title: A549 cells treated with 5 mM sodium phenylbutyrate

city: Wenzhou

first: xiaoqiang

last: xiao

state: zhejiang

address: No 270.Xueyuan road

institute: Wenzhou Medical University

description: mRNA expression data from 5 mM sodium phenylbutyrate treated A549 cell line

hyb_protocol: he microarray was pre-hybridized and hybridized using the GeneChip hybridization, wash and staining kit (Affymetrix, Inc., CA, USA) in a GeneChip hybridization oven

scan_protocol: Microarray were scanned using Affymetrix Genechip Scanner 3000.

data_processing: primary data in DAT format were transformed into CEL format using the AGCC software. The Expression Console software was used for the Quality control of the primary data from the scanning the microarray, and Partek software was used for RMA processing and data analysis.

source_name: A549 cell line

label_protocol: biotinylated-labeled RNA were prepared according to Genechip 3'IVT express kit protocol from 500 ng total RNA  from affymetrix)

growth_protocol: A549 cells were loaded on 10 cm cell culture plate and cultured in RPMI 1640 medium containing 10% fetal bovine serium and 100 mg/ml streptomycin, and 100 U/ml penicillin for 24 hours .Cells were grown at 37oC under 5% CO2.

extract_protocol: Total RNAs were extracted with Trizol based on the manufacture's instruction.

treatment_protocol: 5mM sodium butyrate or sodium 4-phenybutyrate were added into the medium after 24 hours loading and cells were harvested after 24 hours treatment.

value: 5 mM sodium phenylbutyrate

value: non-small cell lung cancer


title: Patient H_005

status: Public on Jun 10 2017

type: RNA

city: Yokohama-shi, Tsurumi-ku

first: Ryo

last: Matoba

state: Kanagawa-ken

country: Japan

institute: DNAChipResearchInc

hyb_protocol: A total of 600 ng of Cy3 labeled RNA was hybridized to custom-made microarrays at 60C for 17 hours and subsequently washed according to the Agilent standard hybridization protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The data with low signal intensities were excluded from additional investigation, and with each sample, the intensity values were subjected to Quantile Equalization algorithm to correct background noise and for normalization.

molecule: total RNA

organism: Homo sapiens

source_name: prospect study_recurrent-free case

label_protocol:
After monitoring the RNA using 260nm absorbance, one microgram total RNA was converted to cDNA, and was amplified using the Low RNA Input Fluorescent Labeling Kit (Agilent Technologies, Santa Clara, CA).
The cRNA was labeled with Cyanine 3(Cy3)-CTP during in vitro transcription.

extract_protocol: The tumor specimens were cut into approximately 8.0 mm square pieces within 2 hours of surgical resection, immediately put into RNAlaterTM (Ambion, Austin, TX), and stored at -80ºC until use. Total RNA was extracted using TRIzol reagent (Invitrogen, San Diego, CA) as described in the manufacturer’s protocol.

tag: age

tag: gender

value: Male

tag: stage (dukes)

value: B

tag: study group

value: prospect

tag: recurrency

value: recurrent-free

tag: tissue

value: colorectal cancer


title: milk fat globules Polish White Improved goat_2

city: Warszawa

first: Joanna

last: Pławińska-Czarnak

address: Nowoursynowska 159

country: Poland

institute: WULS-SGGW

hyb_protocol: according to the manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Capra hircus

source_name: milk fat globules (MFG)

extract_protocol: isolation of total RNA from goat MSC and MFG the RNeasy Lipid Tissue Mini Kit (Qiagen, USA); the RNA isolationfrom goat PNCB was conducted by using Total RNA mini Kit (A & A Biotechnology, POLAND)

treatment_protocol: MSC and FMC was protected with Qiazol reagent from the RNeasy Lipid Tissue Mini Kit Qiagen (Qiagen, USA); Blood from vein was mixed with erythrocyte lysis buffer RBCL and protected with fenozol from Total RNA mini Kit (A & A Biotechnology,POLAND)

tag: breed

value: Polish White

tag: Sex

value: female

value: milk fat globules

source_name: common reference sample composed of 7 healthy goats

value: peripheral nuclear blood cells

value: Polish breeds (PWI=4 & PFI=3)

tag: lactation stage


title: milk fat globules Polish Fawn Improved goat_4

label_protocol: according to the manufacturer's protocol

value: Polish Fawn


title: milk fat globules Polish Fawn Improved goat_3


title: milk fat globules Polish White Improved goat_3


title: milk fat globules Polish Fawn Improved goat_1


title: peripheral nuclear cells blood Polish Fawn Improved goat_4

source_name: peripheral nuclear cells blood (PNCB)


title: milk fat globules Polish Fawn Improved goat_2


title: peripheral nuclear cells blood Polish Fawn Improved goat_1


title: AVR3

city: Bristol

first: Costanza

last: Emanueli

address: Research Floor Level 7, Bristol Royal Infirmary, Upper Maudlin Street

department: School of Clinical Science

country: United Kingdom

institute: Bristol Heart Institute, University of Bristol

description:
AVR3 global normalisation
AVR3 global normalisation

data_processing:
For the bioinformatics analyses, the processing setting were as follows: 1) detection scoring: miRNAs not detectable in all 3 samples or Ct ≥ 37 in at least 2 patients were not considered for future calculations; 2) average of inter-plate calibrator (UniSp3 IPC) was calculated for each run (representing one sample) and the median was subtracted to each miRNAs Ct; 3) expression of each miRNA was derived using the 2−ΔΔCT method. On the basis of these criteria, arrays data were inspected using the NormFinder algorithm to assess the variance in expression levels. The best normalizer was found to be the average of assays detected in all 3 AVR samples (global normalisation); therefore it was used to normalize the array.
Matrix non-normalized worksheet reports CT value

label: SYBR

source_name: Pericardial fluid (PF)

label_protocol: Total RNA was converted to cDNA using a reverse transcription kit (Universal cDNA Synthesis Kit, Exiqon, Woburn, MA) following the Manufacturer’s instructions. Three (unpooled) PF samples of the AVR surgical patients’ groups were randomly selected to be run in a PCR-based miRNA array enabling the profiling of 752 human miRNAs (miRNACURY LNA™ microRNA polymerase chain reaction (PCR) human panels I and II (version 3, Exiqon). The miRNA array plates were run using a LightCycler 480 (Roche) with 95˚C, 10 min and  45 amplifi cation cycles at 95˚C, 10 s 60˚C, 1 min

extract_protocol: Total RNA was extracted using the miRNeasy (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: PF was centrifuged at 13,500 g for 15min at RT. Total RNA was extracted from 200uLof platelet-poor PF.

tag: subject status

value: patient undergoing aortic valve replacement (AVR) surgery

tag: subject id

value: Patient number 3

tag: sample type

value: pericardial fluid (PF)


title: peripheral nuclear cells blood Polish Fawn Improved goat_2


title: AVR2

description:
AVR2 global normalisation
AVR2 global normalisation

value: Patient number 2


title: AVR1

description:
AVR1 global normalisation
AVR1 global normalisation

value: Patient number 1


title: peripheral nuclear cells blood Polish Fawn Improved goat_3


title: peripheral nuclear cells blood Polish White Improved goat_3


title: milk fat globules Polish White Improved goat_4


title: milk fat globules Polish White Improved goat_1


title: milk somatic cells Polish Fawn Improved goat_3

source_name: milk somatic cells (MSC)

value: milk somatic cells


title: peripheral nuclear cells blood Polish White Improved goat_2


title: milk somatic cells Polish White Improved goat_3


title: milk somatic cells Polish Fawn Improved goat_1


title: peripheral nuclear cells blood Polish White Improved goat_4


title: milk somatic cells Polish Fawn Improved goat_4


title: milk somatic cells Polish White Improved goat_2


title: milk somatic cells Polish Fawn Improved goat_2


title: milk somatic cells Polish White Improved goat_4


title: peripheral nuclear cells blood Polish White Improved goat_1


title: milk somatic cells Polish White Improved goat_1


title: TM-MSC_rep1

status: Public on Jun 09 2017

city: Singapore

first: Padmapriya

last: Sathiyanathan

address: Genome, 60 Biopolis Street

department: Stem Cell & Regenerative Biology

country: Singapore

institute: Genome Institute of Singapore

description:
Replicate 1
SAMPLE 10

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: Biotin

source_name: TM-MSC

label_protocol: RNA was amplified using the Ambion TotalPrep RNA amplication kit into biotinylated cRNA

extract_protocol: Total RNA was extracted with Trizol reagent, followed by purification and DNase I treatment with the Qiagen RNeasy miniprep kit according to the manufacturer's instructions.

value: Cultured cells

tag: cell type

value: trabecular meshwork-derived mesenchymal stem cells


title: TM_rep2

description:
Replicate 2
SAMPLE 2

source_name: Trabecular meshwork

value: Tissue

value: Trabecular meshwork


title: TM-MSC_rep3

description:
Replicate 3
SAMPLE 12


title: Cornea_rep3

description:
Replicate 3
SAMPLE 6

source_name: Cornea

value: Cornea


title: Cornea_rep1

description:
Replicate 1
SAMPLE 4


title: Sclera_rep3

description:
Replicate 3
SAMPLE 9

source_name: Sclera

value: Sclera


title: TM_rep3

description:
Replicate 3
SAMPLE 3


title: Sclera_rep1

description:
Replicate 1
SAMPLE 7


title: Cornea_rep2

description:
Replicate 2
SAMPLE 5


title: Sclera_rep2

description:
Replicate 2
SAMPLE 8


title: TM-MSC_rep2

description:
Replicate 2
SAMPLE 11


title: TM_rep1

description:
Replicate 1
SAMPLE 1


title: ccRCC [G3_644]

type: genomic

city: Rostock

first: Dirk

last: Koczan

address: Schillingallee 70

department: Institute for Immunology

country: Germany

institute: University of Rostock

description: Hybridized to Genome-Wide Human SNP 6.0 Array

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). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Genotyping Console 4.2.0. and Birdseed algoritm and Affymetrix Copy Number Analysis Tool (CNAT) softwares using default values.

molecule: genomic DNA

source_name: clear cell renal cell carcinoma tissue

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Tissue samples were taken immediately after resection of the kidney and cryoconserved in liquid nitrogen.

extract_protocol: About 30 mg tissue was disrupted using mortar and pestle immersed in liquid nitrogen. Genomic DNA was extracted with the QIAamp® DNA Mini Kit (Qiagen, Hilden) according to the manufacturers protocol.

tag: tumour grading


title: ccRCC [G3_362]


title: ccRCC [G3_541]


title: ccRCC [G3_593]


title: ccRCC [G3_65]


title: ccRCC [G3_713]


title: ccRCC [G3_138]


title: ccRCC [G3_576]


title: ccRCC [G3_537]


title: ccRCC [G2_48]


title: ccRCC [G3_531]


title: ccRCC [G3_563]


title: ccRCC [G3_39]


title: ccRCC [G3_287]


title: ccRCC [G3_241]


title: ccRCC [G1_365]


title: ccRCC [G3_457]


title: ccRCC [G3_21]


title: ccRCC [G3_603]


title: ccRCC [G1_346]


title: ccRCC [G3_183]


title: ccRCC [G3_30]


title: ccRCC [G2_37]


title: ccRCC [G1_327]


title: ccRCC [G1_34]


title: ccRCC [G1_94]


title: ccRCC [G3_526]


title: ccRCC [G1_359]


title: ccRCC [G1_326]


title: genomic DNA from purified CD19+ B cells TJITB121

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

country: Spain

institute: Vall d'Hebron Hospital Research Institute

description: Positively selected CD19+ B cells from healthy individual

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to  Illumina HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy3 and Cy5

source_name: healthy control sample 72

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted  from purified CD19+ B cells using Qiagen DNeasy Kit according to standard instructions

tag: disease state

value: Healthy Control


title: genomic DNA from purified CD19+ B cells TJITB119

source_name: healthy control sample 70


title: genomic DNA from purified CD19+ B cells TJITB116

source_name: healthy control sample 68


title: genomic DNA from purified CD19+ B cells TJITB115

description: Positively selected CD19+ B cells from rheumatoid arthritis patient

source_name: rheumatoid arthritis sample 48

value: Rheumatoid Arthritis


title: genomic DNA from purified CD19+ B cells TJITB1

source_name: rheumatoid arthritis sample 1


title: genomic DNA from purified CD19+ B cells TJITB118

source_name: healthy control sample 69


title: genomic DNA from purified CD19+ B cells TJITB122

source_name: healthy control sample 73


title: genomic DNA from purified CD19+ B cells TJITB120

source_name: healthy control sample 71


title: ccRCC [G1_320]


title: genomic DNA from purified CD19+ B cells TJITB114

source_name: healthy control sample 67


title: ccRCC [G1_357]


title: ccRCC [G1_22]


title: genomic DNA from purified CD19+ B cells TJITB117

source_name: rheumatoid arthritis sample 49


title: ccRCC [G1_301]


title: ccRCC [G1_294]


title: ccRCC [G1_185]


title: genomic DNA from purified CD19+ B cells TJITB112

source_name: healthy control sample 66


title: ccRCC [G1_290]


title: genomic DNA from purified CD19+ B cells TJITB113

source_name: rheumatoid arthritis sample 47


title: ccRCC [G1_286]


title: ccRCC [G1_321]


title: genomic DNA from purified CD19+ B cells TJITB111

source_name: healthy control sample 65


title: genomic DNA from purified CD19+ B cells TJITB106

source_name: rheumatoid arthritis sample 46


title: ccRCC [G1_196]


title: ccRCC [G1_262]


title: genomic DNA from purified CD19+ B cells TJITB105

source_name: rheumatoid arthritis sample 45


title: genomic DNA from purified CD19+ B cells TJITB109

source_name: healthy control sample 63


title: genomic DNA from purified CD19+ B cells TJITB107

source_name: healthy control sample 61


title: ccRCC [G1_111]

source_name: clear cell renal cell carcinoma tissue


title: ccRCC [G1_288]


title: genomic DNA from purified CD19+ B cells TJITB104

source_name: rheumatoid arthritis sample 44


title: genomic DNA from purified CD19+ B cells TJITB110

source_name: healthy control sample 64


title: ccRCC [G1_101]


title: ccRCC [G1_267]


title: genomic DNA from purified CD19+ B cells TJITB101

source_name: rheumatoid arthritis sample 41


title: genomic DNA from purified CD19+ B cells TJITB103

source_name: rheumatoid arthritis sample 43


title: genomic DNA from purified CD19+ B cells TJITB108

source_name: healthy control sample 62


title: ccRCC [G1_142]


title: genomic DNA from purified CD19+ B cells TJITB102

source_name: rheumatoid arthritis sample 42


title: genomic DNA from purified CD19+ B cells TJITB99

source_name: healthy control sample 59


title: Tumor-3x8Gy-24hrs-3

city: New York

first: Sandra

last: Demaria

state: New York

address: 1300 York avenue, Room A-279

department: Radiation Oncology

country: USA

institute: Weill Cornell Medicine

hyb_protocol: Purified cRNA was fragmented to uniform size and applied to Agilent Mouse Gene Expression 4x44 v2 Microarray (Agilent Technologies, design ID 026655) in hybridization buffer. Arrays were hybridized at 37° C for 18 hrs. in a rotating incubator.

scan_protocol: Arrays were scanned on an Agilent G2505B Microarray Scanner

data_processing: All arrays were processed with Agilent Feature Extraction software and data was analyzed with GeneSpring GX software (Agilent Technologies).

organism: Mus musculus

source_name: TSA mammary tumor

label_protocol: Total RNA was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence.  After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer as indicated for Total RNA analysis.

extract_protocol: Total RNA was extracted after homogenization of the sample using miRNeasy Mini kit (Qiagen) according to the manufacturer's protocol.

value: mammary tumor


title: genomic DNA from purified CD19+ B cells TJITB97

source_name: healthy control sample 57


title: genomic DNA from purified CD19+ B cells TJITB98

source_name: healthy control sample 58


title: genomic DNA from purified CD19+ B cells TJITB96

source_name: healthy control sample 56


title: Tumor-20Gy-24hrs-1


title: genomic DNA from purified CD19+ B cells TJITB94

source_name: rheumatoid arthritis sample 40


title: Tumor-20Gy-24hrs-3


title: Tumor-3x8Gy-24hrs-2


title: genomic DNA from purified CD19+ B cells TJITB95

source_name: healthy control sample 55


title: genomic DNA from purified CD19+ B cells TJITB92

source_name: rheumatoid arthritis sample 38


title: Tumor-20Gy-24hrs-2


title: genomic DNA from purified CD19+ B cells TJITB100

source_name: healthy control sample 60


title: Tumor-3x8Gy-24hrs-1


title: genomic DNA from purified CD19+ B cells TJITB91

source_name: rheumatoid arthritis sample 37


title: Tumor-0Gy-24hrs-2


title: Tumor-0Gy-24hrs-3


title: Tumor-20Gy-4hrs-3


title: genomic DNA from purified CD19+ B cells TJITB85

source_name: healthy control sample 51


title: Tumor-0Gy-24hrs-1


title: genomic DNA from purified CD19+ B cells TJITB89

source_name: rheumatoid arthritis sample 35


title: genomic DNA from purified CD19+ B cells TJITB88

source_name: healthy control sample 54


title: genomic DNA from purified CD19+ B cells TJITB86

source_name: healthy control sample 52


title: genomic DNA from purified CD19+ B cells TJITB90

source_name: rheumatoid arthritis sample 36


title: ccRCC [G1_140]

source_name: clear cell renal cell carcinoma tissue


title: Tumor-20Gy-4hrs-2


title: genomic DNA from purified CD19+ B cells TJITB84

source_name: healthy control sample 50


title: Tumor-20Gy-4hrs-1


title: genomic DNA from purified CD19+ B cells TJITB87

source_name: healthy control sample 53


title: genomic DNA from purified CD19+ B cells TJITB83

source_name: healthy control sample 49


title: genomic DNA from purified CD19+ B cells TJITB81

source_name: rheumatoid arthritis sample 33


title: Tumor-3x8Gy-4hrs-3

source_name: TSA mammary tumor


title: Tumor-3x8Gy-4hrs-2


title: Tumor-3x8Gy-4hrs-1


title: genomic DNA from purified CD19+ B cells TJITB79

source_name: rheumatoid arthritis sample 31


title: genomic DNA from purified CD19+ B cells TJITB78

source_name: rheumatoid arthritis sample 30


title: genomic DNA from purified CD19+ B cells TJITB82

source_name: rheumatoid arthritis sample 34


title: genomic DNA from purified CD19+ B cells TJITB77

source_name: rheumatoid arthritis sample 29


title: genomic DNA from purified CD19+ B cells TJITB75

source_name: healthy control sample 47


title: genomic DNA from purified CD19+ B cells TJITB74

source_name: healthy control sample 46


title: genomic DNA from purified CD19+ B cells TJITB80

source_name: rheumatoid arthritis sample 32


title: Tumor-0Gy-4hrs-3


title: genomic DNA from purified CD19+ B cells TJITB93

source_name: rheumatoid arthritis sample 39


title: breast cancer, Tam, patient 133

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

description: Gene expression data of primary breast tumor

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Cel files were processed using the affy and rma R packages, available at www.bioconductor.org.

label: biotin

source_name: Snap frozen primary breast tumor

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted with RNABee (Campro, Veenendaal, the Netherlands) according to the manufacturer procedure

tag: response

value: PD


title: Tumor-0Gy-4hrs-1


title: breast cancer, Tam, patient 143


title: genomic DNA from purified CD19+ B cells TJITB73

source_name: healthy control sample 45


title: breast cancer, Tam, patient 124

value: SD


title: breast cancer, Tam, patient 126


title: Tumor-0Gy-4hrs-2


title: genomic DNA from purified CD19+ B cells TJITB76

source_name: healthy control sample 48


title: breast cancer, Tam, patient 123


title: genomic DNA from purified CD19+ B cells TJITB66

source_name: rheumatoid arthritis sample 25


title: breast cancer, Tam, patient 134


title: genomic DNA from purified CD19+ B cells TJITB70

source_name: healthy control sample 42


title: breast cancer, Tam, patient 125


title: genomic DNA from purified CD19+ B cells TJITB67

source_name: rheumatoid arthritis sample 26


title: genomic DNA from purified CD19+ B cells TJITB68

source_name: rheumatoid arthritis sample 27


title: breast cancer, Tam, patient 127


title: genomic DNA from purified CD19+ B cells TJITB64

source_name: rheumatoid arthritis sample 23


title: breast cancer, Tam, patient 128


title: genomic DNA from purified CD19+ B cells TJITB69

source_name: rheumatoid arthritis sample 28


title: genomic DNA from purified CD19+ B cells TJITB71

source_name: healthy control sample 43


title: breast cancer, Tam, patient 131


title: breast cancer, Tam, patient 129


title: genomic DNA from purified CD19+ B cells TJITB65

source_name: rheumatoid arthritis sample 24


title: breast cancer, Tam, patient 130


title: breast cancer, Tam, patient 132

value: PR


title: genomic DNA from purified CD19+ B cells TJITB62

source_name: healthy control sample 41


title: genomic DNA from purified CD19+ B cells TJITB63

source_name: rheumatoid arthritis sample 22


title: breast cancer, Tam, patient 113


title: breast cancer, Tam, patient 122


title: breast cancer, Tam, patient 111


title: genomic DNA from purified CD19+ B cells TJITB59

source_name: healthy control sample 38


title: breast cancer, Tam, patient 117


title: breast cancer, Tam, patient 120

value: CR


title: genomic DNA from purified CD19+ B cells TJITB57

source_name: healthy control sample 36


title: genomic DNA from purified CD19+ B cells TJITB60

source_name: healthy control sample 39


title: genomic DNA from purified CD19+ B cells TJITB61

source_name: healthy control sample 40


title: genomic DNA from purified CD19+ B cells TJITB58

source_name: healthy control sample 37


title: breast cancer, Tam, patient 121

source_name: Snap frozen primary breast tumor


title: breast cancer, Tam, patient 110


title: breast cancer, Tam, patient 107


title: genomic DNA from purified CD19+ B cells TJITB55

source_name: healthy control sample 34


title: breast cancer, Tam, patient 115


title: genomic DNA from purified CD19+ B cells TJITB72

source_name: healthy control sample 44


title: breast cancer, Tam, patient 114


title: genomic DNA from purified CD19+ B cells TJITB56

source_name: healthy control sample 35


title: genomic DNA from purified CD19+ B cells TJITB52

source_name: rheumatoid arthritis sample 21


title: breast cancer, Tam, patient 100


title: genomic DNA from purified CD19+ B cells TJITB51

source_name: rheumatoid arthritis sample 20


title: genomic DNA from purified CD19+ B cells TJITB50

source_name: rheumatoid arthritis sample 19


title: breast cancer, Tam, patient 93


title: genomic DNA from purified CD19+ B cells TJITB48

source_name: rheumatoid arthritis sample 17


title: genomic DNA from purified CD19+ B cells TJITB53

source_name: healthy control sample 32


title: genomic DNA from purified CD19+ B cells TJITB54

source_name: healthy control sample 33


title: genomic DNA from purified CD19+ B cells TJITB49

source_name: rheumatoid arthritis sample 18


title: breast cancer, Tam, patient 99


title: genomic DNA from purified CD19+ B cells TJITB45

source_name: healthy control sample 29


title: ccRCC [G1_269]

source_name: clear cell renal cell carcinoma tissue


title: breast cancer, Tam, patient 97


title: genomic DNA from purified CD19+ B cells TJITB47

source_name: healthy control sample 31


title: genomic DNA from purified CD19+ B cells TJITB41

source_name: healthy control sample 25


title: genomic DNA from purified CD19+ B cells TJITB42

source_name: healthy control sample 26


title: genomic DNA from purified CD19+ B cells TJITB44

source_name: healthy control sample 28


title: genomic DNA from purified CD19+ B cells TJITB43

source_name: healthy control sample 27


title: genomic DNA from purified CD19+ B cells TJITB46

source_name: healthy control sample 30


title: breast cancer, Tam, patient 95

source_name: Snap frozen primary breast tumor


title: breast cancer, Tam, patient 91


title: breast cancer, Tam, patient 92


title: breast cancer, Tam, patient 101


title: ccRCC [G1_293]


title: breast cancer, Tam, patient 76


title: breast cancer, Tam, patient 94


title: breast cancer, Tam, patient 88


title: breast cancer, Tam, patient 85


title: genomic DNA from purified CD19+ B cells TJITB35

source_name: rheumatoid arthritis sample 15


title: breast cancer, Tam, patient 77


title: breast cancer, Tam, patient 89


title: breast cancer, Tam, patient 84


title: breast cancer, Tam, patient 86


title: genomic DNA from purified CD19+ B cells TJITB38

source_name: healthy control sample 22


title: breast cancer, Tam, patient 21

description: Gene expression data of primary breast tumor, M1

data_processing: Cel files were processed using the affy and frma R packages, available at www.bioconductor.org using median polish as summarize setting in fRMA.


title: genomic DNA from purified CD19+ B cells TJITB34

source_name: rheumatoid arthritis sample 14


title: breast cancer, Tam, patient 62


title: genomic DNA from purified CD19+ B cells TJITB40

source_name: healthy control sample 24


title: breast cancer, Tam, patient 80


title: breast cancer, Tam, patient 82


title: genomic DNA from purified CD19+ B cells TJITB32

source_name: rheumatoid arthritis sample 12


title: genomic DNA from purified CD19+ B cells TJITB36

source_name: rheumatoid arthritis sample 16


title: breast cancer, Tam, patient 17


title: genomic DNA from purified CD19+ B cells TJITB33

source_name: rheumatoid arthritis sample 13


title: genomic DNA from purified CD19+ B cells TJITB29

source_name: rheumatoid arthritis sample 9


title: breast cancer, Tam, patient 83


title: genomic DNA from purified CD19+ B cells TJITB31

source_name: rheumatoid arthritis sample 11


title: genomic DNA from purified CD19+ B cells TJITB39

source_name: healthy control sample 23


title: genomic DNA from purified CD19+ B cells TJITB28

source_name: rheumatoid arthritis sample 8


title: breast cancer, Tam, patient 108


title: breast cancer, Tam, patient 74


title: breast cancer, Tam, patient 109


title: breast cancer, Tam, patient 69


title: genomic DNA from purified CD19+ B cells TJITB27

source_name: healthy control sample 20


title: breast cancer, Tam, patient 67


title: genomic DNA from purified CD19+ B cells TJITB26

source_name: healthy control sample 19


title: breast cancer, Tam, patient 78


title: genomic DNA from purified CD19+ B cells TJITB37

source_name: healthy control sample 21


title: genomic DNA from purified CD19+ B cells TJITB30

source_name: rheumatoid arthritis sample 10


title: breast cancer, Tam, patient 73


title: genomic DNA from purified CD19+ B cells TJITB24

source_name: healthy control sample 17


title: breast cancer, Tam, patient 64

source_name: Snap frozen primary breast tumor


title: genomic DNA from purified CD19+ B cells TJITB21

source_name: healthy control sample 14


title: genomic DNA from purified CD19+ B cells TJITB23

source_name: healthy control sample 16


title: genomic DNA from purified CD19+ B cells TJITB25

source_name: healthy control sample 18


title: genomic DNA from purified CD19+ B cells TJITB19

source_name: healthy control sample 12


title: breast cancer, Tam, patient 63


title: genomic DNA from purified CD19+ B cells TJITB20

source_name: healthy control sample 13


title: genomic DNA from purified CD19+ B cells TJITB18

source_name: healthy control sample 11


title: breast cancer, Tam, patient 75


title: genomic DNA from purified CD19+ B cells TJITB22

source_name: healthy control sample 15


title: genomic DNA from purified CD19+ B cells TJITB17

source_name: rheumatoid arthritis sample 7


title: breast cancer, Tam, patient 44


title: genomic DNA from purified CD19+ B cells TJITB16

source_name: rheumatoid arthritis sample 6


title: breast cancer, Tam, patient 71


title: breast cancer, Tam, patient 19


title: breast cancer, Tam, patient 25


title: breast cancer, Tam, patient 65


title: breast cancer, Tam, patient 66


title: breast cancer, Tam, patient 68


title: genomic DNA from purified CD19+ B cells TJITB12

source_name: healthy control sample 8


title: genomic DNA from purified CD19+ B cells TJITB11

source_name: healthy control sample 7


title: genomic DNA from purified CD19+ B cells TJITB15

source_name: rheumatoid arthritis sample 5


title: genomic DNA from purified CD19+ B cells TJITB13

source_name: healthy control sample 9


title: breast cancer, Tam, patient 57


title: genomic DNA from purified CD19+ B cells TJITB14

source_name: healthy control sample 10


title: breast cancer, Tam, patient 40


title: breast cancer, Tam, patient 61


title: breast cancer, Tam, patient 41


title: breast cancer, Tam, patient 43


title: breast cancer, Tam, patient 32


title: breast cancer, Tam, patient 5


title: breast cancer, Tam, patient 35


title: genomic DNA from purified CD19+ B cells TJITB7

source_name: healthy control sample 3


title: genomic DNA from purified CD19+ B cells TJITB5

source_name: healthy control sample 1


title: genomic DNA from purified CD19+ B cells TJITB4

source_name: rheumatoid arthritis sample 4


title: breast cancer, Tam, patient 11

source_name: Snap frozen primary breast tumor


title: breast cancer, Tam, patient 2


title: genomic DNA from purified CD19+ B cells TJITB6

source_name: healthy control sample 2


title: genomic DNA from purified CD19+ B cells TJITB9

source_name: healthy control sample 5


title: breast cancer, Tam, patient 45


title: genomic DNA from purified CD19+ B cells TJITB10

source_name: healthy control sample 6


title: genomic DNA from purified CD19+ B cells TJITB8

source_name: healthy control sample 4


title: post genomic DNA from whole blood of C7

city: Tokushima

first: Kensei

last: Nishida

state: Tokushima

address: 3-18-15 Kuramoto-cho

institute: Tokushima University Graduate school

description: post-intervention, LcS

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

data_processing: Illumina® GenomeStudio V2011.1

label: Cy5 and Cy3

source_name: whole blood

extract_protocol: genomic DNA was extracted and purified from whole blood samples using Qiagen DNeasy Kit according to standard instructions

value: Female

tag: condition

value: post-intervention

tag: intervention

value: LcS


title: breast cancer, Tam, patient 52


title: breast cancer, Tam, patient 6


title: breast cancer, Tam, patient 53


title: genomic DNA from purified CD19+ B cells TJITB3

source_name: rheumatoid arthritis sample 3


title: breast cancer, Tam, patient 50


title: breast cancer, Tam, patient 49


title: breast cancer, Tam, patient 24


title: post genomic DNA from whole blood of C3

description: post-intervention, LcS

tag: gender


title: post genomic DNA from whole blood of C12

description: post-intervention, LcS


title: post genomic DNA from whole blood of C10

description: post-intervention, LcS


title: breast cancer, Tam, patient 22


title: post genomic DNA from whole blood of C6

description: post-intervention, LcS


title: post genomic DNA from whole blood of C11

description: post-intervention, LcS


title: breast cancer, Tam, patient 51


title: post genomic DNA from whole blood of C5

description: post-intervention, LcS


title: genomic DNA from purified CD19+ B cells TJITB2

source_name: rheumatoid arthritis sample 2


title: breast cancer, Tam, patient 15


title: post genomic DNA from whole blood of C9

description: post-intervention, LcS


title: breast cancer, Tam, patient 54


title: post genomic DNA from whole blood of C2

description: post-intervention, LcS


title: breast cancer, Tam, patient 8


title: post genomic DNA from whole blood of C1

description: post-intervention, LcS


title: breast cancer, Tam, patient 9


title: MKN45T_MKN45

city: Tokyo

first: Takashi

last: Kobunai

address: 1-2-4, Uchikanda, Chiyoda-ku

institute: Taiho Pharmaceutical Co., Ltd.

hyb_protocol: The labeled DNA was hybridized to the Agilent Human Genome CGH Microarray Kit 244K and processed according to the manufacturer's protocol.

scan_protocol: Fluorescent array images were acquired with an Agilent DNA microarray scanner.

data_processing: The log2 ratios were corrected for the GC content wave effect using 1 Mb windows for genome GC content. Outliers were smoothed and the normalized log2 ratios were segmented using circular binary segmentation analysis.

source_name: gastric cancer cell line MKN45T (5-FU resistant)

label_protocol: The extracted DNA from MKN45 was labeled using an Agilent Genomic DNA Enzymatic Labeling Kit (Cy3-dUTP), while those DNA from MKN45T was labeled with Cy5-dUTP.

extract_protocol: Total DNA extacted using Qiagen DNA extraction kit.

tag: cell line

value: gastric cancer cell line

source_name: gastric cancer cell line MKN45 (parental)


title: post genomic DNA from whole blood of C4

description: post-intervention, LcS


title: pre genomic DNA from whole blood of C9

description: pre-intervention, LcS

value: pre-intervention


title: post genomic DNA from whole blood of C8

description: post-intervention, LcS


title: pre genomic DNA from whole blood of C10

description: pre-intervention, LcS


title: pre genomic DNA from whole blood of C12

description: pre-intervention, LcS


title: pre genomic DNA from whole blood of C11

description: pre-intervention, LcS


title: pre genomic DNA from whole blood of C8

description: pre-intervention, LcS


title: pre genomic DNA from whole blood of C6

description: pre-intervention, LcS


title: breast cancer, Tam, patient 4


title: breast cancer, Tam, patient 7


title: breast cancer, Tam, patient 1


title: breast cancer, Tam, patient 14


title: breast cancer, Tam, patient 149


title: pre genomic DNA from whole blood of C7

description: pre-intervention, LcS


title: pre genomic DNA from whole blood of C4

description: pre-intervention, LcS


title: breast cancer, Tam, patient 13


title: breast cancer, Tam, patient 47


title: pre genomic DNA from whole blood of C3

description: pre-intervention, LcS


title: breast cancer, Tam, patient 12


title: pre genomic DNA from whole blood of C2

description: pre-intervention, LcS


title: breast cancer, Tam, patient 3 replicate1


title: pre genomic DNA from whole blood of C5

description: pre-intervention, LcS


title: breast cancer, Tam, patient 150


title: breast cancer, Tam, patient 10


title: post genomic DNA from whole blood of A10

description: post-intervention, placebo

value: placebo


title: pre genomic DNA from whole blood of C1

description: pre-intervention, LcS


title: post genomic DNA from whole blood of A12

description: post-intervention, placebo


title: breast cancer, Tam, patient 20


title: breast cancer, Tam, patient 151


title: post genomic DNA from whole blood of A8

description: post-intervention, placebo


title: post genomic DNA from whole blood of A9

description: post-intervention, placebo


title: post genomic DNA from whole blood of A11

description: post-intervention, placebo


title: breast cancer, Tam, patient 27


title: breast cancer, Tam, patient 18


title: post genomic DNA from whole blood of A5

description: post-intervention, placebo


title: 26c

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: ES_11_48297_14t_slide543_S01_CGH_107_Sep09

hyb_protocol: Labeled DNA was hybridized to Agilent 1M CGH arrays for 40 hours at 60°C.

scan_protocol: After washing, the slides were scanned and images quantified using Feature Extraction 9.1 (Agilent).

data_processing:
The aCGH data were first processed using a normalization procedure to correct for block, row, column or intensity effects as well as any artifact such as dependence of log-ratios on the genomic GC content. The normalized data were then segmented using the Circular Binary Segmentation algorithm (CBS) to compute copy number regions and alterations. The RAE method is then used to analyze cohort-wide CNAs in the tumor samples and assigns a copy number status (diploid, gain, loss) to all contiguous regions in each sample of the genome [Taylor BS, Barretina J, Socci ND, Decarolis P, Ladanyi M, Meyerson M, Singer S, Sander C. Functional copy-number alterations in cancer. PLoS One 2008;3:e3179.] The 'GeneMatrix.txt' is obtained by assigning a copy number status to genes in the regions.
The sample data table contains normalized data included in the LogRatio column (in *GCNormV4b.txt file). The normalized data were generated using both the genomic artificial models and lowess normalization method, which are described at http://cbio.mskcc.org/CGCC/

source_name: retroperitoneal metastasis

label_protocol: 3 mg of DNA was then heat-fragmented and labeled with the ULS Labeling V3.4 kit, according to the manufacturer’s instructions (Agilent).

extract_protocol: Genomic DNA from FFPE samples was extracted using the Agilent protocol for oligonucleotide array-based CGH for genomic DNA analysis. DNA integrity was verified on a 1% agarose gel.

tag: patient id

tag: patient gender

value: male

tag: patient age at resection

value: retroperitoneal metastasis

source_name: Roche Human Genomic DNA

value: reference

tag: reference dna info.

value: Roche catalog. 11691112001


title: 20

source_name: lymph node metastasis

tag: tissue

value: lymph node metastasis


title: 22

source_name: primary liver tumor

value: female

value: primary liver tumor


title: 26a


title: breast cancer, Tam, patient 46

value: PD


title: post genomic DNA from whole blood of A7

description: post-intervention, placebo


title: breast cancer, Tam, patient 28

value: SD


title: breast cancer, Tam, patient 26


title: breast cancer, Tam, patient 38


title: post genomic DNA from whole blood of A3

description: post-intervention, placebo


title: post genomic DNA from whole blood of A2

description: post-intervention, placebo


title: 25


title: pre genomic DNA from whole blood of A12

description: pre-intervention, placebo


title: post genomic DNA from whole blood of A6

description: post-intervention, placebo


title: 21b

source_name: recurrent liver tumor

value: recurrent liver tumor


title: 26b


title: 24


title: 23

description: MC_03_574_1_TM2_slide105_S01_CGH_107_Sep09


title: pre genomic DNA from whole blood of A11

description: pre-intervention, placebo


title: breast cancer, Tam, patient 29


title: post genomic DNA from whole blood of A4

description: post-intervention, placebo


title: breast cancer, Tam, patient 23


title: pre genomic DNA from whole blood of A9

description: pre-intervention, placebo


title: 17

description: ES_12_17135_12TC_slide544_S01_CGH_107_Sep09


title: 21a


title: breast cancer, Tam, patient 81


title: 15a


title: post genomic DNA from whole blood of A1

description: post-intervention, placebo


title: breast cancer, Tam, patient 16


title: breast cancer, Tam, patient 37


title: 19


title: pre genomic DNA from whole blood of A10

description: pre-intervention, placebo


title: 16b

description: ES_05_29058_14LN_slide558_S01_CGH_107_Sep09


title: breast cancer, Tam, patient 37 replicate


title: 16a

description: ES_02_42478_1TSC10_slide516_S01_CGH_107_Sep09


title: 18

description: ES_99_29783_1U1_slide515_S01_CGH_107_Sep09

source_name: peritoneal metastasis

value: peritoneal metastasis


title: 13


title: 15b

description: ES_03_14401_1T11_slide517_S01_CGH_107_Sep09


title: breast cancer, Tam, patient 33


title: breast cancer, Tam, patient 119 replicate


title: pre genomic DNA from whole blood of A8

description: pre-intervention, placebo

value: Female


title: 14b

description: MC_10_4006_31_1nl_slide125_S01_CGH_107_Sep09


title: pre genomic DNA from whole blood of A7

description: pre-intervention, placebo


title: pre genomic DNA from whole blood of A5

description: pre-intervention, placebo


title: pre genomic DNA from whole blood of A2

description: pre-intervention, placebo


title: 12


title: pre genomic DNA from whole blood of A6

description: pre-intervention, placebo


title: pre genomic DNA from whole blood of A1

description: pre-intervention, placebo


title: pre genomic DNA from whole blood of A4

description: pre-intervention, placebo


title: 14a

description: MC_10_4006_12_1nl_slide126_S01_CGH_107_Sep09


title: Adipocyte Culture N°10, Day 15

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

hyb_protocol: 600ng of labelled cRNA was then fragmented in the appropriate buffer (Agilent) for 30 min at 60°C before dilution (v/v) in hybridization buffer. Hybridizations were performed in a microarray hybridization oven (Agilent) overnight at 65°C, using two high-density oligonucleotide microarray slides.  Following hybridization, the slides were rinsed in gene expression wash buffers 1 and 2 (Agilent)

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits)

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09). Normalization and statistical analysis were performed using GeneSpring software (Agilent).

organism: Oncorhynchus mykiss

source_name: white adipose tissue

label_protocol: 150ng of total RNA from cells at different developmental stages (days 3, 8, 15 and 21) from four independent cultures was labelled with Cy3 according to the manufacturer’s instructions (Agilent). Briefly, RNA was first reverse transcribed, using a polydTT7 primer, Cy3 was incorporated by a T7 polymerase mediated transcription and excess dye was removed using an RNeasy kit (Quiagen). The level of dye incorporation was evaluated using a spectrophotometer (Nanodrop ND1000, LabTech).  and scanned at a 3 μm resolution using an Agilent G2505 microscanner.

growth_protocol: Rainbow trout (Oncorhynchus mykiss Walbaum 1792) weighting from 200 to 250 g were obtained from the “Truites del Segre” fish farm (Lleida, Spain). Fish were acclimatized to a 12 h light:12 h dark photoperiod and 14 ± 1°C in a closed circuit flow system located in the Faculty of Biology at the University of Barcelona. Fish were fed daily ad libitum on a commercial diet based on fishmeal and fish oil (Dibaq Diproteg, Segovia, Spain). All animal handling procedures were approved by the Ethics and Animal Care Committee of the University of Barcelona, following the regulations and procedures established by the EU, and by the Spanish and Catalan governments (permits reference numbers CEEA 237/12 and DAAM 6755).

extract_protocol: Total RNA from adipocyte cells was extracted using the TriReagent method (Ambion, Alcobendas, Spain) following the manufacturer’s recommendations. The quantity of isolated RNA was determined by spectrophotometry with a ND-2000 NanoDrop (Thermo Fisher Scientific, Alcobendas, Spain) and the quality was assessed using a Bionalyzer (Agilent).

treatment_protocol: Fish were fasted 24 h before the experiments. The animals were killed by a blow to the head under anesthesia (3-aminobenzoic acid ethyl ester, MS-222; 100 μg/ml), which was followed by immersion in 70% ethanol for 30 s to sterilize the external surfaces. Cells for each experiment were isolated from a pool of white adipose tissue of 6-7 fish and cultured as described elsewhere (Bouraoui et al., 2008). The use of pooled tissue minimizes fish-specific variation in the experimental measurements. Briefly, the dissected visceral fat tissue was washed with Krebs-HEPES buffer (pH 7.4) and was digested for 1 h with type II collagenase 130 UI/mL containing 1% bovine serum albumin in Krebs-HEPES buffer at 18°C. The resulting cell suspension was filtered (100 μm) and centrifuged at 700 g for 10 min and the pellet was treated with erythrocyte lysing buffer (0.154 M NH4Cl, 10 mM KHCO3, and 0.1 mM EDTA) for 5 min at room temperature. After washing, the cells were centrifuged again at 700 g for 10 min. The cell pellet was resuspended in growth medium, consisting on Leibovitz’s L-15 medium containing 10% fetal bovine serum, 2 mM L-glutamine and 1% antibiotic/antimycotic solution. Cells were counted, diluted, seeded in pretreated flasks or six-well plates (25 cm2 or 9.6 cm2/well respectively), with 1% gelatin at a density of 2·104 cells/cm2 and kept at 18°C. For each experimental condition either one flask (RNA extraction) or two wells pooled together (Western blot) were used. After confluence (day 8), cells were induced to differentiate by means of a growth medium supplemented with 10 μg/mL insulin, 0.5 mM 3-isobutyl-1-methylxanthine (IBMX), 0.25 μM dexamethasone and 10 μL/mL lipid mixture. Media were changed every 2 days during the whole procedure. Samples were collected at day 3 (mesenchymal stem cells), day 8 (proliferated cells), day 15 (committed preadipocytes) and day 21 (mature adipocytes).

tag: number of culture

tag: time-course


title: breast cancer, Tam, patient 103

source_name: Snap frozen primary breast tumor


title: pre genomic DNA from whole blood of A3

description: pre-intervention, placebo


title: breast cancer, Tam, patient 98


title: breast cancer, Tam, patient 42


title: breast cancer, Tam, patient 118 replicate


title: 10


title: breast cancer, Tam, patient 119


title: Adipocyte Culture N°10, Day 21


title: Adipocyte Culture N°10, Day 8


title: Adipocyte Culture N°9, Day 15


title: Adipocyte Culture N°10, Day 3


title: Adipocyte Culture N°9, Day 21


title: breast cancer, Tam, patient 112


title: 7


title: 11


title: Adipocyte Culture N°8, Day 21


title: 9a


title: Adipocyte Culture N°9, Day 3


title: breast cancer, Tam, patient 118


title: breast cancer, Tam, patient 105


title: breast cancer, Tam, patient 116 replicate


title: 9b

description: ES_04_18926_32LLN_slide518_S01_CGH_107_Sep09


title: breast cancer, Tam, patient 116


title: Adipocyte Culture N°8, Day 15


title: Small HRS cells of L1236

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
Unsupported Human Gene 1.0 ST Array CDF Files
HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

label_protocol: Samples were labelled with Encore biotin module (NuGEN) washed and stained using the HWS Kit (Affymetrix).

growth_protocol: RPMI + 10% FCS

extract_protocol: RNA was amplified using the One-direct-Kit from NuGEN applied for 500- 2000 microdissected cells

treatment_protocol: After washing in PBS, smears of the cell line suspensions were performed

value: Small HRS


title: Adipocyte Culture N°8, Day 8


title: Small HRS cells of L428


title: 6

description: ES_09_38637_22RS_slide561_S01_CGH_107_Sep09


title: Adipocyte Culture N°9, Day 8


title: breast cancer, Tam, patient 87


title: breast cancer, Tam, patient 102


title: Big HRS cells of L428

value: Big HRS


title: Big HRS cells of L1236


title: breast cancer, Tam, patient 90


title: 5


title: breast cancer, Tam, patient 106


title: Adipocyte Culture N°4, Day 21


title: 8


title: breast cancer, Tam, patient 96


title: Adipocyte Culture N°4, Day 15


title: breast cancer, Tam, patient 104


title: Adipocyte Culture N°8, Day 3


title: Adipocyte Culture N°4, Day 8


title: Adipocyte Culture N°4, Day 3


title: KoAdeL_0 vs KoAdeL_BS

city: A Coruña

first: Maria

last: Tomas-Carmona

address: As Xubias, 84

department: Microbiology Department

institute: Instituto de Investigación Biomédica de A Coruña (INIBIC) / Complexo Hospitalario Universitario de A Coruña (CHUAC)

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol.

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

organism: Acinetobacter baumannii ATCC 17978

source_name: mid exponential growth phase cultures

label_protocol: Two-color microarray-based prokaryote analysis Fair Play III Labeling v1.3 (Agilent)

growth_protocol: 50 ng of the Dnase-treated RNA was obtained from mid exponential growth phase cultures (optical density of 0.5 at 600 nm).

extract_protocol: RNA was isolated using hot phenol extraction and subjected to DNase I treatment (Invitrogen).  Next, the RNA was cleaned on an RNeasy column (Qiagen) following the manufacturer’s mini cleanup protocol

treatment_protocol: The cultures were treated with a bile salt mixture containing 50% each of cholic acid (CA) sodium salt and deoxycholic acid (DCA) sodium salt, at a final concentration of 0,5% (wt/vol), and incubated in a static culture until it reached an optical density of 0,5 (600nm) before samples were removed for RNA extraction.

tag: strain

value: KoAdeL

tag: absence (0) or presence (bs) of 0.5% bile salts

value: BS


title: breast cancer, Tam, patient 34


title: KoAdeL_BS vs KoAdeL_0


title: KoAdeB_BS vs KoAdeB_0 1

value: KoAdeB


title: 1c1

description: MC_10_7783_1_2U_slide297_S01_CGH_107_Sep09

value: male

tag: sample type


title: KoAdeB_0 vs KoAdeB_BS 2


title: breast cancer, Tam, patient 58


title: KoAdeB_BS vs KoAdeB_0 2


title: 4b

description: ES_09_40165_48U_slide560_S01_CGH_107_Sep09


title: breast cancer, Tam, patient 79


title: 3

description: ES_94_22212_34T_slide514_S01_CGH_107_Sep09


title: 1c2

description: MC_10_7783_18_add_slide298_S01_CGH_107_Sep09


title: breast cancer, Tam, patient 60

description: Gene expression data of primary breast tumor


title: breast cancer, Tam, patient 70


title: breast cancer, Tam, patient 72


title: ATCC_BS vs ATCC_0

value: ATCC


title: breast cancer, Tam, patient 59


title: ATCC_0 vs ATCC_BS 2


title: 1a

description: MC_03_574_1_T10_slide149_S01_CGH_107_Sep09

value: reference


title: ATCC_0 vs ATCC_BS 1


title: 4a

description: ES_08_38198_18TF_slide559_S01_CGH_107_Sep09

value: Roche catalog. 11691112001


title: 679N_(HTA-2_0)

city: Luxembourg

first: Arnaud

last: Muller

address: 84 Val Fleuri

department: DONC

country: Luxembourg

institute: LIH

hyb_protocol: Hybridation has been made using standard Affymetrix protocols.

scan_protocol: Scanning has been made using standard Affymetrix protocols.

data_processing:
Pre-processing of Affymetrix CEL-files was performed with Partek® Genomics Suite version 6.6 (Partek® GS) using the robust multi-chip analysis (RMA) algorithm, which performs background adjustment, quantile normalisation and probe summarisation {Irizarry, 2003 #2}. GC-content correction was used, as suggested by the default pipeline of Partek® GS. Gene level expression was estimated using mean of probe set log expression. Further analysis was performed in R/Bioconductor {Team, 2005 #3}.
probe group file: HTA-2_0.r1.pgf
meta-probeset file: HTA-2_0.na33.hg19.probeset.csv

source_name: adjacent-SCC

label_protocol: Labeling has been made using standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from biological samples using miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. RNA quantity was determined using the NanoDrop Spectrophotometer. RNA quality was checked using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Diegem, Belgium) and  only RNAs with a RIN number >7 were taken forward for microarray experiments.

tag: tissue type

value: Adjacent normal lung tissue

tag: Stage

value: I

tag: technology

value: Microarray


title: 679_(HTA-2_0)

source_name: tumor-SCC

value: Lung squamous cell carcinoma


title: 667N_(HTA-2_0)


title: 2

value: female

value: primary liver tumor


title: KoAdeL_0 vs KoAdeL_BS 1


title: KoAdeL_BS vs KoAdeB_BS


title: 1d

description: ES_12_9225_14LN_slide545_S01_CGH_107_Sep09

value: lymph node metastasis


title: ATCC_BS vs KoAdeB_BS


title: KoAdeB_BS vs KoAdeL_BS


title: breast cancer, Tam, patient 36

tag: response

value: SD


title: breast cancer, Tam, patient 30


title: breast cancer, Tam, patient 39


title: breast cancer, Tam, patient 56

value: PR


title: breast cancer, Tam, patient 31


title: breast cancer, Tam, patient 55 replicate


title: ATCC_BS vs KoAdeL_BS


title: KoAdeB_BS vs ATCC_BS


title: 405N_(HTA-2_0)


title: MCF10A_48h_nonspecific stapled-Peptide

first: Tetsuro

last: Yoshimaru

department: Institute for Genome Research

institute: Tokushima University

description: Gene expression after 48hr in non-specific stapled-peptide-treated MCF-10A cells

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 microL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to  Agilent SurePrint G3 Human Gene Expression 8x60K v2 arrays (G4851B, Design ID 039494) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then immediately put the slides with Agilent barcode facing up in a slide holder with an ozone-barrier slide cover on top of the array.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MCF-10A cells, 48hr, non-specific Stapled-Peptide

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by NucleoSpin RNA II system (Takara-Clontech). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Samples were thawed on ice and mixed by repeat pipet disruption with 70% ethanol according to the procedure described in the technical protocol of the NucleoSpin RNA II system (Takara-Clontech), which was used for subsequent purification according to the manufacturer instructions. This included an on-column DNase digestion. The total RNAs were eluted once with 50 µL of RNase-free water.

treatment_protocol: MCF-10A cells were seeded in 6-well plates (3 × 10^5 cells/mL) in MEBM (Lonza) supplemented with SingleQuots Kit (BPE, hydrocortisone, hEGF, insulin, and gentamicin/amphotericin-B) and 100 ng/mL choleratoxin.  Forty-eight hours later, the cells were treated with 10 microM stapled-peptide or unspecific stapled-peptide for 24 hr or 48 hr at 37 ºC in a humidified incubator with 5% CO2..

value: MCF-10A  breast epithelial cell line

tag: treatment

value: control

tag: time


title: KoAdeL_BS vs ATCC_BS

value: KoAdeL

value: BS


title: breast cancer, Tam, patient 140


title: breast cancer, Tam, patient 142

value: PD


title: breast cancer, Tam, patient 139

value: CR


title: MCF10A_24h_stapled-Peptide

description: Gene expression after 24hr in stapled-peptide-treated MCF-10A cells

source_name: MCF-10A cells, 24hr, stapled-Peptide

tag: cell line

value: stapled-Peptide


title: 449_(HTA-2_0)


title: breast cancer, Tam, patient 55


title: breast cancer, Tam, patient 136 replicate


title: breast cancer, Tam, patient 141


title: 1b

description: ES_04_38025_11U_slide557_S01_CGH_107_Sep09

tag: patient id

value: male

value: recurrent liver tumor

value: reference

value: Roche catalog. 11691112001


title: breast cancer, Tam, patient 137


title: MCF10A_48h_stapled-Peptide

description: Gene expression after 48hr in stapled-peptide-treated MCF-10A cells

source_name: MCF-10A cells, 48hr, stapled-Peptide


title: breast cancer, Tam, patient 136


title: breast cancer, Tam, patient 137 replicate


title: breast cancer, Tam, patient 135


title: breast cancer, Tam, patient 48


title: breast cancer, Tam, patient 143 replicate3


title: breast cancer, Tam, patient 138


title: breast cancer, Tam, patient 133 replicate


title: 405_(HTA-2_0)

value: Lung squamous cell carcinoma

value: Microarray


title: breast cancer, Tam, patient 132 replicate


title: breast cancer, Tam, patient 135 replicate


title: 667_(HTA-2_0)


title: breast cancer, Tam, patient 143 replicate2


title: breast cancer, Tam, patient 143 replicate5


title: breast cancer, Tam, patient 143 replicate4


title: 450N_(HTA-2_0)

value: Adjacent normal lung tissue

value: I


title: breast cancer, Tam, patient 146


title: breast cancer, Tam, patient 155

value: SD


title: MCF10A_24h_nonspecific stapled-Peptide

description: Gene expression after 24hr in non-specific stapled-peptide-treated MCF-10A cells

source_name: MCF-10A cells, 24hr, non-specific Stapled-Peptide


title: 327N_(HTA-2_0)


title: breast cancer, Tam, patient 144


title: breast cancer, Tam, patient 148


title: breast cancer, Tam, patient 3 replicate


title: 349_(HTA-2_0)


title: 450_(HTA-2_0)


title: breast cancer, Tam, patient 152

value: PR


title: breast cancer, Tam, patient 153


title: breast cancer, Tam, patient 3


title: 45 min incubation in egg white model medium at 45°C or 0 min incubation in egg white model medium

first: Florence

last: Baron

address: 65 rue de Saint Brieuc

institute: Agrocampus Ouest

description: Mean of 3 biological replicates and 2 technical replicates of S. Enteritidis exposed to egg-white model medium for 45min compared to a reference (0 min of incubation, i.e. S. Enteritidis washed with egg-white filtrate)

hyb_protocol: The microarray, containing 3971 ORFs (representing 94.4% of S. Enteritidis gene composition) (NC_011294.1), was designed using Agilent’s e-array software (https:\\earray.chem.agilent.com\earray\). The custom oligonucleotide microarray was manufactured by Agilent Technologies using an 8x15K format and included each probe in duplicate. Microarray hybridization and data analysis were performed by the Pasteur Institute (Transcriptome and Epigenome Platform PF2, Paris, France). S. Enteritidis exposed to egg-white model medium for 7, 25 and 45 min was compared to a reference (0 min of incubation, i.e. S. Enteritidis washed with egg-white filtrate). For each time point, three arrays were hybridized with three independent biological replicates in duplicate (giving three biological replicates and two technical replicates). Cy3 and Cy5 dye-swap design was included in order to reduce dye specific effects.

scan_protocol: Images of the microarrays were scanned using an Axon 4000a scanner (Axon, Instruments, CA, USA) and intensity data were extracted using the GenepixPro 6.1 software.

data_processing:
Raw microarray data were first normalized using the LOWESS (Locally Weighted Scatter Plot Smoother) regression option in the R software suite, version 2.10.1 (http://www.r-project.org/), to correct for dye-bias within the array, followed by median normalization to normalize across all arrays.
Changes in gene expression upon incubation in egg-white model medium compared to the control were recorded as log2 fold differences. Statistical significance was estimated with a moderated t-test using the LIMMA package (Smyth 2004) of the R software suite (version 2.10.1). The adjustment of raw p-values was then performed to account for multiple comparisons, using the method of Benjamini and Yekutieli (BY) (Benjamini and Yekutieli, 2001)
Genes that exhibited ≥2.0 fold changes in expression (with respect to the control) and P≤0.05 were considered as differentially regulated.

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: 0 min incubation in egg white model medium at 45°C or 45min incubation in egg white model medium at 45°C

label_protocol: The resultant total RNA (500 ng of each sample) was reverse transcribed and labeled using the SuperScriptTM Indirect cDNA Labeling System (Invitrogen, Life Technologies, Courtaboeuf, France) according to the protocol provided by the manufacturer, except that the hexamer solution was replaced with the pdN6 hexamer solution (Roche Diagnostics, Meylan, France).

extract_protocol: After incubation, cells were centrifuged at 10,000 x g at 4 °C for 5 min, pellets were immediately frozen in liquid nitrogen and stored at -80 °C. After defrosting on ice, cells were disrupted by treatment with TE (Tris-HCl 10 mM pH7, EDTA 1 mM) buffer, containing 20 mg/mL lysozyme, for 30 min at 37 °C followed by mechanical lysis with zirconium beads using a FastPrep-24 instrument (MP Biomedicals, Illkirch, France) with two cycles of 30 s at 30 Hz interspaced with 30 s cooling periods. Total RNA was then isolated by phenol-chloroform extraction. The evaluation of RNA quantity and quality was assessed spectrophotometrically by measuring the ultraviolet absorbance profile (NanoDrop, NanoDrop Technologies, Inc., Rockland, Wilmington, DE, USA) at 230, 260 and 280 nm. For the microarray experiment, additional analysis for RNA integrity was performed using a RNA 6000 Nano LabChip kit (2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA, USA; (Mueller et al., 2000). The RNA samples were then DNase treated using a DNA-free kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions. Quantification of the RNA and any contamination by proteins was again assessed using a NanoDrop ND-1000 and RNA integrity again confirmed using a 2100 Bioanalyzer.

treatment_protocol: After propagation in tryptic soy broth, bacterial suspensions were centrifuged at 5,600 x g and 15 °C for 7 min, and cells were washed three times with egg-white filtrate. The final pellet was resuspended in the original volume of egg-white filtrate and was used to inoculate egg-white model medium at a final concentration of 7.3 ± 0.2 log10 cfu/mL. Cells were incubated for 7, 25 or 45 min at 45 °C. Egg-white model medium was prepared with egg-white filtrate (Baron et al., 1997) supplemented by 10% egg-white.


title: breast cancer, Tam, patient 147


title: 449N_(HTA-2_0)


title: breast cancer, Tam, patient 145


title: 354_(HTA-2_0)


title: breast cancer, Tam, patient 143 replicate1


title: 7 min incubation in egg white model medium at 45°C or 0 min incubation in egg white model medium

description: Mean of 3 biological replicates and 2 technical replicates of S. Enteritidis exposed to egg-white model medium for 7 min compared to a reference (0 min of incubation, i.e. S. Enteritidis washed with egg-white filtrate)

source_name: 0 min incubation in egg white model medium at 45°C or 7 min incubation in egg white model medium at 45°C


title: Embryon 2 E11.5, left motoneurons, biological repeat 2

status: Public on Jun 08 2017

city: Lyon

first: joel

last: lachuer

address: 8 avenue rockefeller

institute: university Lyon1

description: gene expression of the left GFP+ pool collected from embryo 2

hyb_protocol: Following fragmentation, 15 µg of labeled cRNA were hybridized on GeneChip Mouse 430 2.0 Arrays (Affymetrix) following affymetrix protocol

scan_protocol: microarrays were scanned using the GeneChip scanner 3000 7G

data_processing: Data normalisation as performed using MAS5 protocol with Expression Console software (Affymetrix)

source_name: Motoneurons of the left cervical spinal cord

label_protocol: RNA were labeled with biotin usingusing BioArray HighYield RNA Transcript Labeling (ENZO)

growth_protocol: Embryos were collected from time pregant mouse

extract_protocol: Samples were microdissected using laser capture microdissection (Arturus PixCell II), RNA purification with RNAeasy microkit (Qiagen) and RNA amplified with ExpressArt mRNA amplification PICO kit (AmpTec, France)

treatment_protocol: Embryos were frozen in isopentane (-45°C) and cryo-sectioned (12um sections). Sections were collected on superfrost glass slides kept on dry ice and stored at -80°C. Sections were dehydrated (ethanol) and cleared (xylene) prior laser capture of the left and right GFP+ regions (PixCell II LCM system, Arcturus Engineerin).

tag: genotype

value: HB9::GFP transgenic mice

tag: age


title: Embryon 3 E11.5, right motoneurons, biological repeat 3

description: gene expression of the right GFP+ pool collected from embryo 3

source_name: Motoneurons of the right cervical spinal cord


title: 25 min incubation in egg white model medium at 45°C or 0 min incubation in egg white model medium

description: Mean of 3 biological replicates and 2 technical replicates of S. Enteritidis exposed to egg-white model medium for 25 min compared to a reference (0 min of incubation, i.e. S. Enteritidis washed with egg-white filtrate)

source_name: 0 min incubation in egg white model medium at 45°C or 25min incubation in egg white model medium at 45°C


title: breast cancer, Tam, patient 154


title: Embryon 3 E11.5, left motoneurons, biological repeat 3

description: gene expression of the left GFP+ pool collected from embryo 3

value: Motoneurons of the left cervical spinal cord


title: Embryon 2 E11.5, right motoneurons, biological repeat 2

description: gene expression of the right GFP+ pool collected from embryo 2

value: Motoneurons of the right cervical spinal cord


title: 349N_(HTA-2_0)


title: 354N_(HTA-2_0)


title: Embryon 1 E11.5, left motoneurons, biological repeat 1

description: gene expression of the left GFP+ pool collected from embryo 1


title: 328_(HTA-2_0)


title: iDC_M7015_vehicle_24h

city: Spring House

first: Alice

last: Walsh

state: PA

address: Welsh & McKean Roads

department: Immunology

institute: Janssen R&D

hyb_protocol: Microarray hybridization was performed on GeneChip Human Genome U133 Plus 2.0 Array according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data were normalized using Robust Multi-array Average (RMA) algorithm and log base 2 transformed using ArrayStudio (Omicsoft)

source_name: immature dendritic cells

label_protocol: Subject cDNA was amplified through utilization of the NuGEN Ovation Pico WTA System V2 (NuGEN, San Carlos, CA, USA).

growth_protocol: Monocytes from healthy donor peripheral blood were purified and cultured in complete RPMI media with 50ng/ml GM-CSF and 50ng/ml IL4 for 3 days; fresh media was added and culture continued until day 6.

extract_protocol: RNA was extracted from cell cultures with the Qiagen RNeasy Kit in 96-well plates.

treatment_protocol: On day 7, cells were stimulated with recombinant CD40L (1µg/ml, R&D systems, CAT#6420-CL-025) at 3x10^4 cells/well in 96-well plates for 1, 3 or 24hr before harvest for RNA extract.

tag: donor

tag: cell type

value: immature dendritic cells (iDC)

value: vehicle

tag: treatment time


title: iDC_M6807_sCD40L_24h


title: iDC_M7015_vehicle_1h


title: iDC_M6807_vehicle_24h


title: iDC_M6807_vehicle_3h


title: iDC_M7015_sCD40L_1h


title: iDC_M6807_sCD40L_1h


title: iDC_M7015_sCD40L_24h


title: iDC_M6807_sCD40L_3h


title: 327_(HTA-2_0)


title: iDC_M6801_vehicle_3h


title: iDC_M6807_vehicle_1h


title: iDC_M7015_vehicle_3h


title: 328N_(HTA-2_0)


title: iDC_M6801_sCD40L_1h


title: Embryon 1 E11.5 , right motoneurons, biological repeat 1

description: gene expression of the right GFP+ pool collected from embryo 1

tag: tissue


title: iDC_M5772_sCD40L_3h


title: iDC_M6801_vehicle_24h


title: iDC_M6801_sCD40L_3h


title: iDC_M5772_sCD40L_24h


title: iDC_M5772_vehicle_24h


title: iDC_M5772_sCD40L_1h


title: iDC_M5772_vehicle_1h


title: iDC_M6801_sCD40L_24h


title: iDC_M5137_sCD40L_1h


title: iDC_M5137_vehicle_24h


title: iDC_M5137_sCD40L_24h


title: Bcell_Donor6-SCD40L-3

data_processing: Data were normalized using Robust Multi-array Average (RMA) algorithm and log base 2 transformed using R/Bioconductor.

source_name: Naïve B cells purified from peripheral blood

growth_protocol: Naïve B cells were purified from healthy donor PBMC using negative selection beads (Miltenyi)

treatment_protocol: Naïve B cells were cultured with sCD40L at 2.5ug/ml for 6 hours.

value: naive B cells

tag: replicsate


title: iDC_M5137_vehicle_3h


title: Bcell_Donor6-SCD40L-2


title: iDC_M5772_vehicle_3h


title: Bcell_Donor6-NS-2

value: mock treated


title: iDC_M5137_vehicle_1h


title: Bcell_Donor6-SCD40L-1


title: Bcell_Donor5-SCD40L-1


title: Bcell_Donor5-SCD40L-3


title: iDC_M5137_sCD40L_3h


title: Bcell_Donor5-NS-4


title: Bcell_Donor6-NS-1


title: Bcell_Donor5-SCD40L-2


title: Bcell_Donor4-SCD40L-1


title: Bcell_Donor5-NS-3


title: Bcell_Donor5-NS-2


title: Bcell_Donor3-SCD40L-3


title: Bcell_Donor3-SCD40L-2


title: Bcell_Donor4-NS-2


title: Bcell_Donor4-SCD40L-2


title: Bcell_Donor4-NS-4


title: Bcell_Donor4-NS-3


title: Bcell_Donor4-NS-1


title: Bcell_Donor5-NS-1


title: Bcell_Donor3-SCD40L-1


title: Bcell_Donor4-SCD40L-3


title: Bcell_Donor3-NS-1


title: Bcell_Donor2-SCD40L-3


title: Bcell_Donor3-NS-4


title: Bcell_Donor3-NS-3


title: Bcell_Donor3-NS-2


title: Bcell_Donor2-NS-4


title: Bcell_Donor2-SCD40L-1


title: Bcell_Donor2-NS-2


title: Bcell_Donor1-SCD40L-2


title: SCLC_49

status: Public on Jun 07 2017

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Genome Studio V2011.2
processed data: Average Beta
raw data: Unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: Lung

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

tag: health state

value: cancer


title: Bcell_Donor2-NS-1


title: iDC_M7015_sCD40L_3h


title: Bcell_Donor1-SCD40L-3


title: SCLC_52


title: Bcell_Donor1-SCD40L-1


title: SCLC_51


title: SCLC_50


title: SCLC_56


title: Bcell_Donor2-NS-3


title: iDC_M6801_vehicle_1h


title: SCLC_55


title: Bcell_Donor1-NS-2


title: Bcell_Donor2-SCD40L-2


title: SCLC_54


title: SCLC_46


title: SCLC_45


title: Bcell_Donor1-NS-3


title: SCLC_44


title: SCLC_48


title: SCLC_53


title: SCLC_47


title: Bcell_Donor1-NS-1


title: SCLC_42


title: SCLC_40


title: Bcell_Donor1-NS-4


title: SCLC_39


title: SCLC_43


title: SCLC_38


title: SCLC_32


title: SCLC_37


title: SCLC_35


title: SCLC_26


title: SCLC_34


title: SCLC_33


title: Blood_16

source_name: Haematopoietic & Lymphoid

value: normal


title: Blood_19


title: Blood_15


title: Blood_9


title: Blood_13


title: Blood_12


title: SCLC_30


title: Blood_20


title: Blood_17


title: Blood_10


title: SCLC_28


title: SCLC_24


title: Blood_14


title: Blood_7


title: Blood_18


title: Blood_6


title: Blood_3


title: Blood_4


title: Blood_2


title: SCLC_27


title: SCLC_29


title: PC_10

source_name: Prostate


title: PC_17


title: PC_19


title: PC_15


title: PC_21


title: PC_11


title: PC_12


title: PC_9


title: PC_13


title: PC_23


title: PC_14


title: PC_20


title: PC_18


title: SCLC_31


title: SCLC_25


title: PC_8


title: PC_7


title: Blood_11


title: Blood_1


title: PC_6


title: SCLC_41


title: PC_24


title: PC_22


title: Blood_8


title: Blood_5


title: PC_16


title: PC_3


title: NB_18

source_name: Autonomic Ganglia


title: PC_25


title: Liver_8

source_name: Liver


title: PC_5


title: Liver_9


title: NB_15


title: NB_12


title: NB_8


title: NB_9


title: PC_2


title: NB_14


title: NB_16


title: Liver_6


title: NB_11


title: PC_1


title: NB_6


title: Liver_5


title: NB_17


title: Liver_7


title: NB_19


title: Liver_10


title: NB_10


title: NB_5


title: NB_3


title: NB_4


title: NB_2


title: LYMPH_23


title: LYMPH_18


title: NB_7


title: NB_13


title: NB_1


title: LYMPH_21


title: SCLC_22


title: PC_4


title: LC_222


title: LC_228


title: LYMPH_19


title: LYMPH_20


title: SCLC_23


title: LYMPH_22


title: LC_217


title: LC_225


title: LYMPH_17


title: LC_227


title: LC_226


title: LC_220


title: LC_224


title: LC_212


title: LC_219


title: LC_209


title: LC_213


title: LC_204


title: LC_215


title: LC_211


title: LC_221


title: LC_208


title: LC_216


title: LC_218


title: LC_223


title: LC_206


title: LC_210


title: LC_214


title: LC_207


title: LC_203


title: LC_205


title: LC_196


title: LC_200


title: LC_201


title: LC_192


title: LC_191


title: LC_199


title: LC_198


title: LC_187


title: LC_184


title: LC_193


title: LC_182


title: LC_202


title: LC_176


title: LC_177


title: LC_183


title: LC_197


title: LC_174


title: LC_173


title: LC_194


title: LC_195


title: LC_175


title: LC_172


title: LC_185


title: LC_188


title: LC_170


title: LC_186


title: LC_168


title: LC_166


title: LC_171


title: LC_189


title: LC_164


title: LC_163


title: LC_160


title: LC_159


title: LC_158


title: LC_180


title: LC_179


title: LC_181


title: LC_169


title: LC_153


title: LC_152


title: LC_151


title: LC_165


title: LC_167


title: LC_178


title: LC_190


title: LC_147


title: LC_145


title: LC_146


title: LC_162


title: LC_142


title: LC_140


title: LC_138


title: LC_132


title: LC_133


title: LC_157


title: LC_156


title: LC_131


title: LC_128


title: LC_129


title: LC_154


title: LC_149


title: LC_150


title: LC_143


title: LC_161


title: LC_124


title: LC_123


title: LC_144


title: LC_122


title: LC_137


title: LC_120


title: LC_139


title: LC_117


title: LC_148


title: LC_114


title: LC_115


title: LC_155


title: LC_113


title: LC_109


title: LC_134


title: LC_126


title: LC_106


title: LC_136


title: LC_102


title: LC_127


title: LC_125


title: LC_101


title: LC_110


title: LC_100


title: LC_130


title: LC_94


title: LC_118


title: LC_93


title: LC_135


title: LC_141


title: LC_121


title: LC_112


title: LC_119


title: LC_87


title: LC_111


title: LC_108


title: LC_116


title: LC_104


title: LC_86


title: LC_105


title: LC_79


title: LC_78


title: LC_75


title: LC_103


title: LC_73


title: LC_72


title: LC_97


title: LC_95


title: LC_107


title: LC_96


title: LC_91


title: LC_69


title: LC_90


title: LC_84


title: LC_98


title: LC_66


title: LC_92


title: LC_85


title: LC_61


title: LC_60


title: LC_58


title: LC_89


title: LC_88


title: LC_57


title: LC_82


title: LC_56


title: LC_80


title: LC_55


title: LC_83


title: LC_77


title: LC_52


title: LC_81


title: LC_68


title: LC_42


title: LC_67


title: LC_40


title: LC_74


title: LC_39


title: LC_38


title: LC_65


title: LC_36


title: LC_76


title: LC_34


title: LC_33


title: LC_70


title: LC_41


title: LC_32


title: LC_71


title: LC_31


title: LC_64


title: LC_62


title: LYMPH_16


title: LC_35


title: LC_54


title: CLL_41


title: SCLC_21


title: LC_50


title: LC_29


title: LC_63


title: LC_59


title: LC_51


title: LC_47


title: CLL_35


title: CLL_36


title: LC_44


title: LC_53


title: CLL_34


title: LC_46


title: CLL_33


title: LC_43


title: LC_48


title: CLL_31


title: CLL_39


title: CLL_32


title: LC_49


title: LC_45


title: CLL_29


title: LC_30


title: LYMPH_15


title: LC_28


title: LC_37


title: CLL_27


title: CLL_25


title: CLL_24


title: CLL_42


title: LC_27


title: CLL_23


title: CLL_37


title: CLL_30


title: LU990

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Illumina hybridization protocol

scan_protocol: Standard Illumina iScan scanning protocol; scan setting file: Direct Hyb

data_processing: The data were normalized using quantile normalisation implemented in BASE, http://base.thep.lu.se/

source_name: Lung tumor

extract_protocol: Total RNA from fresh frozen lung tumor tissue was extracted using the Qiagen AllPrep kit according to manufacturer's instructions. RNA concentrations were measured using a Nanodrop (NanoDrop Technologies). RNA integrity was determined by an Agilent Bioanalyzer.

tag: histology

value: SqCC

tag: Sex

value: M


title: LU976

value: AC

value: F


title: LU965


title: CLL_40


title: SCLC_36


title: SCLC_19


title: CLL_38


title: SCLC_18


title: LYMPH_14


title: CLL_26


title: CLL_28


title: LU983


title: LU968


title: LU867


title: LU998

value: LCNEC


title: SCLC_20


title: Grey_matter_5

source_name: Central Nervous System


title: Prostate_3


title: LU876


title: LU85


title: LU87


title: LYMPH_12


title: LU887


title: Prostate_4


title: LU835

value: LCC


title: LU987


title: LU859


title: LYMPH_9


title: Prostate_1


title: LU826


title: LYMPH_13


title: Prostate_2


title: LU851


title: LU866


title: LU856


title: LU821


title: LU800


title: LU847


title: Liver_2


title: LU818


title: LC_26


title: LC_24


title: LC_23


title: Prostate_5


title: LYMPH_10


title: LU788


title: LYMPH_11


title: Liver_3


title: Liver_4


title: LC_21


title: Liver_1


title: LYMPH_8


title: LU782


title: LU785


title: LU755


title: LC_19


title: LU820


title: LU797


title: LU804


title: LC_18


title: LU749


title: LU752


title: LU812


title: LU738


title: LU79


title: LYMPH_7


title: LU775


title: LC_11


title: LC_10


title: LC_22


title: LU773


title: LC_9


title: LU727


title: LU681


title: LU768


title: LC_25


title: LC_20


title: LC_5


title: LU673


title: LU672


title: LU667


title: LU745


title: LC_7


title: LC_14


title: LU648


title: LC_15


title: LC_13


title: LC_16


title: LU660


title: LU735


title: LC_12


title: LC_17


title: LYMPH_4


title: LYMPH_3


title: LU631


title: LU737


title: LC_8


title: LU616


title: LC_4


title: LC_6


title: LYMPH_5


title: LU709


title: LU605


title: LU717


title: LU704


title: LYMPH_6


title: LU583


title: LC_2


title: LC_1


title: LU716


title: LC_3


title: LU66


title: CLL_19


title: LU558


title: ALL_61


title: LU647


title: SCLC_15


title: LU635


title: LU627


title: LU641


title: LU500


title: Grey_matter_4


title: LU464


title: Grey_matter_2


title: SCLC_12


title: CLL_22


title: CLL_20


title: CLL_21


title: Grey_matter_3


title: SCLC_9


title: LU565


title: LU591


title: SCLC_17


title: SCLC_8


title: LU580


title: SCLC_6


title: Grey_matter_1


title: LU436


title: SCLC_5


title: LU546


title: SCLC_14


title: SCLC_11


title: SCLC_3


title: LU505


title: LU418


title: SCLC_10


title: LU411


title: SCLC_16


title: LU427


title: LU473


title: LU402

value: SCLC


title: LU460


title: LU468


title: LU492


title: SCLC_2


title: CLL_16


title: SCLC_7


title: LU444


title: LU400


title: CLL_17


title: LU485


title: LU510


title: CLL_12


title: SCLC_4


title: CLL_11


title: CLL_15


title: CLL_9


title: LU375


title: LU449


title: CLL_18


title: CLL_14


title: CLL_13


title: LU382


title: CLL_8


title: LU352


title: SCLC_1


title: LU434


title: LU332


title: CLL_5


title: LU387


title: LU328


title: LU398


title: LU318


title: CLL_10


title: CLL_2


title: LU376


title: ALL_60


title: LU370


title: CLL_6


title: CLL_7


title: CLL_4


title: SCLC_13


title: LU330


title: LU350


title: CLL_3


title: LU292


title: ALL_55


title: LU294


title: LU302


title: ALL_53


title: LU277


title: LU271


title: LU219


title: LU324


title: LU295


title: LU372


title: LU209


title: CLL_1


title: LU190


title: LU438


title: ALL_59


title: LU2


title: ALL_57


title: LU164


title: ALL_48


title: ALL_50


title: ALL_47


title: ALL_58


title: ALL_56


title: ALL_46


title: LU154


title: LU257


title: LU262


title: LU276


title: ALL_45


title: LU195


title: LYMPH_2


title: ALL_49


title: ALL_52


title: LU136


title: ALL_38


title: ALL_39


title: ALL_51


title: LU123


title: LU14


title: ALL_40


title: ALL_43


title: LU1170


title: LU143


title: LU1167


title: ALL_42


title: LU137


title: LU119


title: ALL_37


title: ALL_36


title: LU16


title: LU145


title: LU12


title: ALL_44


title: LU1157


title: ALL_41


title: LU1152


title: LU1162


title: ALL_33


title: ALL_32


title: ALL_34


title: LU1151


title: LYMPH_1


title: ALL_27


title: ALL_35


title: LU1153


title: ALL_31


title: ALL_25


title: ALL_28


title: ALL_30


title: ALL_29


title: LU1134


title: LU114


title: LU1121


title: LU1149


title: ALL_24


title: ALL_23


title: ALL_26


title: LU1124


title: LU1136


title: LU1138


title: LU1114


title: ALL_22


title: LU1115


title: LU1118


title: ALL_20


title: LU1117


title: ALL_21


title: ALL_19


title: LU1110


title: LU10


title: LU1163


title: ALL_17


title: ALL_16


title: LNCaP Insulin R1881 replicate 3

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

description: RNA from LNCaP cells treated with 10 nM insulin and 1 nM R1881 for 48 hours was hybridized to a custom 105K Agilent microarray.

hyb_protocol: Agilent Single Channel Gene Expression Hybridization Protocol

scan_protocol: Scanning was performed using Agilent High Resolution Microarray Scanner and feature extraction was performed using Agilent Feature Extraction software (version 10.5.1)

data_processing: The raw data were normalized using quantile between array normalization method in the bioconductor package, LIMMA (version 2.9.2).

source_name: LNCaP prostate cancer cell line

label_protocol: Agilent's Quick Amp Labelling Kit (Agilent) using 500 ng of total RNA according to manufacturer’s instructions.

growth_protocol: LNCaP cells were cultured in 5% FBS RPMI minus phenol red for 48hrs.

extract_protocol: TriReagent extraction of RNA.

treatment_protocol: Before a 48hr pre-incubation in 5% CSS RPMI, cells were treated for 24hr with either 1nM R1881 (Sigma) in CSS RPMI or equal volume 20% EtOH (vehicle), then in either serum free RPMI with R1881 or EtOH for 24hr. 10nM insulin was then added for 10hr.

tag: agent

value: 10 nM insulin + 1 nM R1881


title: LNCaP Insulin R1881 replicate 1


title: ALL_12


title: LU1113


title: LU1094


title: LNCaP R1881 replicate 2

description: RNA from LNCaP cells treated with 1 nM R1881 for 48 hours was hybridized to a custom 105K Agilent microarray.


title: LNCaP Insulin-EtOH replicate 1

description: RNA from LNCaP cells treated with 10 nM insulin for 48 hours was hybridized to a custom 105K Agilent microarray.

value: 10 nM insulin + EtOH


title: ALL_11


title: LNCaP R1881 replicate 1


title: ALL_54


title: LNCaP R1881 replicate 3


title: LNCaP Insulin R1881 replicate 2


title: ALL_18


title: ALL_13


title: LNCaP EtOH replicate 1

description: RNA from LNCaP cells treated with an ethanol vehicle control for 48 hours was hybridized to a custom 105K Agilent microarray.

value: EtOH vehicle control


title: ALL_7


title: LU1096


title: ALL_14


title: LU1084


title: ALL_15


title: ALL_5


title: LNCaP Insulin-EtOH replicate 2


title: LU101


title: LU1054


title: ALL_10


title: ALL_9


title: LU1020


title: LU1098


title: ALL_6


title: ALL_4


title: LU1074


title: LU1041


title: LU1080


title: ALL_2


title: LU1040


title: ALL_8


title: LU1090


title: LNCaP EtOH replicate 3


title: ALL_3


title: LU1068


title: LNCaP EtOH replicate 2


title: LU1089


title: ALL_1


title: replicate 2 KO run

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
gene expression data from HDAC4 knockout mouse after 2 weeks forced running exercise
KO_pos_1150

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

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of mouse430_2-type from Affymetrix. A Custom CDF Version 12 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: KO run

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

growth_protocol: Animals were running on a treadmill for 2x 5 days with age of 8 weeks

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

treatment_protocol: animals were sacrified at day 14 of treatment protocol and heart were collected in liquid nitrogen

tag: genotype/variation

value: KO

tag: protocol

value: exercise

value: heart


title: replicate 2 WT sham

description:
gene expression data from control mouse without running exercise
WT_neg_1186

source_name: WT sham

value: WT

value: without exercise


title: replicate 3 KO run

description:
gene expression data from HDAC4 knockout mouse after 2 weeks forced running exercise
KO_pos_1151


title: replicate 1 KO sham

description:
gene expression data from HDAC4 knockout mouse without running exercise
KO_neg_1177

source_name: KO sham


title: replicate 3 WT sham

description:
gene expression data from control mouse without running exercise
WT_neg_1187


title: NT2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: mSCC non transfected (Rep2)

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and differential analysis using Limma package in R / Bioconductor.

label_protocol: Agilent - Low RNA input QuickAmp

growth_protocol: mSCC-38 cells were grown in 35mm dishes DMEM medium supplemented with gutamine and 10% of FCII fetal calf serum.

extract_protocol: ARN were extracted in 800µl Qiazol + 170µl Chloroform and purified using miRNeasy minikit (Qiagen).

tag: amount in (µg)

tag: rin number

tag: transfection


title: replicate 1 WT sham

description:
gene expression data from control mouse without running exercise
WT_neg_1185


title: Si1AK-4

description: mSCC after a 72h treatment with Si1AK (rep4)

tag: cell line


title: NT4

description: mSCC non transfected (Rep4)


title: replicate 2 WT run

description:
gene expression data from control mouse after 2 weeks forced running exercise
WT_pos_1157

source_name: WT run


title: Si1AK-3

description: mSCC after a 72h treatment with Si1AK (rep3)


title: replicate 3 WT run

description:
gene expression data from control mouse after 2 weeks forced running exercise
WT_pos_1158


title: replicate 1 KO run

description:
gene expression data from HDAC4 knockout mouse after 2 weeks forced running exercise
KO_pos_1149


title: Si2AK-3

description: mSCC after a 72h treatment with Si2AK (rep3)


title: replicate 1 WT run

description:
gene expression data from control mouse after 2 weeks forced running exercise
WT_pos_1152


title: NC2

description: mSCC after a 72h treatment with control siRNA (Rep2)

value: control siRNA


title: replicate 2KO sham

description:
gene expression data from HDAC4 knockout mouse without running exercise
KO_neg_1178


title: Si2AK-1

description: mSCC after a 72h treatment with Si2AK (rep1)


title: NC3

description: mSCC after a 72h treatment with control siRNA (Rep3)


title: replicate 3 KO sham

description:
gene expression data from HDAC4 knockout mouse without running exercise
KO_neg_1179


title: SiC1

description: mSCC after a 72h treatment with control si RNA (Rep1)


title: NT1

description: mSCC non transfected (Rep1)


title: T3

description: RNA extracted from a biopsy of DMBA/TPA-induced tumor (sample T6)

extract_protocol: ARN were extracted from healthy skin and tumor biopsies in 800µl Qiazol + 170µl Chloroform and purified using miRNeasy minikit (Qiagen).

tag: sample type

value: Biopsy of DMBA/TPA induced mouse skin Tumor (cSCC)

value: female

tag: strain

value: FVB/N


title: NT3

description: mSCC non transfected (Rep3)


title: S3

description: RNA extracted from a biopsy of healthy skin (sample S7)

value: Biopsy of mouse healthy skin


title: Si1AK-1

description: mSCC after a 72h treatment with Si1AK (rep1)


title: S2

description: RNA extracted from a biopsy of healthy skin (sample S5)


title: Si1AK-2

description: mSCC after a 72h treatment with Si1AK (rep2)


title: T2

description: RNA extracted from a biopsy of DMBA/TPA-induced tumor (sample T4)


title: Si2AK-2

description: mSCC after a 72h treatment with Si2AK (rep2)


title: 37_degree_2A

status: Public on Jun 06 2017

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

country: China

institute: College of Life Sciences, Zhejiang University

description:
Genotypes of spore of KZ37-2A
37-2A

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 48 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°.

scan_protocol: We acquired the microarray images with a GenePix 4000B scanner and analyzed the images with the GenePix Pro 6.0 software

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio.

organism: Saccharomyces cerevisiae

source_name: cell culture of strain KZ37-2A

label_protocol: The DNA was labeled using either Cy3-dUTP (control) or Cy5-dUTP (samples) using Invitrogen Bioprime Array CGH Genome Labeling Module using the kit protocol.

growth_protocol: Yeast cells were grown in YPD medium at 30 degree.

extract_protocol: Approximately 55 mg of the pelleted culture was resuspended in 500 ml of a melted agarose solution (0.5% low melt agarose, 100 mM EDTA pH 7.5 at approximately 42°), and then 20 μl of a 25 mg/ml Zymolase solution was added. This cell-agarose mixture was distributed into five plug molds and allowed to solidify. The plugs were then incubated in 700 μl of an EDTA/Tris solution (500 mM EDTA, 10 mM Tris, pH 7.5) overnight at 37°.  The next day, 400 μl of a sarcosyl/proteinase K solution (5% sarcosyl, 5 mg/ml proteinase K, 500 mM EDTA pH 7.5) was added to the tubes containing the plugs, and they were incubated at 50° for five hours to overnight. DNA was isolated from three plugs per strain analyzed using the Fermentas Life Sciences GeneJet Gel Extraction Kit. Following the addition of the “Binding” buffer from the kit, the samples were incubated at room temperature (~25°) until the agarose had melted and were then incubated on ice for 5 minutes. These samples were sonicated using a BioRupter sonicater for two 15-minute sessions of 30-second high pulses, followed by 30 seconds without sonication, resulting in DNA fragments of about 200-300 bp. Following sonication, the samples were treated according to the kit protocol.

treatment_protocol: Yeast cells were collected after culture in YPD medium for 20 hours.

tag: temperature

value: 37 degree

source_name: cell culture of JSC24-2


title: 37_degree_3D

description:
Genotypes of spore of KZ37-3D
37-3D

source_name: cell culture of strain KZ37-3D


title: 37_degree_4D

description:
Genotypes of spore of KZ37-4D
37-4D

source_name: cell culture of strain KZ37-4D


title: 37_degree_3C

description:
Genotypes of spore of KZ37-3C
37-3C

source_name: cell culture of strain KZ37-3C


title: 37_degree_5B

description:
Genotypes of spore of KZ37-5B
37-5B

source_name: cell culture of strain KZ37-5B


title: 37_degree_4B

description:
Genotypes of spore of KZ37-4B
37-4B

source_name: cell culture of strain KZ37-4B


title: 37_degree_4C

description:
Genotypes of spore of KZ37-4C
37-4C

source_name: cell culture of strain KZ37-4C


title: 37_degree_1C

description:
Genotypes of spore of KZ37-1C
37-1C

source_name: cell culture of strain KZ37-1C


title: 37_degree_5D

description:
Genotypes of spore of KZ37-5D
37-5D

source_name: cell culture of strain KZ37-5D


title: 30_degree_11D

description:
Genotypes of spore of KZ30-11D
30-11D

source_name: cell culture of strain KZ30-11D

value: 30 degree


title: 37_degree_3B

description:
Genotypes of spore of KZ37-3B
37-3B

source_name: cell culture of strain KZ37-3B


title: 37_degree_2B

description:
Genotypes of spore of KZ37-2B
37-2B

source_name: cell culture of strain KZ37-2B


title: S1

description: RNA extracted from a biopsy of healthy skin (sample S3)


title: 30_degree_11B

description:
Genotypes of spore of KZ30-11B
30-11B

source_name: cell culture of strain KZ30-11B


title: 37_degree_1D

description:
Genotypes of spore of KZ37-1D
37-1D

source_name: cell culture of strain KZ37-1D


title: 30_degree_11A

description:
Genotypes of spore of KZ30-11A
30-11A

source_name: cell culture of strain KZ30-11A


title: T1

description: RNA extracted from a biopsy of DMBA/TPA-induced tumor (sample T2)


title: 37_degree_4A

description:
Genotypes of spore of KZ37-4A
37-4A

source_name: cell culture of strain KZ37-4A


title: 37_degree_5A

description:
Genotypes of spore of KZ37-5A
37-5A

source_name: cell culture of strain KZ37-5A


title: 37_degree_3A

description:
Genotypes of spore of KZ37-3A
37-3A

source_name: cell culture of strain KZ37-3A

source_name: cell culture of JSC24-2


title: 37_degree_1A

description:
Genotypes of spore of KZ37-1A
37-1A

source_name: cell culture of strain KZ37-1A


title: 37_degree_5C

description:
Genotypes of spore of KZ37-5C
37-5C

source_name: cell culture of strain KZ37-5C


title: 37_degree_2C

description:
Genotypes of spore of KZ37-2C
37-2C

source_name: cell culture of strain KZ37-2C


title: 37_degree_2D

description:
Genotypes of spore of KZ37-2D
37-2D

source_name: cell culture of strain KZ37-2D


title: 37_degree_1B

description:
Genotypes of spore of KZ37-1B
37-1B

source_name: cell culture of strain KZ37-1B


title: 30_degree_10C

description:
Genotypes of spore of KZ30-10C
30-10C

source_name: cell culture of strain KZ30-10C


title: 30_degree_10D

description:
Genotypes of spore of KZ30-10D
30-10D

source_name: cell culture of strain KZ30-10D


title: 30_degree_10A

description:
Genotypes of spore of KZ30-10A
30-10A

source_name: cell culture of strain KZ30-10A


title: 30_degree_9D

description:
Genotypes of spore of KZ30-9D
30-9D

source_name: cell culture of strain KZ30-9D


title: 30_degree_11C

description:
Genotypes of spore of KZ30-11C
30-11C

source_name: cell culture of strain KZ30-11C


title: 30_degree_9C

description:
Genotypes of spore of KZ30-9C
30-9C

source_name: cell culture of strain KZ30-9C


title: 30_degree_9A

description:
Genotypes of spore of KZ30-9A
30-9A

source_name: cell culture of strain KZ30-9A


title: 30_degree_10B

description:
Genotypes of spore of KZ30-10B
30-10B

source_name: cell culture of strain KZ30-10B


title: 30_degree_8A

description:
Genotypes of spore of KZ30-8A
30-8A

source_name: cell culture of strain KZ30-8A


title: 30_degree_9B

description:
Genotypes of spore of KZ30-9B
30-9B

source_name: cell culture of strain KZ30-9B


title: 30_degree_8C

description:
Genotypes of spore of KZ30-8C
30-8C

source_name: cell culture of strain KZ30-8C


title: 30_degree_8D

description:
Genotypes of spore of KZ30-8D
30-8D

source_name: cell culture of strain KZ30-8D

source_name: cell culture of JSC24-2


title: 30_degree_8B

description:
Genotypes of spore of KZ30-8B
30-8B

source_name: cell culture of strain KZ30-8B