title: CCRF-CEM transduced with shTOX-1

city: Charlestown

last: Langenau

state: Massachusetts

address: 149 13th Street, Room 6027

institute: Massachusetts General Hospital

description: Gene expression data of CCRF-CEM after transduction with TOX shRNA #1

hyb_protocol: Following fragmentation and labeling, 2.3 ug of ss-cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 St. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with AffySTExpressionFileCreator from Genepattern, using quantile normalization and background correction.

source_name: CCRF-CEM T-ALL cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip WT plus Quick Reference Card, 2013, Affymetrix).

growth_protocol: T-ALL cell lines are grown in RPMI, 10%FBS, 1% Pen/Strep/Glutamine

extract_protocol: Cells were harvested and total RNA were extracted using RNAeasy kit.

treatment_protocol: T-ALL cell lines were transduced with shRNA against TOX or a scramble control by spinoculation, 90min, 2250rpm at 32°C. The cells were then selected for the integrative transgene with puromycine. At least 2 weeks were waited to ensure stability of the cells for the shRNA

value: T-cell Acute Lymphoblastic Leukemia cell line


title: Patient_220_Baseline

status: Public on Sep 01 2017

type: RNA

city: Lund

first: Ingrid

last: Hedenfalk

address: Medicon Village

department: Div of Omcology & Pathology, Dept of Clinical Sciences

country: Sweden

institute: Lund University

description: Direct Hyb

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing: The data were normalised using quantile normalisation with BASE

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Primary breast cancer

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevD, (Modification of Amplification kit v 2.2)

extract_protocol: Qiagen Allprep DNA/RNA mini kit, with a QIAcube

tag: treatment

value: Baseline (no treatment)

tag: tissue

value: Breast


title: Patient_223_Baseline

description: Direct Hyb


title: Patient_218_Surgery

description: Direct Hyb

value: Surgery (chemo+bevacizumab)


title: Patient_216_Baseline

description: Direct Hyb


title: CCRF-CEM transduced with scramble

first: David

country: USA

description: Gene expression data of CCRF-CEM after transduction with scramble shRNA

tag: cell type


title: HPB-ALL untransduced

description: Gene expression data of untransduced HPB-ALL

source_name: HPB-ALL T-ALL cell line


title: CCRF-CEM untransduced

description: Gene expression data of untransduced CCRF-CEM


title: Patient_222_Cycle 2

description: Direct Hyb

value: Cycle 2 (chemo only)


title: Patient_217_Baseline

description: Direct Hyb


title: Patient_213_Cycle 2

description: Direct Hyb


title: HPB-ALL transduced with scramble

description: Gene expression data of HPB-ALL after transduction with scramble shRNA


title: Patient_211_Surgery

description: Direct Hyb


title: HPB-ALL transduced with shTOX-1

description: Gene expression data of HPB-ALL after transduction with TOX shRNA #1


title: CCRF-CEM transduced with shTOX-2

description: Gene expression data of CCRF-CEM after transduction with TOX shRNA #2


title: Patient_217_Cycle 2

description: Direct Hyb


title: Patient_220_Surgery

description: Direct Hyb


title: Patient_213_Surgery

description: Direct Hyb


title: Patient_218_Cycle 2

description: Direct Hyb


title: Patient_213_Baseline

description: Direct Hyb


title: HPB-ALL transduced with shTOX-2

description: Gene expression data of HPB-ALL after transduction with TOX shRNA #2


title: Patient_211_Cycle 2

description: Direct Hyb


title: A549_Tumor_3

city: Shiraoka

first: Ayako

last: Otani

state: Saitama

address: 1470 Shiraoka

department: Medical Materials group

country: Japan

institute: Nissan Chemical Industries

description: Gene expression data from A549 cells which were isolated from xenograft tumor tissue.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.

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

data_processing: The data were analyzed with Affimetrix Expression Console Softwere ver.1.3.0 using RMA-Sketch (RMA-Gene-Default) algorithm.

source_name: A549 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Affimetrix GeneChip WT PLUS Reagent Kit).

growth_protocol: Non-small lung cancer cells A549 were cultured in DMEM supplemented with 10% FBS.

extract_protocol: Extraction of total RNA was performed with Quiagen RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: 5 × 10^6 A549 cells in 100 μL PBS was injected subcutaneously into one or both scapulars of 7-8 week old male BALB/cAJcl-nu/nu mice. Tumors greater than 5 mm in diameter (range = 3-5 mm) were observed within 21 days in all the mice inoculated. The tumors were harvested and trimmed of adipose and connective tissue.

tag: tissue type

value: A549 cells from xenograft tumor

value: Non-small lung cancer cell


title: Patient_214_Baseline

description: Direct Hyb


title: A549_Tumor_2


title: Patient_222_Baseline

description: Direct Hyb


title: Patient_215_Baseline

description: Direct Hyb


title: A549_2D_1

description: Gene expression data from A549 cells which were isolated from 2D cultured A549 cells.

value: A549 cells


title: A549_2D_3


title: Patient_209_Surgery

description: Direct Hyb


title: A549_Tumor_1


title: Patient_209_Baseline

description: Direct Hyb


title: Patient_210_Cycle 2

description: Direct Hyb


title: Patient_210_Surgery

description: Direct Hyb


title: A549_2D_2


title: Patient_210_Baseline

description: Direct Hyb


title: RH30_VISMODEGIB

city: Barcelona

first: Ana

last: Almazán

address: Passeig Vall d'Hebron 119-129

country: Spain

institute: VHIR

description: RH30 cell line harbors a GLI1-amplification

hyb_protocol: Approximately 5μg of fragmented and labeled ssDNA was hybridized per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45°C at 60rpm using an Affymetrix hybridization oven

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G.

data_processing: RMA algorithm was used to normalize the arrays and to summarize the probes. Bioconductor packages and R statistical software were used to analyze the raw data.     RMA algorithm was used to normalize the arrays and to summarize the probes. Bioconductor packages and R statistical software were used to analyze the raw data.  RMA algorithm was used to normalize the arrays and to summarize the probes. Bioconductor packages and R statistical software were used to analyze the raw data.     RMA algorithm was used to normalize the arrays and to summarize the probes. Bioconductor packages and R statistical software were used to analyze the raw data.

source_name: RH30 RMS cell line treated with vehicle (DMSO)

label_protocol: 5.5μg of ssDNA were fragmented and labeled using the Terminal Labeling kit (Affymetrix) following protocol guides.

growth_protocol: RMS cell lines were grown in MEM media and mantained at 37°C in a 5% CO2 water-jacketed incubator.

extract_protocol: Total RNA from cells was extracted using the RNeasy Mini Kit (Qiagen), following the manufacturer's instructions,

treatment_protocol: Cells were treated for 48 hours with 50µM Vismodegib. Control plates were treated with equal volumes of vehicle (DMSO).

tag: cell line

value: RH30 RMS

tag: rms subtype

value: alveolar RMS

value: Vismodegib


title: Patient_208_Surgery

description: Direct Hyb


title: RD_VISMODEGIB

source_name: RD RMS cell line treated with vehicle (DMSO)

value: RD RMS

value: embryonal RMS


title: Patient_206_Baseline

description: Direct Hyb


title: RH30_DMSO

source_name: RH30 RMS cell line treated with Vismodegib

value: DMSO


title: Patient_205_Cycle 2

description: Direct Hyb


title: RH4_DMSO

source_name: RH4 RMS cell line treated with Vismodegib

value: RH4 RMS


title: Patient_207_Surgery

description: Direct Hyb


title: Patient_206_Cycle 2

description: Direct Hyb


title: Patient_207_Baseline

description: Direct Hyb


title: Patient_208_Baseline

description: Direct Hyb


title: RH4_VISMODEGIB

source_name: RH4 RMS cell line treated with vehicle (DMSO)


title: RD_DMSO

source_name: RD RMS cell line treated with Vismodegib


title: gastric adjacent tissue Zheng

city: beijing

first: HUI

last: GUO

state: beijing

address: NO.5 Dong Dan San Tiao, Dongcheng District

department: Department of Biochemistry and Molecular Biology

country: China

institute: Peking Union Medical College & Chinese Academy of Medical Sciences

description: lncRNA expression profiling for 4 paired human gastric samples

hyb_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 10 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: gastric adjacent tissue

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: gastric adjacent tissue

tag: gender

value: male


title: Patient_205_Baseline

description: Direct Hyb


title: gastric adjacent tissue WGQ_N


title: gastric adjacent tissue 13N_QY


title: gastric adjacent tissue HSN_Zheng


title: gastric tumor tissue 13Ca

source_name: gastric tumor tissue

value: gastric tumor tissue


title: gastric tumor tissue WGQ


title: gastric tumor tissue 4Ca


title: gastric tumor tissue cancer


title: Patient_204_Surgery

description: Direct Hyb


title: Patient_204_Cycle 2

description: Direct Hyb


title: Patient_204_Baseline

description: Direct Hyb

value: Baseline (no treatment)


title: Patient_203_Cycle 2

description: Direct Hyb

value: Breast


title: Patient_205_Surgery

description: Direct Hyb

value: Surgery (chemo+bevacizumab)


title: N4

city: Jinan

first: Peng

last: Gao

address: Wen Hua Xi Road 44

institute: Shandong University

description: Gene expression microarray was utilized to screen the differentially expressed genes between metastatic and nonmetastatic gastric cancers. Little was known on the comprehensive understanding of genetic expression patterns in metastatic human gastric cancer.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 6 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: Patient 11, primary gastric cancer

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Tissues from samples were microdissected with a 25G needle under a dissecting microscope.Total RNAs was extracted using TRIzol reagent.Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.RNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

value: primary gastric cancer without lymph node metastasis


title: N1

source_name: Patient 8, primary gastric cancer


title: N5

source_name: Patient 12, primary gastric cancer


title: Patient_202_Surgery

description: Direct Hyb


title: N2

source_name: Patient 9, primary gastric cancer


title: Patient_158_Surgery

description: Direct Hyb


title: M2

source_name: Patient 4, primary gastric cancer

value: primary gastric cancer with lymph node metastasis


title: M1

source_name: Patient 3, primary gastric cancer


title: Patient_201_Cycle 2

description: Direct Hyb

source_name: Primary breast cancer

value: Cycle 2 (chemo only)


title: Patient_202_Baseline

description: Direct Hyb


title: Patient_159_Cycle 2

description: Direct Hyb


title: M4

source_name: Patient 6, primary gastric cancer


title: Patient_160_Cycle 2

description: Direct Hyb


title: M5

source_name: Patient 7, primary gastric cancer


title: N3

source_name: Patient 10, primary gastric cancer


title: Patient_159_Baseline

description: Direct Hyb


title: M3

source_name: Patient 5, primary gastric cancer


title: Patient_160_Surgery

description: Direct Hyb


title: Patient_158_Cycle 2

description: Direct Hyb


title: Patient_201_Baseline

description: Direct Hyb


title: Patient_158_Baseline

description: Direct Hyb


title: G2

source_name: Patient 2, gastric ulcer

value: normal gastric mucosa


title: Patient_156_Baseline

description: Direct Hyb


title: Patient_157_Baseline

description: Direct Hyb


title: G1

source_name: Patient 1, gastric ulcer


title: Patient_155_Surgery

description: Direct Hyb


title: Patient_155_Cycle 2

description: Direct Hyb


title: Patient_157_Surgery

description: Direct Hyb


title: Patient_153_Surgery

description: Direct Hyb


title: Heart MR-Cadio + aldosterone treatment sample 3 (mouse n° 206)

city: Ottawa

first: Smail

last: Messaoudi

state: Ontario

address: 451 smyth road

department: BMI

country: Canada

institute: University of Ottawa

description: Hearts were rinsed in cold PBS,  frozen in liquid nitrogen, and kept at –80°C.

hyb_protocol: 825 ng of Cy5-labelled samples and 825 ng of Cy3-labelled references were incubated at 60° for 30 min in fragmentation buffer.  Hybridization buffer was then added, and sample/reference couples (1 couple per microarray) were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an G2505 Agilent scanner. Images were quantified using Agilent Feature Extraction Software (version v 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.Data were processed using  genespring software v11.0.

organism: Mus musculus

source_name: Heart MR-Cadio + aldosterone treatment

label_protocol: Labelling of the RNAs weas performed according to Agilent's instruction. Briefly, 100 ng of total RNA + spikes  were primed with 1,8µl of T7 promoter primer mix at 70°C for 10 min, then reversed transcribed at 40°C for 2 h in presence of a mix containing first strand buffer, 20 mM DTT, 2 mM DNTP mix and AffinityScript rnase block mix. Reaction was stopped by heating samples at 70° foc 15 min. New synthetized cDNA was then labelled and amplified at 40° for 2h in presence of a mix containing transcription buffer, NTP mix, 20mM DTT, T7 RNA polymerase and CY3-CTP or CY5-CTP.

extract_protocol: Total RNA was prepared from ventricle samples with the RNeasy Mini Kit (Qiagen S.A) according to the manufacturer's instructions and its quality was assessed with Bioanalyzer 2100 (Agilent technologies)

tag: Sex

tag: genotype

value: Transgenic (cardiomyocytes targeted mineralocorticoid receptor overexpression)

value: Aldosterone

tag: treatment duration

value: 7 days

value: Heart

source_name: Total RNA pooled  from several tissues (liver, brain, heart kidney, spleen), labeled with Cyanine-3, used as reference

tag: tissues

value: liver, brain, heart kidney, spleen


title: Heart MR-Cadio + aldosterone treatment sample 5 (mouse n° 205)


title: Heart MR-Cadio + aldosterone treatment sample 1 (mouse n° 204)


title: Heart MR-Cadio + aldosterone treatment sample 4 (mouse n° 231)


title: Patient_155_Baseline

description: Direct Hyb


title: Patient_153_Baseline

description: Direct Hyb


title: Heart MR-Cardio + corticosterone treatment sample 6 (mouse n° 249)

value: Corticosterone


title: Patient_154_Cycle 2

description: Direct Hyb


title: Heart MR-Cadio + aldosterone treatment sample 6 (mouse n° 233)


title: Heart MR-Cardio + corticosterone treatment sample 2 (mouse n° 219)


title: Heart MR-Cardio + corticosterone treatment sample 1 (mouse n° 248)


title: Patient_154_Baseline

description: Direct Hyb


title: Patient_152_Surgery

description: Direct Hyb


title: Patient_152_Cycle 2

description: Direct Hyb


title: Heart MR-Cardio + corticosterone treatment sample 5 (mouse n° 267)


title: Heart MR-Cadio + aldosterone treatment sample 2 (mouse n° 201)


title: Heart MR-Cardio no treatment sample 7 (mouse n° 213)

source_name: Heart MR-Cardio no treatment

value: no treatment


title: Heart MR-Cardio + corticosterone treatment sample 3 (mouse n° 221)


title: Patient_153_Cycle 2

description: Direct Hyb


title: Heart MR-Cardio no treatment sample 6 (mouse n° 212)


title: Patient_151_Surgery

description: Direct Hyb


title: Patient_211_Baseline

description: Direct Hyb


title: Heart MR-Cardio no treatment sample 5 (mouse n° 208)


title: Heart MR-Cardio no treatment sample 4 (mouse n° 224)


title: Heart MR-Cardio no treatment sample 3 (mouse n° 214)


title: Patient_150_Surgery

description: Direct Hyb


title: Heart MR-Cardio no treatment sample 2 (mouse n° 211)


title: Patient_151_Baseline

description: Direct Hyb


title: Patient_150_Cycle 2

description: Direct Hyb


title: Patient_152_Baseline

description: Direct Hyb


title: Heart MR-Cardio no treatment sample 1 (mouse n° 209)


title: Patient_148_Cycle 2

description: Direct Hyb


title: Patient_148_Baseline

description: Direct Hyb


title: Patient_150_Baseline

description: Direct Hyb


title: Heart Ctrl + corticosterone treatment sample 4 (mouse n° 261)

source_name: Heart Ctrl + corticosterone treatment

value: Ctrl (non-transgenic)


title: Heart Ctrl + corticosterone treatment sample 3 (mouse n° 263)

value: male


title: Patient_145_Surgery

description: Direct Hyb


title: Patient_149_Surgery

description: Direct Hyb


title: Heart Ctrl + corticosterone treatment sample 5 (mouse n° 222)


title: Patient_147_Baseline

description: Direct Hyb


title: Patient_147_Surgery

description: Direct Hyb


title: Heart Ctrl + aldosterone treatment sample 5 (mouse n° 226)

source_name: Heart Ctrl + aldosterone treatment


title: Patient_146_Baseline

description: Direct Hyb


title: Heart Ctrl + corticosterone treatment sample 2 (mouse n° 220)


title: Patient_149_Baseline

description: Direct Hyb


title: Heart Ctrl + corticosterone treatment sample 1 (mouse n° 247)


title: Heart Ctrl + aldosterone treatment sample 3 (mouse n° 253)


title: Heart Ctrl + aldosterone treatment sample 4 (mouse n° 257)


title: Patient_145_Cycle 2

description: Direct Hyb


title: Heart Ctrl + aldosterone treatment sample 2 (mouse n° 232)


title: Patient_144_Surgery

description: Direct Hyb


title: Heart Ctrl + aldosterone treatment sample 1 (mouse n° 203)


title: Heart Ctrl no treatment sample 5 (mouse n° 215)

source_name: Heart Ctrl no treatment


title: Patient_143_Surgery

description: Direct Hyb


title: Patient_145_Baseline

description: Direct Hyb


title: Heart Ctrl no treatment sample 3 (mouse n° 223)


title: Heart Ctrl no treatment sample 4 (mouse n° 272)


title: Patient_144_Baseline

description: Direct Hyb


title: Patient_142_Cycle 2

description: Direct Hyb


title: Heart Ctrl no treatment sample 2 (mouse n° 217)


title: Heart Ctrl no treatment sample 1 (mouse n° 210)


title: Patient_138_Cycle 2

description: Direct Hyb


title: Patient_137_Baseline

description: Direct Hyb


title: Patient_141_Cycle 2

description: Direct Hyb


title: Patient_136_Surgery

description: Direct Hyb


title: Patient_140_Baseline

description: Direct Hyb


title: Patient_134_Baseline

description: Direct Hyb


title: Patient_133_Cycle 2

description: Direct Hyb


title: Patient_133_Baseline

description: Direct Hyb


title: Patient_132_Cycle 2

description: Direct Hyb


title: Patient_138_Baseline

description: Direct Hyb


title: Patient_128_Baseline

description: Direct Hyb


title: Heart MR-Cardio + corticosterone treatment sample 4 (mouse n° 262)


title: Patient_129_Cycle 2

description: Direct Hyb


title: Patient_129_Baseline

description: Direct Hyb


title: Patient_135_Baseline

description: Direct Hyb


title: Patient_134_Cycle 2

description: Direct Hyb


title: Patient_139_Baseline

description: Direct Hyb


title: Patient_135_Cycle 2

description: Direct Hyb


title: Patient_141_Baseline

description: Direct Hyb


title: Patient_143_Cycle 2

description: Direct Hyb


title: Patient_127_Cycle 2

description: Direct Hyb


title: Patient_127_Surgery

description: Direct Hyb


title: Patient_125_Baseline

description: Direct Hyb


title: Patient_126_Surgery

description: Direct Hyb


title: Patient_131_Baseline

description: Direct Hyb


title: Patient_126_Cycle 2

description: Direct Hyb


title: Patient_122_Surgery

description: Direct Hyb


title: Patient_123_Baseline

description: Direct Hyb


title: Patient_120_Cycle 2

description: Direct Hyb


title: Patient_126_Baseline

description: Direct Hyb


title: Patient_119_Cycle 2

description: Direct Hyb


title: Patient_113_Baseline

description: Direct Hyb


title: Patient_112_Baseline

description: Direct Hyb


title: Patient_124_Surgery

description: Direct Hyb


title: Patient_119_Surgery

description: Direct Hyb


title: Patient_118_Baseline

description: Direct Hyb


title: Patient_121_Surgery

description: Direct Hyb


title: Patient_118_Surgery

description: Direct Hyb


title: Patient_124_Cycle 2

description: Direct Hyb


title: Patient_114_Baseline

description: Direct Hyb


title: Patient_121_Baseline

description: Direct Hyb


title: Patient_115_Baseline

description: Direct Hyb


title: Patient_115_Cycle 2

description: Direct Hyb


title: Patient_116_Cycle 2

description: Direct Hyb


title: Patient_118_Cycle 2

description: Direct Hyb


title: Patient_114_Surgery

description: Direct Hyb


title: Patient_119_Baseline

description: Direct Hyb


title: Patient_122_Baseline

description: Direct Hyb


title: Patient_120_Baseline

description: Direct Hyb


title: Patient_116_Baseline

description: Direct Hyb


title: Patient_111_Baseline

description: Direct Hyb


title: Patient_115_Surgery

description: Direct Hyb


title: Patient_109_Baseline

description: Direct Hyb


title: Patient_108_Surgery

description: Direct Hyb


title: Patient_108_Cycle 2

description: Direct Hyb


title: Patient_112_Surgery

description: Direct Hyb


title: Patient_107_Baseline

description: Direct Hyb


title: Patient_108_Baseline

description: Direct Hyb


title: Patient_109_Cycle 2

description: Direct Hyb


title: Patient_105_Cycle 2

description: Direct Hyb


title: Patient_105_Surgery

description: Direct Hyb


title: Patient_105_Baseline

description: Direct Hyb


title: Patient_101_Cycle 2

description: Direct Hyb


title: Patient_103_Cycle 2

description: Direct Hyb


title: Patient_102_Cycle 2

description: Direct Hyb


title: Patient_104_Cycle 2

description: Direct Hyb


title: Patient 43

city: Oslo

first: Hege

last: Pihlstrøm

address: P.B. 4950 Nydalen

department: Department of Transplant Medicine

country: Norway

institute: Oslo University Hospital, Rikshospitalet

description: SAMPLE 54

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio  v2011.1 Gene Expression Module 1.9.0” software.

source_name: Kidney biopsy

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™-96 RNA  Amplification Kit

extract_protocol: QIAGEN RNeasy mini kit with DNase I treatment

treatment_protocol: paricalcitol (Zemplar; Abbvie) 2 μg/day in addition to standard care

tag: paricalcitol treated

value: No


title: Patient 44

description: SAMPLE 58


title: Patient 70

description: SAMPLE 60


title: Patient_103_Baseline

description: Direct Hyb

value: Baseline (no treatment)


title: Patient 20

description: SAMPLE 56


title: Patient 56

description: SAMPLE 59


title: Patient_106_Baseline

description: Direct Hyb

value: Breast


title: Patient_101_Baseline

description: Direct Hyb


title: Patient_102_Baseline

description: Direct Hyb


title: Patient 68

description: SAMPLE 52


title: Patient 31

description: SAMPLE 57


title: Patient 53

description: SAMPLE 51


title: Patient 51

description: SAMPLE 48


title: Patient 15

description: SAMPLE 45


title: Patient 17

description: SAMPLE 49


title: Patient_104_Baseline

description: Direct Hyb


title: Patient_102_Surgery

description: Direct Hyb

value: Surgery (chemo+bevacizumab)


title: Patient 9

description: SAMPLE 53


title: Patient 69

description: SAMPLE 55


title: Patient 5

description: SAMPLE 44


title: Patient 28

description: SAMPLE 50


title: Patient 27

description: SAMPLE 47


title: Patient 26

description: SAMPLE 46


title: Patient 4

description: SAMPLE 41


title: Patient 14

description: SAMPLE 42


title: Patient 10

description: SAMPLE 30

value: Yes


title: Patient 11

description: SAMPLE 31


title: Patient 47

description: SAMPLE 36


title: Patient 3

description: SAMPLE 37


title: Patient 2

description: SAMPLE 34


title: Patient 48

description: SAMPLE 39


title: Patient 36

description: SAMPLE 43


title: Patient 60

description: SAMPLE 40


title: Patient 30

description: SAMPLE 28


title: Patient 58

description: SAMPLE 33


title: Patient 52

description: SAMPLE 21


title: Patient 23

description: SAMPLE 38


title: Patient 16

description: SAMPLE 16


title: Patient 61

description: SAMPLE 18


title: Patient 40

description: SAMPLE 17


title: Patient 18

description: SAMPLE 24


title: Patient 67

description: SAMPLE 22


title: Patient 29

description: SAMPLE 25


title: Patient 45

description: SAMPLE 32


title: Patient 22

description: SAMPLE 35


title: Patient 55

description: SAMPLE 29


title: Patient 41

description: SAMPLE 20


title: Patient 6

description: SAMPLE 15


title: Patient 7

description: SAMPLE 19


title: Drosophila melanogaster

type: SRA

city: Walnut Creek

first: Denis

last: Tolkunov

state: CA

address: 2800 Mitchell Dr

institute: DOE Joint Genome Institute

description: [Third-party re-analysis] Raw SMRT sequencing  data was retrieved from: http://datasets.pacb.com.s3.amazonaws.com/2014/Drosophila/reads/list.html. Ref: Kim, K. E. et al. Scientific Data 1, 140045 (2014), doi:10.1038/sdata.2014.45

library_source: genomic

data_processing:
SMRT sequencing reads were processed and mapped to the respective reference genome sequences using the SMRTPortal Analysis platform, v.2.3.0 with BLASR mapping algorithm using the standard mapping protocol and the modifications protocol using default parameters.
Genome_build: FlyBase dm6
The pipeline used to detect the modifications is called “DNA Modification Detection with SMRT Sequencing using R” and can be found at https://github.com/PacificBiosciences/kineticsTools. Interpulse durations (IPDs) were measured for all pulses aligned to each position in the reference sequence. The format of the output CSV/GFF files with modifications is described at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf. The CSV file contains statistical analysis of each position in the reference.  The GFF file includes sequence contexts only for sites of putative modification defined as positions with p-values of 0.01 or less.
Supplementary_files_format_and_content: GFF and CSV files

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Drosophila melanogaster_Whole organism

value: Whole organism


title: Patient 50

description: SAMPLE 13


title: Patient 65

description: SAMPLE 14


title: Patient 13

description: SAMPLE 7


title: Patient 49

description: SAMPLE 10


title: Patient 21

description: SAMPLE 2


title: Patient 25

description: SAMPLE 9


title: Patient 35

description: SAMPLE 8


title: Patient 37

description: SAMPLE 12


title: Patient 32

description: SAMPLE 3


title: Resected glioma M6 second surgery

type: genomic

city: Toyoake

first: Shunsuke

last: Nakae

state: Aichi

address: 1-98 Dengakubakubo Kutsukakecho

institute: human

description: SAMPLE 19

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). CEL files were produced by Affymetrix GeneChip® Command Console®, then processed with OncoScan Consple software to make OSCHP files.
Copy number

source_name: Glioma patient M5

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from freshly frozen tissue using DNeasy blood and tissue kits and from FFPE samples using DNA FFPE tissue kits.DNA was quantified with absorptiometric methods.

tag: subject status

value: Glioma patient

tag: subject id

value: recurrent tumor


title: Patient 59

description: SAMPLE 6


title: Patient 66

description: SAMPLE 11


title: P9_T3

city: Jena

first: S.

last: Lambeck

address: Erlanger Allee 101

country: Germany

institute: JUH

description: in vivo

scan_protocol: Arrays were readout with the detection system iScan from Illumina.

data_processing: Raw data was pre-processed using GenomeStudio (v 1.9.0). Robust spline normalization (rsn) and detection filtering were performed via the lumi package within Bioconductor and R statistics software (version 3.03). Detection (p<0.01) was required in at least four samples from the 34 initial samples. Ten further samples were taken for validation (techn. replicates). Annotation was mapped using HumanHT-12_V4_0_R2_15002873_B from Illumina.

source_name: male patient, no treatment

label_protocol: Amplification and biotinylation of RNA were carried out using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip®.

growth_protocol: All samples were taken after official registration (ClinicalTrials.gov Identifier: NCT01067703) and written consent.

extract_protocol: Blood was drawn before CPB (T1), 30 min after CPB (T2) and at 8:00 on the first postoperative day (T3) and prepared with 200 μl PAXgene reagent (PreAnalytix®, Qiagen, Hilden, Germany). Biotinylated probes were prepared from 500 ng of total RNA, using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip®. Amplification of RNA was in agreement to the protocol of the Illumina® for the BeadArray Reader 500 X.

treatment_protocol: Patients undergoing heart surgery on CPB were recruited in a prospective, multicenter, randomized, double-blind study. In brief, RIPC was induced during standardized anesthesia by four 5-min cycles of upper limb ischemia and 5-min reperfusion using a blood-pressure cuff inflated to a pressure 200 mm Hg, whereas the pressure was at least 20 mm Hg greater than the systolic arterial pressure measured via the arterial line. The study intervention was performed by un-blinded staff either on the patient’s arm (RIPC) or on a standardized dummy arm (control). The 12 Patients were approx. 60 years old (mean: RIPC 61.2, CTRL 57.6; sd: RIPC 10.9, CTRL 11.2).


title: P11_T3_VALIDATION

description: in vivo

hyb_protocol: Biotinylated probes were prepared from 500 ng of total RNA, using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip®. Amplification of RNA was in agreement to the protocol of the Illumina® for the BeadArray Reader 500 X.

source_name: female patient, no treatment

value: female


title: P9_T3_VALIDATION

description: in vivo


title: P11_T1_VALIDATION

description: in vivo


title: P10_T3

description: in vivo

source_name: male patient, remote ischaemic preconditioning (PIPC)


title: P11_T2_VALIDATION

description: in vivo


title: P9_T1_VALIDATION

description: in vivo


title: Patient 1

description: SAMPLE 1


title: Patient 8

description: SAMPLE 23


title: P10_T1_VALIDATION

description: in vivo


title: P12_T3_VALIDATION

description: in vivo

source_name: female patient, remote ischaemic preconditioning (PIPC)


title: P10_T3_VALIDATION

description: in vivo


title: P12_T1_VALIDATION

description: in vivo


title: P12_T2_VALIDATION

description: in vivo


title: Resected glioma M5 second surgery

description: SAMPLE 11


title: Resected glioma M11 first surgery

description: SAMPLE 13

value: primary tumor


title: Resected glioma M11 second surgery

description: SAMPLE 15


title: P12_T3

description: in vivo


title: P12_T2

description: in vivo


title: Resected glioma M10 second surgery

description: SAMPLE 7

source_name: Glioma patient M10


title: Resected glioma M10 first surgery

description: SAMPLE 5


title: Resected glioma M6 first surgery

description: SAMPLE 17


title: Resected glioma M8 second surgery

description: SAMPLE 3

source_name: Glioma patient M8


title: Resected glioma M8 first surgery

description: SAMPLE 1


title: P11_T2

description: in vivo


title: P11_T1

description: in vivo


title: Resected glioma M5 first surgery

description: SAMPLE 9


title: P7_T2

description: in vivo


title: P12_T1

description: in vivo


title: P8_T2

description: in vivo


title: P8_T3

description: in vivo


title: P11_T3

description: in vivo


title: P5_T3

description: in vivo


title: P7_T3

description: in vivo


title: P10_T1

description: in vivo


title: P5_T2

description: in vivo


title: P6_T3

description: in vivo


title: P7_T1

description: in vivo


title: P6_T2

description: in vivo


title: P8_T1

description: in vivo


title: P6_T1

description: in vivo


title: Patient 42

description: SAMPLE 26


title: P1_T3

description: in vivo


title: P4_T3

description: in vivo


title: P4_T2

description: in vivo


title: P2_T2

description: in vivo


title: P2_T3

description: in vivo


title: P3_T3

description: in vivo


title: P9_T1

description: in vivo


title: P5_T1

description: in vivo


title: Human epidermal keratinocytes, leptin treated, biological replicate 2

city: Seoul

first: Minsoo

last: Noh

address: 1 Gwanak-ro, Gwanak-gu

department: Pharmacy

country: South Korea

institute: Seoul National University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 oligonucleotide arrays. GeneChips were hybridized and washed using the Affymetrix Fluidics Station 450

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

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

source_name: Cultured human primary epidermal keratinocytes, formaledhyde treated, 24 hours

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

growth_protocol: Normal human keratinocytes (NHK) from neonatal foreskin were purchased from Lonza (Basel, Switzerland) and cultured in KBM medium with KGM2 growth supplements according to the manufacturer's instuction

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

treatment_protocol: At passge 2, when NHKs were confluent in culture,10 ng/ml of leptin were treated. After 24 hours in culture, NHKs were harvested for total RNA isolation.

tag: cell

value: human epidermal keratinocytes


title: P1_T2

description: in vivo


title: P3_T2

description: in vivo


title: Human epimermal keratinocytes, vehicle treated, biological replicate 2


title: Patient 19

description: SAMPLE 27


title: Human epidermal keratinocytes, leptin treated, biological replicate 1

source_name: Cultured human primary epidermal keratinocytes, vehicle treated, 24 hours


title: P4_T1

description: in vivo


title: P3_T1

description: in vivo


title: DMSO-2

city: South San Francisco

first: Matthew

last: Brauer

state: California

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description: HT29 cells treated with DMSO-2

hyb_protocol: Hybridization was performed according to methods developed by Affymetrix, using Human gene U133 Plus 2.0 arrays.

scan_protocol: Samples were scanned on a GeneChip Scanner 3000

data_processing: Probe intensities were normalized using RMA and imported into R version 2.10 (R Development Core Team, 2010) and non-specifically filtered by variance using the nsFilter method from the 'genefilter' package

source_name: HT-29 cells

label_protocol: Labeling was performed according to methods developed by Affymetrix

growth_protocol: HT-29 cells were grown in RPMI media suplemented with 10% FBS.

extract_protocol: mRNA extraction and cRNA synthesis were performed according to methods developed by Affymetrix

treatment_protocol: Cells were exposed to 5 uM gemcitabine for 30 minutes which was thenwashed out aand replaced with fresh media and cells were grown for a further 24 hours.

tag: concentration

tag: delivery

tag: time


title: P1_T1

description: in vivo

extract_protocol: Blood was drawn before CPB (T1), 30 min after CPB (T2) and at 8 am on the first postoperative day (T3) and prepared with 200 μl PAXgene reagent (PreAnalytix®, Qiagen, Hilden, Germany). Biotinylated probes were prepared from 500 ng of total RNA, using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip®. Amplification of RNA was in agreement to the protocol of the Illumina® for the BeadArray Reader 500 X.


title: Human epimermal keratinocytes, vehicle treated, biological replicate 1


title: gem-4

description: HT29 xenograft treated with Gemcitabine

source_name: HT-29 tumors

growth_protocol: NCR.nude mice (Taconic) were inoculated with HT-29 cells; when the tumor volumes reached 250-400 mm3, mice were distributed into volume-matched cohorts

treatment_protocol: Animals were administered 60 mg/kg gemcitabine or vehicle, and 24 hours later were administered 25 mg/kg GNE-783 or vehicle. Tumors were harvested 24 hours later.

tag: treatment

value: Gemcitabine


title: 5uM 0.5 h pulse-3

description: HT29 cells treated with G783-5uM 0.5 h pulse-3

value: pulse


title: DMSO-1

description: HT29 cells treated with DMSO-1


title: P2_T1

description: in vivo


title: combo-4

description: HT29 xenograft treated with GNE-783+Gemcitabine


title: Patient 34

description: SAMPLE 5


title: 5uM 0.5 h pulse-1

description: HT29 cells treated with G783-5uM 0.5 h pulse-1


title: gem-3

description: HT29 xenograft treated with Gemcitabine


title: DMSO-3

description: HT29 cells treated with DMSO-3


title: gem-5

description: HT29 xenograft treated with Gemcitabine


title: combo-2


title: 5uM 0.5 h pulse-2

description: HT29 cells treated with G783-5uM 0.5 h pulse-2


title: combo-3


title: Caenorhabditis elegans

description: [Third-party re-analysis] Raw SMRT sequencing  data was retrieved from: http://datasets.pacb.com.s3.amazonaws.com/2014/c_elegans/list.html. Ref: Kim, K. E. et al. Scientific Data 1, 140045 (2014), doi:10.1038/sdata.2014.45

data_processing:
SMRT sequencing reads were processed and mapped to the respective reference genome sequences using the SMRTPortal Analysis platform, v.2.3.0 with BLASR mapping algorithm using the standard mapping protocol and the modifications protocol using default parameters.
Genome_build: WormBase, WS245
The pipeline used to detect the modifications is called “DNA Modification Detection with SMRT Sequencing using R” and can be found at https://github.com/PacificBiosciences/kineticsTools. Interpulse durations (IPDs) were measured for all pulses aligned to each position in the reference sequence. The format of the output CSV/GFF files with modifications is described at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf. The CSV file contains statistical analysis of each position in the reference.  The GFF file includes sequence contexts only for sites of putative modification defined as positions with p-values of 0.01 or less.
Supplementary_files_format_and_content: GFF and CSV files

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans_Whole organism

tag: tissue


title: G783-5

description: HT29 xenograft treated with GNE-783


title: G783-4

description: HT29 xenograft treated with GNE-783


title: vehicle-3

description: HT29 xenograft treated with Vehicle

value: Vehicle


title: vehicle-2

description: HT29 xenograft treated with Vehicle


title: combo-1


title: vehicle-4

description: HT29 xenograft treated with Vehicle


title: G783-2

description: HT29 xenograft treated with GNE-783


title: vehicle-1

description: HT29 xenograft treated with Vehicle


title: G783-3

description: HT29 xenograft treated with GNE-783


title: G783-1

description: HT29 xenograft treated with GNE-783


title: gem-1

description: HT29 xenograft treated with Gemcitabine


title: gem-2

description: HT29 xenograft treated with Gemcitabine


title: gem 24hr-3

treatment_protocol: Cells were exposed to 1 uM gemcitabine for 30 minutes which was then washed out aand replaced with fresh media. Either DMSO or 1 uM GNE-783 was added for a further 24 hours.

value: Gem


title: G783 24hr-3


title: G783 24hr-1


title: Patient 12

description: SAMPLE 4


title: urine_pEMT_pos_11

city: Paris

first: Pierre

last: Galichon

address: 4 rue de la Chine

department: Hopital Tenon - Urgences Nephrologiques et Transplantation Renale

country: France

institute: Assistance Publique - Hopitaux de Paris

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer Oligo Microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, Santa Clara, CA, USA)

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using the Agilent Microarray Scanner System (Agilent Technologies, Santa Clara, CA, USA)

data_processing: Agilent Feature Extraction Software was used to read out and process the microarray image files, determining feature intensities (including background substraction), and normalization by the median intensity

source_name: urine

label_protocol: To produce C3-labeled cRNAs, the RNA samples were amplified and labeled using the Agilent low input quick Amp labeling kit following the manufacturer’s instructions

extract_protocol: 50 mL of urine was harvested, centrifuged at 15°C, 2000 rpm for 20 min, washed with 15 mL 1X phosphate buffered serum, and centrifuged again for 10 min. The pellet was resuspended in 150 µL of RNAlater (Qiagen, Courtaboeuf, France) and stored at -80°C. RNA isolation was performed using RNeasy micro kit (Qiagen, Courtaboeuf, France) following the provider’s protocol for mRNA isolation following laser capture microdissection

tag: pemt


title: urine_pEMT_pos_12


title: gem 24hr-2


title: gem 24hr-1


title: urine_pEMT_pos_13


title: G783 24hr-2


title: vehicle 24hr-2

value: DMSO


title: Lot_D_0.1_Gy

city: Kyoto

first: Aya

last: Fujishiro

address: Sakyo-ku

department: Transfusion Medicine and Cell Therapy

institute: Kyoto University Hospital

description: Gene expression of BM-MSCs of lot D 24 hours after 0.1 Gy irradiated

hyb_protocol: Hybridization was performed by using SurePrint G3 Human GE Microarray Kit (Agilent Technologies) following the manufacturer's recommendations.

scan_protocol: Microarray slides were scanned immediately after washing on the Microarray Scanner G2565CA (Agilent) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 039494_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: BM-MSCs, 0.1 Gy-irradiated,lot C

label_protocol: The amount of 150 ng of RNA extracted from each sample was used for complementary DNA (cDNA) and complementary RNA (cRNA) syntheses, and labeling cRNA with Cyanine3. These were performed with the use of Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies) following the manufacturer's recommendations.

growth_protocol: 2.5~3.0×105 of BM-MSCs were seeded in 10 cm dish and incubated until being confluent (for about 7~9 days) .

extract_protocol: Total RNA was isolated from irradiated or non-irradiated BM-MSCs by RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations. RNA integrities of all samples were evaluated by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), using the RNA 6000 Nano Kit.

treatment_protocol: BM-MSCs were exposed to 0.1 Gy of γ-radiation (Cesium-137) at a rate of 0.8 Gy/min using a Gammacell Irradiator (Best Theratronics, Ontario, Canada).

value: Bone marrow mesenchymal stromal/stem cells

tag: dose


title: urine_pEMT_pos_14


title: vehicle 24hr-3


title: combo 24hr-3


title: Lot_C_0.1_Gy

description: Gene expression of BM-MSCs of lot C 24 hours after 0.1 Gy irradiated


title: Lot_D_0_Gy

description: Gene expression of non-irradiated BM-MSCs of lot D

source_name: BM-MSCs, non-irradiated,lot C

value: 0 Gy


title: urine_pEMT_pos_9


title: urine_pEMT_pos_8


title: urine_pEMT_pos_10


title: vehicle 24hr-1


title: combo 24hr-2


title: Lot_C_0_Gy

description: Gene expression of non-irradiated BM-MSCs of lot C


title: combo 24hr-1


title: Lot_B_0.1_Gy

description: Gene expression of BM-MSCs of lot B 24 hours after 0.1 Gy irradiated

source_name: BM-MSCs, 0.1 Gy-irradiated,lot B


title: urine_pEMT_pos_7


title: urine_pEMT_pos_6


title: urine_pEMT_pos_5


title: col-0

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: control

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Genotypic designed Custom Arabidopsis 8x60K (AMADID No: 037661) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 3 micron resolution.

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift.

organism: Arabidopsis thaliana

source_name: seeds

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Seeds were sterilized and placed on MS agr plate and kept at 4 degree for 2 days. Then allowed to grow at 23 degree with 16/8 h light/dark cycle to allow the germination.

extract_protocol: RNA isolation was done by using QIAGEN RNeasy mini kit (Cat#74904)  as per the manufacturer’s protocols.

value: radicle emerged seeds

tag: genotype/variation

value: control

tag: ecotye


title: Lot_B_0_Gy

description: Gene expression of non-irradiated BM-MSCs of lot B

source_name: BM-MSCs, non-irradiated,lot B


title: urine_pEMT_pos_4


title: Lot_A_0.1_Gy

description: Gene expression of BM-MSCs of lot A 24 hours after 0.1 Gy irradiated

source_name: BM-MSCs, 0.1 Gy-irradiated,lot A


title: urine_pEMT_pos_1


title: urine_pEMTneg_9


title: HepG2_BFA_rep1

city: Tokyo

first: Kiyoshi

last: Yamaguchi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Clinical Genome Research

institute: The University of Tokyo

description: Gene expression in HepG2 cells treated with BFA

hyb_protocol: 600 ng of Cy3-labeled RNA was hybridized at 65⁰C for 17 hours.

scan_protocol: The signals were detected by using the DNA microarray scanner (Agilent Technologies).

data_processing: The scanned images were extracted with Feature Extraction software (Version 10.7.3.1; Agilent Technologies) using default parameters.

source_name: HepG2, BFA

label_protocol: 200 μg of total RNA were amplified and labeled using the Low Input QuickAmp Labeling kit (Agilent Technologies) according to the manufacturer’s protocols.

growth_protocol: HepG2 cells were grown in EMEM supplemented with 10% FBS (Thermo Fisher Scientific) and antibiotic/antimycotic solution (Sigma).

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen).

treatment_protocol: HepG2 cells were treated with DMSO or Brefeldin A (300 nM) for 24 hours.

value: liver

tag: cell line

tag: agent

value: BFA


title: urine_pEMTneg_11


title: urine_pEMT_pos_2


title: urine_pEMTneg_12


title: styk1

description: Gne expression compared to wild-type

source_name: germinated seeds

treatment_protocol: RNA isolation was done by using QIAGEN RNeasy mini kit (Cat#74904)  as per the manufacturer’s protocols.

value: T-dna knock-out


title: Lot_A_0_Gy

description: Gene expression of non-irradiated BM-MSCs of lot A

source_name: BM-MSCs, non-irradiated,lot A


title: HepG2_BFA_rep3


title: urine_pEMTneg_10


title: urine_pEMT_pos_3


title: HepG2_DMSO_rep1

description: Gene expression in HepG2 cells treated with DMSO

source_name: HepG2, DMSO


title: HepG2_BFA_rep2


title: styk2

description: Gne expression compared to wild-type


title: urine_pEMTneg_8


title: Z138 control

first: Patricia

last: Pérez-Galán

state: Barcelona

address: Centre Esther Koplowitz, Hemato-oncology dept, Rosello 149-153, 2nd floor

department: Hemato-oncology

institute: IDIBAPS

description: Gene expression data control cells

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the Gene Titan instrument.

data_processing:
Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software (AGCC) (Affymetrix).
Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm implemented in the Expression Console Software v1.1 (Affymetrix).

source_name: Z138 Mantle Cell Lymphoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA

growth_protocol: MCL cells at exponential phase  were set at  5x105 cells/ml  for  the experiment

extract_protocol: Total RNA was extracted using the Trizol  reagent

treatment_protocol: MCL cells were treated with 1 uM CC-292 for 48h


title: Z138 1mM CC-292 48h

description: Gene expression data CC-292  treated cells


title: HepG2_DMSO_rep3


title: HepG2_DMSO_rep2


title: urine_pEMTneg_6


title: REC 1mM CC-292 48h

source_name: REC-1 Mantle Cell Lymphoma cell line


title: urine_pEMTneg_7


title: urine_pEMTneg_4


title: urine_pEMTneg_5


title: urine_pEMTneg_3


title: HepG2_siCtrl_rep1

description: Gene expression in HepG2 cells treated with control siRNA

source_name: HepG2, siCtrl

treatment_protocol: HepG2 cells were transfected with siRNAs using Lipofectamine RNAiMAX for 48 hours.

tag: transfection

value: siCtrl


title: HepG2_siβ-catenin-10_rep2

description: Gene expression in HepG2 cells treated with β-catenin-10 siRNA

source_name: HepG2, β-catenin-10 siRNA

value: β-catenin-10 siRNA

value: beta-catenin knockdown


title: urine_pEMTneg_2


title: HepG2_siCtrl_rep2


title: HepG2_siβ-catenin-9_rep2

description: Gene expression in HepG2 cells treated with β-catenin-9 siRNA

source_name: HepG2, β-catenin-9 siRNA

value: β-catenin-9 siRNA


title: 50 DAA endosperm of RL4452, biological rep2

city: Winnipeg

first: Belay

middle: T.

last: Ayele

state: MB

address: 222 Agriculture Building

department: Plant Science

institute: University of Manitoba

description: Gene expression data from 50 DAA endosperm of RL4452

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

scan_protocol: GeneChips were scanned using an Affymetrix Scanner 3000.

data_processing:
Gene expression data of each genotype was normalized with the Robust Multi-array Average (RMA) algorithm of FlexArray software (http://genomequebec.mcgill.ca/FlexArray, Blazejczyk et al., 007).
Reference
Blazejczyk M, Miron M, Nadon R. 2007. FlexArray: a statistical data analysis software for gene expression microarrays. Genome Quebec, Montreal, Canada http://genomequebec.mcgill.ca/FlexArra

organism: Triticum aestivum

source_name: 50 DAA maturing seed of RL4452

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT Labelling Kit and the GeneChip Sample Cleanup Module

growth_protocol: Wheat plants of both genotypes (AC Domain and RL4452) were grown in a greenhouse at 22oC/18oC (day/night) under a 16/8 h photoperiod until harvest

extract_protocol: Total RNA of the embryo tissue was extracted using RNeasy Plant Mini Kit according to the manufacturer's instruction; mRNA from the endosperm tissue was isolated using PolyATtract kit according to the manufacturer's instructions.

treatment_protocol: Maturing seeds were harvested at 20, 30, 40 and 50 days after anthesis (DAA). The embryo and endosperm tissues were dissected from the maturing seeds harvested from the middle region of each spike

value: seed

tag: genotype

tag: age

value: 50 days after anthesis (DAA)


title: HepG2_siβ-catenin-9_rep1


title: LBR10216_0009

city: Atlanta

first: Sandeep

last: Kumar

state: GA

address: 1760 Haygood Dr.

department: Biomedical Engineering

institute: Emory University

description:
8294816087_B
WT Sample 5 e-LCA2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Illumina HiScan Scanner.

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio 2011.1.

source_name: carotid artery, WT, disturbed flow

label_protocol: Standard Illumina labeling protocol.

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

tag: strain/background

value: WT

value: carotid artery

value: disturbed flow


title: 50 DAA endosperm of RL4452, biological rep1


title: 50 DAA embryo of RL4452, biological rep2

description: Gene expression data from 50 DAA embryo of RL4452


title: HepG2_siβ-catenin-10_rep1


title: 30 DAA endosperm of RL4452, biological rep2

description: Gene expression data from 30 DAA endosperm of RL4452

source_name: 30 DAA maturing seed of RL4452

value: 30 days after anthesis (DAA)


title: REC control 48h

description: Gene expression data control cells


title: LBR10216_0010

description:
8294816056_E
WT Sample 2 e-RCA 2

source_name: carotid artery, WT, stable flow

value: stable flow


title: 20 DAA endosperm of RL4452, biological rep2

description: Gene expression data from 20 DAA endosperm of RL4452

source_name: 20 DAA maturing seed of RL4452

value: 20 days after anthesis (DAA)


title: 40 DAA endosperm of RL4452, biological rep2

description: Gene expression data from 40 DAA endosperm of RL4452

source_name: 40 DAA maturing seed of RL4452

value: 40 days after anthesis (DAA)


title: LBR10216_0008

description:
8294816087_E
WT Sample 6 e-LCA3


title: 20 DAA endosperm of RL4452, biological rep1


title: 30 DAA endosperm of RL4452, biological rep1


title: 40 DAA embryo of RL4452, biological rep2

description: Gene expression data from 40 DAA embryo of RL4452


title: urine_pEMTneg_1

source_name: urine


title: LBR10216_0011

description:
8294816087_A
WT Sample 4 e-LCA1


title: 50 DAA embryo of RL4452, biological rep1


title: LBR10216_0007

description:
8294816056_B
WT Sample 1 e-RCA 1


title: LBR10216_0012

description:
8294816056_F
WT Sample 3 e-RCA 3


title: 40 DAA endosperm of RL4452, biological rep1


title: 40 DAA embryo of RL4452, biological rep1


title: 30 DAA embryo of RL4452, biological rep2

description: Gene expression data from 30 DAA embryo of RL4452


title: SGC7901: Negative control

description: Differential expression analysis of global gene profiling were performed in gastric cancer cells transfected with siKIF26B or negative control.

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1).

source_name: gastric cancer cell SGC7901

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers.For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

extract_protocol: SGC7901 cells were transfected of KIF26B siRNA or the negative control respestively.Total RNAs was extracted using TRIzol reagent.Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.RNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

tag: cell type

value: gastric cancer

value: transfected with negative control


title: SGC7901: siKIF26B

description: Differential expression analysis of global gene profiling were performed in gastric cancer cells transfected with siKIF27B or negative control.

value: transfected with siKIF26B


title: 20 DAA embryo of RL4452, biological rep2

description: Gene expression data from 20 DAA embryo of RL4452


title: 30 DAA embryo of RL4452, biological rep1


title: 20 DAA embryo of RL4452, biological rep1


title: Blood-PCI-24h-Rep1

description:
Illumina MouseWG-6 v2.0 expression beadchip
SAMPLE 8

hyb_protocol: Whole-Genome Gene Expression with IntelliHybTM Seal protocoll (Revision B) from Illumina® (San Diego, CA, USA)

scan_protocol: Scanning of arrays was done with the BeadArray Reader 500 X from Illumina® (San Diego, CA, USA).

data_processing: Gene chips were scanned and pre-processed using BeadStudio (version 3.23). Data analysis was carried out using R statistics software (version 2.92) and BioConductor (version 2.4.1)

source_name: Blood samples from mice challenged by PCI after 24 hours

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays. Amplification and biotinylation of RNA was performed according to the protocol of the Illumina® TotalPrep RNA Amplifikation Kit from Ambion (Applied Biosystems, Darmstadt, Germany)

growth_protocol: 8 weeks old female C57/BL6 Jackson mice

extract_protocol: Sample preparation, RNA isolation, array hybridization were performed according to standard protocols (Mouse-WG6 v2.0, Illumina®, San Diego, USA) . Samples prepared with 200µl PAXgene reagent (PreAnalytix®, Qiagen, Hilden, Germany). Additional clearing from globin RNA according to the GLOBINclearTM Mouse/Rat Kit by Ambion® (Applied Biosystems, Darm-stadt, Germany).

treatment_protocol: Intraperitoneal injection of 200 µl of a human faeces suspension (KBE 75 x 106/ml) leading to peritoneal contamination and infection (PCI) in mice. Sham controls received intraperitoneal injection of 200 µl of saline.

tag: gender

value: Female

tag: strain

value: C57/BL6 Jackson mice

value: 8 weeks old

value: challenged by PCI after 24 hours


title: Blood-PCI-24h-Rep3

description:
Illumina MouseWG-6 v2.0 expression beadchip
SAMPLE 10


title: Blood-PCI-6h-Rep4

description:
Illumina MouseWG-6 v2.0 expression beadchip
SAMPLE 7

source_name: Blood samples from mice challenged by PCI after 6 hours

value: challenged by PCI after 6 hours


title: Blood-PCI-24h-Rep4

description:
Illumina MouseWG-6 v2.0 expression beadchip
SAMPLE 11


title: Blood-PCI-24h-Rep2

description:
Illumina MouseWG-6 v2.0 expression beadchip
SAMPLE 9


title: Blood-PCI-6h-Rep2

description:
Illumina MouseWG-6 v2.0 expression beadchip
SAMPLE 5


title: 50 DAA endosperm of AC Domain, biological rep2

description: Gene expression data from 50 DAA endosperm of AC Domain

source_name: 50 DAA maturing seed of AC Domain

value: seed

value: AC Domain


title: 50 DAA endosperm of AC Domain, biological rep1

value: 50 days after anthesis (DAA)


title: Blood-PCI-6h-Rep3

description:
Illumina MouseWG-6 v2.0 expression beadchip
SAMPLE 6


title: 40 DAA endosperm of AC Domain, biological rep2

description: Gene expression data from 40 DAA endosperm of AC Domain

source_name: 40 DAA maturing seed of AC Domain


title: Blood-Sham-6h-Rep2

description:
Illumina MouseWG-6 v2.0 expression beadchip
SAMPLE 2

source_name: Blood samples from mice challenged to sham treatment

value: sham treatment


title: Blood-Sham-6h-Rep3

description:
Illumina MouseWG-6 v2.0 expression beadchip
SAMPLE 3


title: Blood-PCI-6h-Rep1

description:
Illumina MouseWG-6 v2.0 expression beadchip
SAMPLE 4


title: 30 DAA endosperm of AC Domain, biological rep2

description: Gene expression data from 30 DAA endosperm of AC Domain

source_name: 30 DAA maturing seed of AC Domain


title: 40 DAA endosperm of AC Domain, biological rep1


title: K562, Imatinib treated, sample #2

city: BORDEAUX

first: Bruno

last: CARDINAUD

address: 146 rue Leo Saignat

department: INSERM U1035

institute: Bordeaux University

hyb_protocol: The totality of the labeled RNA were resuspended in 45ul of a mix containing 18ul of nuclease-free water, 4.5 ul of 10X GE Blocking agent, 22.5ul of 2xHi-RPM Hybridization buffer. After a 100°C/5min incubation, the labeled RNA were hybridized to Agilent-019118 Human miRNA Microarray 2.0 for 16 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) then 5 minutes with 37°C GE Wash buffer 2 (Agilent). Slides were then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent B DNA Microarray Scanner using settings for 4x44k one color slides (eXtended Dynamic Range, scan area 61x21.6 mm, Scan resolution 5um, dye channel is set to Green).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol miRNA_V1_95_May07_Feb07 and Grid: 019118_D_20080214) to obtain background subtracted and spatially detrended Processed Signal intensities.
Normalized signal intensity (quantile normalization, BRB array tools)

source_name: K562, Imatinib treated

label_protocol: 200ng of total RNA were Cy3-labeled using the miRNA complete labeling kit (5190-0456), following the manufacturer's instructions. After removal of the unincorporated nucleotides using a BioRad micro Bio-Spin 6 columns (Biorad), the labeled RNA were dried using a vacuum concentrator at 45°C

growth_protocol: K562 cells (DSMZ, Germany) were grown at 37°C / 5% CO2 in RPMI medium (Invitrogen) supplemented with 10% foetal calf serum and penicillin/streptomycin, and splitted every 2-3 days. The day before the treatment, cells were seeded at 250.000 cells per well of a 24-wells plate, in a volume of 1ml. Ten 10 microliters of either Imatinib 100microM or PBS were added to the wells. After 24h, cells were centrifuged, the pellets were washed once with PBS then resuspended in 1ml Trizol (ThermoFisher) and homogeneized.

extract_protocol: The first steps of the RNA extraction were performed following the manufacturer's recommendations. After phases separation, ethanol (1.5 volume) was added to the aqueous phase and the mix was deposited onto a RNeasy column (Qiagen) and RNA were purified following the "RNA cleanup" protocol supplied by the manufacturer. After elution, RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored using agarose gel electrophoresis.


title: K562, Imatinib treated, sample #1


title: K562, Imatinib treated, sample #3


title: Blood-Sham-6h-Rep1

description:
Illumina MouseWG-6 v2.0 expression beadchip
SAMPLE 1


title: K562, not treated, sample #3

source_name: K562, not treated


title: 30 DAA endosperm of AC Domain, biological rep1


title: 20 DAA endosperm of AC Domain, biological rep2

description: Gene expression data from 20 DAA endosperm of AC Domain

source_name: 20 DAA maturing seed of AC Domain


title: K562, not treated, sample #2


title: 20 DAA endosperm of AC Domain, biological rep1


title: K562, not treated, sample #1


title: carbon source ferulic acid 2

city: Yangling

first: Can

last: Chen

address: No.3 Taicheng Road

institute: Northwest A&F University

description: experimental group 2

hyb_protocol: Each Slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit in Hybridization Oven according to the manufacturer's insrtuctions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan, Scan resolution 3um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Corynebacterium glutamicum ATCC 13032

source_name: carbon source ferulic acid

label_protocol: RNA was labled by low Input Quick Amp Labeling Kit, One-Color, following the manufacture' instructions.

growth_protocol: C. glutamicum strains were routinely grown in LB medium or in mineral salts medium supplemented with 0.05 g l-1 of yeast extract to meet the requirement of vitamins for the strains on a rotary shaker at 30°C

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Samples were collected during the mid-logarithmic growth phase in minimal medium with added glucose (control sample: 100 mM) or ferulic acid as the sole carbon source (3 mM), respectively.

tag: carbon source

value: ferulic acid


title: carbon source ferulic acid 1

description: experimental group 1


title: T4-S2-R4

hyb_protocol: For hybridisation, the Whole-Genome Gene Expression with IntelliHybTM Seal protocoll (Revision B) from Illumina® (San Diego, CA, USA) was used.

scan_protocol: Scanning of arrays was done with the BeadArray Reader 500 X from Illumina®, San Diego, CA, USA).

data_processing: Gene chips from 44 samples (four tissues; four replicates for 6 h and 24 h post-infection and three replicates sham) were scanned and pre-processed using BeadStudio (version 3.23). Data analysis was carried out using R statistics software (version 2.92) and BioConductor (version 2.3). A robust spline normalization, combining the features of quantile and loess normalization, was conducted for the tissue separated sample groups (liver, lung, spleen and blood) and log 2 signals were obtained.

source_name: blood samples from mice challenged to PCI treatment were monitored after 6 hours

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

extract_protocol: Preparation of total RNA from lung, liver and spleen. Tissue homogenization was conducted with the tissue lyser by Qiagen (Retsch, Haan, Germany) with a 5mm steel ball for 4 minutes at 30hz and processed for total RNA isolation as described by the manufacturer using RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA-Isolation from whole blood was performed according to the protocol of PAXgene Blood RNA Kit (PreAnalytix®, Qiagen, Hilden, Germany). Additional clearing from globin RNA was used for RNA from whole blood samples according to the GLOBINclearTM Mouse/Rat Kit by Ambion® (Applied Biosystems, Darmstadt, Germany) RNA integrity and concentration analyses were performed with the Bioanalyzer 2100 (Agilent Technologies®, Palo Alto, CA, USA) according to the manufacturers protocol RNA 6000 Nano Assay using RNA 6000 Nano LabChip® Kits by Agilent Technologies®.

treatment_protocol: 1. faecal Peritonitis: intraperitoneal injection of 200µl of a human faeces suspension (KBE 75 x 10^6/ml), 2. Sham controls: intraperitoneal injection of 200µl of physiological sodium chloride

tag: sex

value: female

value: 8 weeks


title: 50 DAA embryo of AC Domain, biological rep1

description: Gene expression data from 50 DAA embryo of AC Domain


title: DNA methylation in HGEC6B

city: Chuo-ku

first: Naoko

last: Iida

state: Tokyo

address: 5-1-1 Tsukiji

institute: National Cancer Center in Japan.

description: SAMPLE 5

hyb_protocol: Standard Illumina Protocol

scan_protocol: The array was scanned with an iScan System.

data_processing:
The data were analyzed using GenomeStudio Methylation Module Software (v1.9.0）
The 'Matrix_signal_intensity.txt' contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: DNA methylation in normal cells.

label_protocol: Standard Illumina Protocol

growth_protocol: AGS, HSC39, HSC57, KATO III, MKN45 and SW480 were maintained in RPMI1640 medium with 10% FBS. HT29 was maintained in McCoy's 5A medium with 10% FBS. HGEC6B was Keratinocyte-SFM medium with 5ng/ml EGF, bovine pituitary extract, 10% FBS, 2mM NAC, 0.2mM Ascorbic acid 2-phosphate 3Na.

extract_protocol: Genomic DNA was extracted by standard phenol/chloroform method, and was quantified using a Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies).

value: Normal human gastric epithelial cell line


title: T4-S3-R2

source_name: blood samples from mice challenged to PCI treatment were monitored after 24 hours


title: carbon source glucose 3

description: control group 3

source_name: carbon source glucose

value: glucose


title: T4-S3-R1


title: T4-S2-R3


title: T4-S3-R4


title: 50 DAA embryo of AC Domain, biological rep2


title: T4-S3-R3


title: Y7_2

city: Clayton

first: Justin

last: StJohn

state: Victoria

address: 27-31 Wright Street

department: Centre for Genetic Diseases

country: Australia

institute: Hudson Institute of Medical Research

description: SAMPLE 24

hyb_protocol: Samples were hybridized according to the Infinium HD Assay Ultra protocol

scan_protocol: Samples were scanned according to the Infinium HD Assay Ultra protocol

data_processing:
Genomic DNA extracted from pig blood samples was genotyped using Illumina PorcineSNP60 v2 BeadChip
Image processing and SNP calling were performed using the genotyping module of Illumina GenomeStudio software (GenCall cutoff for failed genotypes of 0.15,  = software versions 1.9.4 and 2011.1, respectively).

organism: Sus scrofa

source_name: Blood

label_protocol: Samples were labelled according to the Infinium HD Assay Ultra protocol

growth_protocol: Blood was drawn from live pigs

extract_protocol: Extraction of genomic DNA from fresh blood was performed using the Isolate II Genomic DNA kit (Bioline, London, UK) including proteinase K and RNase treatments, according to the manufacturer’s instructions.

treatment_protocol: No treatments were performed

tag: individual

value: mini-pig Y7

value: blood


title: DNA methylation in KATO III

description: SAMPLE 4

source_name: DNA methylation in cancer cell line

value: KATO III

value: Gastric cancer cell line


title: DNA methylation in HSC57

description: SAMPLE 3


title: 40 DAA embryo of AC Domain, biological rep1

description: Gene expression data from 40 DAA embryo of AC Domain

tag: tissue

value: 40 days after anthesis (DAA)


title: 40 DAA embryo of AC Domain, biological rep2


title: Y6_2

description: SAMPLE 23

value: mini-pig Y6


title: carbon source glucose 2

description: control group 2


title: carbon source glucose 1

description: control group 1


title: DNA methylation in MKN45

description: SAMPLE 6


title: DNA methylation in SW480

description: SAMPLE 8

value: Colon cancer cell line


title: Ovarian non-tumor tissue [R85C]

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

description:
R85C
Non-tumor

data_processing:
Raw data were processed by REST2009 software (Pfaffl et al. Nucleic Acids Res. 2000, 30, e36).
Mean expression of reference genes (PPIA, UBC, and YWHAZ) was used for normalization.

label: FAM

source_name: Ovarian non-tumor

label_protocol: cDNA was synthesized using 0.5 µg of total RNA by help of RevertAidTM First Strand cDNA Synthesis Kit (MBI Fermentas, Vilnius, Lithuania) with random hexamer primers according to manufacturer´s protocol and stored at -20 °C. cDNA was preamplified using 5x PerfeCTa PreAmp SuperMix (Quanta Biosciences, Beverly, MA). qPCR was performed in ViiA7 Real-Time PCR System (Life Technologies, Carlsbad, CA) with 45 cycles at 95 °C for 15 seconds and 60 °C for 60 seconds.

extract_protocol: Total RNA was isolated from frozen tissues using AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Hildesheim, Germany) according to manufacturer's protocol.

value: Ovarian non-tumor

tag: age at diagnosis


title: Ovarian non-tumor tissue [R94C]

description:
R94C
Non-tumor


title: DNA methylation in AGS

description: SAMPLE 1

value: AGS


title: Y5_2

description: SAMPLE 22

value: mini-pig Y5


title: 30 DAA embryo of AC Domain, biological rep1

description: Gene expression data from 30 DAA embryo of AC Domain

value: seed

value: AC Domain

value: 30 days after anthesis (DAA)


title: Ovarian non-tumor tissue [R84C]

description:
R84C
Non-tumor


title: DNA methylation in HT29

description: SAMPLE 7


title: T4-S2-R1

value: female


title: DNA methylation in HSC39

description: SAMPLE 2


title: 30 DAA embryo of AC Domain, biological rep2


title: Ovarian non-tumor tissue [R83C]

description:
R83C
Non-tumor


title: Y2_2

description: SAMPLE 19

value: mini-pig Y2


title: T4-S1-R2

source_name: blood samples from mice challenged to sham treatment

value: 8 weeks


title: Y3_2

description: SAMPLE 20

value: mini-pig Y3


title: 20 DAA embryo of AC Domain, biological rep3

description: Gene expression data from 20 DAA embryo of AC Domain

value: 20 days after anthesis (DAA)


title: 20 DAA embryo of AC Domain, biological rep4


title: 20 DAA embryo of AC Domain, biological rep2


title: Ovarian non-tumor tissue [R81C]

description:
R81C
Non-tumor


title: Y4_2

description: SAMPLE 21

value: mini-pig Y4

value: blood


title: T3-S3-R4

source_name: spleen samples from mice challenged to PCI treatment monitored after 24 hours


title: T4-S1-R1


title: T4-S1-R3


title: T3-S3-R3


title: Ovarian non-tumor tissue [R74C]

description:
R74C
Non-tumor


title: Ovarian non-tumor tissue [R80C]

description:
R80C
Non-tumor


title: T3-S3-R2


title: 20 DAA embryo of AC Domain, biological rep1


title: Ovarian non-tumor tissue [R73C]

description:
R73C
Non-tumor


title: R1_2

description: SAMPLE 18

value: mini-pig R1


title: G1_2

description: SAMPLE 17

value: mini-pig G1


title: Y1_2

description: SAMPLE 16

value: mini-pig Y1


title: W1

description: SAMPLE 15

value: mini-pig W1


title: Ovarian non-tumor tissue [R72C]

description:
R72C
Non-tumor

value: Ovarian non-tumor


title: Ovarian non-tumor tissue [R68C]

description:
R68C
Non-tumor


title: Ovarian non-tumor tissue [R78C]

description:
R78C
Non-tumor


title: Ovarian non-tumor tissue [R69C]

description:
R69C
Non-tumor


title: Ovarian non-tumor tissue [R67C]

description:
R67C
Non-tumor


title: G1_1

description: SAMPLE 14


title: R17

description: SAMPLE 13

value: mini-pig R17


title: T3-S2-R3

source_name: spleen samples from mice challenged to PCI treatment monitored after 6 hours


title: T3-S2-R2


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL85M]

description:
PL85M
Intraperitoneal metastasis

source_name: Intraperitoneal EOC metastasis

value: Intraperitoneal EOC metastasis

tag: Stage

tag: grade

tag: histological type

value: high grade serous carcinoma

tag: progression, recurrence or death

value: no

tag: progression-free survival [months]

tag: first-line chemotherapy

value: administered


title: R1_1

description: SAMPLE 9


title: T3-S3-R1

value: female


title: R2

description: SAMPLE 10

value: mini-pig R2


title: T4-S2-R2

value: 8 weeks


title: T2-S3-R4

source_name: lung samples from mice challenged to PCI treatment monitored after 24 hours


title: T3-S2-R1


title: T2-S3-R3


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL82M]

description:
PL82M
Intraperitoneal metastasis

value: other than high grade serous carcinoma

value: yes

tag: drug resistance status

value: resistant


title: T3-S1-R2

source_name: spleen samples from mice challenged to sham treatment

tag: age


title: R4

description: SAMPLE 12

value: mini-pig R4

value: blood


title: T3-S1-R1


title: T3-S1-R3


title: T3-S2-R4


title: R3

description: SAMPLE 11

value: mini-pig R3


title: Y8

description: SAMPLE 8

value: mini-pig Y8


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL71M]

description:
PL71M
Intraperitoneal metastasis


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL69M]

description:
PL69M
Intraperitoneal metastasis


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL66M]

description:
PL66M
Intraperitoneal metastasis


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL70M]

description:
PL70M
Intraperitoneal metastasis


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL63M]

description:
PL63M
Intraperitoneal metastasis


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL61M]

description:
PL61M
Intraperitoneal metastasis


title: T2-S3-R2


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL60M]

description:
PL60M
Intraperitoneal metastasis


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL59M]

description:
PL59M
Intraperitoneal metastasis

value: intermediate


title: Y5_1

description: SAMPLE 5

value: mini-pig Y5


title: Y6_1

description: SAMPLE 6

value: mini-pig Y6


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL54M]

description:
PL54M
Intraperitoneal metastasis

value: Intraperitoneal EOC metastasis

value: sensitive


title: T2-S2-R4

source_name: lung samples from mice challenged to PCI treatment monitored after 6 hours


title: Y4_1

description: SAMPLE 4

value: mini-pig Y4


title: T2-S3-R1


title: Y7_1

description: SAMPLE 7

value: mini-pig Y7


title: Y3_1

description: SAMPLE 3

value: mini-pig Y3


title: T2-S2-R3

value: female


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL53M]

description:
PL53M
Intraperitoneal metastasis

value: high grade serous carcinoma

value: not administered


title: E11.5 lung

city: Tsukuba

first: Naoto

last: Ninomiya

state: Ibaraki

address: 1-1-1 Higashi

department: Biotechnology Research Institute for Drug Discovery

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent gene expression blocking agent following the manufacturers protocols. To stop fragmentation reaction, 2x Hi-RPM hybridization buffer was added, and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112F) for 18 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 sec with Acetonitrile (Wako), and then dried immediately.

scan_protocol: Slides were scanned immediately after wash and dried on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10 μm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol: GE1_1105_Oct12, and Grid: 014868_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: E11.5 lung

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 600 ng RNA using the One-Color Quick amp labeling kit (Qiagen) following the manufacturer's instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MEFs and MDF were cultured in DMEM supplemented with 12% FBS and 100U/ml penicillin/streptomycin. iLung cells were cultured in DMEM supplemented with 12% FBS and 100U/ml penicillin/streptomycin for 7 days. On day 7, the medium was changed to Advanced RPMI 1460 supplemented with 0.2% FBS and L-glutamine, and cultured for 10 days.

extract_protocol: Total RNA was prepared using RNeasy Mini kit (Qiagen) following the manufacturer's instructions. The protocol of RNeasy Mini kit includes DNase digestion. Extracted RNA was qualified using a NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: iLung cells were generated by retroviral transduction of transcription factors.

value: ICR

value: E11.5 lung


title: T2-S1-R2

source_name: lung samples from mice challenged to sham treatment

value: 8 weeks


title: T2-S2-R2


title: T2-S2-R1


title: Y2_1

description: SAMPLE 2

value: mini-pig Y2

value: blood


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL50M]

description:
PL50M
Intraperitoneal metastasis

value: yes

value: administered


title: Ovarian non-tumor tissue [R65C]

description:
R65C
Non-tumor

value: Ovarian non-tumor


title: Adult thyroid

source_name: Adult thyroid

value: Adult thyroid


title: Adult trachea

source_name: Adult trachea

value: Adult trachea


title: Adult lung

source_name: Adult lung

value: Adult lung


title: T2-S1-R1


title: T1-S3-R4

source_name: liver samples from mice challenged to PCI treatment monitored after 24 hours


title: T2-S1-R3


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL48M]

description:
PL48M
Intraperitoneal metastasis

value: Intraperitoneal EOC metastasis

value: other than high grade serous carcinoma

value: no

value: sensitive


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL49M]

description:
PL49M
Intraperitoneal metastasis


title: Y1_1

description: SAMPLE 1

value: mini-pig Y1


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL44M]

description:
PL44M
Intraperitoneal metastasis

value: resistant


title: Adult esophagus

source_name: Adult esophagus

value: ICR

value: Adult esophagus


title: T1-S3-R1

value: female

value: 8 weeks


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL42M]

description:
PL42M
Intraperitoneal metastasis

value: high grade serous carcinoma


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL40M]

description:
PL40M
Intraperitoneal metastasis

value: yes

value: intermediate


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL41M]

description:
PL41M
Intraperitoneal metastasis

value: administered


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL43M]

description:
PL43M
Intraperitoneal metastasis


title: iLung (MDF)-2

source_name: iLung cells generated from MDF

value: induced lung progenitor cells


title: iLung (MDF)-1


title: iLung (Limb MEF)-3

source_name: iLung cells generated from limb MEF


title: iLung (Dorsal MEF)-1

source_name: iLung cells generated from Dorsal MEF


title: T1-S3-R2


title: iLung (Limb MEF)-1


title: iLung (MDF)-3


title: iLung (Limb MEF)-2


title: T1-S2-R3

source_name: liver samples from mice challenged to PCI treatment monitored after 6 hours


title: iLung (Dorsal MEF)-2


title: iLung (Dorsal MEF)-3


title: MDF-2

source_name: Mouse dermal fibroblasts

value: Dermal fibroblasts


title: T1-S2-R1


title: T1-S3-R3


title: T1-S2-R4


title: T1-S2-R2


title: T1-S1-R3

source_name: liver samples from mice challenged to sham treatment


title: Spleen Venus+CD138hi cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description:
SP Ve+
Gene-expression profiling of freshly isolated IL-10 Venus+CD138hi cells in spleen

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

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

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

source_name: IL-10 Venus mice spleen

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

growth_protocol: All samples were freshly isolated.

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Quiagen).

treatment_protocol: B220+ and Venus+ CD138hi cells from spleen and bone marrow  of IL-10 Venus mice were sorted by flow cytometric cell sorting on a BD Aria III sorter (Becton Dickinson).

tag: genotype/variation

value: IL-10 Venus reporter mouse

value: spleen

value: Venus+ CD138hi


title: Bone marrow Venus+ CD138hi cells

description:
BM Ve+
Gene-expression profiling of freshly isolated IL-10 Venus+CD138hi cells in bone marrow

source_name: IL-10 Venus mice bone marroe

value: bone marrow

tag: cell type


title: T1-S1-R1

first: S.

last: Lambeck

address: Erlanger Allee 101

institute: JUH


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL3M]

description:
PL3M
Intraperitoneal metastasis

source_name: Intraperitoneal EOC metastasis

value: Intraperitoneal EOC metastasis


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL39M]

description:
PL39M
Intraperitoneal metastasis


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL28M]

description:
PL28M
Intraperitoneal metastasis


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL38M]

description:
PL38M
Intraperitoneal metastasis


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL37M]

description:
PL37M
Intraperitoneal metastasis

value: sensitive


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL26M]

description:
PL26M
Intraperitoneal metastasis

value: resistant


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL13M]

description:
PL13M
Intraperitoneal metastasis

value: not administered


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL18M]

description:
PL18M
Intraperitoneal metastasis


title: Epithelial ovarian carcinoma tissue, primary [PL87T]

description:
PL87T
Primary tumor

source_name: Primary EOC tumor

value: Primary EOC tumor

value: no


title: Epithelial ovarian carcinoma tissue, primary [PL88T]

description:
PL88T
Primary tumor


title: Epithelial ovarian carcinoma tissue, primary [PL86T]

description:
PL86T
Primary tumor


title: MDF-3

value: ICR


title: Epithelial ovarian carcinoma tissue, primary [PL84T]

description:
PL84T
Primary tumor

value: other than high grade serous carcinoma


title: Limb MEF-3

source_name: E13.5 mouse limb fibroblasts

value: Embryonic fibroblasts


title: Epithelial ovarian carcinoma tissue, intraperitoneal metastasis [PL24M]

description:
PL24M
Intraperitoneal metastasis

value: high grade serous carcinoma

value: yes


title: Limb MEF-2


title: Epithelial ovarian carcinoma tissue, primary [PL80T]

description:
PL80T
Primary tumor

value: administered


title: Epithelial ovarian carcinoma tissue, primary [PL83T]

description:
PL83T
Primary tumor


title: Epithelial ovarian carcinoma tissue, primary [PL74T]

description:
PL74T
Primary tumor


title: MDF-1

value: Dermal fibroblasts


title: Spleen B220+ cells

description:
Ctrl
Gene-expression profiling of primary B220+ cells in spleen

source_name: IL-10Venus mice spleen

value: IL-10 Venus reporter mouse


title: T1-S1-R2

value: female

value: 8 weeks


title: Dorsal MEF-2

source_name: E13.5 mouse dorsal fibroblasts


title: Epithelial ovarian carcinoma tissue, primary [PL76T]

description:
PL76T
Primary tumor


title: Dorsal MEF-3


title: Dorsal MEF-1