title: Control (rhLIGHT 0 ng/ml) vs rhLIGHT 200 ng/ml.

city: Ulsan

first: Sook-Kyoung

last: Heo

address: 877 Bangeojinsunhwan-doro

department: Biomedical Research Center

country: South Korea

institute: University of Ulsan College of Medicine

description: Whole Human Genome Microarray 4x44K v2 (Probe Name version)

hyb_protocol: The fragmented cRNA was resuspended with 2× hybridization buffer and directly pipetted onto the microarray, which was placed in the Hybridization Chamber (Agilent Technologies, Inc.). By incubating the hybridization chamber at 42°C for 16 hours with mild agitation, competitive hybridization reactions occurred between labeled targets and probes on the microarray. To eliminate the non-specific binding, hybridized microarrays were washed with Agilent’s Gene Expression Wash Buffer Kit. Finally, microarrays were spin-dried and stored in dark conditions until scanned.

scan_protocol: Scanned images were analyzed using the Feature Extraction program (Agilent Technologies, Inc.).

data_processing: All data manipulations, the selection of genes exhibiting fold-changes, and statistical t-tests were performed using GeneSpring 7.3.1 (Agilent Technologies, Inc.). All numerical data were normalized by intensity-dependent normalization (locally weighted scatterplot smoothing, LOWESS), where the ratio was reduced to the residual of the Lowess fit of the intensity vs. ratio curve using GeneSpring 7.3.1.

source_name: Human bone marrow-derived mesenchymal stem cells

label_protocol: During transcription-amplification, cRNA samples were labeled with Cy3-CTP and Cy5-CTP, respectively. Amplified and labeled cRNA was purified and quantified using an ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE, USA) to check labeling efficiency, followed by fragmentation of cRNA by adding 10× blocking agent and 25× fragmentation buffer and incubating at 60°C for 30 min

growth_protocol: Human BM-MSCs were incubated with 0 and 200 ng/ml rhLIGHT for 72 h, and were analyzed using a 44K oligo-microarray (Agilent Technologies, Inc., Palo Alto, CA, USA)

extract_protocol: For RNA samples, the synthesis of target cRNA probes and hybridization were performed using Agilent’s Low RNA Input Linear Amplification Kit PLUS according to the manufacturer’s instructions. Briefly, 1 μg of total RNA for each sample and T7 promoter primer mix were mixed and incubated at 65°C for 10 min. cDNA master mix (5× first-strand buffer, 0.1 M DTT, 10 mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to RNA and the primer mixture. The samples were incubated at 40°C for 2 h for reverse-transcription and double-strand cDNA (dsDNA) synthesis and terminated by incubation at 65°C for 15 min. The transcription master mix was prepared following the manufacturer’s protocol (4× Transcription buffer, 0.1 M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP), added to the dsDNA reaction mixture, and incubated at 40°C for 2 h for transcription of dsDNA.

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

tag: time point

value: day 3 (72hr)

tag: protocol

value: recombinant human LIGHT 0 ng/ml

value: recombinant human LIGHT 200 ng/ml


title: 18h +Isotype control sample 3

status: Public on Aug 23 2016

type: RNA

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in Partek Genomic Suite

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: 18h +Isotype control sample 3

label_protocol: Biotinylated cRNA were prepared with the TargetAmpTM Nano-gTM Biotin-aRNA Labeling Kit

extract_protocol: Total RNA from all cell samples was isolated using TRIzol Reagent (Invitrogen).

tag: strain

value: DesTCR mice (Tg(KB5.C20-TCR))

tag: age

value: 8-16 weeks

tag: tissue

value: splenic DesTCR T cells


title: 48h +Isotype control sample 2

description: replicate 2

source_name: 48h +Isotype control sample 2


title: 48h +Isotype control sample 3

description: replicate 3

source_name: 48h +Isotype control sample 3


title: WT_WW30m_replicate3

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

description: Gene expression after 30 min of elicitation with Wounding + Water

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent platform GPL21138 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Quantile normalization and log2 transformation was performed for all raw microarray data using the R package “Agi4x44PreProcess”. All probes with signal within 95% confidence interval of the signal of negative control probes were discared from down-stream analysis.  All replicated probes were averaged.

organism: Nicotiana attenuata

source_name: wild type plant leaves, 30 min, Wounding + Water elicitation, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds from N. attenuata wild type and ir-AOC plants were grown in the glasshouse under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

extract_protocol: Total RNA was extracted from leaves using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: For elicitation treatment, leaves were wounded by rolling a fabric-pattern wheel three times on each side of the midvein and the wounds were supplemented with 20 microliters of FAC diluted 1/5 (v/v) in water.

tag: genotype/variation

value: wild type

tag: treatment

value: elicitation with Wounding + Water

value: leaves


title: irAOC_WW30m_replicate2

source_name: irAOC plant leaves, 30 min, Wounding + Water elicitation, replicate 2

value: irAOC


title: irAOC_WW30m_replicate1

source_name: irAOC plant leaves, 30 min, Wounding + Water elicitation, replicate 1


title: irAOC_FAC30m_replicate3

description: Gene expression after 30 min of elicitation with Wounding + FAC

source_name: irAOC plant leaves, 30 min, Wounding + FAC elicitation, replicate 3

value: elicitation with Wounding + FAC


title: 48h +Isotype control sample 1

description: replicate 1

source_name: 48h +Isotype control sample 1


title: 0h sample 3

description: replicate 3

source_name: 0h sample 3


title: Granny_Smith_PH_1-MCP_3

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

country: Italy

institute: University of Trento

description: SAMPLE 18

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User's Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' inst

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization

organism: Malus domestica

source_name: Granny Smith_treated with 1-MCP at harvest and stored for after 1 wk of postharvest shelf life

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User's Guide (V 3.2).

growth_protocol: Plants were manteined following standard agronomical techniques for pruning, thinning and pest-disease control

extract_protocol: Total RNA was isolated from fruit cortex tissue of three biological replicates with the Spectrum Total RNA kit (Sigma). RNA quantity and quality was controlled with a Nanodrop ND-8000 (Thermo Scientific, USA) and an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: 1ppm of 1-methylcyclopropene (1-MCP) was applied after harvest overnight

tag: cultivar

value: Granny Smith

tag: ripening stage

value: postharvest 1-MCP treated

value: fruit flesh


title: 4h +FcMR sample 2

description: replicate 2

source_name: 4h +FcMR sample 2


title: SUM149 cells 6h after ACY1215 treatment

city: Memphis

first: Jiyang

last: Yu

state: TN

address: 262 Danny Thomas Place, MS 1135

department: Computational Biology

country: USA

institute: St. Jude Children's Research Hospital

hyb_protocol: standard Agilent hybridization protocol

scan_protocol: standard Agilent scanning protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides: scan area was 61x21.6 mm, scan resolution 3 µm, dye channel was set to Green, Tiff file dynamic range was 20 bits and Green PMT was set to 100 %.

data_processing: background subtraction, LOWESS and QUANTILE normalization

organism: Homo sapiens

label_protocol: 100 ng of RNA were labelled using Low Input Quick Amp Labeling kit from Agilent Technologies

growth_protocol: SUM149 cells were seeded in 6-well plates and let attach for 24 hours. Next day they were treated with 2.5uM ACY1215 for 3, 6 and 12 hours before RNA extraction.

extract_protocol: RNA was extracted with Rnaeasy following manufacturer instructions.

tag: cell line

source_name: pool of all untreated and treated SUM149 cells


title: SUM149 cells untreated


title: Granny_Smith_PH_1-MCP_1

description: SAMPLE 16


title: 18h +FcMR sample 2

description: replicate 2

source_name: 18h +FcMR sample 2


title: Granny_Smith_PH_1-MCP_2

description: SAMPLE 17


title: SUM149 cells 12h after ACY1215 treatment


title: irAOC_FAC30m_replicate1

source_name: irAOC plant leaves, 30 min, Wounding + FAC elicitation, replicate 1


title: SUM149 cells 3h after ACY1215 treatment


title: African American primary proximal tubule cells K10202

city: Winston Salem

first: Lijun

last: Ma

state: NC

address: 1 Medical Center Blvd

department: Nephrology

institute: Wake Forest School of Medicine

hyb_protocol: Following fragmentation and labeling, 5.2 µg ss-cDNA was hybridized for 16 hr at 45 °C in hybridization oven, rotating at 60 rpm on GeneChip® Human Transcriptome Array 2.0. Cartridges were washed and stained using the GeneChip Fluidics Station according to standard Affymetrix operating procedures (Affymetrix®GeneChip® Fluidics Station 450 User's Guide AGCC (P/N 08-0295), the GeneChip® Expression Wash, Stain, and Scan User Manual for Cartridge Arrays (PN 702731)

scan_protocol: Cartridges were scanned using the GeneChip® Scanner 3000 7G according to the standard Affymetrix protocol (GeneChip® Expression Wash,Stain, and Scan User Manual for Cartridge Arrays (PN 702731) and the Affymetrix® GeneChip® Command Console® User Manual (P/N 702569)).

data_processing: Raw data were generated using TAC software and normalized by the RMA method. Log intensity distributions, pair-wise correlations and internal Affymerix controls were examined to evaluate hybridization quality.

label: Biotin

label_protocol: Approximately 250 ng of purified total RNA was processed to produce amplified and biotinylated sense-strand DNA targets.

extract_protocol: Total RNA was isolated from HEK293 Tet-on APOL1 G0, G1 and G2 cells using the QIAGEN Rneasy Mini Kit (QIAGEN Cat # 74104).

tag: apol1 genotype

tag: cell type

value: primary proximal tubule cells


title: Scramble vector DU145 cell,rep2

city: Guangzhou

first: Yifeng

last: Luo

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Institute of Respiratory Diseases of Sun Yat-sen University

country: China

institute: The First Affiliated Hospital of Sun Yat-sen University

description: Scramble vector DU145 cell as Control

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.

data_processing: 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. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US)

source_name: Scramble vector DU145 cell,rep2

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: Cell are cultured in RPMI 1640 medium (Hyclone, USA) supplemented with 10% fetal bovine serum (Gibico, USA), 2 mM L-glutamine, and antibiotics.

extract_protocol: Cell lysised by TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) and extracted as TRIZOL Kit protocol requirement.Totoal RNA will be 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: After cell grow up to more than 70% confluency, the cell collected.

tag: genotype

value: Control


title: 18h +Isotype control sample 1

description: replicate 1

source_name: 18h +Isotype control sample 1


title: 48h +FcMR sample 1

description: replikate 1

source_name: 48h +FcMR sample 1


title: African American primary proximal tubule cells K10182


title: 0h sample 4

description: replicate 4

source_name: 0h sample 4


title: Granny_Smith_PH_Ctrl_3

description: SAMPLE 15

source_name: Granny Smith_after 1 wk of postharvest shelf life

value: postharvest control


title: Scramble vector DU145 cell,rep1

description: Scramble vector DU145 cell as Control

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.

source_name: Scramble vector DU145 cell,rep1


title: irAOC_FAC30m_replicate2

source_name: irAOC plant leaves, 30 min, Wounding + FAC elicitation, replicate 2


title: 48h +FcMR sample 2

description: replicate 2

source_name: 48h +FcMR sample 2


title: African American primary proximal tubule cells K10018


title: African American primary proximal tubule cells K10203


title: 4h +FcMR sample 1

description: replicate 1

source_name: 4h +FcMR sample 1


title: HCT116 Dicer wildtype cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Dicer wildtype cells

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

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

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

source_name: HCT116 cells

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

growth_protocol: DMEM with 10% FBS with or without tetracycline

extract_protocol: Standard Trizol Reagent for the RNA extraction.

treatment_protocol: For Hct tet100 cells, Dicer gene disrupted HCT116 cells were transduced with tet-on Dicer gene and cultured with 100 pg/ml tetracycline for more than one week.

value: Colon carcinoma


title: African American primary proximal tubule cells K10073


title: Granny_Smith_PH_Ctrl_1

description: SAMPLE 13


title: Granny_Smith_PH_Ctrl_2

description: SAMPLE 14


title: miR-30d overexpression DU145 cell,rep2

description: miR-30d overexpression DU145 cell

source_name: miR-30d overexpression DU145 cell,rep2


title: 18h +FcMR sample 1

description: replicate 1

source_name: 18h +FcMR sample 1


title: African American primary proximal tubule cells K10222


title: miR-195 overexpression DU145 cell,rep2

description: miR-195 overexpression DU145 cell

source_name: miR-195 overexpression DU145 cell,rep2


title: Granny_Smith_H_3

description: SAMPLE 12

source_name: Granny Smith_at harvest

value: harvest


title: miR-30d overexpression DU145 cell,rep1

description: miR-30d overexpression DU145 cell

source_name: miR-30d overexpression DU145 cell,rep1


title: 4h +Isotype control sample 2

description: replicate 2

source_name: 4h +Isotype control sample 2


title: 18h +FcMR sample 3

description: replicate 3

source_name: 18h +FcMR sample 3


title: 4h +Isotype control sample 1

description: replicate 1

source_name: 4h +Isotype control sample 1


title: miR-195 overexpression DU145 cell,rep1

description: miR-195 overexpression DU145 cell

source_name: miR-195 overexpression DU145 cell,rep1


title: Granny_Smith_H_2

description: SAMPLE 11


title: African American primary proximal tubule cells K10219


title: 0h sample 2

description: replicate 2

source_name: 0h sample 2


title: Wildtype LNCap cell,rep3

description: Wildtype LNCap cell line

source_name: Wildtype LNCap cell,rep3

value: LNCap

value: WildType


title: African American primary proximal tubule cells K10217


title: Granny_Smith_H_1

description: SAMPLE 10


title: African American primary proximal tubule cells K10214


title: 0h sample 1

description: replicate 1

source_name: 0h sample 1

value: DesTCR mice (Tg(KB5.C20-TCR))

value: 8-16 weeks


title: Golden_Delicious_PH_1-MCP_2

description: SAMPLE 8

source_name: Gold delicious_treated with 1-MCP at harvest and stored for after 1 wk of postharvest shelf life

value: Golden Delicious


title: Golden_Delicious_PH_1-MCP_3

description: SAMPLE 9


title: Wildtype LNCap cell,rep1

description: Wildtype LNCap cell line

source_name: Wildtype LNCap cell,rep1


title: Scramble vector LNCap cell,rep3

description: Scramble vector LNCap cell as Control

source_name: Scramble vector LNCap cell,rep3


title: Scramble vector LNCap cell,rep2

description: Scramble vector LNCap cell as Control

source_name: Scramble vector LNCap cell,rep2


title: African American primary proximal tubule cells K10210


title: Golden_Delicious_PH_Ctrl_3

description: SAMPLE 6

source_name: Gold delicious_after 1 wk of postharvest shelf life


title: Wildtype LNCap cell,rep2

description: Wildtype LNCap cell line

source_name: Wildtype LNCap cell,rep2


title: SOLmuscle_cSix1 rep3

city: Paris

first: iori

last: sakakibara

address: 22 rue Méchain

country: France

institute: Cochin institut

description: Microarrays analysis of soleus muscles of cSix1

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: the data were RMA normalized  and  analysed with Partek Genomic Suit

source_name: C56BL6N soleus muscle

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

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

treatment_protocol: Soleus muscles were collected from cSix1 KO and control mice. Total RNAs were extracted by Trizol Reagent (Invitrogen) according to manufacturer's instruction.

value: soleus muscle

value: 8 weeks old

value: cSix1 KO


title: Scramble vector LNCap cell,rep1

description: Scramble vector LNCap cell as Control

source_name: Scramble vector LNCap cell,rep1


title: African American primary proximal tubule cells K10211


title: SOLmuscle_cSix1 rep2


title: Golden_Delicious_PH_Ctrl_2

description: SAMPLE 5


title: African American primary proximal tubule cells K10165


title: African American primary proximal tubule cells K10188


title: SOLmuscle_ctl rep3

value: wild type


title: miR-30d overexpression LNCap cell,rep3

description: miR-30d overexpression LNCap cell

source_name: miR-30d overexpression LNCap cell,rep3


title: African American primary proximal tubule cells K10159


title: Golden_Delicious_PH_Ctrl_1

description: SAMPLE 4


title: Golden_Delicious_PH_1-MCP_1

description: SAMPLE 7


title: SOLmuscle_cSix1 rep1


title: Golden_Delicious_H_3

description: SAMPLE 3

source_name: Gold delicious_at harvest


title: African American primary proximal tubule cells K10150


title: Golden_Delicious_H_2

description: SAMPLE 2


title: miR-195 overexpression LNCap cell,rep3

description: miR-195 overexpression LNCap cell

source_name: miR-195 overexpression LNCap cell,rep3


title: SOLmuscle_ctl rep1


title: African American primary proximal tubule cells K10160


title: miR-30d overexpression LNCap cell,rep1

description: miR-30d overexpression LNCap cell

source_name: miR-30d overexpression LNCap cell,rep1


title: miR-30d overexpression LNCap cell,rep2

description: miR-30d overexpression LNCap cell

source_name: miR-30d overexpression LNCap cell,rep2


title: HEK293_Tet-on G2(-)_3

hyb_protocol: Biotinylated cRNA was hybridized to the Illumina Human HT-12 v4 Gene Expression BeadChips according to current Illumina protocols.

scan_protocol: The arrays were washed and scanned according to standard Illumina protocols on a Bead Array Reader system

data_processing: Raw data were generated using GenomeStudio software and normalized by the RMA method. Log intensity distributions, pair-wise correlations and internal Illumina controls were examined to evaluate hybridization quality.

source_name: HEK293 Tet-on APOL1 G2 cells w/o  Dox induction

label_protocol: Total RNA was amplified and labeled using TargetAmp-Nano Labeling Kit .

extract_protocol: Total RNA was isolated from all 24 wells of HEK293 Tet-on cells using the QIAGEN Rneasy Mini Kit (QIAGEN Cat # 74104).

value: embyronic kidney cell


title: HEK293_Tet-on G2(-)_1


title: African American primary proximal tubule cells K10135


title: African American primary proximal tubule cells K10111


title: miR-195 overexpression LNCap cell,rep1

description: miR-195 overexpression LNCap cell

source_name: miR-195 overexpression LNCap cell,rep1


title: miR-195 overexpression LNCap cell,rep2

description: miR-195 overexpression LNCap cell

source_name: miR-195 overexpression LNCap cell,rep2


title: HEK293_Tet-on G1(-)_1

source_name: HEK293 Tet-on APOL1 G1 cells w/o  Dox induction


title: Golden_Delicious_H_1

description: SAMPLE 1


title: African American primary proximal tubule cells K10133


title: HEK293_Tet-on G1(-)_3


title: SOLmuscle_ctl rep2


title: HEK293_Tet-on G1(-)_2


title: HEK293_Tet-on EV(+)_3

source_name: HEK293 Tet-on empty vector cells w  Dox induction


title: African American primary proximal tubule cells K10148


title: HEK293_Tet-on G2(-)_2


title: African American primary proximal tubule cells K10110


title: African American primary proximal tubule cells K10109


title: African American primary proximal tubule cells K10102


title: HEK293_Tet-on EV(+)_2


title: HEK293_Tet-on EV(-)_2

source_name: HEK293 Tet-on empty vector cells w/o Dox induction


title: Genomic DNA from prostate biopsy 47

type: genomic

city: Moscow

first: Elizaveta

last: Babikova

address: Malaya Pirogovskaya 1a

department: Molecular Biology

country: Russia

institute: Research Institute of Physico-Chemical Medicine

description: Normal prostate (cancer unrelated).

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

scan_protocol: Arrays were imaged using iScan Reader using the standard recommended Illumina scanner setting.

data_processing: GenomeStudio Software v2011.1. Average Beta values were normalized using internal controls

label: Cy5 and Cy3

molecule: genomic DNA

source_name: prostate biopsy, normal

label_protocol: Cy5 and Cy3

extract_protocol: Genomic DNA was extracted and purified from Formalin-fixed, paraffin-embedded tissue samples using Qiagen

value: normal prostate

tag: cancer patient

value: yes

tag: sample number


title: HEK293_Tet-on G2(+)_1

source_name: HEK293 Tet-on APOL1 G2 cells w/  Dox induction


title: African American primary proximal tubule cells K10056

value: primary proximal tubule cells


title: African American primary proximal tubule cells K10101


title: HEK293_Tet-on G2(+)_2

source_name: HEK293 Tet-on APOL1 G2 cells w  Dox induction


title: African American primary proximal tubule cells K10023


title: African American primary proximal tubule cells K10095


title: African American primary proximal tubule cells K10015


title: HEK293_Tet-on G2(+)_3


title: HEK293_Tet-on G2(+)_3


title: Genomic DNA from prostate biopsy 48

description: Normal prostate (cancer unrelated).


title: Genomic DNA from prostate biopsy 46

description: Normal prostate (cancer unrelated).


title: HEK293_Tet-on G1(+)_3

source_name: HEK293 Tet-on APOL1 G1 cells w  Dox induction


title: HEK293_Tet-on G2(+)_1


title: African American primary proximal tubule cells K10053


title: HEK293_Tet-on EV(+)_1


title: HEK293_Tet-on EV(-)_3


title: African American primary proximal tubule cells K10075


title: HEK293_Tet-on EV(-)_1


title: HEK293_Tet-on G1(+)_1


title: HEK293_Tet-on G1(+)_2


title: HEK293_Tet-on G0(+)_3

source_name: HEK293 Tet-on APOL1 G0 cells w/  Dox induction


title: HEK293_Tet-on G0(+)_2


title: HEK293_Tet-on G0(-)_3

source_name: HEK293 Tet-on APOL1 G0 cells w/o Dox induction


title: HEK293_Tet-on G0(+)_1


title: HEK293_Tet-on G1(+)_3

source_name: HEK293 Tet-on APOL1 G1 cells w/  Dox induction


title: HEK293_Tet-on G0(+)_1


title: HEK293_Tet-on G0(-)_2


title: HEK293_Tet-on G1(+)_1


title: HEK293_Tet-on G0(+)_3


title: human Urine-Derived Cells-rep2

city: GuangZhou

first: Linli

last: Wang

state: GuangDong

address: Science city Juquan road no. 3

institute: Guangzhou Biocare Cancer Institude

description: repeated sample 2 of human Urine-Derived Cells

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

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

source_name: human Urine-Derived Cells

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix  WT PLUS Reagent Kit(Cat#902280， Affymetrix, Santa Clara, CA, US according to the manufacturer’s instructions to obtain biotin labeled cDNA.

value: Urine-Derived Cells


title: hESCs-rep2

description: repeated sample 2 of human Embryonic Stem Cells

source_name: human Embryonic Stem Cells

value: Embryonic Stem Cells


title: Genomic DNA from prostate biopsy 43

description: Prostate adenocarcinoma.

source_name: prostate biopsy, adenocarcinoma

value: adenocarcinoma


title: hiPSCs-rep2

description: repeated sample 2 of human induced Pluripotent Stem Cells

source_name: human induced Pluripotent Stem Cells

value: induced Pluripotent Stem Cells


title: Genomic DNA from prostate biopsy 40

description: Normal prostate (cancer unrelated).


title: Genomic DNA from prostate biopsy 44

description: Normal prostate (cancer unrelated).


title: Genomic DNA from prostate biopsy 42

description: Normal prostate (cancer unrelated).


title: Genomic DNA from prostate biopsy 45

description: Prostate adenocarcinoma.


title: siDYRK2

city: Tokyo

first: REI

last: MIMOTO

address: 3-25-8 Nishishinbashi, Minato-ku

department: Biochemistry

institute: The Jikei University School of Medicine

description: Gene expression after siRNA transfection

hyb_protocol: cRNA was hybridized to SurePrint G3 Human GE 8x60k Ver.2.0 microarray Kit, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Scanner (G2539) (Agilent Technologies) according to  the “AgilentG3_GX_21Color” protocol. Raw .tif images were then extracted using Agilent “Feature Extraction, version 10.10.1.1”

data_processing: The data were analyzed with median polish summarization and quantile normalization by GeneSpring GX (ver 12.6.0) software, and obtained normalized intensity values.

source_name: siDYRK2 cell

label_protocol: The cRNA was amplified, labeled usingLow Input Quick Amp Labeling Kit, one color  according to the manufacturer's instructions.

extract_protocol: Total RNA extraction was performed using TRIsure(Nippon genetics) following the manufacture's instructuion.

treatment_protocol: MCF-7 cells were transfected with siRNA DYRK2 or non-silencing DYRK2.

value: breast cancer


title: Dye swap of RCC4 and RCC4_STF-62247-treated cells biological replicate 3

city: Moncton

first: Daniel

last: Leger

state: New Brunswick

address: 35 Providence Street

department: IARC

country: Canada

institute: Atlantic Cancer Research Institute

description: Dye swap of experiment BR3.

hyb_protocol: 2.5ug of each labeled target was used per slide (5ug total) and Hybridizations were performed in Ambion SlideHyb#2 buffer (Thermo Scientific) at 42C for 16 h using the automated TECAN 4800 Hybridization station (TECAN)

scan_protocol: Following hybridization, slides were scanned at 10um resolution using an Axon GenePix 4200AL scanner (Molecular Devices) and gridded using SpotReader software (Niles Scientific)

data_processing: Fine tuning of spot rejection was subsequently done by visual inspection of the gridded image and of a scatter plot of M=log(532/635) versus A=log(532)+log(635), special attention being paid to outliers. A GPR file was generated that was subsequently processed to flag spots with a signal to noise ratio of less than 5. Analysis was done with Acuity 4.0. The data was normalized using Lowess and analyzed by various statistical and visual methods sush as SOM (Self Organizing Maps), t-Test, PCA and volcano plot.

source_name: RCC4 Control untreated cells BR 3

label_protocol: 1ug of total RNA was amplified using Ambion's Amino-Allyl MessageAmp II aRNA kit (Life Technologies) following manufacturer's instructions.  20ug of amplified aRNA was reverse transcribed and labeled using a Direct cDNA Labeling kit with Alexa-Fluor 555 and Alexa Fluor 647 - conjugated UTP (Life Technologies)

growth_protocol: RCC4 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) High Glucose (HG) supplemented with 10% Fetal Bovine Serum (FBS), 2mM L-glutamine and 1mM sodium pyruvate.

extract_protocol: Total RNA was isolated using Trizol (Life Technologies) and purified with RNeasy columns (Qiagen) following manufacturer's instructions. Quality of total RNA samples was assessed using the Experion bioanalyzer system with RNA Stdsens chips and associated reagents (BIO-RAD)

treatment_protocol: Cells were treated with 1.25uM of STF-62247 or vehicle (DMSO) for 48 hr.

value: Clear Cell Renal Cell Carcinoma

source_name: RCC4 STF-62247-treated cells BR 3


title: HEK293_Tet-on G0(-)_1


title: hESCs-rep1

description: repeated sample 1 of human Embryonic Stem Cells


title: siControl

source_name: siControl cell


title: Genomic DNA from prostate biopsy 38

description: Normal prostate (cancer unrelated).


title: hiPSCs-rep1

description: repeated sample 1 of human induced Pluripotent Stem Cells


title: Genomic DNA from prostate biopsy 41

description: Prostate adenocarcinoma.


title: Hcc827-8-3

city: Nanjing

first: Ying

last: Wu

address: Baiziting 42

institute: Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province

description: gene expression in gefitinib-resistant HCC827-8-1 cells

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to OE Human lncRNA Microarray V4.0 (Agilent) 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: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: gefitinib-resistant HCC827cells_rep3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The cell line was maintained in RPMI-1640 supplemented with 10% FBS (Gibco) at 37°C, with 5% CO2 and humidified atmosphere

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: To generate a resistant cell line, we exposed HCC827 cells to increasing concentrations of gefitinib  Gefitinib concentrations were increased stepwise from 8 to 100 nM when the cells resumed growth kinetics similar to the untreated parental cells. Cells with the ability to grow in 100 nM of gefitinib were obtained 6 months after the initial drug exposure. HCC827-8-1 cell line was isolated as a clone.

value: lung adenocarcinoma cells

tag: phenotype

value: gefitinib-resistant


title: human Urine-Derived Cells-rep1

description: repeated sample 1 of human Urine-Derived Cells


title: RCC4 and RCC4_STF-62247-treated cells biological replicate 3

description: BR3, two condition experiment, one cell line (RCC4) untreated control versus STF-62247-treated, biological replicate 3.


title: Dye swap of RCC4 and RCC4_STF-62247-treated cells biological replicate 2

description: Dye swap of experiment BR2.

source_name: RCC4 Control untreated cells BR 2

source_name: RCC4 STF-62247-treated cells BR 2


title: Dye swap of RCC4 and RCC4_STF-62247-treated cells biological replicate 1

description: Dye swap of experiment BR1.

source_name: RCC4 Control untreated cells BR 1

source_name: RCC4 STF-62247-treated cells BR 1


title: RCC4 and RCC4_STF-62247-treated cells biological replicate 2

description: BR2, two condition experiment, one cell line (RCC4) untreated control versus STF-62247-treated, biological replicate 2.


title: RCC4 and RCC4_STF-62247-treated cells biological replicate 1

description: BR1, two condition experiment, one cell line (RCC4) untreated control versus STF-62247-treated, biological replicate 1.


title: Genomic DNA from prostate biopsy 39

description: Prostate adenocarcinoma.


title: Hcc827-8-2

source_name: gefitinib-resistant HCC827cells_rep2


title: Genomic DNA from prostate biopsy 36

description: Normal prostate (cancer unrelated).

source_name: prostate biopsy, normal


title: Genomic DNA from prostate biopsy 37

description: Prostate adenocarcinoma.


title: Hcc827-8-1

source_name: gefitinib-resistant HCC827cells_rep1


title: Hcc827-2

description: gene expression in gefitinib-sensitive HCC827 cells

source_name: gefitinib-sensitive HCC827cells_rep2

value: gefitinib-sensitive


title: Genomic DNA from prostate biopsy 33

description: Prostate adenocarcinoma.


title: Genomic DNA from prostate biopsy 35

description: Prostate adenocarcinoma.


title: Genomic DNA from prostate biopsy 34

description: Normal prostate (cancer unrelated).


title: Genomic DNA from prostate biopsy 31

description: Prostate adenocarcinoma.


title: Hcc827-1

source_name: gefitinib-sensitive HCC827cells_rep1


title: Genomic DNA from prostate biopsy 30

description: Normal prostate (cancer unrelated).


title: Genomic DNA from prostate biopsy 32

description: Normal prostate (cancer unrelated).


title: Genomic DNA from prostate biopsy 25

description: Normal prostate (cancer unrelated).


title: Hcc827-3

source_name: gefitinib-sensitive HCC827cells_rep3


title: Genomic DNA from prostate biopsy 27

description: Normal prostate (cancer unrelated).


title: Genomic DNA from prostate biopsy 29

description: Normal prostate (cancer unrelated).


title: Genomic DNA from prostate biopsy 26

description: Normal prostate (cancer unrelated).


title: 14286A-P22

status: Public on Aug 22 2016

city: Odense C

first: Qihua

last: Tan

address: J. B. Winsløws Vej 9B

country: Denmark

institute: University of Southern Denmark

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

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

data_processing: R package minfi

label: cy3 and cy5

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from whole blood according to standard instructions

value: Whole blood

tag: diagnosis

value: PCOS


title: 14286A-P27


title: Genomic DNA from prostate biopsy 28

description: Normal prostate (cancer unrelated).


title: 14286A-P26


title: 14286A-P28


title: 14286A-P24


title: 14286A-P25


title: 14286A-P19


title: 14286A-P15


title: 14286A-P31


title: 14286A-P18


title: 14286A-P20


title: 14286A-P17


title: 14286A-P16


title: 14286A-P14


title: 14286A-P23


title: 14286A-P11


title: 14286A-P13


title: 14286A-P8


title: 14286A-P21


title: 14286A-P12


title: 14286A-P6


title: 14286A-P7


title: 14286A-P5


title: 14286A-P9


title: 14286A-N30

value: healthy control


title: 14286A-P1


title: 14286A-P4


title: 14286A-N17


title: 14286A-N24


title: 14286A-P2


title: 14286A-N27


title: 14286A-N23


title: 14286A-N21


title: 14286A-P30


title: 14286A-N31


title: 14286A-N12


title: 14286A-N29


title: 14286A-N25


title: 14286A-N26


title: 14286A-N16


title: 14286A-P10


title: 14286A-N18


title: 14286A-N28


title: 14286A-N14


title: 14286A-P3


title: 14286A-N10


title: 14286A-N13


title: 14286A-N11


title: 14286A-N19


title: 14286A-N22


title: 14286A-N15


title: 14286A-N9


title: 14286A-N6


title: 14286A-N7


title: 14286A-N5


title: 14286A-N8


title: 14286A-N3


title: tissue_30_oxBS

city: Hanover

first: Kevin

middle: Crowley

last: Johnson

state: NH

address: 72 College Street

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth College

description: tissue30_BS and tissue30_oxBS derived from the same biological sample

hyb_protocol: 1.4ug was carried forward through oxBS conversion with the TrueMethyl protocol, and 1.05ug through the bisulfite conversion arm of the protocol with manufacturer recommended mass and volume.  DNA was then hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

data_processing:
minfi, Aryee et al Bioinformatics 2014
We used maximum likelihood to fit the data generating model under the constraints of each C modification (5C, 5mC, 5hmC) > 0, 5C + 5mC + 5hmC = 1, thus estimating parameters 5C (unmethylated proportion), 5mC  (5mC proportion), and 5hmC (5hmC proportion)
The values in the sample data table are beta values for both 5mC (BS) and 5hmC (oxBS) in a given sample. Importantly, the 5hmC beta values are often near 0 because of the low abundance of 5hmC, but the 5hmC (oxBS) values may take any number between 0 and 1.

extract_protocol: Tumor DNA was extracted with the QIAmp DNeasy tissue kit (Qiagen) according to the manufacturer’s instructions.

tag: gender

value: Male

tag: alive

value: No

tag: survival time (months)

tag: subject age

value: glioblastoma


title: 14286A-N2

tag: tissue


title: tissue_26_BS

description: tissue26_BS and tissue26_oxBS derived from the same biological sample


title: tissue_30_BS


title: tissue_24_BS

description: tissue24_BS and tissue24_oxBS derived from the same biological sample

value: Female


title: tissue_23_oxBS

description: tissue23_BS and tissue23_oxBS derived from the same biological sample


title: tissue_27_BS

description: tissue27_BS and tissue27_oxBS derived from the same biological sample


title: tissue_26_oxBS


title: tissue_29_oxBS

description: tissue29_BS and tissue29_oxBS derived from the same biological sample


title: tissue_28_oxBS

description: tissue28_BS and tissue28_oxBS derived from the same biological sample


title: tissue_27_oxBS


title: 14286A-N4


title: 14286A-N1


title: tissue_23_BS


title: tissue_21_oxBS

description: tissue21_BS and tissue21_oxBS derived from the same biological sample


title: tissue_22_BS

description: tissue22_BS and tissue22_oxBS derived from the same biological sample


title: tissue_29_BS


title: tissue_24_oxBS


title: tissue_25_BS

description: tissue25_BS and tissue25_oxBS derived from the same biological sample


title: tissue_22_oxBS


title: tissue_20_oxBS

description: tissue20_BS and tissue20_oxBS derived from the same biological sample


title: tissue_21_BS


title: tissue_25_oxBS


title: tissue_18_oxBS

description: tissue18_BS and tissue18_oxBS derived from the same biological sample


title: tissue_20_BS


title: tissue_19_BS

description: tissue19_BS and tissue19_oxBS derived from the same biological sample


title: tissue_18_BS


title: tissue_28_BS


title: colon_female_pup_wsd_replicate6

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.26.6).

source_name: colon, female pup of 14 days of age, dam received a Western-style, high fat/cholesterol diet

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Female C57BL/6 mice (five weeks of age) were purchased from Harlan (Horst, The Netherlands) and housed individually in the light- and temperature-controlled facility of the University Medical Center Groningen (lights on 7:00 am-7:00 pm, 21°C). Mice had free access to drinking water and were fed a semi-synthetic, low-fat [control] diet (3.85 kcal/g; 10 E% fat, 20 E% protein, 70 E% carbohydrate; D12450B, Research Diets, New Brunswick, USA), or a semi-synthetic, energy-rich, Western-style high-fat diet (WS diet, 4.73 kcal/g; 45 E% fat, 20 E% protein, 35 E% carbohydrate; D12451, Research Diets) that contained a high cholesterol content from lard (196.5 mg cholesterol/kg). After 6 weeks, mice were mated with males and in case conceiving failed, mice were allowed to re-mate. Mice were allowed to deliver spontaneously and were left undisturbed with their litters for 24 h. Litter sizes were standardized to 5-7 pups, to ensure no litter was nutritionally biased due to lower or higher litter size. By natural circumstances, the litter size of some dams was reduced further, but not changing the overall male/female ratio significantly. Throughout pregnancy and lactation, the dams were kept on the same Western-style high-fat diet.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Two weeks into lactation, pups were sacrificed by heart puncture under isoflurane anaesthesia. Both males and females were included. Pups included were derived from 3 different litters. Small intestine and colon were excised from each pup, snap-frozen in liquid nitrogen, and stored at -80 C until further use.

tag: mouseid

tag: litterid

tag: diet group dam

value: colon

value: wildtype

tag: strain

value: C57BL/6 (Harlan; Horst, The Netherlands)

tag: Sex

value: female

tag: age

value: 14 days


title: tissue_16_BS

description: tissue16_BS and tissue16_oxBS derived from the same biological sample


title: colon_male_pup_wsd_replicate6

source_name: colon, male pup of 14 days of age, dam received a Western-style, high fat/cholesterol diet

value: male


title: tissue_17_oxBS

description: tissue17_BS and tissue17_oxBS derived from the same biological sample


title: tissue_13_oxBS

description: tissue13_BS and tissue13_oxBS derived from the same biological sample


title: SI_male_pup_wsd_replicate6

source_name: small intestine, male pup of 14 days of age, dam received a Western-style, high fat/cholesterol diet

value: small intestine


title: tissue_12_BS

description: tissue12_BS and tissue12_oxBS derived from the same biological sample


title: tissue_17_BS


title: tissue_19_oxBS


title: SI_female_pup_wsd_replicate6

source_name: small intestine, female pup of 14 days of age, dam received a Western-style, high fat/cholesterol diet


title: colon_female_pup_wsd_replicate5

value: Western-style, high fat/cholesterol diet


title: colon_male_pup_wsd_replicate5


title: tissue_15_oxBS

description: tissue15_BS and tissue15_oxBS derived from the same biological sample


title: tissue_13_BS


title: tissue_14_oxBS

description: tissue14_BS and tissue14_oxBS derived from the same biological sample


title: tissue_15_BS


title: tissue_16_oxBS


title: tissue_9_BS

description: tissue9_BS and tissue9_oxBS derived from the same biological sample


title: tissue_10_BS

description: tissue10_BS and tissue10_oxBS derived from the same biological sample


title: tissue_14_BS


title: tissue_11_oxBS

description: tissue11_BS and tissue11_oxBS derived from the same biological sample


title: tissue_8_BS

description: tissue8_BS and tissue8_oxBS derived from the same biological sample


title: tissue_8_oxBS


title: tissue_7_oxBS

description: tissue7_BS and tissue7_oxBS derived from the same biological sample


title: tissue_7_BS


title: tissue_9_oxBS


title: tissue_11_BS


title: tissue_12_oxBS


title: tissue_5_BS

description: tissue5_BS and tissue5_oxBS derived from the same biological sample


title: tissue_10_oxBS


title: tissue_6_oxBS

description: tissue6_BS and tissue6_oxBS derived from the same biological sample


title: SI_male_pup_wsd_replicate5


title: colon_female_pup_wsd_replicate4


title: colon_female_pup_wsd_replicate3


title: tissue_6_BS


title: SI_female_pup_wsd_replicate4


title: tissue_5_oxBS


title: SI_female_pup_wsd_replicate5


title: colon_female_pup_wsd_replicate2


title: SI_female_pup_wsd_replicate3


title: sigC_overexpress_3rd

city: Kyoto

first: Masayuki

last: Inui

address: 9-2 Kizugawadai, Kizugawa

institute: Research institute of Innovative Technology for the Earth (RITE)

description: IPTG was added at the final concentration of 0.5 mM during the exponential phase of growth

hyb_protocol: Labeled cDNA (4.5 μg each) are mixed with 1 × hybridization buffer (6 × SSC, 0.2% SDS, 5 × Denhardt’s solution, 0.1 mg/ml denatured salmon sperm DNA) in a total volume of 340 μl, and denatured at 95˚C for 2 min. The hybridization mixture was hybridized to a microarray in an Agilent Technologies Microarray chamber at 60˚C for 17 h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 5 minutes with wash buffer 1 (2x SSC, 0.2% SDS) at room temperature , 5 minutes with wash buffer 2 (0.2x SSC, 0.2% SDS) at 60˚C, and 5 minutes with wash buffer 3 (0.2x SSC) at room temperature.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) at a resolution of 5 µm. PMT is set to 100% for Cy3 and Cy5 channels.

data_processing: The scanned images were analyzed quantified with Feature Extraction Software 10.5.5.1 (Agilent) using default parameters (protocol GE2-NonAT_105_Dec08). Feature extracted data were analyzed using GeneSpring GX v 12.5 software from Agilent. Normalization of the data was done in GeneSpring GX using the Lowess normalization algorithm without baseline transformation.

organism: Corynebacterium glutamicum R

source_name: The wild-type strain carrying the sigC overexpressing plasmid before IPTG induction

label_protocol: The cDNAs were synthesized from RNA by using reverse transcriptase from 10 μg of total RNAs and labeled with cyanine 3 (Cy3) or cyanine 5 (Cy5) using the SuperScript Indirect cDNA Labeling system (Life Technologies).

growth_protocol: C. glutamicum strains are grown in 100 ml of nutrient rich A medium containing 1% glucose in  500 ml flask at 33˚C

extract_protocol: Total RNA was extracted from C. glutamicum cells using NucleoSpin RNA II kit (Macherey-Nagel, Germany) according to the manufacture's manual.

treatment_protocol: To induce sigC overexpression, isopropyl-β-d-thiogalactopyranoside (IPTG) was added at the final concentration of 0.5 mM to exponentially-growing culture. After 15 min, 1 ml of culture was mixed with 1 ml bacterial RNA protect reagent (Qiagen) for RNA stabilization.

value: Wild type

tag: plasmid

source_name: The wild-type strain carrying the sigC overexpressing plasmid after 15 min of IPTG induction


title: vector_control

source_name: The wild-type strain carrying the vacant vector before IPTG induction

tag: genotype


title: SigC-FLAG_stat_2nd

hyb_protocol: Hybridization was performed using Agilent Oligo aCGH Hybridization kit according to the manufacture’s manual (Agilent). Equal amount (2.5 μg) of each labeled DNA were mixed and hybridized to microarrays in an Agilent Technologies Microarray chamber at 65˚C for 24 h in a rotating Agilent hybridization oven at 20 rpm. After hybridization, microarrays were washed 5 min at room temperature with Oligo aCGH/ChIP-on-chip Wash Buffer 1 (Agilent), 5 min with 31˚C Oligo aCGH/ChIP-on-chip Wash buffer 2 (Agilent Technologies), 10 sec with acetonitrile, and 30 sec with Stabilization and Drying Solution (Agilent) at room temperature.

scan_protocol: Slides were scanned immediately after washing and placement within an Agilent Ozone Barrier Slide cover (Agilent) the Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 4x44k array Scan resolution 5 microns. Scanning was done in both channels and PMT is set to 100% for both Cy3\cy5 channels.

data_processing: Feature extraction software provided by Agilent (version 10.5.1.1, Agilent Technologies, Palo Alto, CA, USA) was used to quantify the intensity of the fluorescent images and to normalize the results by subtracting local background fluorescence, according to the manufacturer’s instructions.

source_name: SigC-FLAG ChIP DNA from the wild-type strain of Corynebacterium glutamicum at the onset of the stationary phase

label_protocol: DNA samples were blunted with T4 DNA polymerase, ligated to linkers, and amplified by PCR. Amplified DNA from reference DNA and immunoprecipitated DNA were differentially labeled with Cy3 and Cy5, respectively, by using CGH labeling kit (Invitrogen) according to the manufacture’s instruction.

growth_protocol: C. glutamicum are grown in 100 ml of nutrient rich A medium containing 1% glucose in  500 ml flask at 33˚C

extract_protocol: C. glutamicum cultures at the late exponential phase and the onset of the stationary phase (at the OD610 of up to 2.5 and 7.0, respectively) were treated with formaldehyde (at the final concentration of 1%) and incubate for 20 min at room temperature. The cross-linking was quenched by addition of glycine (at the final concentration of 125 mM) and incubation for 10 min at room temperature. Cells were then collected by centrifugation, washed twice with Tris-buffered saline (20 mM Tris-HCl pH 7.5, 150 mM NaCl) and stored at -80˚C. Pellets were resuspended in 2 ml IP buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, Roche Antiprotease mini). The cells were mechanically disrupted for nine cycles of 25 s at a speed rating of 6.5 with a FastPrep™ FP120 (BIO 101, Thermo Savant) at room temperature with intermittent cooling on ice for 5 min. The supernatant after centrifugation was sonicated on ice to shear DNA to an average size to 600-1,000 bp. A 50 μl fraction of the supernatant was saved for later analysis (reference DNA). The remainder was subjected to immunoprecipitation with 100μl of magnetic beads coated with Protein G (Invitrogen), which was coupled to the monoclonal anti-FLAG-tag antibody (Sigma). The mixture was incubated overnight on a rotating platform at 4˚C. The beads were washed once with IP buffer, twice with IP buffer containing 400 mM NaCl, eight times with RIPA buffer (50 mM HEPES pH7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Sodium deoxycholate), and twice with TE buffer with 50 mM NaCl. Immunoprecipitated complexes were eluted from the beads by treatment with 210 μl elution buffer (50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS) at 65˚C for 20 min. Cross-links of immunoprecipitated samples and of total DNA samples were reversed by incubation overnight at 65˚C. Samples were then treated with RNase A and proteinase K for 2 h at 55˚C. DNA was extracted with phenol-chloroform and purified with QIAquick PCR purification mini Elute kit (Qiagen).

tag: growth

value: stationary phase

source_name: Reference genomic DNA, no IP treatment control


title: SI_female_pup_wsd_replicate2


title: colon_male_pup_wsd_replicate4


title: SigC-FLAG_stat_1st

source_name: SigC-FLAG ChIP DNA from the wild-type strain of Corynebacterium glutamicum at the exponential phase


title: SigC-FLAG_expo_2nd

value: exponential phase


title: SigC-FLAG_expo_1st


title: SI_male_pup_wsd_replicate4


title: sigC_overexpress_2nd


title: sigC_overexpress_1st


title: colon_female_pup_wsd_replicate1


title: colon_male_pup_wsd_replicate3


title: tissue_4_BS

description: tissue4_BS and tissue4_oxBS derived from the same biological sample


title: tissue_2_oxBS

description: tissue2_BS and tissue2_oxBS derived from the same biological sample


title: SI_female_pup_wsd_replicate1


title: tissue_3_BS

description: tissue3_BS and tissue3_oxBS derived from the same biological sample


title: tissue_4_oxBS


title: tissue_1_BS

description: tissue1_BS and tissue1_oxBS derived from the same biological sample


title: tissue_2_BS


title: tissue_1_oxBS


title: tissue_3_oxBS


title: SI_male_pup_wsd_replicate3


title: SI_male_pup_wsd_replicate2


title: colon_male_pup_wsd_replicate1


title: lung carcinoma, formalin fixed, paraffin embedded (5770)

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

description:
5770_TU_FF
genomic DNA from  lung carcinoma, formalin fixed, paraffin embedded

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

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

data_processing: BeadStudio software v3.2

extract_protocol: genomic DNA was extracted and purified from lung tissue samples using Qiagen QIAmp Kit (Qiagen, Hilden, Germany) according to standard instructions

tag: disease state

value: tumor

value: lung

tag: treatment

value: FFPE


title: lung carcinoma, HOPE fixed, paraffin embedded (5770)

description:
5770_TU_HOPE
genomic DNA from  lung carcinoma, HOPE fixed, paraffin embedded

value: HOPE, paraffin


title: 1210B2-lt-NES (Xf)-2

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

institute: Keio University School of Medicine

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were loaded into R for background correction, quantile normalization and log (base 2)  conversion with the limma package.

source_name: PBMC

label_protocol: Total RNA was reverse-transcribed, labeled with biotin using the Target Amp-Nano Labeling Kit for Illumina Expression BeadChip (Epicentre)

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.

tag: cell type

value: lt-NES cell


title: 1231A3-lt-NES (Xf)-2

description: replicate 2


title: Neurons, derived from ax0016 (line 6)

city: Cambridgeshire

first: Yichen

last: Shi

address: Suite 3, The Science Village Building, Chesterford Research Park, Little Chesterford

country: United Kingdom

institute: Axol Bioscience Limited

description: Gene expression profile

hyb_protocol: SourceBioscience provided the standard services for hybridization

scan_protocol: SourceBioscience provided the standard services for scanning

data_processing: The data were analyzed with Expression Console and Transcriptome Console using Affymetrix default analysis settings

source_name: iPSC-derived Neural Stem Cells

label_protocol: SourceBioscience provided the standard services for labeling

growth_protocol: Axol Human iPSC-Derived Neural Stem Cells were synchronously differentiation to cerebral cortical neurons using a fully-defined neuronal differentiation method.

extract_protocol: QIAGEN All prep DNA/RNA/protein mini kit extracted total RNA according to the manufacturer's instructions

treatment_protocol: No specific treatment

tag: gender

value: Female

tag: hla serotype

tag: genetic modification

tag: starting material

value: Cord blood CD34+ cells


title: colon_male_pup_wsd_replicate2

tag: tissue

value: colon

value: wildtype


title: 1231A3-lt-NES (Xf)-1

description: replicate 1


title: AF22-2

description: replicate 2

source_name: fibroblast


title: AF22-1

description: replicate 1


title: SI_male_pup_wsd_replicate1

tag: mouseid

value: C57BL/6 (Harlan; Horst, The Netherlands)


title: lung carcinoma, cryo-preserved (5770)

description:
5770_NO_HOPE
genomic DNA from lung carcinoma, cryo-preserved

source_name: lung carcinoma, cryo-preserved

value: cryo-preserved


title: normal lung, HOPE fixed, paraffin embedded (5770)

description:
5770_NO_Form
genomic DNA from normal lung, HOPE fixed, paraffin embedded

value: control


title: 201B7-lt-NES (Con)-1

description: replicate 1


title: 1210B2-lt-NES (Xf)-1

description: replicate 1


title: normal lung, cryo-preserved (5770)

description:
5770_ TU_Form
genomic DNA from normal lung, cryo-preserved

source_name: normal lung, cryo-preserved


title: 201B7-lt-NES (Con)-2

description: replicate 2


title: normal lung, formalin fixed, paraffin embedded (5770)

description:
5770_NO_FF
genomic DNA from normal lung, formalin fixed, paraffin embedded


title: lung carcinoma, formalin fixed, paraffin embedded (5285)

description:
5285_NO_HOPE
genomic DNA from  lung carcinoma, formalin fixed, paraffin embedded


title: invivoPGC_4

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description:
Mouse E12.5 embryonic PGC, batch 4
mRNA expression: E12.5 embryonic PGC

hyb_protocol: Labeled cRNA probes were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 microarrays in an Affymetrix Hybridization Oven 645 following the manufacturer's protocol. Hybridized chips were stained and washed using an Affymetrix Fluidic Station 450 with the equipment's built-in protocol EukGE-WS2v5_450.

scan_protocol: Microarray Chips were scanned using an Affymetrix GeneChip Scanner 3000-7G running under Affymetrix Gene Command Console ver 3.2 to generate .CEL files.

data_processing: The .CEL file data were processed using Affymetrix Expression Console software ver 1.3.0.187 to generate RMA-normalized signal intensity values.

source_name: E12.5 mouse embryonic gonads (genital ridges)

label_protocol: Biotin-labeled cRNA probes were synthesized using Affymetrix One-Cycle Target Labeling and Control Reagents following the manufacturer's instruction.

growth_protocol: Mouse embryonci PGCs were isolated from E12.5 embryos of the C57BL/6 strain; sex of the embryos were unknown. PGCLCs and EpiLCs were generated from mouse embryonic stem cells or iPS cells (C57BL/6 x 129/Sv background; all males) following the protocol published by Hayashi et al (2011, Cell 146:519-532).

extract_protocol: Total RNA was isolated from FACS-enriched PGCs or PGCLCs or trypsinized single cell suspension ESCs, iPSCs, or EpiLCs using Qiagen RNeasy kits. Integrities of the RNA samples were examined using an Agilent Bioanalyzer and confirmed to be RIN > 8.0.

tag: genetic background

value: unkown

tag: precursor cell type

tag: facs enrichment


title: 201B7-lt-NES (Xf)-1

description: replicate 1


title: normal lung, cryo-preserved (5285)

description:
5285_ TU_Form
genomic DNA from normal lung, cryo-preserved


title: invivoPGC_1

description:
Mouse E12.5 embryonic PGC, batch 1
mRNA expression: E12.5 embryonic PGC

tag: Sex


title: 201B7-lt-NES (Xf)-2

description: replicate 2


title: invivoPGC_2

description:
Mouse E12.5 embryonic PGC, batch 2
mRNA expression: E12.5 embryonic PGC


title: lung carcinoma, HOPE fixed, paraffin embedded (5285)

description:
5285_TU_FF
genomic DNA from  lung carcinoma, HOPE fixed, paraffin embedded


title: invivoPGC_3

description:
Mouse E12.5 embryonic PGC, batch 3
mRNA expression: E12.5 embryonic PGC


title: lung carcinoma, cryo-preserved (5285)

description:
5285_NO_Form
genomic DNA from lung carcinoma, cryo-preserved


title: lung carcinoma, cryo-preserved (15725)

description:
15725_TU_FF
genomic DNA from lung carcinoma, cryo-preserved


title: iPS_R21-6

description:
iPCS, clone 4
mRNA expression: iPSC

source_name: iPSC cell culture

value: male

value: iPSC


title: iPS_R21-5

description:
iPCS, clone 3
mRNA expression: iPSC


title: 201B7-Neurosphere-2

description: replicate 2

value: Neurosphere


title: lung carcinoma, HOPE fixed, paraffin embedded (15725)

description:
15725_TU_HOPE
genomic DNA from  lung carcinoma, HOPE fixed, paraffin embedded


title: iPS_R21-4

description:
iPCS, clone 2
mRNA expression: iPSC


title: normal lung, HOPE fixed, paraffin embedded (5285)

description:
5285_NO_FF
genomic DNA from normal lung, HOPE fixed, paraffin embedded


title: 201B7-Neurosphere-1

description: replicate 1


title: normal lung, HOPE fixed, paraffin embedded (15725)

description:
15725_NO_HOPE
genomic DNA from normal lung, HOPE fixed, paraffin embedded


title: lung carcinoma, formalin fixed, paraffin embedded (15725)

description:
15725_TU_Form
genomic DNA from  lung carcinoma, formalin fixed, paraffin embedded


title: iPS_R21-2

description:
iPCS, clone 1
mRNA expression: iPSC


title: normal lung, formalin fixed, paraffin embedded (5285)

description:
5285_ TU_HOPE
genomic DNA from normal lung, formalin fixed, paraffin embedded


title: normal lung, formalin fixed, paraffin embedded (15725)

description:
15725_NO_Form
genomic DNA from normal lung, formalin fixed, paraffin embedded


title: iPS_PPF159-2

description:
iPSC, clone 5
mRNA expression: iPSC


title: normal lung, cryo-preserved (15725)

description:
15725_NO_FF
genomic DNA from normal lung, cryo-preserved


title: R21-6_PGCLC

description:
PGCLC, derived from iPSC clone 4
mRNA expression: PGCLC (iPSC derived)

source_name: Embryoid Body, 6-day culture in the PGCLC induction medium

value: PGCLC


title: SAI1-1

description: replicate 1

source_name: fetal hindbrain


title: normal lung, HOPE fixed, paraffin embedded (15724)

description:
15724_NO_HOPE
genomic DNA from normal lung, HOPE fixed, paraffin embedded


title: R21-5_PGCLC

description:
PGCLC, derived from iPSC clone 3
mRNA expression: PGCLC (iPSC derived)


title: R21-6_EpiLC

description:
EpiLC, derived from iPSC clone 4
mRNA expression: EpiLC (iPSC derived)

source_name: EpiLC cell culture

value: EpiLC


title: lung carcinoma, formalin fixed, paraffin embedded (15724)

description:
15724_TU_Form
genomic DNA from  lung carcinoma, formalin fixed, paraffin embedded

value: tumor

value: lung


title: oh-NSC-3-fb-2

description: replicate 2

source_name: fetal forebrain


title: iPS_PPF159-3

description:
iPSC, clone 6
mRNA expression: iPSC


title: R21-4_PGCLC

description:
PGCLC, derived from iPSC clone 2
mRNA expression: PGCLC (iPSC derived)


title: R21-5_EpiLC

description:
EpiLC, derived from iPSC clone 3
mRNA expression: EpiLC (iPSC derived)


title: ES_v65_PGCLC

description:
PGCLC, derived from ESC clone 1
mRNA expression: PGCLC (ESC derived)

value: ESC


title: R21-4_EpiLC

description:
EpiLC, derived from iPSC clone 2
mRNA expression: EpiLC (iPSC derived)


title: R21-2_EpiLC

description:
EpiLC, derived from iPSC clone 1
mRNA expression: EpiLC (iPSC derived)


title: oh-NSC-7-fb-2

description: replicate 2


title: oh-NSC-3-fb-1

description: replicate 1


title: lung carcinoma, cryo-preserved (15724)

description:
15724_TU_FF
genomic DNA from lung carcinoma, cryo-preserved


title: oh-NSC-7-fb-1

description: replicate 1


title: SAI1-2

description: replicate 2

value: lt-NES cell


title: 1231A3-ff-hiPSC-2

description: replicate 2

value: hiPSC


title: R21-2_PGCLC

description:
PGCLC, derived from iPSC clone 1
mRNA expression: PGCLC (iPSC derived)


title: ES_v65_EpiLC

description:
EpiLC, derived from ESC clone 1
mRNA expression: EpiLC (ESC derived)


title: normal lung, formalin fixed, paraffin embedded (15724)

description:
15724_NO_Form
genomic DNA from normal lung, formalin fixed, paraffin embedded

value: FFPE


title: ES_v65

description:
ESC, clone 1
mRNA expression: ESC

source_name: ESC cell culture


title: mtlr_MCMV_S_XCR1+_LT_WT_SetE_2

city: MARSEILLE

first: Marc

last: DALOD

address: Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9

institute: CIML

hyb_protocol: see original GSM record

scan_protocol: see original GSM record

data_processing: GeneChip Mouse Gene 1.0 ST (GPL6246) and GeneChip Mouse Genome 430 2.0 (GPL1261) DAT files were processed using Affymetrix Gene Chip Operating System to generate .CEL files. Normalization of the raw Affymetrix expression data with Robust Multi-chip Analysis were performed through Bioconductor in the R statistical environment (version 3.0.2) using the oligo package (GPL6246) and the affy, affyPLM and yaqcaffy packages (GPL1261). For genes symbol with several probeSets , the most variant probSet has been selected. The two platforms weere merged by the unique genes symbols. Quantile Normalization was applied on the merged expression arrays to generate Matrix 1. PCA analysis revealed a strong platform effect. Partial Least Square (PLS) was performed to remove the platform effect and yield Matrix2 which was used for subsequent analyses. These matrices contain the normalized data for these reanalyzed samples and can be found on the SuperSeries record.  The data matrices contain the Log2 values.

label_protocol: see original GSM record

extract_protocol: see original GSM record

tag: strain

value: CD8a+ dendritic cells (DC)

tag: genotype/variation


title: im_S_XCR1+_LT_Ifnar1-KO_SetE_2

value: IFNAR-KO


title: mtlr_MCMV_S_XCR1+_LT_Ifnar1-KO_SetE_1


title: mtlr_MCMV_S_XCR1+_LT_WT_SetE_1

value: wildtype


title: im_S_XCR1+_LT_WT_SetE_2


title: im_S_XCR1+_LT_Ifnar1-KO_SetE_1


title: im_S_XCR1+_LT_WT_SetE_1


title: 1231A3-ff-hiPSC-1

description: replicate 1


title: ES1_5

description:
ESC, clone 3
mRNA expression: ESC


title: lung carcinoma, HOPE fixed, paraffin embedded (15343)

description:
15343_TU_HOPE
genomic DNA from  lung carcinoma, HOPE fixed, paraffin embedded

value: HOPE, paraffin


title: ES1_2

description:
ESC, clone 2
mRNA expression: ESC


title: ES1_5_EpiLC

description:
EpiLC, derived from ESC clone 3
mRNA expression: EpiLC (ESC derived)


title: ES1_5_PGCLC

description:
PGCLC, derived from ESC clone 3
mRNA expression: PGCLC (ESC derived)


title: 201B7-ff-hiPSC-2

description: replicate 2


title: 1210B2-ff-hiPSC-2

description: replicate 2


title: mtlr_MCMV_S_XCR1+_LT_Ifnar1-KO_SetE_2


title: lung carcinoma, HOPE fixed, paraffin embedded (15724)

description:
15724_TU_HOPE
genomic DNA from  lung carcinoma, HOPE fixed, paraffin embedded


title: normal lung, cryo-preserved (15724)

description:
15724_NO_FF
genomic DNA from normal lung, cryo-preserved

value: control

value: cryo-preserved


title: normal lung, HOPE fixed, paraffin embedded (15343)

description:
15343_NO_HOPE
genomic DNA from normal lung, HOPE fixed, paraffin embedded


title: 1210B2-ff-hiPSC-1

description: replicate 1


title: 201B7-ff-hiPSC-1

description: replicate 1


title: lung carcinoma, cryo-preserved (15343)

description:
15343_TU_FF
genomic DNA from lung carcinoma, cryo-preserved


title: normal lung, formalin fixed, paraffin embedded (15343)

description:
15343_NO_Form
genomic DNA from normal lung, formalin fixed, paraffin embedded


title: lung carcinoma, formalin fixed, paraffin embedded (15343)

description:
15343_TU_Form
genomic DNA from  lung carcinoma, formalin fixed, paraffin embedded


title: mtlr_polyI:C_18hrs_S_XCR1+_CCR7+_LT_SetA_2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430.2 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400 with the EukGE_WS2v5 protocol.

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

data_processing: The data were RMA normalized in R and Bioconductor, using the affy package.

label_protocol: 40 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from sorted cell subsets with the Qiagen RNeasy Micro Kit, with on column DNase digestion, according to the manufacturer protocol.

treatment_protocol: Mice were untreated, or injected i.p. with 10µg polyI:C and organs harvested 18 hours after.

value: Spleen

tag: phenotype

value: TLR-matured (CCR7+) spleen XCR1+ DC


title: mh_S_XCR1+_CCR7+_LT_SetA_3

value: homeostatically-matured (CCR7+) spleen XCR1+ DC

value: Untreated


title: im_S_XCR1+_CCR7-_LT_SetA_3

value: immature (CCR7- ) spleen XCR1+ DC


title: mtlr_polyI:C_18hrs_S_XCR1+_CCR7+_LT_SetA_1


title: mtlr_polyI:C_18hrs_S_XCR1+_CCR7+_LT_SetA_3


title: mh_S_XCR1+_CCR7+_LT_SetA_2


title: im_S_XCR1+_CCR7-_LT_SetA_2


title: im_T_XCR1+_CCR7-_1

value: Thymus

value: immature (CCR7- ) thymic XCR1+ DC


title: mh_T_XCR1+_CCR7+_3

value: homeostatically-matured (CCR7+) thymic XCR1+ DC


title: im_T_XCR1+_CCR7-_3


title: mh_T_XCR1+_CCR7+_1


title: mh_T_XCR1+_CCR7+_2


title: im_T_XCR1+_CCR7-_2


title: HEK293 cell line with stable pBI-CMV2 vector overexpression 2

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

institute: Ludwig-Maximilians-University Munich

data_processing: The data were normalised using quantile normalisation and background substraction with GenomeStudio Software 2011.1 (Illumina).

source_name: HEK293_stable pBI-CMV2 vector overexpression

label_protocol: cRNA was prepared  using the TargetAmp™- Nano Labeling Kit for Illumina Expression BeadChip (Epicentre Biotechnologies, Madison, WI, USA).

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: cell line

tag: cell line cat. #

value: vector (pBI-CMV2) control


title: HEK293 cell line with stable circANRIL overexpression 2

source_name: HEK293_stable circANRIL overexpression

value: stably overexpressing circular ANRIL (circANRIL-pBI-CMV2)


title: HEK293 cell line with stable pBI-CMV2 vector overexpression 3


title: im_S_XCR1+_CCR7-_LT_SetA_1

tag: treatment


title: HEK293 cell line with stable circANRIL overexpression 3


title: mh_S_XCR1+_CCR7+_LT_SetA_1

tag: cell type


title: HEK293 cell line with stable circANRIL overexpression 1


title: HEK293 cell line with stable pBI-CMV2 vector overexpression 1


title: normal lung, cryo-preserved (15343)

description:
15343_NO_FF
genomic DNA from normal lung, cryo-preserved

tag: disease state

value: lung


title: lung carcinoma, HOPE fixed, paraffin embedded (15136)

description:
15136_TU_HOPE
genomic DNA from  lung carcinoma, HOPE fixed, paraffin embedded

value: tumor


title: lung carcinoma, formalin fixed, paraffin embedded (15136)

description:
15136_TU_Form
genomic DNA from  lung carcinoma, formalin fixed, paraffin embedded

value: FFPE


title: lung carcinoma, cryo-preserved (15136)

description:
15136_TU_FF
genomic DNA from lung carcinoma, cryo-preserved


title: normal lung, cryo-preserved (15136)

description:
15136_NO_FF
genomic DNA from normal lung, cryo-preserved


title: normal lung, HOPE fixed, paraffin embedded (15136)

description:
15136_NO_HOPE
genomic DNA from normal lung, HOPE fixed, paraffin embedded


title: normal lung, formalin fixed, paraffin embedded (15136)

description:
15136_NO_Form
genomic DNA from normal lung, formalin fixed, paraffin embedded


title: im_S_XCR1+_LT_SetC_2

value: CD8a+ dendritic cells (DC)

value: wildtype


title: mtlr_polyI:C_3hrs_S_XCR1+_LT_SetC_2


title: mtlr_polyI:C_3hrs_S_XCR1+_LT_SetC_1


title: CCR7+ XCR1+ tDC_GF (BMN_Z-B2r)

hyb_protocol: Following fragmentation and end-labeling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G at a resolution of 0.7 µm.

data_processing: The data were RMA normalized in R and Bioconductor, using the oligo package.

source_name: CCR7+ XCR1+ tDC_GF

label_protocol: 0.7 to 7.3 ng of RNA from each sample was used to synthesize biotinylated probes, using the NuGEN Ovation Pico WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kit, according to NuGEN recommendations, with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from sorted cell subsets with the Qiagen RNeasy PLUS Micro Kit, according to the manufacturer protocol.

treatment_protocol: None. Mice were untreated.

value: wild-type

tag: condition

value: Germ-Free (GF)


title: mtlr_polyI:C_3hrs_L_XCR1+_Int_3

description: GSM605822_EA07068_99776_MoGene_DC.103+.11B-.POLYIC.LU#3

source_name: lung

value: DC.103+11b-.PolyIC.Lu#3, Lung CD103+ DCs


title: mtlr_polyI:C_3hrs_L_XCR1+_Int_2

description: GSM605821_EA07068_99775_MoGene_DC.103+.11B-.POLYIC.LU#2

value: DC.103+11b-.PolyIC.Lu#2, Lung CD103+ DCs


title: mh_MedLN_XCR1+_CCR7+_Mig_2

description: GSM854245_EA07068_142681_MOGENE-1_0-ST-V1_DC.103+11B-.LULN_3_N2

source_name: mediastinal LN

value: DC.103+11b-.LuLN#3, CD103+ migratory DC


title: mh_MedLN_XCR1+_CCR7+_Mig_1

description: GSM854244_EA07068_142680_MOGENE-1_0-ST-V1_DC.103+11B-.LULN_2_N2

value: DC.103+11b-.LuLN#2, CD103+ migratory DC


title: mtlr_polyI:C_3hrs_L_XCR1+_Int_1

description: GSM605820_EA07068_99774_MoGene_DC.103+.11B-.POLYIC.LU#1

value: DC.103+11b-.PolyIC.Lu#1, CD103+ lung DCs


title: CCR7+ XCR1+ tDC_Ifnar1-KO (BMN_Y-B1)

source_name: CCR7+ XCR1+ tDC_Ifnar1-KO

value: Thymus

value: Ifnar1-KO SPF

value: Untreated


title: CCR7- XCR1+ tDC_Ifnar1-KO (BMN_Y-A3r)

source_name: CCR7- XCR1+ tDC_Ifnar1-KO

value: immature (CCR7-) thymic XCR1+ DC


title: im_S_XCR1+_LT_SetC_1


title: CCR7+ XCR1+ tDC_CTRL (BMN_X-A2)

source_name: CCR7+ XCR1+ tDC_CTRL

value: homeostatically-matured (CCR7+) thymic XCR1+ DC

value: SPF (CTRL)


title: CCR7- XCR1+ tDC_CTRL (BMN_X-A1r)

source_name: CCR7- XCR1+ tDC_CTRL


title: CCR7- XCR1+ tDC_Ifnar1-KO (BMN_Y-A2r)


title: CCR7+ XCR1+ tDC_CTRL (BMN_X-B1r)


title: CCR7- XCR1+ tDC_CTRL (BMN_X-B2)


title: CCR7+ XCR1+ tDC_CTRL (BMN_X-B3)


title: CCR7- XCR1+ tDC_Ifnar1-KO (BMN_Y-A1)


title: CCR7- XCR1+ tDC_GF (BMN_Z-A3r)

source_name: CCR7- XCR1+ tDC_GF


title: im_L_XCR1+_Int_3

value: DC.103+11b-.Lu#3, lung CD103+ dendritic cells


title: im_L_XCR1+_Int_2

value: DC.103+11b-.Lu#2, lung CD103+ dendritic cells


title: im_L_XCR1+_Int_1

value: DC.103+11b-.Lu#1, lung CD103+ dendritic cells


title: CCR7- XCR1+ tDC_GF (BMN_Z-A1r)


title: CCR7+ XCR1+ tDC_GF (BMN_Z-B1r)


title: CCR7- XCR1+ tDC_CTRL (BMN_X-A3)


title: CCR7+ XCR1+ tDC_Ifnar1-KO (BMN_Y-B3r)


title: the sigC mutant1 at the exponential phase_2nd

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit according to the manufacture’s manual (Agilent). The labeled cDNA was hybridized to microarrays in an Agilent Technologies Microarray chamber at 65˚C for 17 h 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) at a resolution of 5 µm using single color scan setting for 4x44k array slides. PMT is set to 100% for Cy3 channels.

data_processing: The scanned images were analyzed quantified with Feature Extraction Software 10.5.5.1 (Agilent) using default parameters (protocol GE1_105_Dec08). Feature extracted data were analyzed using GeneSpring GX v 12.5 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended Percentile shift normalization (50th percentile).

source_name: The sigC mutant strain at the exponential phase

label_protocol: The cDNAs were synthesized from RNA by using reverse transcriptase from 10 μg of total RNAs and labeled with cyanine 3 (Cy3) using the SuperScript Indirect cDNA Labeling system (Life Technologies).

extract_protocol: Total RNA was extracted from C. glutamicum cells using the Qiagen RNeasy Mini kit (Qiagen) according to the manufacture's manual.

tag: genotype

value: ΔsigC


title: wt at the exponential phase_2nd (#2)

source_name: The wild-type strain at the exponential phase

value: wild type


title: the sigC mutant2 at the exponential phase_2nd


title: the sigC mutant2 at the exponential phase_1st


title: the sigC mutant1 at the exponential phase_1st


title: CCR7+ XCR1+ tDC_Ifnar1-KO (BMN_Y-B2_2r)


title: wt at the exponential phase_1st (#2)


title: mh_S_XCR1+_CCR7+_Il12b-_LT_SetB_2

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

source_name: homeostatically-matured (CCR7+Il12b- fraction) spleen XCR1+ DC

label_protocol: 3 or 20 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification (using the NuGEN Ovation Pico WTA System V2 Kit and the NuGEN Encore Biotin Module Kit according to NuGEN recommendations) with appropriate quality control to ensure full length synthesis.

extract_protocol: Each cell subset was purified by flow cytometry and total RNA was extracted with the Qiagen RNeasy Plus Micro Kit, according to the manufacturer protocol.

value: Spleen


title: mtlr_STAg_S_XCR1+_LT_SetC_2

hyb_protocol: Following fragmentation and end-labeling, 1.9 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Gene 1.0ST Array. GeneChips were washed and stained in the Affymetrix GeneChip® fluidics station 450 with the FS450-0007 protocol.

source_name: TLR-matured (total) spleen XCR1+ DC

label_protocol: 150 ng of RNA from each sample was used to synthesize biotinylated probes, with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

treatment_protocol: Mice were injected i.v. with 20µg of STAg and spleens were harvested 12 hours after.

value: spleen

value: TLR-matured (total) spleen XCR1+ DC

value: STAg


title: mtlr_STAg_S_XCR1+_LT_SetC_1


title: mh_S_XCR1+_CCR7+_Il12b-_LT_SetB_1

value: homeostatically-matured (CCR7+Il12b- fraction) spleen XCR1+ DC


title: mh_S_XCR1+_CCR7+_Il12b-_LT_SetB_3


title: WT pMIG rep2

city: München

first: Sebastian

last: Mueller

address: Ismaninger Strasse 22

department: Institut für Molekulare Onkologie und Funktionelle Genomik

institute: Klinikum rechts der Isar

description: replicate 2

data_processing: The data were normalised using quantile normalisation as implemented in R

source_name: Lin– BM cells

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

extract_protocol: RNA was extracted using Absolutely RNA Microprep Kit (Agilent Technologies) according to manufacturer’s instructions. Quality control was performedwith Agilent 2100 Bioanalyzer.

value: bone marrow

value: Lin– BM cells pMIG


title: WT FLT3-ITD rep2

description: replicate 2

value: Lin– BM cells FLT3-ITD


title: im_S_XCR1+_CCR7-_Il12b-_LT_SetB_3

source_name: immature (CCR7-Il12b-) spleen XCR1+ DC

value: immature (CCR7-Il12b-) spleen XCR1+ DC


title: WT pMIG rep1

description: replicate 1


title: WT FLT3-ITD rep1

description: replicate 1


title: 1E10_HG-U133_Plus_2_rep1

city: Yokohama

first: Atsushi

last: Fukushima

address: 1-7-22 Suehiro, Tsurumi

department: Center for Sustainable Resource Science

institute: RIKEN

description: ΔSLPI cells were maintained in α-Minimal Essential Medium (Wako, Tokyo, Japan) containing 10% fetal bovine serum (Japan Bio Serum, Tokyo, Japan) and 1% penicillin-streptomycin (Wako) at 37°C in an atmosphere containing 5% CO2.

hyb_protocol: Biotin-labeled cRNA was added to the fragmentation buffer (Affymetrix), and was heated for 35 min at 95°C. Fragmented cRNA (10 μg) was hybridized to GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 integrated with Affymetrix® Microarray Suitesoftware.

data_processing: The data were analyzed with Bioconductor 'simpleaffy' package using RMA as normalization method.

source_name: SLPI-deficient Ca9-22 (ΔSLPI)

label_protocol: Biotin-labeled cRNA was synthesized by in vitro transcription using the BioArray high-yield RNA transcript labeling system (ENZO, Farmingdale, NY, USA).

growth_protocol: Ca9-22 cells were obtained from RIKEN BRC (Ibaraki, Japan). SLPI-deficient (Δ) Ca9-22 cells were generated as previously described (Mikami et al. Mol Immunol, 2015). Cells were maintained in α-Minimal Essential Medium (Wako, Tokyo, Japan) containing 10% fetal bovine serum (Japan Bio Serum, Tokyo, Japan) and 1% penicillin-streptomycin (Wako) at 37°C in an atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy kits (Qiagen, Valencia, CA, USA) according to the manufacturer's instruction.

value: SLPI-deficient


title: mh_S_XCR1+_CCR7+_Il12b+_LT_SetB_1

source_name: homeostatically-matured (CCR7+Il12b+ fraction) spleen XCR1+ DC


title: CCR7+ XCR1+ tDC_GF (BMN_Z-B3.2r)

value: Thymus

value: homeostatically-matured (CCR7+) thymic XCR1+ DC

value: wild-type

value: Germ-Free (GF)

value: Untreated


title: CCR7- XCR1+ tDC_GF (BMN_Z-A2r)

value: immature (CCR7-) thymic XCR1+ DC


title: mh_S_XCR1+_CCR7+_Il12b+_LT_SetB_2

value: homeostatically-matured (CCR7+Il12b+ fraction) spleen XCR1+ DC


title: im_S_XCR1+_CCR7-_Il12b-_LT_SetB_1

value: Spleen


title: im_S_XCR1+_CCR7-_Il12b-_LT_SetB_2


title: Patient 0123, hepatic tissue

status: Public on Aug 21 2016

city: shanghai

first: Mingjie

address: 197 Ruijin Er Road

institute: Ruijin Hospital,Shanghai Jiaotong University,School of Medicine

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0123, Scheuer score: G2S4

hyb_protocol: After fragmentation, 10 ug of RNA were hybridized for 16 hr at 45C on HG U133 Plus 2.0 array. Chips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: All raw data were manipulated in R version 3.1.3. Background adjusted and normalizaed using R package affy utilizing the RMA algorithm, missing values were evaluate using package impute, and batch effects were removed using package sva

source_name: Hepatic tissue from chronic hepatitis B patients 0123

extract_protocol: Total RNA extracted using Trizol following the manufacture's instructions.

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: Patient 0118, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0118, Scheuer score: G1S0

source_name: Hepatic tissue from chronic hepatitis B patients 0118

tag: tissue


title: Patient 0121, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0121, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0121


title: Patient 0116, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0116, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0116


title: Patient 0124, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0124, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0124

value: Female


title: Patient 0122, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0122, Scheuer score: G1S0

source_name: Hepatic tissue from chronic hepatitis B patients 0122


title: Patient 0113, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0113, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0113


title: Patient 0115, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0115, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0115


title: KLF10 knockout Replicate 2 of 3

city: Chiayi

first: Weng

middle: Ching

last: Chieh

address: No.168, Sec. 1, University Rd., Minhsiung

department: Department of Biomedical Sciences

country: Taiwan

institute: National Chung Cheng University

description: Biological replicate 2 of 3. Pdx-1Cre LSL-KrasG12D P53L/L compared with Pdx-1CreLSL-KrasG12D KLF10L/L P53L/L.

hyb_protocol: 0.3 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to a Agilent SurePrint G3 Mouse GE 8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5.

data_processing: Scanned images are analyzed by Feature extraction 10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

source_name: Pdx1-Cre LSL-KrasG12D P53L/L Cell Line

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: Mouse primary PDAC cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, nonessential amino acids, 100 units/ml penicillin and 100 μg/ml streptomycin at 37 °C in a 5% CO2 incubator.

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

value: Pancreatic ductal adenocarcinoma

value: KLF10 wild type

source_name: Pdx-1Cre LSL-KrasG12D KLF10L/L P53L/L Cell Line

value: KLF10 knockout


title: Patient 0117, hepatic tissue

last: Wang

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0117, Scheuer score: G2S0

source_name: Hepatic tissue from chronic hepatitis B patients 0117


title: KLF10 knockout Replicate 3 of 3

description: Biological replicate 3 of 3. Pdx-1Cre LSL-KrasG12D P53L/L compared with Pdx-1CreLSL-KrasG12D KLF10L/L P53L/L.


title: Patient 0120, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0120, Scheuer score: G1S1

source_name: Hepatic tissue from chronic hepatitis B patients 0120


title: Patient 0119, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0119, Scheuer score: G1S0

source_name: Hepatic tissue from chronic hepatitis B patients 0119


title: CU95

city: Lund

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

description: breast tumor

hyb_protocol: According to manufacturer (Agilent) specifications.

scan_protocol: According to manufacturer (Agilent) specifications, microarrays were scanned on an Agilent Microarray Scanner.

data_processing: The raw data was loaded into BioArray Software Environment (BASE) for processing. Background-corrected intensities (ch1: 'gMeanSignal' - 'gBGMedianSignal'; ch2: 'rMeanSignal' - 'rBGMedianSignal') were filtered for values with A>0.5 (A=log10(channel1 * channel2) / 2) and the data normalized using the Lowess algorithm.

source_name: Breast tumor CU95

extract_protocol: QIAGEN RNAeasy

tag: er

value: ER positive

tag: pr

value: PR negative

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

value: INPP4B low

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

value: TP53 wildtype

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumB

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN poor

source_name: Stratagene Universal Human Reference RNA

tag: sample type


title: Patient 0110, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0110, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0110

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: CU86

description: breast tumor

source_name: Breast tumor CU86

label_protocol: According to manufacturer (Agilent) specifications.

tag: er

tag: pr

value: PR positive

tag: her2 status

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

tag: pik3ca mutant

tag: pik3ca aa

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

value: LumA

value: PTEN good

value: Stratagene Universal Human Reference RNA


title: CU81

description: breast tumor

source_name: Breast tumor CU81

tag: er

value: ER negative

tag: pr

value: PR negative

tag: her2 status

value: HER2 positive

value: Ki67 low

value: EGFR ihc positive

value: PIK3CA mutant

value: TP53 mutant

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: unclassified

tag: sample type


title: CU74

description: breast tumor

source_name: Breast tumor CU74

value: ER positive

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

value: INPP4B low

tag: pik3ca mutant

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

value: Normal


title: Patient 0111, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0111, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0111

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: Patient 0114, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0114, Scheuer score: G1S3

source_name: Hepatic tissue from chronic hepatitis B patients 0114


title: Patient 0109, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0109, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0109


title: Patient 0112, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0112, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0112


title: CU75

description: breast tumor

source_name: Breast tumor CU75

tag: er

tag: pr

value: PR negative

tag: her2 status

value: HER2 positive

tag: ki67 ihc

tag: spf status

tag: ln status

value: PIK3CA wildtype

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN good

tag: sample type

value: Stratagene Universal Human Reference RNA


title: CU87

description: breast tumor

source_name: Breast tumor CU87

tag: er

tag: pr

value: PR positive

tag: her2 status

value: HER2 negative

value: Ki67 low

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

tag: pik3ca mutant

tag: pik3ca aa

tag: tp53 mutant

value: TP53 wildtype

value: LumA


title: Patient 0106, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0106, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0106

tag: tissue

tag: gender

value: Female

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: Patient 0107, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0107, Scheuer score: G2S3

source_name: Hepatic tissue from chronic hepatitis B patients 0107


title: CU70

description: breast tumor

source_name: Breast tumor CU70

tag: er

value: ER positive

tag: pr

tag: her2 status

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

value: PTEN ihc positive

value: PTEN wildtype

value: EGFR ihc negative

value: INPP4B low

value: TP53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumB

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN poor

tag: sample type