet T4, biological replicate 5


title: satellite cells adult animal calorie restriction diet T20, biological replicate 5


title: satellite cells adult animal calorie restriction diet T8, biological replicate 4


title: satellite cells adult animal calorie restriction diet T20, biological replicate 4


title: satellite cells adult animal calorie restriction diet T4, biological replicate 2


title: satellite cells adult animal calorie restriction diet T8, biological replicate 5


title: satellite cells adult animal calorie restriction diet T8, biological replicate 1


title: satellite cells adult animal calorie restriction diet T20, biological replicate 2


title: satellite cells adult animal calorie restriction diet T8, biological replicate 2


title: satellite cells adult animal calorie restriction diet T4, biological replicate 6


title: satellite cells adult animal calorie restriction diet T4, biological replicate 1


title: satellite cells adult animal calorie restriction diet T16, biological replicate 4


title: satellite cells adult animal calorie restriction diet T4, biological replicate 3


title: satellite cells adult animal calorie restriction diet T16, biological replicate 2


title: satellite cells adult animal calorie restriction diet T16, biological replicate 1


title: satellite cells adult animal calorie restriction diet T20, biological replicate 1


title: satellite cells adult animal calorie restriction diet T16, biological replicate 3


title: satellite cells adult animal calorie restriction diet T20, biological replicate 3


title: satellite cells adult animal calorie restriction diet T12, biological replicate 3


title: satellite cells adult animal calorie restriction diet T12, biological replicate 4


title: satellite cells adult animal calorie restriction diet T12, biological replicate 5


title: satellite cells adult animal calorie restriction diet T12, biological replicate 6


title: CPZ 10 mg/kg BW 25 days, sample 12

city: Bilthoven

first: Alexa

last: Vitins

address: P.O. Box 1

country: Netherlands

institute: RIVM

description: CPZ high 25d_12

hyb_protocol: According to the Affymetrix Hybridization, Wash and Stain Kit (#901530).

scan_protocol: According to Affymetrix protocols.

data_processing: Cell Intensity Files generated for each GeneChip using the Affymetrix GeneChip Command Console (v3.0) software were normalized using the Robust Multichip Average (RMA) algorithm from http://arrayanalysis.org (BiGCaT Maastricht University). RMA-normalized data were transformed to log2 by arrayanalysis.org for further analysis. Additionally, the quality of microarray images was inspected visually (http://arrayanalysis.org, BiGCaT Maastricht University).

source_name: Mouse liver after 25 day CPZ treatment

label_protocol: According to the protocol provided with the Affymetrix 3' IVT Express Labeling Kit (#901229).

extract_protocol: Upon sacrifice, liver was immediately dissected. Central half of the left lateral lobe was collected in RNAlater and kept for a maximum of one week at 4 oC and frozen at -80 oC until use for RNA isolation. RNA was isolated using the RNeasy Mini Kit.

treatment_protocol: Mice treated for 25 days with vehicle or compound by oral gavage.

tag: strain/background

tag: gender

value: 10 weeks

tag: weight

value: liver

tag: treatment

value: CPZ

value: 25 days


title: satellite cells adult animal calorie restriction diet T16, biological replicate 5


title: satellite cells adult animal calorie restriction diet T12, biological replicate 1


title: CPZ 10 mg/kg BW 25 days, sample 11

description: CPZ high 25d_11


title: satellite cells adult animal calorie restriction diet T0, biological replicate 4


title: Caruncular_nonLactating_14

value: Holstein dairy cow

tag: group


title: satellite cells adult animal calorie restriction diet T12, biological replicate 2


title: CPZ 10 mg/kg BW 25 days,sample 3

description: CPZ high 25d_3


title: satellite cells adult animal calorie restriction diet T0, biological replicate 3


title: CPZ 10 mg/kg BW 25 days, sample 1

description: CPZ high 25d_1


title: CPZ 10 mg/kg BW 25 days, sample 4

description: CPZ high 25d_4


title: CPZ vehicle 25 days, sample 19

description: CPZ v 25d_19

source_name: Mouse liver after 25 day CPZ vehicle treatment

value: CPZ vehicle (PBS)


title: CPZ vehicle 25 days, sample 14

description: CPZ v 25d_14


title: satellite cells adult animal calorie restriction diet T0, biological replicate 1


title: satellite cells adult animal calorie restriction diet T0, biological replicate 2


title: CPZ vehicle 25 days, sample 20

description: CPZ v 25d_20


title: satellite cells aged animal control diet T8, biological replicate 1

value: control

value: 83-97 week old


title: satellite cells adult animal calorie restriction diet T0, biological replicate 5


title: EE2 3.70 mg/kg BW 25 days, sample 17

description: EE2 high 25d_17

source_name: Mouse liver after 25 day EE2 treatment


title: CPZ vehicle 25 days, sample 10

description: CPZ v 25d_10


title: satellite cells aged animal control diet T8, biological replicate 2


title: CPZ vehicle 25 days, sample 7

description: CPZ v 25d_7


title: EE2 3.70 mg/kg BW 25 days, sample 18

description: EE2 high 25d_18


title: satellite cells aged animal control diet T8, biological replicate 4


title: satellite cells aged animal control diet T4, biological replicate 4


title: satellite cells aged animal control diet T4, biological replicate 3


title: satellite cells aged animal control diet T8, biological replicate 3


title: EE2 3.70 mg/kg BW 25 days, sample 13

description: EE2 high 25d_13


title: EE2 3.70 mg/kg BW 25 days, sample 15

description: EE2 high 25d_15


title: satellite cells aged animal control diet T4, biological replicate 2


title: EE2 vehicle 25 days, sample 16

description: EE2 v 25d_16

source_name: Mouse liver after 25 day EE2 vehicle treatment

value: EE2 vehicle (sunflower oil)


title: satellite cells aged animal control diet T4, biological replicate 1


title: Caruncular_nonLactating_8

value: non-Lactating


title: satellite cells aged animal control diet T20, biological replicate 2


title: satellite cells aged animal control diet T20, biological replicate 3


title: EE2 vehicle 25 days, sample 6

description: EE2 v 25d_6

value: male


title: EE2 3.70 mg/kg BW 25 days, sample 9

description: EE2 high 25d_9


title: EE2 vehicle 25 days, sample 5

description: EE2 v 25d_5


title: satellite cells aged animal control diet T20, biological replicate 4


title: EE2 vehicle 25 days, sample 2

description: EE2 v 25d_2


title: satellite cells aged animal control diet T16, biological replicate 4


title: EE2 vehicle 25 days, sample 8

description: EE2 v 25d_8


title: satellite cells aged animal control diet T20, biological replicate 1


title: satellite cells aged animal control diet T12, biological replicate 3


title: satellite cells aged animal control diet T12, biological replicate 1


title: satellite cells aged animal control diet T16, biological replicate 1


title: satellite cells aged animal control diet T0, biological replicate 4


title: satellite cells aged animal control diet T0, biological replicate 2


title: satellite cells aged animal control diet T12, biological replicate 4


title: satellite cells aged animal control diet T12, biological replicate 2


title: satellite cells aged animal control diet T16, biological replicate 3


title: satellite cells aged animal control diet T0, biological replicate 1


title: satellite cells aged animal calorie restriction diet T8, biological replicate 4


title: satellite cells aged animal control diet T16, biological replicate 2


title: satellite cells aged animal calorie restriction diet T8, biological replicate 1


title: satellite cells aged animal calorie restriction diet T4, biological replicate 4


title: satellite cells aged animal calorie restriction diet T8, biological replicate 3


title: satellite cells aged animal control diet T0, biological replicate 3


title: satellite cells aged animal calorie restriction diet T8, biological replicate 2


title: satellite cells aged animal calorie restriction diet T4, biological replicate 2


title: satellite cells aged animal calorie restriction diet T20, biological replicate 4


title: satellite cells aged animal calorie restriction diet T12, biological replicate 5


title: satellite cells aged animal calorie restriction diet T20, biological replicate 2


title: satellite cells aged animal calorie restriction diet T16, biological replicate 4


title: satellite cells aged animal calorie restriction diet T12, biological replicate 4


title: satellite cells aged animal calorie restriction diet T12, biological replicate 2


title: satellite cells aged animal calorie restriction diet T12, biological replicate 3


title: satellite cells aged animal calorie restriction diet T20, biological replicate 1


title: satellite cells aged animal calorie restriction diet T20, biological replicate 3


title: satellite cells aged animal calorie restriction diet T16, biological replicate 2


title: satellite cells aged animal calorie restriction diet T12, biological replicate 1


title: satellite cells aged animal calorie restriction diet T4, biological replicate 1


title: satellite cells aged animal calorie restriction diet T0, biological replicate 4


title: satellite cells adult animal control diet T8, biological replicate 3


title: satellite cells aged animal calorie restriction diet T4, biological replicate 3


title: satellite cells aged animal calorie restriction diet T0, biological replicate 1


title: satellite cells adult animal control diet T8, biological replicate 4


title: satellite cells aged animal calorie restriction diet T16, biological replicate 3


title: satellite cells aged animal calorie restriction diet T0, biological replicate 3


title: satellite cells aged animal calorie restriction diet T16, biological replicate 1


title: satellite cells aged animal calorie restriction diet T0, biological replicate 5


title: satellite cells aged animal calorie restriction diet T0, biological replicate 2


title: satellite cells adult animal control diet T8, biological replicate 1


title: satellite cells adult animal control diet T8, biological replicate 2


title: satellite cells adult animal control diet T4, biological replicate 3


title: satellite cells adult animal control diet T4, biological replicate 4


title: satellite cells adult animal control diet T4, biological replicate 1


title: satellite cells adult animal control diet T16, biological replicate 4


title: VUmc_62

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

hyb_protocol: Hybridization was performed on a human GE 4x44K formatted expression array spotted with 60-mer oligonucleotides representing over 43,000 well-characterized coding and non-coding sequences (G4112F, Agilent Technologies, Amstelveen, The Netherlands).  Input: 825 ng RNA.

scan_protocol: Scanning was performed using a microarray scanner G2505B (Agilent Technologies). Feature Extraction v9.5 using the manufacturers protocols (Agilent Technologies).

data_processing:
Extration of the median signal from the raw data files, no background correction, median and loess within-array normalization (as implemented in the Limma-package).
Data was combined with GSE30788 by limiting both data sets to overlapping probes (performed by Agendia by using their Agilent probe identification). Comparability of the expression data of both datasets is ensured by joint between-array normalization (A-quantile as implemented in the Limma-package) and removal of possible batch effects using the Combat-package (Johnson et al, 2007).

source_name: HNSCC

label_protocol: cDNA synthesis and labeling were performed according to the recommendations of the manufacturer (Agilent Technologies, Amstelveen, The Netherlands), including quality controls (QCs) using a low input labeling and amplification kit (Agilent).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to the protocol of the manufacturer.

treatment_protocol: Tumors were collected immediately after surgery and stored in liquid nitrogen.

tag: tissue type

value: HPV-negative OSCC primary tumor

tag: location

value: Oral Cavity

value: m

tag: survival

tag: deathmonth

tag: pstagetnm

value: IV

tag: pnstage

value: pos

tag: recurrence

value: no

source_name: reference

tag: reference

value: Universal Human Reference RNA (Stratagene)


title: VUmc_66

tag: age

tag: followuptime

value: neg


title: VUmc_63

value: I


title: VUmc_65

value: II


title: satellite cells adult animal control diet T4, biological replicate 2

value: skeletal muscle

tag: time point

tag: diet

tag: genotype/variation

value: Per1-Venus BAC transgenic mice with C57B6/J background


title: VUmc_64

tag: gender

value: yes


title: satellite cells adult animal control diet T16, biological replicate 2

tag: tissue

value: control

value: 83-97 week old


title: satellite cells adult animal control diet T20, biological replicate 1


title: VUmc_58


title: satellite cells adult animal control diet T16, biological replicate 3


title: satellite cells adult animal control diet T16, biological replicate 1


title: VUmc_59

value: f


title: VUmc_61


title: satellite cells adult animal control diet T12, biological replicate 3


title: VUmc_60


title: satellite cells adult animal control diet T12, biological replicate 1


title: VUmc_55


title: VUmc_56


title: satellite cells adult animal control diet T12, biological replicate 2


title: satellite cells adult animal control diet T0, biological replicate 4


title: VUmc_54


title: VUmc_57


title: satellite cells adult animal control diet T0, biological replicate 3


title: VUmc_53


title: satellite cells adult animal control diet T0, biological replicate 1


title: epidermal stem cells adult animal control diet T8, replicate 3

data_processing: Overall array intensity was controlised between arrays and the probe intensity of all probes in a probe set summarised to a single value using RMA (Robust Multichip Average)

source_name: epidermal stem cells

value: epidermis

tag: genotype

value: 47-57 week old


title: VUmc_50

value: HPV-negative OSCC primary tumor

value: Oral Cavity


title: satellite cells adult animal control diet T12, biological replicate 4


title: epidermal stem cells adult animal control diet T8, replicate 1


title: VUmc_51

value: m

value: IV


title: epidermal stem cells adult animal control diet T8, replicate 2


title: epidermal stem cells adult animal control diet T4, replicate 3


title: VUmc_52

value: no


title: VUmc_48

value: pos

value: Universal Human Reference RNA (Stratagene)


title: epidermal stem cells adult animal control diet T4, replicate 4


title: VUmc_47

value: III


title: VUmc_45


title: VUmc_44


title: satellite cells adult animal control diet T0, biological replicate 2


title: epidermal stem cells adult animal control diet T4, replicate 1


title: VUmc_49


title: VUmc_46

value: I

value: neg


title: epidermal stem cells adult animal control diet T12, replicate 2

value: Per1-Venus BAC transgenic mice with C57B6/J background


title: satellite cells adult animal control diet T4, biological replicate 5

value: skeletal muscle


title: epidermal stem cells adult animal control diet T12, replicate 3

value: control


title: VUmc_43


title: epidermal stem cells adult animal control diet T4, replicate 2


title: VUmc_40


title: VUmc_36


title: epidermal stem cells adult animal control diet T20, replicate 4


title: VUmc_39


title: VUmc_30

value: II


title: VUmc_34


title: epidermal stem cells adult animal control diet T20, replicate 1


title: epidermal stem cells adult animal control diet T16, replicate 1


title: VUmc_35

value: f


title: epidermal stem cells adult animal control diet T16, replicate 4

value: epidermis


title: epidermal stem cells adult animal control diet T12, replicate 1

value: 47-57 week old


title: epidermal stem cells adult animal control diet T16, replicate 2


title: epidermal stem cells adult animal control diet T20, replicate 3


title: VUmc_32

value: HPV-negative OSCC primary tumor


title: epidermal stem cells adult animal control diet T16, replicate 3


title: VUmc_41

value: Oral Cavity


title: VUmc_42


title: epidermal stem cells adult animal control diet T12, replicate 4


title: VUmc_38

value: yes


title: VUmc_37

value: m

value: IV


title: VUmc_31

value: no


title: epidermal stem cells adult animal control diet T20, replicate 2


title: epidermal stem cells adult animal control diet T0, replicate 4


title: VUmc_33

value: Universal Human Reference RNA (Stratagene)


title: epidermal stem cells adult animal control diet T0, replicate 3


title: epidermal stem cells adult animal control diet T0, replicate 1


title: epidermal stem cells adult animal calorie restriction diet T4, replicate 4

value: calorie restriction


title: epidermal stem cells adult animal calorie restriction diet T8, replicate 4


title: epidermal stem cells adult animal calorie restriction diet T4, replicate 1


title: epidermal stem cells adult animal control diet T0, replicate 2


title: epidermal stem cells adult animal calorie restriction diet T8, replicate 3


title: epidermal stem cells adult animal calorie restriction diet T4, replicate 2


title: VUmc_29

value: pos


title: VUmc_21

value: III


title: epidermal stem cells adult animal calorie restriction diet T4, replicate 6

value: Per1-Venus BAC transgenic mice with C57B6/J background


title: epidermal stem cells adult animal calorie restriction diet T4, replicate 5


title: VUmc_22

value: neg


title: epidermal stem cells adult animal calorie restriction diet T8, replicate 1


title: VUmc_24


title: VUmc_26


title: VUmc_28


title: VUmc_23


title: VUmc_16


title: epidermal stem cells adult animal calorie restriction diet T20, replicate 5


title: epidermal stem cells adult animal calorie restriction diet T8, replicate 2


title: epidermal stem cells adult animal calorie restriction diet T4, replicate 3


title: VUmc_27


title: VUmc_18


title: VUmc_17


title: VUmc_25


title: epidermal stem cells adult animal calorie restriction diet T20, replicate 4


title: VUmc_19


title: VUmc_20


title: epidermal stem cells adult animal calorie restriction diet T20, replicate 3


title: VUmc_15


title: VUmc_14

value: I


title: VUmc_10

value: II


title: VUmc_11


title: epidermal stem cells adult animal calorie restriction diet T16, replicate 5


title: epidermal stem cells adult animal calorie restriction diet T16, replicate 3


title: epidermal stem cells adult animal calorie restriction diet T12, replicate 5


title: VUmc_12

value: f


title: VUmc_09


title: epidermal stem cells adult animal calorie restriction diet T16, replicate 2

value: epidermis


title: epidermal stem cells adult animal calorie restriction diet T12, replicate 2

value: 47-57 week old


title: epidermal stem cells adult animal calorie restriction diet T16, replicate 4


title: epidermal stem cells adult animal calorie restriction diet T20, replicate 1


title: epidermal stem cells adult animal calorie restriction diet T12, replicate 1


title: epidermal stem cells adult animal calorie restriction diet T20, replicate 2


title: epidermal stem cells adult animal calorie restriction diet T0, replicate 5


title: epidermal stem cells adult animal calorie restriction diet T12, replicate 3


title: VUmc_06

value: HPV-negative OSCC primary tumor


title: VUmc_07

value: Oral Cavity


title: epidermal stem cells adult animal calorie restriction diet T0, replicate 3


title: VUmc_05


title: epidermal stem cells adult animal calorie restriction diet T16, replicate 1


title: epidermal stem cells adult animal calorie restriction diet T0, replicate 4


title: VUmc_03


title: VUmc_01


title: epidermal stem cells adult animal calorie restriction diet T12, replicate 4


title: VUmc_08

value: yes


title: VUmc_04


title: VUmc_02

value: m


title: epidermal stem cells adult animal calorie restriction diet T0, replicate 2


title: White malignant adipocytic tumor_21

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

description: Global gene expression data

hyb_protocol: Biotinylated cDNA was hybridized to GeneChip Gene 1_0 st arrays. Arrays were washed and stained on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was carried out with the GeneChip Scanner 3000 (Affymetrix).

data_processing: Image analysis was perfomed using the GeneChip Operating Software (GCOS, Affymetrix) or command console (Affymetrix). Background correction, normalization and probe summarization was done with the robust multichip average (RMA) algorithm implemented in the Expression Console software (Affymetrix).

source_name: soft tissue

label_protocol: cDNA was labelled with TdT using the WT Terminal Labeling kit (Affymetrix).

extract_protocol: RNA was extracted using the TRIzol reagent (Invitrogen) and purified with Qiagen´s RNeasy kit according to the manufacturers´ instructions.

value: White malignant adipocytic tumor

tag: tissue source

value: tumor biopsy


title: White malignant adipocytic tumor_23

description: Global gene expression data


title: White malignant adipocytic tumor_20

description: Global gene expression data


title: White malignant adipocytic tumor_22

description: Global gene expression data


title: epidermal stem cells adult animal calorie restriction diet T0, replicate 1


title: epidermal stem cells ND control diet T8, replicate 2

value: control

value: 83-97 week old


title: White malignant adipocytic tumor_19

description: Global gene expression data


title: White malignant adipocytic tumor_16

description: Global gene expression data


title: epidermal stem cells ND control diet T4, replicate 4


title: White malignant adipocytic tumor_18

description: Global gene expression data


title: epidermal stem cells ND control diet T8, replicate 1


title: White malignant adipocytic tumor_17

description: Global gene expression data


title: 656116

city: Ames

first: Maria

middle: Guadalupe

last: Salas Fernandez

state: IA

address: 1126E Agronomy Hall

department: Agronomy

institute: Iowa State University

description: Sorghum breeding line

data_processing:
The Fluidigm SNP Genotyping Analysis software automatically analyzes the end-point image of a genotyping chip run and generates genotyping calls for each sample.
SNP calls for each allele

label: SNPtype-FAM, SNPtype-HEX

organism: Sorghum bicolor

source_name: Sorghum Association Panel

label_protocol: SNPtype-FAM, SNPtype-HEX

growth_protocol: grow a single plant in a small pot for each sample

extract_protocol: Total DNA was extracted using CTAB DNA extraction protocol

treatment_protocol: No treatment

value: young leaves


title: White malignant adipocytic tumor_15

description: Global gene expression data


title: 656117

description: Sorghum breeding line


title: 656115

description: Sorghum breeding line


title: 656118

description: Sorghum breeding line


title: 656114

description: Sorghum breeding line


title: 656119

description: Sorghum breeding line


title: epidermal stem cells ND control diet T4, replicate 2


title: epidermal stem cells ND control diet T8, replicate 3


title: 656113

description: Sorghum breeding line


title: White malignant adipocytic tumor_13

description: Global gene expression data


title: White malignant adipocytic tumor_14

description: Global gene expression data


title: White malignant adipocytic tumor_12

description: Global gene expression data


title: epidermal stem cells ND control diet T20, replicate 5


title: epidermal stem cells ND control diet T20, replicate 4


title: epidermal stem cells ND control diet T4, replicate 3


title: 656112

description: Sorghum breeding line


title: 656111

description: Sorghum breeding line


title: 656109

description: Sorghum breeding line


title: 656110

description: Sorghum breeding line


title: 656108

description: Sorghum breeding line


title: 656107

description: Sorghum breeding line


title: 656106

description: Sorghum breeding line


title: 656105

description: Sorghum breeding line


title: epidermal stem cells ND control diet T4, replicate 1


title: 656104

description: Sorghum breeding line


title: White malignant adipocytic tumor_6

description: Global gene expression data


title: White malignant adipocytic tumor_9

description: Global gene expression data


title: White malignant adipocytic tumor_8

description: Global gene expression data


title: White malignant adipocytic tumor_5

description: Global gene expression data


title: White malignant adipocytic tumor_7

description: Global gene expression data


title: White malignant adipocytic tumor_4

description: Global gene expression data


title: White malignant adipocytic tumor_11

description: Global gene expression data


title: White malignant adipocytic tumor_10

description: Global gene expression data


title: 656102

description: Sorghum breeding line


title: 656101

description: Sorghum breeding line


title: epidermal stem cells ND control diet T20, replicate 3


title: epidermal stem cells ND control diet T16, replicate 2


title: epidermal stem cells ND control diet T16, replicate 3


title: epidermal stem cells ND control diet T16, replicate 1


title: epidermal stem cells ND control diet T12, replicate 2


title: epidermal stem cells ND control diet T20, replicate 1


title: epidermal stem cells ND control diet T16, replicate 4


title: White malignant adipocytic tumor_3

description: Global gene expression data


title: 656103

description: Sorghum breeding line


title: 656100

description: Sorghum breeding line


title: epidermal stem cells ND control diet T20, replicate 2


title: epidermal stem cells ND control diet T12, replicate 1


title: epidermal stem cells ND control diet T12, replicate 4


title: epidermal stem cells ND control diet T0, replicate 4


title: 656098

description: Sorghum breeding line


title: 656096

description: Sorghum breeding line


title: White malignant adipocytic tumor_1

description: Global gene expression data


title: 656095

description: Sorghum breeding line


title: White benign adipocytic tumor_47

description: Global gene expression data

value: White benign adipocytic tumor


title: White benign adipocytic tumor_46

description: Global gene expression data


title: 656094

description: Sorghum breeding line


title: White malignant adipocytic tumor_2

description: Global gene expression data


title: White benign adipocytic tumor_48

description: Global gene expression data


title: 656093

description: Sorghum breeding line


title: White benign adipocytic tumor_45

description: Global gene expression data


title: epidermal stem cells ND control diet T0, replicate 3

value: Per1-Venus BAC transgenic mice with C57B6/J background


title: epidermal stem cells ND control diet T12, replicate 3


title: epidermal stem cells ND control diet T0, replicate 2


title: White benign adipocytic tumor_44

description: Global gene expression data


title: 656087

description: Sorghum breeding line


title: 656089

description: Sorghum breeding line


title: White benign adipocytic tumor_43

description: Global gene expression data


title: epidermal stem cells calorie restriction diet T8, replicate 4

value: calorie restriction


title: 656086

description: Sorghum breeding line


title: VUmc_13

tag: tissue type

value: III

value: pos

value: no

value: Universal Human Reference RNA (Stratagene)


title: White benign adipocytic tumor_42

description: Global gene expression data


title: epidermal stem cells calorie restriction diet T8, replicate 2

value: epidermis


title: White benign adipocytic tumor_41

description: Global gene expression data


title: epidermal stem cells calorie restriction diet T8, replicate 3


title: White benign adipocytic tumor_40

description: Global gene expression data


title: 656090

description: Sorghum breeding line


title: White benign adipocytic tumor_37

description: Global gene expression data


title: epidermal stem cells ND control diet T0, replicate 1


title: epidermal stem cells calorie restriction diet T4, replicate 3


title: epidermal stem cells calorie restriction diet T4, replicate 2


title: epidermal stem cells calorie restriction diet T8, replicate 1


title: epidermal stem cells calorie restriction diet T4, replicate 1


title: White benign adipocytic tumor_39

description: Global gene expression data


title: White benign adipocytic tumor_36

description: Global gene expression data


title: epidermal stem cells calorie restriction diet T20, replicate 5


title: 656080

description: Sorghum breeding line


title: 656083

description: Sorghum breeding line


title: 656078

description: Sorghum breeding line


title: 656079

description: Sorghum breeding line


title: 656077

description: Sorghum breeding line


title: 656082

description: Sorghum breeding line


title: epidermal stem cells calorie restriction diet T20, replicate 4


title: White benign adipocytic tumor_38

description: Global gene expression data


title: 656081

description: Sorghum breeding line


title: 656076

description: Sorghum breeding line


title: White benign adipocytic tumor_35

description: Global gene expression data


title: epidermal stem cells calorie restriction diet T20, replicate 3


title: White benign adipocytic tumor_33

description: Global gene expression data


title: epidermal stem cells calorie restriction diet T20, replicate 2


title: 656075

description: Sorghum breeding line


title: White benign adipocytic tumor_32

description: Global gene expression data


title: White benign adipocytic tumor_34

description: Global gene expression data


title: 656074

description: Sorghum breeding line


title: epidermal stem cells calorie restriction diet T20, replicate 1


title: 656073

description: Sorghum breeding line


title: epidermal stem cells calorie restriction diet T16, replicate 4


title: 656072

description: Sorghum breeding line


title: epidermal stem cells calorie restriction diet T16, replicate 3


title: White benign adipocytic tumor_28

description: Global gene expression data


title: White benign adipocytic tumor_31

description: Global gene expression data


title: 656071

description: Sorghum breeding line


title: White benign adipocytic tumor_29

description: Global gene expression data


title: epidermal stem cells calorie restriction diet T12, replicate 4


title: 656068

description: Sorghum breeding line


title: 656066

description: Sorghum breeding line


title: White benign adipocytic tumor_30

description: Global gene expression data


title: White benign adipocytic tumor_27

description: Global gene expression data


title: epidermal stem cells calorie restriction diet T16, replicate 2


title: epidermal stem cells calorie restriction diet T12, replicate 3


title: White benign adipocytic tumor_26

description: Global gene expression data


title: 656065

description: Sorghum breeding line


title: White benign adipocytic tumor_25

description: Global gene expression data


title: epidermal stem cells calorie restriction diet T16, replicate 1


title: epidermal stem cells calorie restriction diet T12, replicate 2


title: epidermal stem cells calorie restriction diet T12, replicate 1


title: White benign adipocytic tumor_24

description: Global gene expression data


title: 656064

description: Sorghum breeding line


title: epidermal stem cells calorie restriction diet T0, replicate 5


title: 656062

description: Sorghum breeding line


title: 656061

description: Sorghum breeding line


title: White benign adipocytic tumor_21

description: Global gene expression data


title: 656063

description: Sorghum breeding line


title: 656059

description: Sorghum breeding line


title: White benign adipocytic tumor_20

description: Global gene expression data


title: White benign adipocytic tumor_23

description: Global gene expression data


title: White benign adipocytic tumor_19

description: Global gene expression data


title: epidermal stem cells calorie restriction diet T0, replicate 2


title: White benign adipocytic tumor_22

description: Global gene expression data


title: 656058

description: Sorghum breeding line


title: epidermal stem cells calorie restriction diet T0, replicate 3


title: 656060

description: Sorghum breeding line


title: epidermal stem cells calorie restriction diet T0, replicate 4


title: 656056

description: Sorghum breeding line


title: 656055

description: Sorghum breeding line


title: White benign adipocytic tumor_18

description: Global gene expression data


title: White benign adipocytic tumor_17

description: Global gene expression data


title: White benign adipocytic tumor_16

description: Global gene expression data


title: epidermal stem cells young animal T8, replicate 3

tag: Sex

value: female

value: wild type

tag: strain

tag: timepoint

value: 8 week old


title: epidermal stem cells calorie restriction diet T0, replicate 1


title: 656054

description: Sorghum breeding line


title: epidermal stem cells young animal T8, replicate 2


title: 656053

description: Sorghum breeding line


title: 656057

description: Sorghum breeding line


title: epidermal stem cells young animal T8, replicate 4


title: White benign adipocytic tumor_15

description: Global gene expression data


title: 656052

description: Sorghum breeding line


title: 656051

description: Sorghum breeding line


title: epidermal stem cells young animal T8, replicate 1


title: White benign adipocytic tumor_13

description: Global gene expression data


title: 656050

description: Sorghum breeding line


title: White benign adipocytic tumor_12

description: Global gene expression data


title: epidermal stem cells young animal T4, replicate 4


title: 656048

description: Sorghum breeding line


title: epidermal stem cells young animal T4, replicate 2


title: White benign adipocytic tumor_10

description: Global gene expression data


title: White benign adipocytic tumor_8

description: Global gene expression data


title: White benign adipocytic tumor_14

description: Global gene expression data


title: White benign adipocytic tumor_11

description: Global gene expression data


title: epidermal stem cells young animal T4, replicate 1


title: White benign adipocytic tumor_7

description: Global gene expression data


title: epidermal stem cells young animal T20, replicate 3


title: epidermal stem cells young animal T20, replicate 4


title: White benign adipocytic tumor_5

description: Global gene expression data


title: White benign adipocytic tumor_9

description: Global gene expression data


title: epidermal stem cells young animal T4, replicate 3


title: 656046

description: Sorghum breeding line


title: epidermal stem cells young animal T20, replicate 2


title: epidermal stem cells young animal T16, replicate 4


title: 656049

description: Sorghum breeding line


title: epidermal stem cells young animal T20, replicate 1


title: 656044

description: Sorghum breeding line


title: White benign adipocytic tumor_6

description: Global gene expression data


title: White benign adipocytic tumor_4

description: Global gene expression data


title: 656047

description: Sorghum breeding line


title: 656041

description: Sorghum breeding line


title: 656040

description: Sorghum breeding line


title: epidermal stem cells young animal T16, replicate 3


title: White benign adipocytic tumor_3

description: Global gene expression data


title: epidermal stem cells young animal T16, replicate 2


title: White benign adipocytic tumor_2

description: Global gene expression data


title: White benign adipocytic tumor_1

description: Global gene expression data


title: 656039

description: Sorghum breeding line


title: 656038

description: Sorghum breeding line


title: 656037

description: Sorghum breeding line


title: 656043

description: Sorghum breeding line


title: epidermal stem cells young animal T16, replicate 1


title: White benign adipocytic tumor_MEN1_deletion

description: Global gene expression data


title: epidermal stem cells young animal T12, replicate 4


title: Hibernoma_12

description: Global gene expression data

value: Hibernoma


title: Hibernoma_14

description: Global gene expression data


title: Hibernoma_11

description: Global gene expression data


title: epidermal stem cells young animal T12, replicate 3


title: 656035

description: Sorghum breeding line


title: epidermal stem cells young animal T0, replicate 2


title: epidermal stem cells young animal T12, replicate 2


title: 656036

description: Sorghum breeding line


title: epidermal stem cells young animal T0, replicate 4


title: epidermal stem cells young animal T12, replicate 1


title: epidermal stem cells young animal T0, replicate 3


title: 656034

description: Sorghum breeding line


title: epidermal stem cells young animal T0, replicate 1


title: 656033

description: Sorghum breeding line


title: 656032

description: Sorghum breeding line