title: mouse Ba/F3-N cells_NADA 12h_rep1

city: Shanghai

first: Min

last: Wu

address: Scientific and technology plaza, Ruijin Road II

institute: Shanghai Institute of hematology

description: Gene expression data from 1μM NADA treated Ba/F3-N cells for 12 hours.

hyb_protocol: On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Mouse Genome 430 2.0 for 16 hours at 45°C in a rotating hybridization oven at the rotation speed of 60 rpm. After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer A according to the user manual of the Hybridization, Wash, and Stain Kit (Affymetrix, #900720).

scan_protocol: The arrays were scanned using a GeneChip® Scanner 3000 (Affymetrix, #3000).

data_processing: The scanned images were saved as DAT files and were transformed to JPG images. The signal intensities were extracted from the JPG images with Affymetrix® GeneChip® Command Console® Software (AGCC software) and were saved as CEL files. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Robust Multi-Chip Average (RMA) as normalization method.Then the significance analysis of microarray package rooted in R was used to calculate the intensity ratios and fold changes.

source_name: mouse Ba/F3-N cells, 1μM NADA, 12h

label_protocol: After the synthesis of the double-stranded cDNA, the cRNA was labelled with a biotinylated ribonucleotide analogue and was fragmented with fragmentation buffer using the MessageAmp™ Premier RNA Amplification Kit (Ambion, #1792).

growth_protocol: The Ba/F3-N cells were cultured in RPMI 1640 (Gibco) including 10% fetal bovine serum (FBS, Gibco) medium. The cells were growing in a 37℃ incubator, supplying with 5% CO2.

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

treatment_protocol: The cultured Ba/F3-N cells were counted and re-seeded at the concentration of 2×105/ml. The NADA treated group were added with 10mM NADA stock solution diluting to the final work concentration of 1μM. The vehicle control group were treated with equal volume of vehicle. 12 hours later, the NADA and vehicle treated Ba/F3-N cells were harvested for the miroarray assay.

tag: cell line source

value: a murine bone marrow-derived cell line transformed with oncogenic NRAS-G12D


title: mouse Ba/F3-N cells_vehicle control 12h_rep2

status: Public on Sep 08 2016

type: RNA

country: China

description: Gene expression data from vehicle control treated Ba/F3-N cells for 12 hours.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse Ba/F3-N cells, equal volume vehicle control, 12h


title: 4F_Day12

city: Barcelona

first: Miki

last: Ebisuya

address: PRBB Building, C/ Dr. Aiguader, 88

department: EMBL Barcelona

country: Spain

institute: EMBL

description:
4F_Day12
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 12.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol with Affymetrix Scanner 3000 7G

data_processing: The probeset signals were calculated using Agilent GeneSpring software.

label_protocol: Biotinylated cRNAs were prepared from 120 ng (rep1) or 300 ng (the others) total RNAs according to the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay manual.

growth_protocol: MEFs were maintained in Dulbecco's Modified Eagle's medium (DMEM) containing 10% foetal bovine serum (FBS).

extract_protocol: Total RNAs were extracted using the Qiagen RNeasy kit according to the manufacturer's protocol. On-column DNase digestion was performed.

treatment_protocol: MEFs were infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), three transcription factors (Oct4, Sox2 and Klf4) or GFP (control) at day 0.

tag: cell type

value: mouse embryonic fibroblasts (MEFs)

tag: retrovirus

value: infected with retroviruses encoding 4 transcription factors (Oct4, Sox2, Klf4 and c-Myc)

tag: time

value: day 12


title: mouse Ba/F3-N cells_vehicle control 12h_rep3


title: mouse Ba/F3-N cells_NADA 12h_rep2


title: mouse Ba/F3-N cells_NADA 12h_rep3


title: Tbr2 +/+;Foxg1::Cre rep3

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

hyb_protocol: Hybridization, blocking and washing procedures were performed with MouseWG-6 v2.0 Expression BeadChip (Illumina), according to the manufacturer's instructions.

scan_protocol: Scanning and image acquisition were performed with the BeadArray Microarray Technology (Illumina), according to the manufacturer's instructions.

data_processing: Data processing was performed with the GenomeStudio Software package (Illumina). GenomeStudio version 2010.3 normalized (quantile) signal intensities with p-values.

source_name: E14.5 dorsal cortex_control

label_protocol: RNA amplification was carried out with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion®), according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated with the TRI Reagent® RNA Isolation Reagent (Sigma), according to the manufacturer's instructions.

tag: strain

tag: genotype

value: Tbr2 +/+;Foxg1::Cre

tag: developmental stage

tag: tissue

value: brain

tag: brain region

value: dorsal cortex


title: Tbr2 fl/fl;Foxg1::Cre rep3

source_name: E14.5 dorsal cortex_Tbr2knockout

value: Tbr2 fl/fl;Foxg1::Cre


title: IMR5_75 DAC+EPZ6438 replicate 2

type: genomic

city: Heidelberg

first: Manuel

last: Wiesenfarth

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to llumina HumanMethylation450 BeadChips using the standard Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Raw data files generated by the iScan array scanner were read and preprocessed using minfi Bioconductor package (Aryee et al., 2014). With the minfi package the same preprocessing steps as in Illumina's Genomestudio software were performed, except for one modification. Namely, in the R-function call normalize.illumina.control() the reference value was set fixed as 10000 rather than the sum of averages of green and red intensities of the first patient.   The following filtering criteria were applied: Removal of probes targeting the X and Y chromosomes (n = 11,551), removal of probes containing a single nucleotide polymorphism (dbSNP132 Common) within five base pairs of and including the targeted CpG-site (n = 24,536), and probes not mapping uniquely to the human reference genome (hg19) allowing for one mismatch (n = 9,993). In total, 438,370 probes were kept for analysis. No batch correction has been applied (since cell lines are analyzed independently).

molecule: genomic DNA

organism: Homo sapiens

source_name: IMR5-75 neuroblastoma cell line

label_protocol: Standard Illumina Protocol

growth_protocol: Cells were grown in RPMI medium (10%FCS) under standard conditions.

extract_protocol: Genomic DNA was extracted from neuroblastoma cell lines using standard procedures.

treatment_protocol: The neuroblastoma cell lines Be(2)-C and IMR5-75 were treated with a combination of DAC (1µM, 72h) and EPZ-6438 (1µM 96h). Controls were treated with solvent (DMSO).

tag: agent

tag: cell line

value: IMR5-75 neuroblastoma cell line


title: 4F_Day10

description:
4F_Day10
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 10.

value: day 10


title: mouse Ba/F3-N cells_vehicle control 12h_rep1


title: IMR5_75 DMSO replicate 2

value: DMSO


title: Tbr2 +/+;Foxg1::Cre rep1


title: IMR5_75 DAC+EPZ6438 replicate 1


title: Be2C DAC+EPZ6438 replicate 2

source_name: Be(2)-C neuroblastoma cell line

value: Be(2)-C neuroblastoma cell line


title: Tbr2 +/+;Foxg1::Cre rep2


title: genomic DNA from neuroblastoma tumor 105

first: Maral

last: Saadati

department: Biostatistics

description: neuroblastoma

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to llumina HumanMethylation450 BeadChips using the standard Illumina protocol.

data_processing: Probes were removed based on the following criteria: (i) proportion of non-detectable beta values >.3 (n=379) (ii) single nucleotide polymorphism at/near the targeted CpG site according to R-Forge package IMA (https://rforge.net/IMA/ )   (n=92,600) (iii) control probes (n=65) (iv) mapping to the X or Y chromosome (n=10,351). Together, n= 382,182 probes were kept for further analysis. The k-nearest neighbors method was used to impute missing values. Finally, a subset quantile normalization as suggested by Touleimat and  Tost was applied (Touleimat N, Tost J. Complete pipeline for Infinium((R)) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation. Epigenomics. 2012)

label: biotin/DNP

source_name: neuroblastoma 105

extract_protocol: genomic DNA was extracted from snap-frozen neuroblastoma tissue using standard procedures.

tag: inss stage

tag: current risk category

value: high-risk

tag: age at diagnosis

value: >=1.5 years

tag: mycn status

value: MYCN-amplified

tag: 1p status

tag: 11q status

tag: 17q status


title: genomic DNA from neuroblastoma tumor 104

description: neuroblastoma

source_name: neuroblastoma 104


title: genomic DNA from neuroblastoma tumor 100

description: neuroblastoma

source_name: neuroblastoma 100


title: genomic DNA from neuroblastoma tumor 103

description: neuroblastoma

source_name: neuroblastoma 103

value: low-risk

value: <1.5 years

value: MYCN-nonamplified

value: 11q-whole loss

value: 17q-whole gain


title: Be2C DAC+EPZ6438 replicate 1


title: genomic DNA from neuroblastoma tumor 97

description: neuroblastoma

source_name: neuroblastoma 97


title: genomic DNA from neuroblastoma tumor 98

description: neuroblastoma

source_name: neuroblastoma 98


title: genomic DNA from neuroblastoma tumor 101

description: neuroblastoma

source_name: neuroblastoma 101


title: Tbr2 fl/fl;Foxg1::Cre rep2


title: Tbr2 fl/fl;Foxg1::Cre rep1


title: GC33P-normal

first: Beiqin

last: Yu

address: No.197 Ruijin Er Road

department: Ruijin Hospital

institute: Shanghai Jiao Tong University School of Medicine

hyb_protocol: Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456)

scan_protocol: An Agilent Microarray Scanner and Feature Extraction software 9.5.3 were applied to scan each slide

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 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.

source_name: gastric

extract_protocol: mirVana™ RNA Isolation Kit (Applied Biosystem p/n AM1556) extract total RNA

tag: gender

value: male

value: normal


title: cSCCHN (6508593048_I)

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

hyb_protocol: Labelled cRNA was hybridized to HumanHT-12 v4 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

data_processing: Data were extracted in GenomeStudio (Illumina) using default analysis settings and no normalization method.  Resulting data were imported into GeneSpring GX v12.5 (Agilent Technologies, Santa Clara, CA, USA).  Expression values were normalized using quantile normalization with default settings.

source_name: Cutaneous SCC of the head and neck with no neural involvement

label_protocol: Biotinylated cRNA was prepared with the Illumina® Whole-Genome DASL® HT Assay as per the manufacturer’s instructions.

extract_protocol: Total RNA was extracted and purified including an RNase-free DNase I digestion step using the RNeasy® FFPE Kit (Qiagen, Hilden, Germany), and quantified (NanoDrop® ND-1000; Thermo Scientific, Waltham, USA).  RNA from each sample was then divided into two aliquots, one aliquot was used in pre-qualification analysis, and the other reserved for expression profiling.

tag: disease state

value: cSCCHN

tag: pni

value: no neural involvement

tag: primary site

value: Scalp

tag: differentiation

value: Mod diff


title: cSCCHN clinical PNI (6508593048_K)

scan_protocol: Labelled cRNA was hybridized to HumanHT-12 v4 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

source_name: Cutaneous SCC of the head and neck with clinical perineural invasion

value: clinical perineural invasion

value: Unknown


title: genomic DNA from neuroblastoma tumor 102

description: neuroblastoma

source_name: neuroblastoma 102


title: cSCCHN clinical PNI (6508593048_L)

value: Cheek

value: Poorly diff


title: GC33T-tumor

label_protocol: Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456)

value: tumor


title: cSCCHN clinical PNI (6508593048_J)

value: Preauricular


title: genomic DNA from neuroblastoma tumor 99

description: neuroblastoma

source_name: neuroblastoma 99

value: high-risk


title: GC32P-normal

value: female


title: genomic DNA from neuroblastoma tumor 96

description: neuroblastoma

source_name: neuroblastoma 96

value: low-risk

value: <1.5 years

value: MYCN-nonamplified


title: cSCCHN clinical PNI (6508593048_H)


title: GC31P-normal

value: male


title: GC32T-tumor


title: GC31T-tumor


title: cSCCHN clinical PNI (6508593048_G)

value: Cheek/Temple


title: GC30P-normal

value: normal


title: genomic DNA from neuroblastoma tumor 95

description: neuroblastoma

source_name: neuroblastoma 95

value: >=1.5 years

value: 17q-whole gain


title: cSCCHN incidental PNI (6508593048_D)

source_name: Cutaneous SCC of the head and neck with incidental perineural invasion

value: cSCCHN

value: incidental perineural invasion

value: Neck

value: Mod-poorly diff


title: genomic DNA from neuroblastoma tumor 92

description: neuroblastoma

source_name: neuroblastoma 92


title: genomic DNA from neuroblastoma tumor 94

description: neuroblastoma

source_name: neuroblastoma 94

value: MYCN-amplified


title: genomic DNA from neuroblastoma tumor 85

description: neuroblastoma

source_name: neuroblastoma 85


title: genomic DNA from neuroblastoma tumor 93

description: neuroblastoma

source_name: neuroblastoma 93


title: cSCCHN incidental PNI (6508593048_C)

value: Cheek

value: Mod diff


title: GC30T-tumor

value: tumor


title: genomic DNA from neuroblastoma tumor 91

description: neuroblastoma

source_name: neuroblastoma 91

value: high-risk


title: cSCCHN incidental PNI (6508593048_B)

value: Poorly diff


title: genomic DNA from neuroblastoma tumor 90

description: neuroblastoma

source_name: neuroblastoma 90


title: genomic DNA from neuroblastoma tumor 87

description: neuroblastoma

source_name: neuroblastoma 87


title: cSCCHN clinical PNI (6508593048_F)

value: clinical perineural invasion

value: Unknown

value: Well diff


title: genomic DNA from neuroblastoma tumor 88

description: neuroblastoma

source_name: neuroblastoma 88

value: MYCN-nonamplified


title: GC29P-normal

value: male

value: normal


title: genomic DNA from neuroblastoma tumor 86

description: neuroblastoma

source_name: neuroblastoma 86

value: >=1.5 years


title: GC29T-tumor

source_name: gastric


title: cSCCHN incidental PNI (6508593048_A)

value: cSCCHN

value: Nose


title: genomic DNA from neuroblastoma tumor 81

description: neuroblastoma

source_name: neuroblastoma 81

value: intermediate-risk

value: <1.5 years


title: genomic DNA from neuroblastoma tumor 84

description: neuroblastoma

source_name: neuroblastoma 84


title: cSCCHN incidental PNI (6508593034_L)

value: incidental perineural invasion

value: Temple


title: GC28P-normal

value: female


title: genomic DNA from neuroblastoma tumor 82

description: neuroblastoma

source_name: neuroblastoma 82

value: MYCN-amplified


title: GC28T-tumor

value: tumor


title: cSCCHN clinical PNI (6508593048_E)

source_name: Cutaneous SCC of the head and neck with clinical perineural invasion

value: Mod diff


title: genomic DNA from neuroblastoma tumor 83

description: neuroblastoma

source_name: neuroblastoma 83

value: high-risk


title: genomic DNA from neuroblastoma tumor 80

description: neuroblastoma

source_name: neuroblastoma 80

value: 17q-whole gain


title: GC27P-normal


title: GC26P-normal


title: GC26T-tumor


title: cSCCHN incidental PNI (6508593034_J)

source_name: Cutaneous SCC of the head and neck with incidental perineural invasion

value: Neck


title: cSCCHN (6508593034_H)

source_name: Cutaneous SCC of the head and neck with no neural involvement

value: no neural involvement

value: Mod-well diff


title: genomic DNA from neuroblastoma tumor 78

description: neuroblastoma

source_name: neuroblastoma 78

value: low-risk

value: MYCN-nonamplified


title: cSCCHN (6508593034_F)

value: cSCCHN


title: GC25P-normal

value: male

value: normal


title: cSCCHN incidental PNI (6508593034_K)

value: Lower eyelid


title: GC25T-tumor


title: GC27T-tumor


title: cSCCHN (6508593034_G)

value: Scalp


title: cSCCHN clinical PNI (6508593034_I)

value: clinical perineural invasion

value: Parotid skin


title: GC24P-normal

value: female


title: cSCCHN (6508593034_C)

value: Ear


title: GC24T-tumor

value: tumor


title: genomic DNA from neuroblastoma tumor 89

description: neuroblastoma

source_name: neuroblastoma 89

value: high-risk

value: >=1.5 years

value: MYCN-amplified


title: cSCCHN (6508593034_B)

value: no neural involvement

value: Forehead

value: Mod diff


title: cSCCHN (6508593034_D)

value: Cheek


title: GC23P-normal


title: genomic DNA from neuroblastoma tumor 76

description: neuroblastoma

source_name: neuroblastoma 76

value: intermediate-risk

value: <1.5 years

value: MYCN-nonamplified

value: 17q-whole gain


title: genomic DNA from neuroblastoma tumor 75

description: neuroblastoma

source_name: neuroblastoma 75


title: genomic DNA from neuroblastoma tumor 74

description: neuroblastoma

source_name: neuroblastoma 74

value: 11q-whole loss


title: GC23T-tumor

value: male


title: GC22P-normal

value: normal


title: ISHAL3

first: Eva

last: Colas

address: Pg. Vall Hebron 119-129

institute: Vall Hebron Research Institute

description: Replicate 3

hyb_protocol: Standard as recommended by illumina

scan_protocol: Standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.22.0). It was log2 transformed and quantile normalized.

source_name: Cell culture

label_protocol: Standard as recommended by illumina

growth_protocol: Hec1A (ATCC®HTB-122TM) and Ishikawa (#99040201, Sigma-Aldrich) EC cell lines were used.  in McCoy’s and DMEM F-12 culture media (BioWest, Nuaillé, France), respectively, supplemented with 10% FBS and 1% penicillin-streptomycin in a 5% CO2 humidified atmosphere at 37ºC.

extract_protocol: Total RNA from cell cultures and tissues was obtained using the RNeasy Mini kit (Qiagen, Valencia, CA, USA). cDNA synthesis was performed using SuperScript III reverse transcription enzyme (Invitrogen, Life technologies, Carlsbad, CA).

treatment_protocol: To generate downregulated stably transfected cells we used the lentiviral pGIPZ vectors: shALCAM1 (V3LHS-3600072), shALCAM2 (V3LHS-3600074) and the empty control vector, shControl (GE Healthcare Bio-Sciences, Pittsburgh, USA).

tag: cell type

value: Ishikawa cell line with shAlcam


title: genomic DNA from neuroblastoma tumor 73

description: neuroblastoma

source_name: neuroblastoma 73


title: ISHAL2

description: Replicate 2


title: GC22T-tumor

tag: tissue


title: GC21P-normal


title: genomic DNA from neuroblastoma tumor 69

description: neuroblastoma

source_name: neuroblastoma 69


title: GC21T-tumor

source_name: gastric


title: cSCCHN (6508593034_A)

value: cSCCHN

value: Ear


title: genomic DNA from neuroblastoma tumor 70

description: neuroblastoma

source_name: neuroblastoma 70

value: low-risk

value: 1p-whole gain


title: genomic DNA from neuroblastoma tumor 72

description: neuroblastoma

source_name: neuroblastoma 72

value: high-risk

value: MYCN-amplified


title: genomic DNA from neuroblastoma tumor 71

description: neuroblastoma

source_name: neuroblastoma 71


title: ISHAL1

description: Replicate 1


title: ISHI1

description: Replicate 1

value: Ishikawa cell line with shControl


title: genomic DNA from neuroblastoma tumor 66

description: neuroblastoma

source_name: neuroblastoma 66


title: GC20P-normal


title: HSHAL3

description: Replicate 3

value: Hec1a cell line with shAlcam


title: ISHI2

description: Replicate 2


title: ISHI3

description: Replicate 3


title: genomic DNA from neuroblastoma tumor 77

description: neuroblastoma

source_name: neuroblastoma 77

value: >=1.5 years


title: genomic DNA from neuroblastoma tumor 67

description: neuroblastoma

source_name: neuroblastoma 67


title: GC18P-normal


title: GC20T-tumor

value: tumor


title: HSHAL2

description: Replicate 2


title: genomic DNA from neuroblastoma tumor 65

description: neuroblastoma

source_name: neuroblastoma 65


title: genomic DNA from neuroblastoma tumor 68

description: neuroblastoma

source_name: neuroblastoma 68

value: <1.5 years


title: genomic DNA from neuroblastoma tumor 64

description: neuroblastoma

source_name: neuroblastoma 64

value: MYCN-nonamplified


title: GC18T-tumor


title: HSHAL1

description: Replicate 1


title: GC17P-normal

value: female


title: H3

description: Replicate 3

value: Hec1a cell line with shControl


title: genomic DNA from neuroblastoma tumor 63

description: neuroblastoma

source_name: neuroblastoma 63


title: genomic DNA from neuroblastoma tumor 62

description: neuroblastoma

source_name: neuroblastoma 62

value: 11q-whole loss

value: 17q-whole gain


title: GC17T-tumor


title: GC16P-normal

value: male

value: normal


title: H2

description: Replicate 2


title: genomic DNA from neuroblastoma tumor 79

description: neuroblastoma

source_name: neuroblastoma 79


title: genomic DNA from neuroblastoma tumor 61

description: neuroblastoma

source_name: neuroblastoma 61

value: intermediate-risk


title: GC15P-normal


title: GC15T-tumor


title: GC16T-tumor


title: GC14P-normal


title: GC14T-tumor


title: H1

description: Replicate 1

source_name: Cell culture


title: genomic DNA from neuroblastoma tumor 59

description: neuroblastoma

source_name: neuroblastoma 59


title: genomic DNA from neuroblastoma tumor 58

description: neuroblastoma

source_name: neuroblastoma 58

value: low-risk


title: A204 Parental No Drug

city: Aurora

first: Karen

last: Ryall

state: Colorado

address: Mail Stop 8117, 12801 East 17th Avenue

department: Medical Oncology

country: USA

institute: University of Colorado Denver

description: A204 Parental with No Drug replicate 2

hyb_protocol: Hybridization to HumanHT-12 v4 Expression BeadChip following the Illumina Whole-Genome Gene Expression Direct Hybridization assay

scan_protocol: BeadChips were scanned using the Illumina iScan System.

data_processing: The data were analyzed with the R-Bioconductor beadarray package using default settings. We used BeadArray to quantile normalize the log2 transformed data.

source_name: A204 Parental No Drug

label_protocol: Sample was labeled using the Ambion Illumina Total Prep RNA amplification kit (#AMIL1791)

growth_protocol: Dasatinib, Pazopanib, and Sunitinib (LC laboratories) were used to induce resistance in the A204 cells. Cells were grown initially in DMEM media containing drug concentration of 500 nM. The drug was incremented when the cells had proliferated to near-confluency alongside minimal visible cell death. Drug concentration was incremented from 2µM, 3µM, and 5µM in a stepwise manner over 6 weeks. A final drug concentration of 5µM was maintained in resistant cells. Media and drug were replenished twice weekly.

extract_protocol: RNA extraction with TRIzol following standard procedures.

treatment_protocol: Cells were treated with 5µM Dasatinib, Pazopanib, or Sunitinib as indicated.


title: genomic DNA from neuroblastoma tumor 57

description: neuroblastoma

source_name: neuroblastoma 57


title: A204 Sunitinib Resistant

description: A204 Sunitinib Resistant with 5 uM Sunitinib

source_name: A204 Sunitinib Resistant


title: A204 Pazopanib Resistant

description: A204 Pazopanib Resistant with 5uM Pazopanib

source_name: A204 Pazopanib Resistant


title: A204 Dasatinib Resistant

description: A204 Dasatinib Resistant with 5uM Dasatinib

source_name: A204 Dasatinib Resistant


title: A204 Parental (No Drug)

description: A204 Parental with No Drug replicate 1

source_name: A204 Parental (No Drug)


title: GC13P-normal

source_name: gastric


title: genomic DNA from neuroblastoma tumor 53

description: neuroblastoma

source_name: neuroblastoma 53


title: genomic DNA from neuroblastoma tumor 55

description: neuroblastoma

source_name: neuroblastoma 55


title: GC12P-normal


title: A204 Parental 5uM Sunitinib

description: A204 Parental with 5uM Sunitinib

source_name: A204 Parental 5uM Sunitinib


title: genomic DNA from neuroblastoma tumor 56

description: neuroblastoma

source_name: neuroblastoma 56


title: GC12T-tumor


title: GC11P-normal


title: GC13T-tumor


title: A204 Parental 5uM Pazopanib

description: A204 Parental with 5uM Pazopanib

source_name: A204 Parental 5uM Pazopanib


title: genomic DNA from neuroblastoma tumor 52

description: neuroblastoma

source_name: neuroblastoma 52


title: genomic DNA from neuroblastoma tumor 49

description: neuroblastoma

source_name: neuroblastoma 49

value: 11q-whole gain


title: A204 Parental 5uM Dasatinib

description: A204 Parental with 5uM Dasatinib

source_name: A204 Parental 5uM Dasatinib


title: GC11T-tumor


title: YUGASP IFI6 shRNA#2replicate 1

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Signal intensities of probes were log2-transformed and Quantile normalized (lumi package in R/Bioconductor)

source_name: YUGASP cell line

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

growth_protocol: YUGASP NS shRNA,YUGASP PEA15 shRNA#1 and YUGASP PEA15 shRNA #2 cell lines were grown in DEMEM media with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instruction

treatment_protocol: YUGASP cells that either expressed Non-silencing shRNA (NS shRNA) or shRNAs targetingIFI6  (IFI6 shRNA #1 and IFI6 shRNA #2 were used for preparing the total RNA and to perfrom gene expression array.

value: YUGASP

tag: expression

value: IFI6 shRNA #2


title: GC10P-normal


title: YUGASP IFI6 shRNA#1replicate 2

value: IFI6 shRNA #1


title: genomic DNA from neuroblastoma tumor 60

description: neuroblastoma

source_name: neuroblastoma 60


title: genomic DNA from neuroblastoma tumor 48

description: neuroblastoma

source_name: neuroblastoma 48


title: genomic DNA from neuroblastoma tumor 51

description: neuroblastoma

source_name: neuroblastoma 51

value: high-risk

value: MYCN-amplified


title: genomic DNA from neuroblastoma tumor 47

description: neuroblastoma

source_name: neuroblastoma 47


title: genomic DNA from neuroblastoma tumor 50

description: neuroblastoma

source_name: neuroblastoma 50


title: GC09P-normal


title: GC08P-normal


title: GC09T-tumor

value: tumor


title: YUGASP IFI6 shRNA#2replicate 2


title: GC10T-tumor


title: YUGASP NS shRNA replicate 2

value: non-silencing shRNA


title: YUGASP IFI6 shRNA#1replicate 1


title: genomic DNA from neuroblastoma tumor 45

description: neuroblastoma

source_name: neuroblastoma 45

value: <1.5 years

value: MYCN-nonamplified


title: GC08T-tumor


title: YUGASP NS shRNA replicate 1


title: MEL-ST KRASv12, replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Signal intensities of probes were log2-transformed and quantile normalized (lumi package in R/Bioconductor).

source_name: MEL-ST cell line, KRASv12

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

growth_protocol: MEL-ST cells either stably expressing empty vector (pBABE-puro) or RAS gene (NRASQ61K, HRASV12, KRASV12) were grown in DEMEM media with 10% fetal bovine serum and Penicilline and Streptomycin at 37 C under 5% CO2 condition.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) as per the instructions from the manufacturer and then purified using RNeasy mini columns (Qiagen) as per the manufacturer's instructions.

treatment_protocol: MEL-ST cells either stably expressing empty vector (pBABE-puro) or RAS gene (NRASQ61K, HRASV12, KRASV12) were used to prepare total RNA for gene expression arrays.

value: MEL-ST

value: immortalized human melanocytes

tag: stable expression


title: GC07P-normal

source_name: gastric


title: genomic DNA from neuroblastoma tumor 44

description: neuroblastoma

source_name: neuroblastoma 44

value: >=1.5 years


title: MEL-ST KRASv12, replicate 1

tag: cell line


title: genomic DNA from neuroblastoma tumor 42

description: neuroblastoma

source_name: neuroblastoma 42

tag: inss stage


title: GC07T-tumor

value: male


title: GC06P-normal

value: normal


title: MEL-ST KRASv12, replicate 3


title: genomic DNA from neuroblastoma tumor 41

description: neuroblastoma

source_name: neuroblastoma 41

tag: current risk category

value: 1p-whole gain

value: 17q-whole gain


title: MEL-ST HRASv12, replicate 1

source_name: MEL-ST cell line, HRASv12


title: MEL-ST HRASv12, replicate 2


title: MEL-ST HRASv12, replicate 3


title: genomic DNA from neuroblastoma tumor 46

description: neuroblastoma

source_name: neuroblastoma 46

value: low-risk

tag: age at diagnosis

value: 11q-whole loss


title: genomic DNA from neuroblastoma tumor 54

description: neuroblastoma

source_name: neuroblastoma 54

tag: mycn status


title: GC06T-tumor


title: GC05P-normal


title: GC05T-tumor


title: genomic DNA from neuroblastoma tumor 43

description: neuroblastoma

source_name: neuroblastoma 43

tag: 1p status


title: MEL-ST NRASQ61K, replicate 3

source_name: MEL-ST cell line, NRASQ61K


title: MEL-ST NRASQ61K, replicate 2


title: genomic DNA from neuroblastoma tumor 35

description: neuroblastoma

source_name: neuroblastoma 35

tag: 11q status


title: genomic DNA from neuroblastoma tumor 37

description: neuroblastoma

source_name: neuroblastoma 37

tag: 17q status


title: MEL-ST vector, replicate 3

source_name: MEL-ST cell line, empty vector

value: empty pBABE-puro vector


title: genomic DNA from neuroblastoma tumor 39

description: neuroblastoma

source_name: neuroblastoma 39


title: CFPAC-1 CPI203 10 hrs 2

city: Boston

first: Andrew

middle: S

last: Liss

state: MA

address: 55 Blossom St

department: Surgery

institute: Massachusetts General Hospital

description: replicate 2

hyb_protocol: 0.75 ug of cDNA were hybridized for 16 hr at 48oC on Illumina HT-12 v4 Array in an Illumina Hybridization Oven (Illumina SE-901-1001). BeadChips were washed and stained in the using standard Illumina protocols.

scan_protocol: BeadChips were scanned using the Illumina iScan Scanner running Illumina iSCAN control software v 3.3.28

data_processing: The data were analyzed with Illumina GenomeStudio ver 2011

source_name: Pancreatic ductal adenocarcinoma

label_protocol: Biotinylated cDNA were prepared according to the standard Illumina protocol from 0.05 ug total RNA using amplification kit NuGEN Ovation Pico SL WTA v2, Lot # 1203210-A, followed by labeling 3 ug cDNA using kit NuGEN Encore Biotin IL Module, Lot # 1109226-A.

growth_protocol: Cell lines were cultured in a 50:50 mix of Dulbecco's Modified Eagle Medium and Ham's F-12 media (Mediatech) supplemented with 10% fetal bovine serum (Life Technologies), penicillin (100 U/ml), and streptomycin (100 μg/ml) at 37°C in 5% CO2.   3X10^5 cells were plated in 6 well dishes 16 hours prior to treatment.

extract_protocol: RNA was isolated from cells using a RNeasy micro kit (Qiagen 74004)

treatment_protocol: Cells were exposed to 1.6 uM CPI203 or an equal volume of DMSO for 5 or 10 hours prior to harvesting for RNA.

tag: treatment

tag: time


title: MEL-ST vector, replicate 2


title: genomic DNA from neuroblastoma tumor 40

description: neuroblastoma

source_name: neuroblastoma 40


title: genomic DNA from neuroblastoma tumor 38

description: neuroblastoma

source_name: neuroblastoma 38


title: MEL-ST vector, replicate 1


title: genomic DNA from neuroblastoma tumor 33

description: neuroblastoma

source_name: neuroblastoma 33


title: genomic DNA from neuroblastoma tumor 34

description: neuroblastoma

source_name: neuroblastoma 34


title: CFPAC-1 CPI203 10 hrs 1

description: replicate 1


title: CFPAC-1 DMSO 5 hrs 2

description: replicate 2

value: DMSO

value: 5 h


title: CFPAC-1 DMSO 10 hrs 1

description: replicate 1


title: CFPAC-1 DMSO 10 hrs 2

description: replicate 2


title: genomic DNA from neuroblastoma tumor 29

description: neuroblastoma

source_name: neuroblastoma 29


title: CFPAC-1 CPI203 5 hrs 2

description: replicate 2


title: genomic DNA from neuroblastoma tumor 31

description: neuroblastoma

source_name: neuroblastoma 31

value: high-risk


title: genomic DNA from neuroblastoma tumor 32

description: neuroblastoma

source_name: neuroblastoma 32


title: CFPAC-1 DMSO 5 hrs 1

description: replicate 1


title: CFPAC-1 CPI203 5 hrs 1

description: replicate 1


title: cSCCHN (6508593034_E)

source_name: Cutaneous SCC of the head and neck with no neural involvement

tag: disease state

value: cSCCHN

tag: pni

value: no neural involvement

value: Cheek/Zygoma

value: Mod diff


title: genomic DNA from neuroblastoma tumor 36

description: neuroblastoma

source_name: neuroblastoma 36

value: <1.5 years

value: MYCN-nonamplified


title: genomic DNA from neuroblastoma tumor 27

description: neuroblastoma

source_name: neuroblastoma 27

value: intermediate-risk


title: genomic DNA from neuroblastoma tumor 30

description: neuroblastoma

source_name: neuroblastoma 30

value: >=1.5 years

value: MYCN-amplified


title: genomic DNA from neuroblastoma tumor 26

description: neuroblastoma

source_name: neuroblastoma 26


title: MEL-ST NRASQ61K, replicate 1

source_name: MEL-ST cell line, NRASQ61K

value: MEL-ST

value: immortalized human melanocytes


title: genomic DNA from neuroblastoma tumor 25

description: neuroblastoma

source_name: neuroblastoma 25


title: 1312 CPI203 5 hrs 1

description: replicate 1


title: 1312 CPI203 10 hrs 1

description: replicate 1


title: 1312 DMSO 10 hrs 2

description: replicate 2


title: 1312 CPI203 10 hrs 2

description: replicate 2


title: genomic DNA from neuroblastoma tumor 20

description: neuroblastoma

source_name: neuroblastoma 20


title: 1312 DMSO 10 hrs 1

description: replicate 1


title: genomic DNA from neuroblastoma tumor 18

description: neuroblastoma

source_name: neuroblastoma 18

value: low-risk

value: 17q-whole gain


title: genomic DNA from neuroblastoma tumor 23

description: neuroblastoma

source_name: neuroblastoma 23


title: 1312 CPI203 5 hrs 2

description: replicate 2

source_name: Pancreatic ductal adenocarcinoma


title: genomic DNA from neuroblastoma tumor 22

description: neuroblastoma

source_name: neuroblastoma 22

value: 11q-whole loss


title: genomic DNA from neuroblastoma tumor 21

description: neuroblastoma

source_name: neuroblastoma 21


title: CFPAC-1 untreated 1

description: replicate 1

value: Untreated

value: control


title: 1312 DMSO 5 hrs 2

description: replicate 2

value: DMSO

value: 5 h


title: genomic DNA from neuroblastoma tumor 28

description: neuroblastoma

source_name: neuroblastoma 28

value: high-risk


title: genomic DNA from neuroblastoma tumor 24

description: neuroblastoma

source_name: neuroblastoma 24


title: genomic DNA from neuroblastoma tumor 19

description: neuroblastoma

source_name: neuroblastoma 19


title: 1312 DMSO 5 hrs 1

description: replicate 1


title: 1312 untreated 1

description: replicate 1


title: genomic DNA from neuroblastoma tumor 17

description: neuroblastoma

source_name: neuroblastoma 17


title: genomic DNA from neuroblastoma tumor 12

description: neuroblastoma

source_name: neuroblastoma 12


title: genomic DNA from neuroblastoma tumor 16

description: neuroblastoma

source_name: neuroblastoma 16


title: BxPc3 DMSO 10 hrs 1

description: replicate 1


title: genomic DNA from neuroblastoma tumor 15

description: neuroblastoma

source_name: neuroblastoma 15


title: BxPc3 CPI203 10 hrs 2

description: replicate 2


title: genomic DNA from neuroblastoma tumor 13

description: neuroblastoma

source_name: neuroblastoma 13


title: BxPc3 DMSO 10 hrs 2

description: replicate 2


title: genomic DNA from neuroblastoma tumor 14

description: neuroblastoma

source_name: neuroblastoma 14


title: BxPc3 CPI203 10 hrs 1

description: replicate 1


title: 1312 untreated 2

description: replicate 2


title: BxPc3 CPI203 5 hrs 1

description: replicate 1


title: genomic DNA from neuroblastoma tumor 11

description: neuroblastoma

source_name: neuroblastoma 11


title: genomic DNA from neuroblastoma tumor 10

description: neuroblastoma

source_name: neuroblastoma 10


title: genomic DNA from neuroblastoma tumor 8

description: neuroblastoma

source_name: neuroblastoma 8


title: genomic DNA from neuroblastoma tumor 9

description: neuroblastoma

source_name: neuroblastoma 9


title: BxPc3 CPI203 5 hrs 2

description: replicate 2


title: BxPc3 DMSO 5 hrs 2

description: replicate 2


title: BxPc3 DMSO 5 hrs 1

description: replicate 1


title: BxPc3 untreated 2

description: replicate 2


title: genomic DNA from neuroblastoma tumor 7

description: neuroblastoma

source_name: neuroblastoma 7


title: CFPAC-1 untreated 2

description: replicate 2

source_name: Pancreatic ductal adenocarcinoma


title: genomic DNA from neuroblastoma tumor 5

description: neuroblastoma

source_name: neuroblastoma 5


title: genomic DNA from neuroblastoma tumor 6

description: neuroblastoma

source_name: neuroblastoma 6


title: Spiderbiofilm grown LR107 hht1 mutant (replicate 2)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

hyb_protocol: The labeled cRNA samples were hybridized on to a Whole Genome Candida albicans 8x15k (AMADID: 026377). 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Slides were scanned using the Agilent Microarray Scanner G2505C at 3 micron resolution.

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

organism: Candida albicans

source_name: Spider biofilm grown hht1 mutant

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: RNA was isolated from C. albicans strains by the RNA Ambion kit (Cat. No. AM1560). For the biofilm induced cells, biofilm was developed in the Spider medium for 48 hours at 37°C

tag: medium

value: Spider biofilm grown

tag: genotype/variation

value: LR107 hht1 mutant


title: 1108 DMSO 10 hrs 2

description: replicate 2


title: 1108 CPI203 10 hrs 2

description: replicate 2


title: 1108 CPI203 10 hrs 1

description: replicate 1


title: Spider biofilm grown SC5314 wild type (replicate 2)

source_name: Spider biofilm grown SC5314 wild type

value: SC5314 wild type


title: Spiderbiofilm grown LR107 hht1 mutant (replicate 1)


title: 1108 DMSO 10 hrs 1

description: replicate 1


title: BxPc3 untreated 1

description: replicate 1


title: genomic DNA from neuroblastoma tumor 4

description: neuroblastoma

source_name: neuroblastoma 4

value: <1.5 years

value: MYCN-nonamplified


title: genomic DNA from neuroblastoma tumor 2

description: neuroblastoma

source_name: neuroblastoma 2

value: >=1.5 years


title: H1299_FBS

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

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

department: PEBC

institute: IDIBELL

description:
sample name: H1299_FBS
Cancer cell line

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

label: Cy3, Cy5

source_name: Lung

label_protocol: Standard Illumina labelling protocol

growth_protocol: Cells where growth on RPMI media with 10% FBS, 1% PS

extract_protocol: Total DNA  where extrated using Trizol Reagent.

treatment_protocol: GCRA: Dexamethasone (1uM) + Retinoic Acid (1uM) 120hours; COMB: Dexamethasone (1uM) + Retinoic Acid (1uM) + Aza (0.2uM) + SAHA (0.2uM) 120 hours

tag: individual

value: Diseased donor

tag: cell line type

value: BRG1 mutant

value: FBS


title: Spider biofilm grown SC5314 wild type (replicate 1)


title: H1299_COMB

description:
sample name: H1299_COMB
Cancer cell line

value: COMB


title: genomic DNA from neuroblastoma tumor 1

description: neuroblastoma

source_name: neuroblastoma 1

value: intermediate-risk


title: 1108 CPI203 5 hrs 2

description: replicate 2


title: LR108 hht1 mutant (replicate 2)

description: LR108 hht1 mutant (replicate 2)

source_name: YPD grown hht1 mutant

value: YPD grown

value: LR108 hht1 mutant


title: LR107 hht1 mutant (replicate 1)

description: LR107 hht1 mutant (replicate 1)


title: 1108 CPI203 5 hrs 1

description: replicate 1


title: genomic DNA from neuroblastoma tumor 3

description: neuroblastoma

source_name: neuroblastoma 3

value: low-risk

value: 17q-whole gain


title: SC5314 wild type (replicate 2)

description: SC5314 wild type (replicate 2)

source_name: YPD grown wild type


title: 1108 untreated 2

description: replicate 2

value: Untreated

value: control


title: SC5314 wild type (replicate 1)

description: SC5314 wild type (replicate 1)


title: 1108 DMSO 5 hrs 2

description: replicate 2

value: DMSO

value: 5 h


title: 1108 DMSO 5 hrs 1

description: replicate 1


title: H460_shBRG1_2_COMB_2

description:
M0114_2016_MA__1400257236312224__Cy3_2332_1_4
Cancer cell line

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 total volume of 25ul following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanner Agilent G2565CA Feature extraction 10.7

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Non Small Cell Lung Cancer (NSCLC)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 45ng total RNA using a LowInput QuickAmp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA were extracted using Trizol Reagent.

value: NSCLC cell line H460

value: MYC amplified


title: 1108 untreated 1

description: replicate 1


title: A549_COMB

description:
Sample name: a549COMB
Cancer cell line

treatment_protocol: GCRA: Dexamethasone (1uM) + Retinoic Acid (1uM) 120hours; COMB: Dexamethasone (1uM) + Retinoic Acid (1uM) + Aza (0.2uM) + SAHA (0.2uM) 120 hours. shRNA targeting BRG1 (an ATPase of the SWI/SNF Chromatin Remodeling Complex).

value: NSCLC cell line A549


title: H460_shBRG1_2_COMB_1

description:
M0113_2016_MA__2300257236312223__Cy3_2331_2_3
Cancer cell line


title: MH-3

city: Sapporo

first: Norihisa

last: Ichinohe

state: Hokkaido

address: South-1, West-17, Chuo-ku,

department: Department of Tissue Development and Regeneration

country: Japan

institute: Sapporo Medical University School of Medicine

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction. Expression profiles were analyzed using an oligo microarray (SurePrint G3 Rat Gene Expression v2 G4853B).

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction

organism: Rattus norvegicus

source_name: Mature hepatocytes isolated  from fresh livers.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: Mature hepatocytes(MH) were isolated from fresh livers. CD44+ cells were isolated from small hepatocytes colonies by using MACS methods. Mat  were passaged and cultured cells  on matrigel-coated dishes. Mat-BGOL were cultured Mat cells treated with matrigel-overlay.

extract_protocol: Total RNAs of prepared cells were extracted using the RNeasy Mini Kit (Qiagen).

tag: strain

value: F344 [dipeptidylpeptidase IV (DPPIV)+ strain; Sankyo Lab Service Corp.Inc., Tokyo, Japan]

tag: gender

value: male

tag: tissue

value: Liver

tag: cell type

value: Mature hepatocytes isolated form fresh livers


title: H1299_GCRA

description:
sample name: H1299_GCRA
Cancer cell line

value: Diseased donor

tag: cell line

value: BRG1 mutant

value: GCRA


title: DMS114_COMB

description:
Sample name: dms114COMB
Cancer cell line

value: SCLC cell line DMS114

value: COMB


title: MH-2


title: A549_GCRA

description:
Sample name: a549GCRA
Cancer cell line


title: H460_shBRG1_2_GCRA_3

description:
M0124_2016_MA__2300257236312226__Cy3_2322_2_3
Cancer cell line


title: DMS114_GCRA

description:
Sample name: dms114GCRA
Cancer cell line


title: Mat-BGOL-2

source_name: Passaged and cultured  cells with matrigel-overlay treatment

value: Differentiated cells treated with matrigel overlay treatment


title: Mat-BGOL-3


title: H460_shBRG1_2_GCRA_1

description:
M0110_2016_MA__2100257236312225__Cy3_2321_2_1
Cancer cell line


title: Mat-BGOL-1


title: H460_shBRG1_2_FBS_2

description:
M0122_2016_MA__2400257236312223__Cy3_2312_2_4
Cancer cell line


title: H460_shBRG1_2_FBS_3

description:
M0123_2016_MA__2300257236312224__Cy3_2313_2_3
Cancer cell line


title: H460_shBRG1_GCRA

description:
Sample name: h460shGCRA
Cancer cell line


title: Mat-2

source_name: Passaged and cultured cells on matrigel-coated dishes

value: Hepatocytic progenitor cells passaged on matrigel coated dishes


title: H460_shBRG1_FBS

description:
Sample name: h460shFBS
Cancer cell line


title: Mat-3


title: H460_shBRG1_2_FBS_1

description:
M0121_2016_MA__2200257236312226__Cy3_2311_2_2
Cancer cell line


title: H460_COMB

description:
Sample name: h460scCOMB
Cancer cell line


title: H460_shBRG1_2_GCRA_2

description:
M0112_2016_MA__1200257236312226__Cy3_2323_1_2
Cancer cell line


title: N2_HSP-6;DVE-1_rep1

city: Ann Arbor

first: Ana

middle: Rodrigues

last: Grant

address: 100 Washtenaw Avenue

department: Computational Medicine & Bioinformatics

institute: University of Michigan

description: HSP-6;DVE-1 1

scan_protocol: Scanner: GeneChip scanner 3000 7G as described in the Affymetrix GeneChip Expression Analysis Technical Manual

data_processing: Software used to generate the CEL files: GCOS v1.4. Data were processed using Biocondutor. Standard data quality validation as suggested by Affymetrix was carried out with the 'simpleaffy' package followed by 'affyPLM', which identified no problematic chips. The raw data were preprocessed according to the GC-RMA method (implemented in 'gcrma').

organism: Caenorhabditis elegans

label_protocol: Labeling kit: 3' IVT kit for expression array from Affymetrix as described in the Affymetrix GeneChip Expression Analysis Technical Manual

growth_protocol: Synchronized N2 worms were grown on E.coli HT115 RNAi plates from day 1 adult for 3 days.

extract_protocol: Worms were harvested after 3 days on RNAi plates to isolate RNA for microarray.

treatment_protocol: Plates were washed-off with M9 every other day to get rid of eggs and larvae.

tag: age

value: day 3 Adults

tag: RNAi


title: H82_shBRG1_GCRA

description:
Sample name: h82shGCRA
Cancer cell line

value: SCLC cell line H82


title: H460_shBRG1_COMB

description:
Sample name: h460shCOMB
Cancer cell line


title: A549_FBS

description:
Sample name: a549FBS
Cancer cell line

value: FBS


title: H82_shBRG1_2_COMB_2

description:
M0105_2016_MA__1200257236312223__Cy3_1332_1_2
Cancer cell line

source_name: Small Cell Lung Cancer (SCLC)


title: N2_HSP-6;HSF-1_rep2

description: HSP-6;HSF-1 2

hyb_protocol: as described in the Affymetrix GeneChip Expression Analysis Technical Manual


title: H82_shBRG1_COMB

description:
Sample name: h82shCOMB
Cancer cell line


title: N2_HSP-6;HSF-1_rep3

description: HSP-6;HSF-1 3


title: H460_FBS

description:
Sample name: h460scFBS
Cancer cell line

value: NSCLC cell line H460


title: N2_HSP-6;DVE-1_rep2

description: HSP-6;DVE-1 2


title: H82_shBRG1_FBS

description:
Sample name: h82hsFBS
Cancer cell line

value: MYC amplified


title: N2_HSP-6;DVE-1_rep3

description: HSP-6;DVE-1 3


title: H460_GCRA

description:
Sample name: h460scGCRA
Cancer cell line


title: DMS114_FBS

description:
Sample name: dms114FBS
Cancer cell line


title: CD44+-2

source_name: Isolated CD44+ cells from small hepatocytes by using MACS methods.

value: Isolated CD44+ cells from small hepatocytes colonies by using MACS methods.


title: Mat-1

value: F344 [dipeptidylpeptidase IV (DPPIV)+ strain; Sankyo Lab Service Corp.Inc., Tokyo, Japan]


title: H82_shBRG1_2_GCRA_3

description:
M0103_2016_MA__1400257236312225__Cy3_1323_1_4
Cancer cell line


title: H82_shBRG1_2_COMB_3

description:
M0106_2016_MA__2400257236312224__Cy3_1333_2_4
Cancer cell line


title: H82_FBS

description:
Sample name: h82scFBS
Cancer cell line


title: N2_HSP-6;HSF-1_rep1

description: HSP-6;HSF-1 1


title: H82_shBRG1_2_COMB_1

description:
M0104_2016_MA__1100257236312226__Cy3_1331_1_1
Cancer cell line


title: N2_HSP-6_rep3

description: HSP-6 3


title: N2_HSP-6_rep2

description: HSP-6 2


title: H82_shBRG1_2_GCRA_2

description:
M0102_2016_MA__1100257236312224__Cy3_1322_1_1
Cancer cell line


title: MH-1

value: male


title: CD44+-1

value: Liver


title: H82_GCRA

description:
Sample name: h82scGCRA
Cancer cell line


title: H82_COMB

description:
Sample name: h82scCOMB
Cancer cell line


title: H82_shBRG1_2_GCRA_1

description:
M0101_2016_MA__1300257236312223__Cy3_1321_1_3
Cancer cell line


title: N2_HSP-6_rep1

description: HSP-6 1


title: Adipose_control diet_32week_rep2

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

description: control diet, 32 week

hyb_protocol: Labeled DNA was hybridized to the Arraystar Mouse ReqSeq Promoter Array.

scan_protocol: Array was scanned with Agilent Scanner G2505C.

data_processing: After normalization, raw data was input into SignalMap Software to observe and evaluate the methylation peaks.

label: Cy 5

source_name: MeDIP DNA from control diet, 32 week

label_protocol: Immunoprecipitated methylated DNA was labeled with Cy5 fluorophere and the input genomic DNA was labeled with Cy3 fluorophere.

extract_protocol: Genomic DNA was extracted from fat samples using Dneasy Blood & Tissue Kit.

value: adipose

value: 32 week

label: Cy 3

source_name: input DNA from control diet, 32week


title: N2_EV_rep3

description: EV 3

value: Empty Vector


title: N2_EV_rep2

description: EV 2


title: H82_shBRG1_2_FBS_3

description:
M0100_2016_MA__2400257236312225__Cy3_1313_2_4
Cancer cell line

value: Diseased donor


title: H82_shBRG1_2_FBS_2

description:
M0099_2016_MA__1200257236312224__Cy3_1312_1_2
Cancer cell line


title: H82_shBRG1_2_FBS_1

description:
M0098_2016_MA__2100257236312223__Cy3_1311_2_1
Cancer cell line


title: Adipose_control diet_32week_rep3

description: control diet, 32 week


title: TEM Sample 20

status: Public on Sep 07 2016

city: Cleveland

first: AARTHI

last: TALLA

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University School of Medicine

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using Genome Studio software (Illumina).

data_processing: Raw probe intensities were preprocessed using the R statistical language. Missing values were imputed using the KNN algorithm followed by log2 transformation and quantile normalization using the Bioconductor software package limma.

organism: Macaca mulatta

source_name: Sorted PBMC (CD8+ TEM )

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

extract_protocol: total RNA was extracted using Agencourt RNAdvance Blood Kit. The isolated total RNA was checked for quantity and quality using a NanoDrop 2000c (Thermo Fisher Scientific) and an Experion Electrophoresis System. Samples with an RQI classification ≥7.0 were selected to proceed downstream to amplification. Samples were normalized at 50ng for input and amplified using Illumina TotalPrep RNA amplification kits (Ambion) according to the manufacturer’s protocol.

tag: donorid

tag: cell count

tag: timepoint

value: Pre Treatment

value: Anti-IL15 Ab


title: TEM Sample 21

value: Post Treatment

tag: treatment


title: TEM Sample 22


title: TEM Sample 19


title: TEM Sample 23


title: Adipose_maternal chromium restriction diet_32week_rep3

source_name: MeDIP DNA from maternal chromium restriction diet, 32week

source_name: input DNA from maternal chromium restriction diet, 32week


title: TEM Sample 15


title: Adipose_maternal chromium restriction diet_32week_rep2

description: maternal chromium restriction diet, 32week


title: TEM Sample 17


title: Adipose_maternal chromium restriction diet_32week_rep1


title: TEM Sample 12

value: IgG1 Control Ab


title: Adipose_control diet_32week_rep1

description: control diet, 32 week


title: TEM Sample 14


title: N2_EV_rep1

description: EV 1

value: day 3 Adults


title: TEM Sample 16


title: TEM Sample 11


title: TEM Sample 13


title: TEM Sample 18


title: TEM Sample 8


title: TEM Sample 9


title: TEM Sample 10


title: TEM Sample 7


title: TEM Sample 5


title: TEM Sample 1


title: TEM Sample 6


title: TCM Sample 45

source_name: Sorted PBMC (CD4+ TCM )

tag: technical replicate

value: No


title: TEM Sample 3


title: TEM Sample 2


title: TCM Sample 43


title: TCM Sample 47


title: TCM Sample 48

source_name: Sorted PBMC (CD8+ TCM )


title: TCM Sample 42


title: TCM Sample 40


title: TCM Sample 44


title: TCM Sample 36


title: TCM Sample 41


title: TCM Sample 34


title: TCM Sample 37


title: TCM Sample 46


title: TCM Sample 29


title: TCM Sample 35


title: TCM Sample 33


title: TEM Sample 4


title: TCM Sample 39


title: TCM Sample 38


title: TCM Sample 31


title: Cortex_CircadianControl_ZT11_rep6

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

hyb_protocol: ss-cDNA was hybridized to a Mouse Gene 2.1 ST 96-Array Plate using GeneTitan Hybridization, Wash and Stain Kit for WT Array Plates. The array plate was washed and stained in the GeneTitan multi-channel instrument.

scan_protocol: Gene 1.1 ST Array Plates were scanned using the GeneTitan® Multi-channel Instrument.

data_processing: RMA normalization using Affymetrix powertools

label_protocol: Biotinylated sense-strand cDNA were prepared from 300 ng total RNA at the UPENN molecular profiling core using the Affymetrix WT Plus Kit.

growth_protocol: The left hemisphere of mouse cortex was dissected from C57BL/6J mice. For each replication, 13 C57BL/6J adult male mice (2 months of age) were obtained from Jackson laboratories and housed individually for a week in the experimental room on a 12 hr/12 hr light/dark schedule with lights on at 7:30 am (Zeitgeber time (ZT) 0). Food and water were available ad libitum throughout the experiment.

extract_protocol: Cortical dissections were performed by a single experimenter, and tissue was collected at 0 (ZT0), 6 (ZT6), 7 (ZT7), 8 (ZT8), and 11 (ZT11) hours into the experimental protocol. Tissue was rapidly dissected and immersed in chilled RNAlater (Qiagen), kept overnight at 4 °C, then frozen at -80 °C. Animals that were handled but not sleep deprived were dissected at the same time of day to control for variations due to circadian rhythms. The protocol was repeated 7 times so that 7 independent experiments are represented in each time point and all animals for each group were dissected at the same time of day. RNA extraction was performed using the RNAEasy Microarray Tissue kit from Qiagen.

treatment_protocol: To acclimate the mice to the experimenter each animal was handled daily for 6 days prior to the experimental day. Handling consisted of 10 minutes of intermittent light brushing of the animals with a paintbrush and tapping on cages.

tag: strain background

value: 2 month old

tag: sample group

value: Circadian Control, ZT11

value: cortex


title: Cortex_CircadianControl_ZT11_rep5


title: TCM Sample 30


title: Cortex_6HrSDw1HrRecovery_ZT7_rep7

value: 6hrSD and 1Hr Recovery, ZT7


title: Cortex_CircadianControl_ZT11_rep4


title: TCM Sample 24

value: Prost Treatment


title: TCM Sample 28


title: TCM Sample 26


title: TCM Sample 27


title: TCM Sample 25


title: Cortex_CircadianControl_ZT11_rep7

value: male


title: TCM Sample 32


title: Cortex_CircadianControl_ZT11_rep3


title: TCM Sample 23


title: TCM Sample 22


title: TCM Sample 20


title: Cortex_CircadianControl_ZT11_rep1


title: TCM Sample 19


title: TCM Sample 21


title: Cortex_5HrSDw6HrRecovery_rep7

value: 5HrSD and 6Hr Recovery, ZT11


title: Cortex_5HrSDw6HrRecovery_rep6


title: TCM Sample 17


title: TCM Sample 18


title: TCM Sample 13


title: TCM Sample 14


title: Cortex_5HrSDw6HrRecovery_rep3


title: TCM Sample 15


title: TCM Sample 10


title: Cortex_5HrSDw6HrRecovery_rep2


title: TCM Sample 16


title: TCM Sample 9


title: Cortex_CircadianControl_ZT8_rep6

value: Circadian Control, ZT8


title: TCM Sample 11


title: TCM Sample 12


title: Cortex_5HrSDw6HrRecovery_rep4


title: TCM Sample 5


title: TCM Sample 8


title: Cortex_CircadianControl_ZT8_rep7


title: Cortex_5HrSDw6HrRecovery_rep1


title: Cortex_5HrSDw6HrRecovery_rep5


title: TCM Sample 3


title: Cortex_CircadianControl_ZT8_rep3


title: TCM Sample 6 rep2


title: TCM Sample 7


title: TCM Sample 2


title: TCM Sample 4


title: Cortex_6HrSDw2HrRecovery_ZT8_rep2

value: 6HrSD and 2Hr Recovery, ZT8


title: Cortex_CircadianControl_ZT8_rep1


title: Cortex_6HrSDw2HrRecovery_ZT8_rep3


title: Thyroid_Wistar_Fipronil_rep10

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

description:
FIP10
Replicate 10

hyb_protocol: For each microarray, 825 ng of Cy3-labelled cRNA and 825 ng of Cy5-labeled RNA were mixed and fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-014879 Whole Rat Genome Oligo Microarrays (G4131F) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min) and Stabilization and Drying Solution (Agilent Technologies, 30 sec).

scan_protocol: Slides were scanned immediately after washing on a GenePix™ 4000B array scanner.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014879_D_20070207). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot):
myfunw<-function(x)
{okType<-x[,ControlType]==0
okFoundRed<-x[,rIsFound]==1
okFoundGreen<-x[,gIsFound]==1
okSatRed<-x$rIsSaturated==0
okSatGreen<- x$gIsSaturated==0
okManualFlag<-x$IsManualFlag==0
okAbBGRed<-x$rIsWellAboveBG==1
okAbBGGreen<-x$gIsWellAboveBG==1
as.numeric(okType & okFoundRed & okFoundGreen & okSatRed & okSatGreen & okManualFlag & okAbBGRed & okAbBGGreen)}
We selected the spots with a weight of 1 for 8 out of 10 microarrays. Replicated probes on the array (identical ProbeName) were resolved by taking the median signal of the replicated probe. At this step, 18016 spots out of 45018 were selected. Data were then normalized between arrays using loess and between arrays using Aquantile methods (limma functions normalizeWithinArrays and normalizeBetweenArrays). The resulting matrix has 18016 rows, each corresponding to a unique ProbeName. The data were further analyzed using a separate channel analysis as described in the user's guide of the limma package from Bioconductor.

source_name: Thyroid gland, Wistar, Fipronil

label_protocol: For each sample, Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 600 ng of total RNA using the Low RNA Input Linear Amplification kit PLUS, Two-Color kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Courtaboeuf, France). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 2- to 3-month-old female Wistar rat (225-250 g at the end of the experiment) were housed at room temperature on a 12h light/dark cycle (lights on at 7:00 am) and had free access to food (A04, SAFE, Augy, France) and tap water.

extract_protocol: Following euthanasia, the thyroid gland was promptly removed, snap-frozen in liquid nitrogen and kept at -80°C until RNA extraction. Total RNA was extracted from frozen thyroid gland samples with RNeasy mini kit (Qiagen) following the manufacturer's instructions. Total RNA samples were controlled for integrity on an Agilent 2100 Bioanalyzer (Agilent Technologies) and assayed at 260nm on a NanoDrop ND-1000 spectrophotometer (Thermo Scientific).

treatment_protocol: Rats were randomly allocated to vehicle (n = 10) or fipronil-treated (n = 10) groups and received a daily oral dose of vehicle (aqueous methylcellulose (0.5%, w/v) and Tween 80 (0.01%, w/v) solution) or fipronil suspension (3 mg/kg/day) through feeding needles for 14 days.

tag: strain/background

value: Wistar Crl:WI

value: female

value: 2-3 months

value: thyroid gland

value: Fipronil, 3mg/kg/d, per os for 14 days


title: Cortex_CircadianControl_ZT8_rep5


title: TCM Sample 1

value: Pre Treatment

value: IgG1 Control Ab


title: Cortex_CircadianControl_ZT8_rep4


title: Cortex_CircadianControl_ZT8_rep2


title: Cortex_6HrSDw2HrRecovery_ZT8_rep1


title: Cortex_5HrSDw3HrRecovery_ZT8_rep6

value: 5HrSD and 3Hr Recovery, ZT8


title: Cortex_5HrSDw3HrRecovery_ZT8_rep7

value: 2 month old


title: Cortex_6HrSDw2HrRecovery_ZT8_rep4


title: Thyroid_Wistar_Fipronil_rep6

description:
FIP6
Replicate 6


title: Thyroid_Wistar_Fipronil_rep8

description:
FIP8
Replicate 8


title: Cortex_5HrSDw3HrRecovery_ZT8_rep4


title: Cortex_5HrSDw3HrRecovery_ZT8_rep3


title: Cortex_5HrSDw3HrRecovery_ZT8_rep5


title: Thyroid_Wistar_Vehicle_rep7

description:
Ctrl7
Replicate 7

source_name: Thyroid gland, Wistar, Vehicle

value: Vehicle per os for 14 days


title: Thyroid_Wistar_Vehicle_rep9

description:
Ctrl9
Replicate 9


title: C57BL/6 IFNabRKO_BMDM_media_6 (rep 3)

city: London

first: Christina

last: Taubert

address: The Ridgeway

country: United Kingdom

institute: The Francis Crick Institute, MH

description:
9253994045_B
replicate 3

data_processing: Using GeneSpring GX12.6.1, lower threshold of signal intensity was set to 10, the expression values log transformed (base2) and scaled to the 75th percentile for normalization. The expression values of each gene were then normalized to the median of expression of that gene in all samples, and gene probes quality filtered for those ‘present’ (p<0.01) in at least one sample

source_name: C57BL/6 IFNabRKO_BMDM_media_6

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

value: Female

tag: genotype/variation

value: IFNabRKO

value: BMDM

value: media

tag: time

tag: experiment


title: Thyroid_Wistar_Vehicle_rep5

description:
Ctrl5
Replicate 5

tag: gender


title: C57BL/6 IFNabRKO_BMDM_media_6 (rep 1)

description:
9253994024_D
replicate 1

tag: strain


title: Cortex_5HrSDw3HrRecovery_ZT8_rep1

value: male

tag: tissue

value: cortex


title: Cortex_CircadianControl_ZT7_rep7

value: Circadian Control, ZT7


title: Thyroid_Wistar_Fipronil_rep4

description:
FIP4
Replicate 4

value: Wistar Crl:WI


title: Thyroid_Wistar_Vehicle_rep3

description:
Ctrl3
Replicate 3

value: female


title: C57BL/6 IFNabRKO_BMDM_media_6 (rep 2)

description:
9253994047_C
replicate 2

tag: cell type


title: C57BL/6_BMDM_media_6 (rep 2)

description:
9253994018_A
replicate 2

value: WT


title: C57BL/6_BMDM_media_6 (rep 1)

description:
9253994013_C
replicate 1


title: BALB/c_BMDM_media_6 (rep 3)

description:
9253994018_D
replicate 3

value: BALB/c


title: BALB/c_BMDM_media_6 (rep 1)

description:
9231438033_F
replicate 1


title: Cortex_CircadianControl_ZT7_rep6

tag: age


title: Thyroid_Wistar_Fipronil_rep2

description:
FIP2
Replicate 2

value: 2-3 months

value: thyroid gland

value: Fipronil, 3mg/kg/d, per os for 14 days


title: Thyroid_Wistar_Vehicle_rep1

description:
Ctrl1
Replicate 1


title: Cortex_CircadianControl_ZT7_rep5


title: C57BL/6 IFNabRKO_BMDM_media_3 (rep 3)

description:
9253601019_A
replicate 3

source_name: C57BL/6 IFNabRKO_BMDM_media_3


title: Cortex_5HrSDw3HrRecovery_ZT8_rep2

value: 5HrSD and 3Hr Recovery, ZT8


title: C57BL/6_BMDM_media_6 (rep 3)

description:
9231438097_E
replicate 3


title: C57BL/6 IFNabRKO_BMDM_media_3 (rep 2)

description:
9253994025_A
replicate 2


title: BALB/c_BMDM_media_6 (rep 2)

description:
9231438070_C
replicate 2


title: Cortex_CircadianControl_ZT11_rep2

value: 2 month old

value: Circadian Control, ZT11


title: C57BL/6 IFNabRKO_BMDM_media_3 (rep 1)

description:
9231438042_D
replicate 1

value: Female


title: C57BL/6_BMDM_media_3 (rep 3)

description:
9253994019_A
replicate 3


title: Thyroid_Wistar_Vehicle_rep10

description:
Ctrl10
Replicate 10

value: Vehicle per os for 14 days


title: Thyroid_Wistar_Fipronil_rep9

description:
FIP9
Replicate 9


title: Thyroid_Wistar_Fipronil_rep7

description:
FIP7
Replicate 7


title: Cortex_CircadianControl_ZT7_rep1


title: C57BL/6_BMDM_media_3 (rep 2)

description:
9231438007_E
replicate 2

value: BMDM


title: BALB/c_BMDM_media_3 (rep 1)

description:
9253994028_B
replicate 1

value: media


title: BALB/c_BMDM_media_3 (rep 2)

description:
9253994007_D
replicate 2


title: BALB/c_BMDM_media_3 (rep 3)

description:
9253601035_F
replicate 3


title: C57BL/6_BMDM_media_3 (rep 1)

description:
9253994036_D
replicate 1


title: Cortex_CircadianControl_ZT7_rep4

value: male


title: Cortex_CircadianControl_ZT7_rep2

value: cortex


title: C57BL/6 IFNabRKO_BMDM_HkBps_6 (rep 2)

description:
9253994039_E
replicate 2

source_name: C57BL/6 IFNabRKO_BMDM_HkBps_6

value: IFNabRKO

value: HkBps


title: Thyroid_Wistar_Vehicle_rep8

description:
Ctrl8
Replicate 8

value: Wistar Crl:WI

value: female


title: Thyroid_Wistar_Fipronil_rep3

description:
FIP3
Replicate 3


title: Cortex_6HrSDw1HrRecovery_ZT7_rep5

value: 6hrSD and 1Hr Recovery, ZT7


title: Thyroid_Wistar_Vehicle_rep6

description:
Ctrl6
Replicate 6

value: 2-3 months


title: C57BL/6_BMDM_HkBps_6 (rep 3)

description:
9253994004_F
replicate 3

value: WT


title: C57BL/6 IFNabRKO_BMDM_HkBps_6 (rep 3)

description:
9253994028_D
replicate 3


title: Thyroid_Wistar_Vehicle_rep4

description:
Ctrl4
Replicate 4

value: thyroid gland


title: Cortex_6HrSDw1HrRecovery_ZT7_rep6


title: Cortex_6HrSDw1HrRecovery_ZT7_rep4


title: BALB/c_BMDM_HkBps_6 (rep 3)

description:
9231438031_C
replicate 3

value: BALB/c


title: Cortex_6HrSDw1HrRecovery_ZT7_rep2

value: 2 month old


title: C57BL/6_BMDM_HkBps_6 (rep 1)

description:
9253994025_D
replicate 1


title: C57BL/6_BMDM_HkBps_6 (rep 2)

description:
9253601016_D
replicate 2


title: TCM Sample 6 rep1

value: Pre Treatment

value: IgG1 Control Ab


title: C57BL/6 IFNabRKO_BMDM_HkBps_6 (rep 1)

description:
9253994019_D
replicate 1

value: Female


title: BALB/c_BMDM_HkBps_6 (rep 2)

description:
9253994036_F
replicate 2

value: BMDM


title: Thyroid_Wistar_Fipronil_rep5

description:
FIP5
Replicate 5

value: Fipronil, 3mg/kg/d, per os for 14 days


title: Cortex_6HrSDw1HrRecovery_ZT7_rep1

value: male


title: Thyroid_Wistar_Vehicle_rep2

description:
Ctrl2
Replicate 2

value: Vehicle per os for 14 days


title: Thyroid_Wistar_Fipronil_rep1

description:
FIP1
Replicate 1


title: C57BL/6 IFNabRKO_BMDM_HkBps_3 (rep 3)

description:
9253994007_F
replicate 3

source_name: C57BL/6 IFNabRKO_BMDM_HkBps_3

value: IFNabRKO


title: Cortex_CircadianControl_ZT6_rep7

value: Circadian Control, ZT6

value: cortex


title: C57BL/6 IFNabRKO_BMDM_HkBps_3 (rep 2)

description:
9231438032_F
replicate 2

value: HkBps


title: BALB/c_BMDM_HkBps_6 (rep 1)

description:
9253601035_D
replicate 1


title: C57BL/6 IFNabRKO_BMDM_HkBps_3 (rep 1)

description:
9253994045_C
replicate 1


title: Cortex_CircadianControl_ZT6_rep3


title: Cortex_CircadianControl_ZT6_rep6


title: Cortex_CircadianControl_ZT6_rep5


title: Cortex_CircadianControl_ZT6_rep4


title: C57BL/6_BMDM_HkBps_3 (rep 3)

description:
9253994010_C
replicate 3


title: Preadipo-2_rep1

city: Singapore

first: Vivien

last: Koh

address: 1E Kent Ridge Road

country: Singapore

institute: National University Health System

description:
Replicate 1
SAMPLE 16

data_processing: Data were processed by rank invariant normalization and background subtraction using Genome Studio software.

label: Biotin

source_name: Preadipocytes in subcutaneous fat from SGBS patient

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

growth_protocol: Total RNA was isolated using TRIZOL (Invitrogen) or RNeasy Mini Kit (QIAGEN) according to the respective manufacturer’s instructions. RNA was quantified using NanoDrop ND-1000 spectrophotometer and quality was verified by agarose gel electrophoresis.

extract_protocol: none provided by submitter

value: SGBS cell line


title: Adipo_14days-2_rep1

description:
Replicate 1
SAMPLE 18


title: MEA+NACl treated at Day1, biological rep3

city: Truro

first: Balakrishnan

last: Prithiviraj

state: Nova Scotia

address: 50,Pictou Road

department: Plant, Food and Environmental Sciences

country: Canada

institute: Dalhousie University

description: Arabidopsis treated with MEA+NaCl

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Arabidopsis genome ATH1 array.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Arabidopsis thaliana

source_name: Arabidopsis plant treated with methanolic extract of ANE and NaCl (after 1 day of treatment)

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly (A) + mRNA present in the isolated total RNA (10 µg total RNA starting material each sample reaction) using the SuperScript double-stranded cDNA synthesis kit (Invitrogen) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase.

growth_protocol: 2 weeks old Arabidopsis plants

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

treatment_protocol: Arabidopsis was initially exposed to 150 mM NaCl for 24 hours, after which plants were treated with either the methanol extract of A. nodosum (MEA) or the ethyl acetate sub-fraction of A. nodosum (EAA). Control plants were also exposed to 150 mM NaCl but were treated with 0.1% aqueous methanol.

value: Arabidopsis leaves


title: MEA+NACl treated at Day5, biological rep3

description: Arabidopsis treated with MEA+NaCl

source_name: Arabidopsis plant treated with methanolic extract of ANE and NaCl (after 5 day of treatment)


title: MEA+NACl treated at Day5, biological rep2

description: Arabidopsis treated with MEA+NaCl


title: C57BL/6_BMDM_HkBps_3 (rep 1)

description:
9253601029_D
replicate 1

value: WT


title: BALB/c_BMDM_HkBps_3 (rep 2)

description:
9253994020_E
replicate 2


title: Adipo_7days-1_rep1

description:
Replicate 1
SAMPLE 14


title: C57BL/6_BMDM_HkBps_3 (rep 2)

description:
9253994046_E
replicate 2


title: MEA+NACl treated at Day5, biological rep1

description: Arabidopsis treated with MEA+NaCl


title: MEA+NACl treated at Day1, biological rep2

description: Arabidopsis treated with MEA+NaCl


title: Cortex_CircadianControl_ZT6_rep2


title: Adipo_7days-2_rep1

description:
Replicate 1
SAMPLE 17


title: EAA+NACl treated at Day5, biological rep3

description: Arabidopsis treated with EAA+NaCl

source_name: Arabidopsis plant treated with ethyl acetate extract of ANE and NaCl  (after 5day of treatment)


title: Cortex_6HrSleepDep_ZT6_rep7

value: 6HrSleepDep, ZT6


title: MEA+NACl treated at Day1, biological rep1

description: Arabidopsis treated with MEA+NaCl


title: BALB/c_BMDM_HkBps_3 (rep 3)

description:
9231438042_E
replicate 3

value: BALB/c


title: EAA+NACl treated at Day5, biological rep2

description: Arabidopsis treated with EAA+NaCl


title: Cortex_CircadianControl_ZT6_rep1

value: 2 month old


title: Adipo_14days-1_rep1

description:
Replicate 1
SAMPLE 15


title: Donor3_Adipo_48h_rep1

description:
Replicate 1
SAMPLE 12

source_name: Healthy donor (adult)

value: Human monocytes


title: BALB/c_BMDM_HkBps_3 (rep 1)

description:
9253601016_A
replicate 1


title: EAA+NACl treated at Day5, biological rep1

description: Arabidopsis treated with EAA+NaCl


title: Cortex_6HrSleepDep_ZT6_rep6


title: Preadipo-1_rep1

description:
Replicate 1
SAMPLE 13


title: LPS/zVAD/Nec-1

first: Alexei

last: Degterev

address: 37 tyler street

department: Biochemistry

institute: Tufts University

description: Quality Control and Gene-level signal: Affymetrix Expression Console Software

hyb_protocol: Following fragmintation, about 2.5μg of cRNA were hybridized for 16 hours at 45 degree C on Gene Chip Mouse Gene ST 1.0 Array. GeneChips were washed and stained in the Affymetrix fluidics station 450.

scan_protocol: GeneChips were scanned using Affymetrix GENEChip® Scanner 30007G.

data_processing: The data were analyzed wth Affymetrix® Expression Console™Software using Affymetrix default analysis settings.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA ( Ambion WT expression kit, Affymetrix).

growth_protocol: BMDMs were prepared by flushing bone marrows from femurs and tibias. BMDMs were allowed to differentiate for 7 days in the presence of conditioned media from L929 cells, containing Macrophage Colony Stimulating Factor (M-CSF)-30% L929 media, 20% FBS and 1% PSA (penicillin/streptomycin/antimycotic solution) in RPMI1640. Medium was replenished on day 3. 48 hours before treating the cells, the medium was exchanged to 10% L929 media, 10% FBS and 1% PSA in RPMI1640. On day 7, the adherent cells were collected using PBS and centrifuged at 430g for 5 min and replated for the experiments at density of 2 millons BMDMs per well.

extract_protocol: Total RNA were extracted using Qiagen RNeasy Plus Kit.

treatment_protocol: BMDMs were treated under 4 different conditions: Control, LPS, LPS/zVAD and LPS/zVAD/Nec-1. LPS=10ng/ml, zVAD=50μM, Nec-1=30μM.

value: Bone marrow

value: BalbC


title: Cortex_6HrSleepDep_ZT6_rep4


title: Donor3_Pre_48h_rep1

description:
Replicate 1
SAMPLE 11


title: EAA treated at Day5, biological rep3

description: Arabidopsis treated with EAA

source_name: Arabidopsis plant treated with NaCl (after 5 day of treatment)


title: Cortex_6HrSleepDep_ZT6_rep5


title: Cortex_6HrSleepDep_ZT6_rep1


title: Donor3_Adipo_24h_rep1

description:
Replicate 1
SAMPLE 10


title: Donor2_Pre_48h_rep1

description:
Replicate 1
SAMPLE 7


title: P-REX1 RNAi #2 with HRG, biological rep 2

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

hyb_protocol: Hybridization was done over Affymetrix GeneChip Human Gene 1.0 ST Array according to the standard protocols at the University of Pennsylvania Microarray Facility.

scan_protocol: Affymetrix Gene ChIP Scanner.

data_processing: The Robust Multichip Average algorithm was employed for background adjustment, quantile normalization and probe set values summarization.

source_name: Breast cancer cell line

label_protocol: Total RNA was reversed transcribed to cDNA (GeneChip® Whole Transcript cDNA Synthesis and Amplification Kit, Affymetrix; Santa Clara, CA), fragmented and end labeled (GeneChip® WT Terminal Labelling Kit, Affymetrix) for further hybridization.

growth_protocol: T-47D cells were obtained from ATCC (Manassas, VA) and were grown in DMEM medium (Lonza; Basel, Switzerland) supplemented with 10% FBS (Hyclone; Logan, UT).

extract_protocol: Total RNA for each sample were obtained using the miRNeasy kit (Qiagen; Valencia, CA). RNA quality was analyzed using Agilent Bioanalyzer Nano assay.

treatment_protocol: T-47D cells were serum starved and then stimulated with HRG (20 ng/ml) or vehicle (PBS) for 6 h in 60-mm plates.

tag: cells

value: T-47D cell line


title: EAA+NACl treated at Day1, biological rep1

description: Arabidopsis treated with EAA+NaCl

source_name: Arabidopsis plant treated with ethyl acetate extract of ANE and NaCl (after 1 day of treatment)


title: Donor2_Adipo_48h_rep1

description:
Replicate 1
SAMPLE 8


title: Cortex_6HrSleepDep_ZT6_rep3


title: Cortex_CircadianControl_ ZT0anchor_rep7

source_name: Cortex_CircadianControl_ ZT0anchor

value: Circadian Control, ZT0


title: Cortex_6HrSleepDep_ZT6_rep2

value: male


title: LPS

source_name: Female BalbC mouse_bone_marrow_LPS

value: Female


title: Donor2_Adipo_24h_rep1

description:
Replicate 1
SAMPLE 6


title: Donor3_Pre_24h_rep1

description:
Replicate 1
SAMPLE 9


title: Control

source_name: Female BalbC mouse_bone_marrow_control


title: EAA+NACl treated at Day1, biological rep3

description: Arabidopsis treated with EAA+NaCl


title: EAA+NACl treated at Day1, biological rep2

description: Arabidopsis treated with EAA+NaCl

source_name: Arabidopsis plant treated with ethyl acetate extract of ANE and NaCl  (after 1day of treatment)


title: Donor2_Pre_24h_rep1

description:
Replicate 1
SAMPLE 5


title: EAA treated at Day5, biological rep2

description: Arabidopsis treated with EAA


title: P-REX1 RNAi #2 with HRG, biological rep 3


title: P-REX1 RNAi #2 with HRG, biological rep 1


title: Cortex_CircadianControl_ ZT0anchor_rep6


title: LPS/zVAD

source_name: Female BalbC mouse_bone_marrow_LPS/zVAD


title: EAA treated at Day1, biological rep3

description: Arabidopsis treated with EAA

source_name: Arabidopsis plant treated with NaCl (after 1 day of treatment)


title: EAA treated at Day5, biological rep1

description: Arabidopsis treated with EAA

source_name: Arabidopsis plant treated with NaCl(after 5 day of treatment)


title: Donor1_Adipo_48h_rep1

description:
Replicate 1
SAMPLE 4


title: P-REX1 RNAi #2 without HRG, biological rep 3


title: Donor1_Adipo_24h_rep1

description:
Replicate 1
SAMPLE 2


title: P-REX1 RNAi #1 with HRG, biological rep 2


title: P-REX1 RNAi #2 without HRG, biological rep 2


title: Cortex_CircadianControl_ ZT0anchor_rep2


title: Donor1_Pre_48h_rep1

description:
Replicate 1
SAMPLE 3


title: Donor1_Pre_24h_rep1

description:
Replicate 1
SAMPLE 1


title: Cortex_CircadianControl_ ZT0anchor_rep4


title: EAA treated at Day1, biological rep1

description: Arabidopsis treated with EAA


title: P-REX1 RNAi #1 with HRG, biological rep 3


title: P-REX1 RNAi #2 without HRG, biological rep 1


title: Cortex_CircadianControl_ ZT0anchor_rep5


title: P-REX1 RNAi #1 without HRG, biological rep 2


title: NTC RNAi with HRG, biological rep 2

description: NTC RNAi with HRG, biological rep 2


title: CD8_TILs_SP_rep1

city: CAMBRIDGE

first: Meromit

last: Singer

state: MASSACHUSETTS

address: 415 main st, ROOM 6031

institute: Broad Institute of MIT and Harvard

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: .CEL files were RMA normalized and merged to an expression matrix using the ExpressionFileCreator of GenePattern with default parameters (Reich et al., 2006).

source_name: CD8+Tim3-PD1+ TILs from CT26 colon carcinoma-bearing Balb/c mice

label_protocol: standard Affymetrix protocol

value: CD8+Tim3-PD1+ TILs


title: Cortex_CircadianControl_ ZT0anchor_rep3


title: NTC RNAi with HRG, biological rep 3

description: NTC RNAi with HRG, biological rep 3


title: P-REX1 RNAi #1 without HRG, biological rep 1


title: EAA treated at Day1, biological rep2

description: Arabidopsis treated with EAA


title: P-REX1 RNAi #1 without HRG, biological rep 3


title: Late diabetes MDSC

city: Torrance

first: Robert

last: Gelfand

state: CA

address: 1124 W. Carson St

department: surgery

institute: LABiomed at Harbor UCLA,  and Charles Drew Univ

hyb_protocol: per UCLA pathology lab protocol according to Affymetrix protocol.

data_processing: Values were calculated as rma values per Affymetrix system calculations.

source_name: male obese Zucker fa/fa rats

label_protocol: RNA was processed and analyzed at the UCLA pathology DNA lab according to the Affymetrix protocol.

growth_protocol: Cells were grown in plastic 6 well plates in Dulbeccor's Modified Eagle's Medium plus 20% fetal bovine serum in the presence of 5.6 mM glucose or 22 mM glucose.

extract_protocol: Cells from individual wells of 6 well plates were washed 1x with phosphate buffered saline, and RNA was extracted using the RNeasy Plus Micro kit per the manufacturer's instructions.

treatment_protocol: Cells were carried in culture until RNA isolation.

value: skeletal muscle stem cells

value: Zucker obese fa/fa


title: NTC RNAi with HRG, biological rep 1

description: NTC RNAi with HRG, biological rep 1


title: CD8_TILs_SP_rep2


title: Early diabetes MDSC

scan_protocol: per UCLA pathology lab protocol according to Affymetrix protocol.


title: CD8_naive_rep3

source_name: CD62LhiCD44low CD8+ cells from non tumor-bearing Balb/c mice

value: CD62LhiCD44low CD8+ cells


title: CD8_naive_rep2


title: CD8_naive_rep1


title: CD8_naive_rep4


title: T-47D parenta with HRG, biological rep 3


title: NTC RNAi without HRG, biological rep 1

description: NTC RNAi without HRG, biological rep 1


title: CD8_Eff_Mem_rep1

source_name: CD62LlowCD44hi CD8+ cells from non tumor-bearing Balb/c mice

value: CD62LlowCD44hi CD8+ cells


title: CD8_Eff_Mem_rep3


title: HepG2, Negative Control, Rep 3

first: QING

middle: K

last: WANG

state: Ohio

address: 9500 Euclid Ave

department: Molecular Cardiology

institute: Cleveland Clinic

description: Gene expression data from HepG2 cells treated by negative control siRNA

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00‐0331‐220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00‐0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00‐00212, Affymetrix,Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA,US) with default settings.

data_processing: Raw probe intensities were further normalized by Robust Multi-array Average (RMA) algorithm, which was implemented by Gene Spring Software 11.0 (Agilent technologies). A total of 49,293 expression probes with intensities distinguishable from background noise (detection P value < 0.05) in all RNA samples were filtered out for downstream differential analysis.

source_name: HepG2 cell line treated by negative control siRNA

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: A HepG2 cell line was purchased from ATCC (American Type Culture Collection) and maintained in the Dulbecco's Modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Gibco Life Technologies). All cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596‐018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase‐Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Small interfering RNA (siRNA) specific to human ADTRP (ADTRP siRNA) and negative control siRNA (NC siRNA) were purchased from Genepharma. The sequences of  ADTRP siRNA were （5'-GGAUCCUCUUUCUCUACAATT-3' (sense) and（5'-UUGUAGAGAAAGAGGAUCCTT-3' (antisense).  The sequences of  NC siRNA were （5'- UUCUCCGAACGUGUCACGUTT-3' (sense) and（5'- ACGUGACACGUUCGGAGAATT-3' (antisense).   Transfection of siRNA (100 nM) was performed using Lipofectamine® RNAi MAX according to the manufacturer’s protocol (Invitrogen, Thermo Fisher).

tag: cell line


title: T-47D parenta with HRG, biological rep 1


title: T-47D parenta with HRG, biological rep 2


title: CD8_TILs_DP_rep2

source_name: CD8+Tim3+PD1+ TILs from CT26 colon carcinoma-bearing Balb/c mice

value: CD8+Tim3+PD1+ TILs


title: CD8_Eff_Mem_rep2


title: CD8_TILs_DP_rep3


title: CD8_TILs_DP_rep1


title: NTC RNAi without HRG, biological rep 3

description: NTC RNAi without HRG, biological rep 3


title: HepG2, Negative Control, Rep 2


title: NTC RNAi without HRG, biological rep 2

description: NTC RNAi without HRG, biological rep 2


title: CD8_TILs_DN_rep2

source_name: CD8+Tim3-PD1- TILs from CT26 colon carcinoma-bearing Balb/c mice

value: CD8+Tim3-PD1- TILs


title: T-47D parenta without HRG, biological rep 3


title: CD8_TILs_DN_rep3


title: HepG2, ADTRP siRNA, Rep 3

description: Gene expression data from HepG2 cells treated by ADTRP siRNAs

source_name: HepG2 cell line treated by ADTRP siRNA


title: T-47D parenta without HRG, biological rep 2

source_name: Breast cancer cell line


title: T-47D parenta without HRG, biological rep 1


title: HepG2, ADTRP siRNA, Rep 2


title: HepG2, Negative Control, Rep 1


title: BAT_CAAM_4hr_no7

status: Public on Sep 06 2016

city: Kawasaki

first: Fumika

last: SHINOZAKI

address: 3-25-13 Tonomachi, Kawasaki-ku

institute: Kanagawa Institute of Industrial Science and Technology

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

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

data_processing: CEL files were quantified with the Distribution Free Weighted method (DFW), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

source_name: BAT of mouse administrated CAAM

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA ( GeneChip 3'IVT Express Kit User Manual, P/N702646 Rev.8, Affymetrix).

value: ddY

tag: Sex

value: Male

value: brown adipose tissue (BAT)


title: BAT_CAAM_4hr_no5


title: BAT_DW_4hr_no2

source_name: BAT of mouse administrated water


title: CD8_TILs_DN_rep1


title: BAT_DW_4hr_no3


title: BAT_CAAM_4hr_no6


title: BAT_DW_4hr_no6


title: WAT_CAAM_4hr_no7

source_name: WAT of mouse administrated CAAM

value: white adipose tissue (WAT)


title: HepG2, ADTRP siRNA, Rep 1


title: P-REX1 RNAi #1 with HRG, biological rep 1


title: WAT_DW_4hr_no7

source_name: WAT of mouse administrated water


title: BAT_DW_4hr_no5


title: BAT_DW_4hr_no4


title: BAT_DW_4hr_no7


title: BAT_CAAM_4hr_no4


title: BAT_CAAM_4hr_no2


title: WAT_CAAM_4hr_no4


title: WAT_CAAM_4hr_no5


title: Cortex_CircadianControl_ ZT0anchor_rep1

source_name: Cortex_CircadianControl_ ZT0anchor

value: 2 month old

value: cortex


title: WAT_CAAM_4hr_no2


title: WAT_CAAM_4hr_no6


title: CD8_TILs_SP_rep3


title: WAT_DW_4hr_no6


title: WAT_DW_4hr_no5


title: WAT_DW_4hr_no4


title: WAT_DW_4hr_no2


title: BAT_DW_4hr_no1


title: Liver_CAAM_4hr_no7

source_name: Liver of mouse administrated CAAM

value: Liver


title: Liver_CAAM_4hr_no6


title: WAT_DW_4hr_no3


title: Liver_DW_4hr_no5

source_name: Liver of mouse administrated water


title: Liver_DW_4hr_no6


title: Liver_CAAM_4hr_no2


title: Liver_CAAM_4hr_no4


title: Liver_CAAM_4hr_no5


title: BAT_VAAM_4hr_no4

source_name: BAT of mouse administrated VAAM


title: BAT_DW_4hr_no6


title: BAT_VAAM_4hr_no1


title: Liver_DW_4hr_no1


title: Liver_DW_4hr_no3


title: BAT_DW_4hr_no2


title: BAT_DW_4hr_no5


title: BAT_VAAM_4hr_no6


title: BAT_DW_4hr_no3


title: BAT_DW_4hr_no4


title: BAT_DW_4hr_no7


title: BAT_VAAM_4hr_no7


title: Liver_DW_4hr_no2


title: BAT_VAAM_4hr_no2


title: Liver_DW_4hr_no7


title: WAT_VAAM_4hr_no3

source_name: WAT of mouse administrated VAAM


title: WAT_DW_4hr_no1


title: WAT_VAAM_4hr_no5


title: BAT_VAAM_4hr_no5


title: BAT_VAAM_4hr_no3


title: WAT_VAAM_4hr_no6


title: BAT_DW_4hr_no1


title: WAT_VAAM_4hr_no4


title: WAT_VAAM_4hr_no7


title: WAT_VAAM_4hr_no2


title: WAT_DW_4hr_no6


title: WAT_VAAM_4hr_no1


title: WAT_DW_4hr_no2


title: WAT_DW_4hr_no5


title: WAT_DW_4hr_no3


title: Liver_VAAM_4hr_no7

source_name: Liver of mouse administrated VAAM


title: WAT_DW_4hr_no4


title: WAT_DW_4hr_no7


title: Liver_VAAM_4hr_no1


title: Liver_VAAM_4hr_no2


title: Liver_VAAM_4hr_no5


title: Liver_VAAM_4hr_no6


title: Liver_DW_4hr_no7


title: Liver_VAAM_4hr_no3


title: Liver_DW_4hr_no5


title: Liver_DW_4hr_no6


title: Liver_DW_4hr_no2


title: HEK/RPF1 Tet- rep3

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

description:
RPF1_4256231024_B.AVG
4256231024_B.AVG

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalization with BeadStudio software

source_name: HEK/RPF Tet- (induced HEK/RPF1)

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

growth_protocol: HEK/RPF1 cells were cultured 48 h in Tet-depleted medium (Tet-)

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

value: HEK293/RPF-1 transfectants

value: HEK/RPF Tet- (induced HEK/RPF1)


title: HEK/RPF1 Tet- rep2

description:
RPF1_4256231024_A.AVG
4256231024_A.AVG


title: Liver_DW_4hr_no3


title: Liver_DW_4hr_no4


title: Liver_VAAM_4hr_no4


title: HEK/RPF1 Tet+ rep1

description:
19plus_4256231023_E.AVG
4256231023_E.AVG

source_name: HEK/RPF Tet+ (control for induced HEK/RPF1)

growth_protocol: HEK/RPF1 cells were cultured 48 h in Tet-supplemented medium (Tet+)


title: HEK/RPF1 Tet- rep1

description:
RPF1_4256231023_H.AVG
4256231023_H.AVG


title: HEK/RPF1 Tet+ rep2

description:
19plus_4256231023_F.AVG
4256231023_F.AVG

value: HEK/RPF Tet+ (control for induced HEK/RPF1)


title: HEK/Mock Tet+ rep1

description:
Mplus_4256231019_G.AVG
4256231019_G.AVG

source_name: HEK/Mock Tet+ (reference for uninduced HEK/RPF1)

growth_protocol: HEK/Mock cells were cultured 48 h in Tet-supplemented medium (Tet+)


title: HEK/RPF1 Tet+ rep3

description:
19plus_4256231023_G.AVG
4256231023_G.AVG


title: HEK/Mock Tet+ rep2

description:
Mplus_4256231019_H.AVG
4256231019_H.AVG

value: HEK/Mock Tet+ (reference for uninduced HEK/RPF1)


title: Liver_DW_4hr_no1


title: HEK/Mock Tet- rep2

description:
Mminus_4256231023_C.AVG
4256231023_C.AVG

source_name: HEK/Mock Tet- (reference for induced HEK/RPF1)

growth_protocol: HEK/Mock cells were cultured 48 h in Tet-depleted medium (Tet-)


title: HEK/Mock Tet+ rep3

description:
Mplus_4256231023_A.AVG
4256231023_A.AVG


title: HEK/Mock Tet- rep1

description:
Mminus_4256231023_B.AVG
4256231023_B.AVG

value: HEK/Mock Tet- (reference for induced HEK/RPF1)


title: HEK/Mock Tet- rep3

description:
Mminus_4256231023_D.AVG
4256231023_D.AVG