title: WG0041908-DNA_B11_RM4135

value: Passed QC

value: Blood

value: AD


title: WG0041908-DNA_C03_RM5449

status: Public on May 01 2012

type: genomic

city: Toronto

first: Ekaterina

last: Rogaeva

address: 6 Queen’s Park Crescent West

country: Canada

institute: Tanz Centre for Neurodegenerative Diseases

hyb_protocol: Samples were applied to beadchips and the loaded beadchips were incubated overnight in the Illumina Hybridization oven. Unhybridized and non-specifically hybridized DNA was washed away, and beadchips were prepared for staining and extension.

scan_protocol: The beadchips were scanned on the Illumina BeadArray Reader using default settings.

data_processing:
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%.
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: 750ng of DNA was denatured and neutralized before amplification. The denatured DNA was isothermally amplified in an overnight step, and the amplified product was them enzymatically fragmented (i.e. End-point fragmentation), precipitated with isopropanol, collected by centrifugation at 4 degrees celciums, and resuspended in hybridization buffer. C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled.

extract_protocol: DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.

tag: qc status

tag: cell type

tag: disease status


title: WG0041908-DNA_B09_RX0458

description: C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled


title: hippocampus adult Sedentary technical replicate of 6

type: RNA

city: Urbana

first: Rachel

middle: Ann

last: Kohman

state: IL

address: 405 N Mathew

department: Psychology

country: USA

institute: University of Illinois

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: hippocampus from adult sedentary

label_protocol: Biotinylated cRNA was prepared with the AMIL1791 Illumina® TotalPrep™ RNA Amplification Kit.

growth_protocol: Mice were weaned at the age of 4 weeks, and afterwards supplied with standard nutrition until sacrification.

extract_protocol: Animals were sacrificed by rapid decapitation without anesthesia. Hippocampal samples were dissected on a chilled glass dish and immediately placed into RNAlater solution (Qiagen, Valencia, CA) and stored at -20ºC until RNA isolation. Hippocampal samples were homogenized and RNA purified with the RNeasy Mini kit (Qiagen, Valencia, CA), then quantified and assessed for purity using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and an Agilent 2100 bioanalyzer.

treatment_protocol: Mice were individually housing with or without a running wheel for 8 weeks.

tag: gender

value: Male

tag: strain

value: BALB/c

tag: age

value: 3.5 months-old

tag: exercise condition

value: Sedentary

tag: tissue

value: hippocampus


title: 1_BCC

city: Bochum

first: Michael

last: Sand

state: NRW

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

country: Germany

institute: Ruhr-University Bochum

hyb_protocol: Labeled miRNA samples  were  hybridized  at  55°C  for  20hrs  on  separate  Human  miRNA  Microarrays Release 16.0 (8x60K format, (Agilent Technologies, Santa Clara, USA). Afterwards, microarrays  were  washed  with  increasing  stringency  using  Gene  Expression Wash Buffers  (Agilent Technologies, Santa Clara, USA) followed by drying with acetonitrile (Sigma-Aldich, St.Louis, USA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies, Santa Clara, USA) on the Agilent DNA Microarray Scanner.

data_processing: Fluorescent signal intensities were extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA). All the steps described were carried out according to the manufacturer's instructions.

source_name: BCC biopsy

label_protocol: For assessment of labeling and hybridization efficiencies total RNA samples were spiked with in-vitro synthesized oligonucleotides by using the MicroRNA Spike-In Kit (Agilent Technologies, Santa Clara, USA). A total of 100 ng total RNA per sample were introduced into a labeling reaction. The  spiked  total  RNA  was  treated  with  alkaline  calf  intestine  phosphatase  (CIP).  The dephosphorylated RNA was labeled with the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, USA) according to the manufacturer´s instructions using T4 RNA ligase, incorporating Cyanine 3-Cytidine biphosphate (pCp). The Cyanine-3-labeled miRNA samples were prepared for One-Color based hybridization with Complete miRNA Labeling and Hyb Kit (Agilent Technologies, Santa Clara, USA) according to the manufacturer's instructions.

extract_protocol: miRNAs was isolated using the miRNeasy Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer's protocol. RNA concentration and purity was determined by NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). RNA integrity control (RIN) was determined by means of capillary electrophoresis with the 2100 Bioanalyzer and the RNA 6000 NanoLabCHip Kits (both Agilent Technologies, Santa Clara, USA).

treatment_protocol: All cutaneous specimens were harvested in the operating room, immediately stored in RNAlater (Quiagen, Hilden, Germany) and kept at - 80 °C until RNA isolation.

value: female

tag: tissue origin

value: skin

value: Basal cell carcinoma (BCC)


title: miR-206 KO; mdx-1

city: Dallas

first: Ning

last: Liu

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: UT Southwestern Medical Center

description: replicate 1

source_name: Mus musculus skeletal muscle

label_protocol: Cy3-labeled cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

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: genetic background

value: 3 months

value: tibialis anterior muscle

tag: genotype

value: miR-206 KO, mdx


title: WG0041908-DNA_B10_RX0427

value: Unaffected


title: WG0041908-DNA_B07_RX0497


title: WG0041908-DNA_C04_RM6726


title: WG0041908-DNA_D01_RM5079


title: AP2-L KO liver stage 7

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

hyb_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from total 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91_0806 and Grid: 031544_D_F_20101207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Plasmodium berghei

source_name: AP2-L KO liver stage

label_protocol: 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 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to custome P. berghei Microarrays 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  1 minute at room temperature with acetonitrile.

growth_protocol: Liver stage parasites were cultured on a 8-wells chamber slide using HepG2 cells. The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the total RNA Purification kit (Promega) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: Stage

value: liver stage cultured for 24h after infection

value: AP2-L KO


title: AP2-L KO liver stage 6


title: AP2-L KO liver stage 5


title: hippocampus aged sedentary no. 20

source_name: hippocampus from aged sedentary


title: hippocampus aged sedentary technical replicate of 3


title: hippocampus aged exercise no. 19

source_name: hippocampus from aged with running wheel

value: Exercise


title: hippocampus aged sedentary no. 18


title: WG0041908-DNA_B08_RM6377

value: Passed QC

value: Blood


title: hippocampus adult exercise no. 22

source_name: hippocampus from adult with running wheel

value: Male


title: hippocampus adult exercise no. 15

value: BALB/c


title: hippocampus adult exercise no. 13

value: 3.5 months-old


title: hippocampus adult Sedentary no. 14

value: Sedentary


title: hippocampus adult exercise no. 12

value: hippocampus


title: hippocampus aged exercise no. 16


title: AP2-L KO liver stage 4


title: WG0041908-DNA_B05_RX0514

value: AD


title: hippocampus adult exercise no. 10


title: WG0041908-DNA_B06_RM5087


title: AP2-L KO liver stage 2


title: hippocampus aged exercise no. 11


title: AP2-L KO liver stage 3


title: hippocampus adult Sedentary no. 8


title: hippocampus adult Sedentary no. 21


title: hippocampus aged exercise technical replicate of 19


title: hippocampus aged sedentary no. 7


title: WG0041908-DNA_B01_RM5551

value: Failed QC


title: wild type liver stage 10

source_name: wild type liver stage

value: wild type


title: hippocampus adult Sedentary no. 6


title: hippocampus aged sedentary no. 3


title: wild type liver stage 9


title: WG0041908-DNA_B04_RM5533


title: hippocampus adult Sedentary no. 4


title: hippocampus aged exercise no. 2


title: WG0041908-DNA_A10_RM5805


title: wild type liver stage 8


title: MI with T4 treatment biological rep 8 technical rep 2

city: Brookings

first: Xijin

last: Ge

state: SD

address: SDSU box 2220C

department: Mathematics and Statistics

institute: South Dakota State University

description: biological rep 8 technical rep 2

organism: Rattus norvegicus

source_name: MI (myocardial infarction) with thyroid hormone treatment

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

value: Sprague-Dawley

value: 3 months

value: heart (left ventricular non-infarcted areas)

tag: treatment

value: T4 pellet 3.3mg_60 days release_implanted subcutaneously immediately following MI


title: WG0041908-DNA_B03_RX0470

value: Unaffected


title: wild type liver stage 7

value: liver stage cultured for 24h after infection


title: MI with T4 treatment biological rep 7 technical rep 2

description: biological rep 7 technical rep 2


title: MI with T4 treatment biological rep 8 technical rep 1

description: biological rep 8 technical rep 1


title: hippocampus adult exercise technical replicate of 13

value: Exercise


title: WG0041908-DNA_A06_RM5520

value: Passed QC


title: MI with T4 treatment biological rep 7 technical rep 1

description: biological rep 7 technical rep 1


title: WG0041908-DNA_A08_RM6414

value: Blood


title: AP2-L KO liver stage 1

value: AP2-L KO


title: wild type liver stage 6


title: wild type liver stage 5


title: MI with T4 treatment biological rep 6 technical rep 2

description: biological rep 6 technical rep 2


title: WG0041908-DNA_A05_RM6592


title: MI with T4 treatment biological rep 5 technical rep 2

description: biological rep 5 technical rep 2


title: hippocampus adult exercise no. 5

value: Male

value: BALB/c


title: MI with T4 treatment biological rep 5 technical rep 1

description: biological rep 5 technical rep 1


title: MI with T4 treatment biological rep 6 technical rep 1

description: biological rep 6 technical rep 1


title: MI biological rep 7 technical rep 1

description: biological rep 7 technical rep 1

source_name: MI (myocardial infarction)


title: wild type liver stage 4


title: wild type liver stage 2


title: MI biological rep 8 technical rep 1

description: biological rep 8 technical rep 1


title: MI biological rep 7 technical rep 2

description: biological rep 7 technical rep 2


title: wild type liver stage 3


title: WG0041908-DNA_A03_RM5291


title: WG0041908-DNA_A02_RM6731


title: WG0041908-DNA_A04_RX0828


title: MI biological rep 8 technical rep 2

description: biological rep 8 technical rep 2


title: WG0041907-DNA_H12_RM4014


title: MI biological rep 6 technical rep 2

description: biological rep 6 technical rep 2


title: WG0041907-DNA_H11_RM5437


title: WG0041908-DNA_A07_RX0427


title: sham biological rep 4 technical rep 2

description: biological rep 4 technical rep 2

source_name: sham MI (myocardial infarction)


title: MI biological rep 6 technical rep 1

description: biological rep 6 technical rep 1


title: wild type liver stage 1


title: MI biological rep 5 technical rep 1

description: biological rep 5 technical rep 1


title: sham biological rep 4 technical rep 1

description: biological rep 4 technical rep 1


title: WG0041907-DNA_H10_RX0287


title: WG0041908-DNA_A11_RX1216


title: sham biological rep 3 technical rep 2

description: biological rep 3 technical rep 2


title: DMSO_0H-replicate 1

city: Singapore

first: Archana

middle: P

last: Gupta

address: 60 Nanyang Drive

department: School Of Biological Sciences

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Lowess normalization and subsequent filtering for quality control were carried out using Acuity 4.0 (Axon Instruments). Spots were considered of good quality when they were unflagged and had a median intensity greater than the local background plus 2 times the standard deviation of the background for each dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy5) divided by the corresponding measurement in the reference channel (Cy3, P. falciparum RNA reference pool).

organism: Plasmodium falciparum

source_name: Trophozoite stage P. falciparum parasites treated with DMSO for 0H from biologocal replicate 1

label_protocol: Labeling  carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

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

treatment_protocol: Treatment of P. falciparum infected erythrocytes with HDAC inhibitors (IC90 concentrations) was carried out using trophozoite-stage parasites (~30-36h post invasion) at 5% parasitemia and 5% hematocrit.

value: Lab strain treated with DMSO control

source_name: RNA pooled from all stages of 3D-7 intraerythrocytic cycle


title: DMSO_0H-replicate 2

source_name: Trophozoite stage P. falciparum parasites treated with DMSO for 0H from biologocal replicate 2

value: RNA pooled from all stages of 3D-7 intraerythrocytic cycle


title: sham biological rep 3 technical rep 1

description: biological rep 3 technical rep 1


title: DMSO_0H-replicate 2_technical duplicate 1


title: MI biological rep 5 technical rep 2

description: biological rep 5 technical rep 2


title: WG0041908-DNA_B02_RX0388

value: AD


title: WG0041907-DNA_H07_RM6659

value: Failed QC


title: sham biological rep 2 technical rep 1

description: biological rep 2 technical rep 1


title: DMSO_0H-replicate 1_technical duplicate 2


title: WG0041907-DNA_H08_RM6578


title: sham biological rep 2 technical rep 2

description: biological rep 2 technical rep 2


title: sham biological rep 1 technical rep 1

description: biological rep 1 technical rep 1


title: WG0041907-DNA_H09_RM5798


title: DMSO_0H-replicate 1_technical duplicate 1


title: sham biological rep 1 technical rep 2

description: biological rep 1 technical rep 2


title: DMSO_0H-replicate 2_technical duplicate 2


title: 2-ASA-9 treated 2h+-replicate 2

source_name: Trophozoite stage P. falciparum parasites treated with 2-ASA-9 for 2h

tag: developmental stage

value: Trophozoite

value: 2-ASA-9 treated 2h+

value: Lab strain treated with HDAC inhibitor 2-ASA-9

source_name: reference pool

tag: reference

value: P. falciparum reference pool consisting of DMSO 0h, DMSO 2h and DMSO 2h+/2h- RNA


title: 4T1_Tw1KD/Twist1/S42D, rep1

city: Basel

first: Gongda

last: Xue

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Gene expression data from mouse breast cancer cells

hyb_protocol: Affymetrix GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing: Probesets were summarized and probeset-level values normalized with justRMA() function from R (version 2.10.0) / Bioconductor (version 2.5) package affy using the CDF environment MoGene-1_0-st-v1.r3.cdf (as provided by Bioconductor) and annotation from Netaffx (www.netaffx.com) (as provided in the attached file).

source_name: mouse breast cancer cell line 4T1 derivative

label_protocol: 100ng of RNA were processed with the Ambion® WT Expression Kit (#4411974 ) following the manufacturer's instructions.

growth_protocol: All cells were grown to 70% confluency in standard DMEM growth medium containing 4ug/ml Puromycin and 800ug/ml G418.

extract_protocol: Total RNA was extracted with Qiagen RNeasy kit.

treatment_protocol: All cells were washed with PBS three times before extraction of RNA.

tag: genotype/variation

value: compensatory expression of Twist1/S42A\D in 4T1_Tw1KD


title: 4T1_Tw1KD/Twist1/S42D, rep3

value: mouse breast cancer cell line 4T1 derivative


title: 4T1_Tw1KD/Twist1/S42D, rep2


title: 4T1_Tw1KD/Twist1/S42A, rep2

value: compensatory expression of Twist1/S42A in 4T1_Tw1KD


title: WG0041907-DNA_H05_RM5663

source_name: Blood


title: WG0041907-DNA_H04_RM5328

value: Unaffected


title: TSA treated 2h+/2h--replicate 2

source_name: Trophozoite stage P. falciparum parasites treated with TSA for 2h, washed and cultured for another 2h

value: TSA treated 2h+/2h-

value: Lab strain treated with HDAC inhibitor TSA


title: 4T1_Tw1KD/Twist1/S42A, rep3


title: WG0041907-DNA_H06_RM5999

value: Passed QC

value: Blood


title: 4T1_Tw1KD/Twist1, rep3

value: compensatory expression of wildtype Twist1 in 4T1_Tw1KD


title: 4T1_Tw1KD/Twist1, rep2


title: TSA treated 2h+-replicate 2

source_name: Trophozoite stage P. falciparum parasites treated with TSA for 2h

value: TSA treated 2h+


title: 4T1_Tw1KD/Twist1/S42A, rep1


title: SAHA treated 2h+/2h--replicate 2

source_name: Trophozoite stage P. falciparum parasites treated with SAHA for 2h, washed and cultured for another 2h

value: SAHA treated 2h+/2h-

value: Lab strain treated with HDAC inhibitor SAHA


title: 2-ASA-9 treated 2h+/2h--replicate 2

source_name: Trophozoite stage P. falciparum parasites treated with 2-ASA-9 for 2h, washed and cultured for another 2h

value: 2-ASA-9 treated 2h+/2h-


title: 4T1_Tw1KD/Twist1, rep1


title: S.cerevisiae FZF1 allele at t=15min replicate 1

city: Saint Louis

first: Justin

last: Fay

state: Missouri

address: Center for Genome Sciences Rm 5526, 4444 Forest Park Pkwy

institute: Washington University

hyb_protocol: cDNA are paired and balanced by mass and mixed with hybridization buffer (Agilent 2X Gene Expression buffer, Agilent 10X Blocking agent, water) and applied to arrays.  Hybridization is carried out at 65C for 20 hours.  Washing procedures follow Agilent gene expression protocols.

scan_protocol: Scanned on an Axon 4000B scanner.  Gridding and analysis of images is performed using Genepix v6.1 (Axon)

data_processing: BioConductor marray package in R was used for log transformation (log2 ((sample median foreground - sample median background)/(reference pool median foreground - reference pool median background))) followed by global median normalization

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Scer FZF1 t=15min

label_protocol: First strand cDNA on 10ug total RNA is generated by oligo-dT primed reverse transcription utilizing the Superscript Plus Indirect labeling system (Invitrogen) according to manufacturer's instructions.  First-strand cDNA is purified with Zymo Research Clean and Concentrator 5 clean-up columns according to manufacturer’s instructions.  First-strand cDNA is dried down to a volume of 3ul and coupled with the appropriate dye (Alexa Fluor 555 or 647) according to the Superscript Plus Indirect labeling system (Invitrogen) protocol.  Coupling reactions are quenched with 3M sodium acetate (20ul).  Fluorescently labeled cDNAs are purified with Zymo Research Clean and Concentrator 5 clean-up columns according to manufacturer’s instructions.

growth_protocol: Strains were grown overnight in YPD + 75mM L-tartaric acid buffered to pH 3.5 (YPD +TA).  Strains were resuspended in fresh YPD + TA at an OD600 of 0.25 for a total of 100mL.  Cultures were grown at 30 degrees Celcius at 200rpm.

extract_protocol: RNA was isolated using Qiagen's Rnaeasy Mini Kit, following the manufacturer's instructions

treatment_protocol: After 3 hours growth in YPD+TA, each culture was sampled for t=0.  Sodium sulfite was immediately added to the cultures to a final concentration of 1mM.  A second sample was taken 15 minutes after sulfite addition t=15min.

tag: fzf1 allele

value: Scer FZF1

tag: time

source_name: reference pool made up of all samples

value: All alleles

value: All times


title: WG0041907-DNA_H03_RM5016

tag: qc status

tag: cell type

value: AD


title: 4T1_Tw1KD cells, rep3

value: 4T1 cells with depleted of endogenous Twist1 (4T1_Tw1KD)


title: 4T1_Tw1KD cells, rep2

value: mouse breast cancer cell line 4T1 derivative


title: SAHA treated 2h-replicate 2

source_name: Trophozoite stage P. falciparum parasites treated with SAHA for 2h

value: Trophozoite

value: SAHA treated 2h

value: P. falciparum reference pool consisting of DMSO 0h, DMSO 2h and DMSO 2h+/2h- RNA


title: 5' S.paradoxus-S.cerevisiae FZF1 allele at t=0min replicate 2

source_name: 5'SparScer FZF1 t=0min

value: 5'SparScer FZF1


title: 5' S.cerevisiae-S.paradoxus FZF1 allele at t=15min replicate 3

source_name: 5'ScerSpar FZF1 15min

value: 5'ScerSpar FZF1


title: WG0041907-DNA_H01_RX0343

value: Passed QC

value: Blood

tag: disease status

value: Unaffected


title: DMSO control 2h+/2h--replicate 2

source_name: Trophozoite stage P. falciparum parasites treated with DMSO for 2h, washed and cultured for another 2h

value: DMSO control 2h+/2h-

value: Lab strain treated with DMSO control


title: 4T1_Tw1KD cells, rep1


title: DMSO control 2h-replicate 2

source_name: Trophozoite stage P. falciparum parasites treated with DMSO for 2h

value: DMSO control 2h


title: 5' S.cerevisiae-S.paradoxus FZF1 allele at t=0min replicate 1

source_name: 5'ScerSpar FZF1 t=0min


title: parental 4T1 cells, rep3

source_name: mouse breast cancer cell line 4T1

value: mouse breast cancer cell line 4T1

value: metastatic breast cancer cell line 4T1


title: S.paradoxus FZF1 allele at t=0min replicate 1

source_name: Spar FZF1 t=0min

value: Spar FZF1

value: All alleles

value: All times


title: 5' S.paradoxus-S.cerevisiae FZF1 allele at t=15min replicate 2

source_name: 5'SparScer FZF1 15min


title: 2-ASA-9 treated 2h+/2h--replicate 1

value: 2-ASA-9 treated 2h+/2h-

value: Lab strain treated with HDAC inhibitor 2-ASA-9

source_name: reference pool


title: 2-ASA-9 treated 2h+-replicate 1

source_name: Trophozoite stage P. falciparum parasites treated with 2-ASA-9 for 2h

value: Trophozoite

value: 2-ASA-9 treated 2h+


title: S.paradoxus FZF1 allele at t=0min replicate 3

source_name: Spar FZF1 0min


title: parental 4T1 cells, rep2


title: S.cerevisiae FZF1 allele at t=0min replicate 1

source_name: Scer FZF1 t=0min

value: Scer FZF1


title: parental 4T1 cells, rep1


title: 5' S.cerevisiae-S.paradoxus FZF1 allele at t=15min replicate 1

source_name: 5'ScerSpar FZF1 t=15min

value: 5'ScerSpar FZF1


title: WG0041907-DNA_H02_RM6325

source_name: Blood

value: Passed QC


title: 55 hr sample from LB growth, rep2

city: Boston

first: Qasim

middle: K

last: Beg

state: MA

address: 44 Cummington St

department: Biomedical Engineering

institute: Boston University

description: Gene expression data from wild-type S. oneidensis MR-1

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on a high-density Shewanella custom microarray manufactured by Affymetrix. The arrays were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000

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

organism: Shewanella oneidensis MR-1

source_name: Cells from batch growth in nutritionally rich LB medium

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were at 30oC at close to 20% dissolved O2 in Bioflo110 bioreactor (New Brunswick Scientific, Edison, NJ) containing 1.2 L of growth medium (pH 7.2). Lactate minimal medium was supplemented with 50 mM D,L-lactate

extract_protocol: RNA easy kit (Qiagen)

treatment_protocol: Culture samples different time intevals were centrifuged at 10,000 x g for 10 min (4oC), treated with RNA protect solution (Qiagen) and flash frozen in liquid nitrogen prior to total RNA extraction.

tag: strain

value: Wild type strain

tag: growth medium

value: nutritionally rich LB medium

tag: growth time


title: TSA treated 2h+-replicate 1

source_name: Trophozoite stage P. falciparum parasites treated with TSA for 2h

value: TSA treated 2h+

value: Lab strain treated with HDAC inhibitor TSA

value: P. falciparum reference pool consisting of DMSO 0h, DMSO 2h and DMSO 2h+/2h- RNA


title: WG0041907-DNA_G10_RM5313

value: Failed QC

value: Blood

value: Unaffected


title: TSA treated 2h+/2h--replicate 1

source_name: Trophozoite stage P. falciparum parasites treated with TSA for 2h, washed and cultured for another 2h

value: TSA treated 2h+/2h-


title: 5' S.cerevisiae-S.paradoxus FZF1 allele at t=0min replicate 3

source_name: reference pool made up of all samples

value: All alleles

value: All times

source_name: 5'ScerSpar FZF1 0min


title: 55 hr sample from LB growth, rep1


title: SAHA treated 2h+/2h--replicate 1

source_name: Trophozoite stage P. falciparum parasites treated with SAHA for 2h, washed and cultured for another 2h

value: SAHA treated 2h+/2h-

value: Lab strain treated with HDAC inhibitor SAHA


title: WG0041907-DNA_G12_RM5590


title: 50 hr sample from LB growth, rep2


title: WG0041907-DNA_G09_RM5012


title: WG0041907-DNA_G11_RM6594


title: S.paradoxus FZF1 allele at t=15min replicate 2

source_name: Spar FZF1 t=15min

value: Spar FZF1


title: SAHA treated 2h-replicate 1

source_name: Trophozoite stage P. falciparum parasites treated with SAHA for 2h

value: Trophozoite

value: SAHA treated 2h


title: 5' S.paradoxus-S.cerevisiae FZF1 allele at t=15min replicate 1

source_name: 5'SparScer FZF1 t=15min

value: 5'SparScer FZF1


title: 50 hr sample from LB growth, rep1

value: Wild type strain


title: WG0041907-DNA_G07_RX0361

value: Passed QC

value: AD


title: DMSO control 2h+/2h--replicate 1

source_name: Trophozoite stage P. falciparum parasites treated with DMSO for 2h, washed and cultured for another 2h

value: DMSO control 2h+/2h-

value: Lab strain treated with DMSO control


title: 47 hr sample from LB growth, rep2

value: nutritionally rich LB medium


title: DMSO control 2h-replicate 1

source_name: Trophozoite stage P. falciparum parasites treated with DMSO for 2h

value: DMSO control 2h

value: P. falciparum reference pool consisting of DMSO 0h, DMSO 2h and DMSO 2h+/2h- RNA


title: S.cerevisiae FZF1 allele at t=15min replicate 2

source_name: Scer FZF1 t=15min

value: Scer FZF1


title: WG0041907-DNA_G06_RM5548

value: Blood

value: Unaffected


title: 47 hr sample from LB growth, rep1


title: 5' S.cerevisiae-S.paradoxus FZF1 allele at t=15min replicate 2

value: 5'ScerSpar FZF1

value: All alleles

value: All times


title: WG0041907-DNA_G05_RM5904


title: 5' S.paradoxus-S.cerevisiae FZF1 allele at t=0min replicate 3

source_name: 5'SparScer FZF1 0min


title: 32 hr sample from LB growth, rep1


title: S.paradoxus FZF1 allele at t=0min replicate 2

source_name: Spar FZF1 t=0min

value: Spar FZF1


title: WG0041907-DNA_G03_RM5342


title: WG0041907-DNA_G08_RM5030


title: 30 hr sample from LB growth, rep2


title: MB100pruR (cy5) vs. MB100 (cy3) rep 3

city: Bronx

last: Berney

state: NY

address: 1301 Morris Park Avenue

department: Department of Microbiology and Immunology

institute: Albert Einstein College of Medicine

description: Biological replicate 3 of 4.

hyb_protocol: Hybrization performed according to SOP M008 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

scan_protocol: Scanned Genepix 4000A scanner . Images were quantified using Spotfinder (TIGR).

data_processing: Total normalization and LOWESS normalization with MIDAS software (TIGR)

organism: Mycolicibacterium smegmatis

source_name: Batch serum vial HdB glycorol proline

label_protocol: 10 µg of total RNA were reverse transcribed and labelled in a two step protocol according to SOP M007 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

growth_protocol: M. smegmatis was grown in Hartmans de Bont (HdB) minimal medium supplemented with 25 mM L-proline and 27 mM glycero in 120 ml sealed serum vials at 37°C with agitation (200 rpm).


title: MB100pruR (cy3) vs. MB100 (cy5) rep 4

description: Biological replicate 4 of 4.


title: S.paradoxus FZF1 allele at t=15min replicate 3

source_name: Spar FZF1 15min


title: WG0041907-DNA_G02_RM6194

source_name: Blood


title: 30 hr sample from LB growth, rep1

source_name: Cells from batch growth in nutritionally rich LB medium


title: MB100pruR (cy5) vs. MB100 (cy3) rep 2

description: Biological replicate 2 of 4.


title: S.cerevisiae FZF1 allele at t=0min replicate 3

source_name: Scer FZF1 0min


title: WG0041907-DNA_F11_RM6423


title: 28 hr sample from LB growth, rep2


title: WG0041907-DNA_G01_RM3607


title: 28 hr sample from LB growth, rep1


title: 32 hr sample from LB growth, rep2


title: WG0041907-DNA_G04_RM6090


title: S.paradoxus FZF1 allele at t=15min replicate 1


title: larvae_IMPDH_rep_04 ChIP-chip

city: Rotterdam

first: Yuri

last: Moshkin

address: Dr. Molewaterplein 50

country: Netherlands

institute: Erasmus University Medical Center

description: IMPDH ChIP larvae Biological Replicate 4

hyb_protocol: according to the manufacturer protocols

scan_protocol: according to the manufacturer protocols

data_processing:
Raw ChIP-chip hybridization intensities were analyzed using R and R/Bioconductor packages. In brief, genome-wide ChIP-chip enrichment was estimated as following: 1) log2-scaled hybridization intensities from the input genomic DNA (5 replicas) were normalized by quantile normalization using Bioconductor package preprocessCore and averaged. 2) log2 – scaled ratios of ChIP hybridization intensities to averaged input were taken and quantile normalized independently for each antibodies giving log2(ChIP/Input) values. 3) The same was done for the Mock ChIP hybridization intensities giving log2(Mock/Input) values. 4) Averaged log2(ChIP/Input) and log2(Mock/Input) ratios were scaled by the median and the log2(Mock/Input)average ratio was subtracted from the log2(ChIP/Input)average ratio giving ChIP-chip enrichment score. Binding sites of IMPDH were selected based on false discovery rate (FDR) estimation using modified procedure described by (Simonis et al., 2006) as following: 1) ChIP-chip enrichment scores were randomly permutated and a running mean with a window of 500 bp was applied. This provides a "null" distribution for FDR estimation 2) FDR was set at < 0.05 by taking the value from the "null" distribution above 95% this distribution. 3) Finally, a running mean with a window of 500 bp was applied to original data and signals (peaks) above the FDR threshold were taken. In addition, we discarded the peaks represented by less than 5 probes. IMPDH binding sites were derived by intersecting the sets of significant ChIP-chip peaks for 4 biological replicates (see larvae_IMPDH_regions.bed file).
larvae_IMPDH_regions.bed
1) .bar files contain ChIP.score for IMPDH calculated for each biological replicate. 2) .sgr files contain chromosome, position and ChIP.score. 3) bed files contain binding sites selected at false discovery rate (FDR) of < 0.05 for each biological replicate. 4) File larvae_IMPDH_regions.bed contains IMPDH binding sites, which were derived by intersecting the sets of significant ChIP-chip peaks for each biological replicate.

organism: Drosophila melanogaster

source_name: larvae IMPDH ChIP DNA replicate 04

label_protocol: according to the manufacturer protocols

growth_protocol: Drosophila larvae were grown at 25°C under standard conditions

extract_protocol: For antibody production, IMPDH (amino acids 1 to 295) was expressed as GST fusion proteins, purified, and used for immunizations. For chromatin preparation, 2 g of larvae were homogenized and fixed for 15 min in homogenization buffer (30 mM KCl, 15 mM NaCl, 2 mM MgCl2, 7.5 mM HEPES pH 7.6, 0.5% Triton X-100 and 0.5 mM DTT) containing 2% formaldehyde. After quenching with 0.125 M glycine, the lysate was filtered through miracloth. Isolated nuclei were resuspended in lyses buffer and sonicated to an apparent length of ~300-500 bp (corresponding to ~200-300 bp of free DNA). 100 ug of cross-linked chromatin was diluted with 9 volumes of dilution buffer (150 mM NaCl, 20 mM Tris-HCl pH8.1, 2 mM EDTA pH8.0, 1% Triton-X100, 0.5 mM PMSF, and 100 ng/ml of leupeptin and aprotinin), pre-cleared with 10 ul (bed volume) protein A agarose blocked with salmon sperm DNA (16-157, Upstate), incubated overnight at 4°C with ~10 ul of appropriate antibodies, followed by 1 hr incubation with 20 ul of pre-blocked protein A agarose. For Mock ChIP, chromatin was incubated with either 10 ul of preimmune serum (4 replicas) or directly with 20 ul of pre-blocked protein A agarose (6 replicas). Beads were washed 5x with a wash buffer (20 mM Tris-HCl pH 8.1, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100, 0.5 mM PMSF, and 100 ng/ml of leupeptin and aprotinin) containing 150 mM NaCl, and 1 x with the wash buffer, containing 500 mM NaCl. DNA was eluted with 250 ul elution buffer (1% SDS, 0.1 M NaHCO3, 500 ug/ml Proteinase K) for 2 hrs at 37°C and overnight at 65°C. DNA was then extracted with QIAquick PCR purification kit (Qiagen Cat. 28106). Isolated DNA was amplified with REPLI-g (Qiagen Cat. 150025), digested with DNase, labeled and hybridized on Affymetrix Drosophila tiling 2.0R arrays.

tag: tissue

value: larvae

tag: antibody

value: IMPDH rabbit polyclonal

source_name: Input/Mock-ChIP DNA

tag: cell line

value: S2 cells

value: preimmune serum (preimmune) or protein A beads (protA)


title: 5' S.cerevisiae-S.paradoxus FZF1 allele at t=0min replicate 2

source_name: 5'ScerSpar FZF1 t=0min

source_name: reference pool made up of all samples


title: larvae_IMPDH_rep_03 ChIP-chip

description: IMPDH ChIP larvae Biological Replicate 3

source_name: larvae IMPDH ChIP DNA replicate 03


title: WG0041907-DNA_F12_RM5489

value: Passed QC


title: 24 hr sample from LB growth, rep2

value: Wild type strain


title: larvae_IMPDH_rep_02 ChIP-chip

description: IMPDH ChIP larvae Biological Replicate 2

source_name: larvae IMPDH ChIP DNA replicate 02


title: WG0041907-DNA_F10_RM3676


title: larvae_IMPDH_rep_01 ChIP-chip

description: IMPDH ChIP larvae Biological Replicate 1

source_name: larvae IMPDH ChIP DNA replicate 01


title: 5' S.paradoxus-S.cerevisiae FZF1 allele at t=0min replicate 1

source_name: 5'SparScer FZF1 t=0min

value: 5'SparScer FZF1


title: 21 hr sample from LB growth, rep2

value: nutritionally rich LB medium


title: 24 hr sample from LB growth, rep1


title: MB100pruR (cy3) vs. MB100 (cy5) rep 1

description: Biological replicate 1 of 4.


title: S.cerevisiae FZF1 allele at t=15min replicate 3

source_name: Scer FZF1 15min


title: 21 hr sample from LB growth, rep1


title: S2_IMPDH_rep_03 ChIP-chip

description:
IMPDH ChIP S2 cells Biological Replicate 3.

Mock ChIPs were performed with preimmune serum (preimmune) or protein A beads (protA).
Input/Mock (control) CEL files: S2_input_1.CEL, S2_input_2.CEL, S2_input_3.CEL, S2_input_4.CEL, S2_input_5.CEL, S2_mock_preimmune_1.CEL, S2_mock_preimmune_2.CEL, S2_mock_preimmune_3.CEL, S2_mock_preimmune_4.CEL, S2_mock_protA_1.CEL, S2_mock_protA_2.CEL, S2_mock_protA_3.CEL, S2_mock_protA_4.CEL, S2_mock_protA_5.CEL, S2_mock_protA_6.CEL

hyb_protocol: According to the manufacturer's protocols.

data_processing:
Raw ChIP-chip hybridization intensities were analyzed using R and R/Bioconductor packages. In brief, genome-wide ChIP-chip enrichment was estimated as following: 1) log2-scaled hybridization intensities from the input genomic DNA (5 replicas) were normalized by quantile normalization using Bioconductor package preprocessCore and averaged. 2) log2 – scaled ratios of ChIP hybridization intensities to averaged input were taken and quantile normalized independently for each antibodies giving log2(ChIP/Input) values. 3) The same was done for the Mock ChIP hybridization intensities giving log2(Mock/Input) values. 4) Averaged log2(ChIP/Input) and log2(Mock/Input) ratios were scaled by the median and the log2(Mock/Input)average ratio was subtracted from the log2(ChIP/Input)average ratio giving ChIP-chip enrichment score. Binding sites of IMPDH were selected based on false discovery rate (FDR) estimation using modified procedure described by (Simonis et al., 2006) as following: 1) ChIP-chip enrichment scores were randomly permutated and a running mean with a window of 500 bp was applied. This provides a "null" distribution for FDR estimation 2) FDR was set at < 0.05 by taking the value from the "null" distribution above 95% this distribution. 3) Finally, a running mean with a window of 500 bp was applied to original data and signals (peaks) above the FDR threshold were taken. In addition, we discarded the peaks represented by less than 5 probes. IMPDH binding sites were derived by intersecting the sets of significant ChIP-chip peaks for 3 biological replicates (see S2_IMPDH_regions.bed file).

.bar files contain ChIP.score for IMPDH calculated for each biological replicate.
.sgr files contain chromosome, position and ChIP.score.
.bed files contain binding sites selected at false discovery rate (FDR) of < 0.05 for each biological replicate.

source_name: S2 IMPDH ChIP DNA

growth_protocol: Drosophila S2 cells were cultured in Schneider's media (Invitrogen 21720-024) supplied with 10% FBS and Penicillin/Streptomycin mixture at 25°C.

extract_protocol: For antibody production, IMPDH (amino acids 1 to 295) was expressed as GST fusion proteins, purified, and used for immunizations. Log-phase S2 cells were fixed for 10 min with 1% formaldehyde. Fixation was stopped by 125 mM glycine, cells were washed with PBS and resuspended in ice-cold L buffer (1% sodium dodecyl sulfate, 10 mM EDTA, 50 mM Tris-HCl pH 8.1, 0.5 mM phenylmethylsulfonyl fluoride - PMSF, and 100 ng/ml of leupeptin and aprotinin). Cross-linked chromatin was sonicated to an apparent length of ~300-500 bp (corresponding to ~200-300 bp of free DNA). 100 mkg of cross-linked chromatin was diluted with 9 volumes of buffer D (150 mM NaCl, 20 mM Tris-HCl pH8.1, 2 mM EDTA pH8.0, 1% Triton-X100, 0.5 mM PMSF, and 100 ng/ml of leupeptin and aprotinin), pre-cleared with 10 mkl (bed volume) protein A agarose blocked with salmon sperm DNA (16-157, Upstate), incubated ON at 4C with ~10 mkl of appropriate antibodies, followed by 1 hr incubation with 20 mkl of pre-blocked protein A agarose. For Mock ChIP, chromatin was incubated with either 10 mkl of preimmune serum (4 replicas) or directly with 20 mkl of pre-blocked protein A agarose (6 replicas). Beads were washed 5x with buffer W (20 mM Tris-HCl pH 8.1, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100, 0.5 mM PMSF, and 100 ng/ml of leupeptin and aprotinin) containing 150 mM NaCl, and 1 x with buffer W/500 mM NaCl. DNA was eluted with 250 mkl buffer E (1% SDS, 0.1 M NaHCO3, 500 mkg/ml Proteinase K) for 2 hrs at 37C and overnight at 65C. DNA was then extracted with QIAquick PCR purification kit (Qiagen Cat. 28106). Isolated DNA was amplified with REPLI-g (Qiagen Cat. 150025), digested with DNase, labeled and hybridized on Affymetrix Drosophila tiling 2.0R arrays.

tag: chip antibody


title: WG0041907-DNA_F08_RM4210

value: AD


title: WG0041907-DNA_F07_RX0317


title: S.cerevisiae FZF1 allele at t=0min replicate 2

source_name: Scer FZF1 t=0min


title: WG0041907-DNA_F06_RM1293


title: Caf40-ChIP

city: Cambridge

first: Sidi

last: Chen

department: Biology

institute: MIT

hyb_protocol: Tecan HS 4800 Pro Hybridization Station

scan_protocol: High-throughput Genome Analysis Core (HGAC) in the Argonne National Laboratory, Affymetrix protocol

data_processing: Affy TAS

source_name: Caf40 ChIP

label_protocol: Affymetrix protocol

growth_protocol: Drosophila cornmeal

extract_protocol: ModEncode ChIP: Biological samples were homogenized in 1.8% of formaldehyde (for cross-linking). The cross-linked chromatin was sonicated to an average size of 500bp.

treatment_protocol: anti-FLAG antibody (Sigma)

tag: fraction

value: Chromatin DNA

value: anti-FLAG

tag: antibody vendor

value: Sigma

source_name: Caf40 input

value: input


title: S2_IMPDH_rep_02 ChIP-chip

description:
IMPDH ChIP S2 cells Biological Replicate 2.

Mock ChIPs were performed with preimmune serum (preimmune) or protein A beads (protA).
Input/Mock (control) CEL files: S2_input_1.CEL, S2_input_2.CEL, S2_input_3.CEL, S2_input_4.CEL, S2_input_5.CEL, S2_mock_preimmune_1.CEL, S2_mock_preimmune_2.CEL, S2_mock_preimmune_3.CEL, S2_mock_preimmune_4.CEL, S2_mock_protA_1.CEL, S2_mock_protA_2.CEL, S2_mock_protA_3.CEL, S2_mock_protA_4.CEL, S2_mock_protA_5.CEL, S2_mock_protA_6.CEL

scan_protocol: According to the manufacturer's protocols.


title: Zeus-ChIP

source_name: Zeus ChIP

source_name: Zeus input


title: WG0041907-DNA_F09_RM2191

source_name: Blood

value: Blood


title: 18 hr sample from LB growth, rep1

source_name: Cells from batch growth in nutritionally rich LB medium


title: S2_IMPDH_rep_01 ChIP-chip

description:
IMPDH ChIP S2 cells Biological Replicate 1.

Mock ChIPs were performed with preimmune serum (preimmune) or protein A beads (protA).
Input/Mock (control) CEL files: S2_input_1.CEL, S2_input_2.CEL, S2_input_3.CEL, S2_input_4.CEL, S2_input_5.CEL, S2_mock_preimmune_1.CEL, S2_mock_preimmune_2.CEL, S2_mock_preimmune_3.CEL, S2_mock_preimmune_4.CEL, S2_mock_protA_1.CEL, S2_mock_protA_2.CEL, S2_mock_protA_3.CEL, S2_mock_protA_4.CEL, S2_mock_protA_5.CEL, S2_mock_protA_6.CEL

label_protocol: According to the manufacturer's protocols.


title: 18 hr sample from LB growth, rep2


title: WG0041907-DNA_F05_RM5465


title: 15 hr sample from LB growth, rep2


title: 15 hr sample from LB growth, rep1


title: 12 hr sample from LB growth, rep2


title: WG0041907-DNA_F04_RM2124

value: Unaffected


title: WG0041907-DNA_F03_RX0493


title: WG0041907-DNA_F02_RM1255


title: 9 hr sample from LB growth, rep2


title: WG0041907-DNA_F01_RM3893


title: WG0041907-DNA_E11_RX0929


title: 5' S.paradoxus-S.cerevisiae FZF1 allele at t=15min replicate 3

source_name: 5'SparScer FZF1 t=15min

value: All alleles

value: All times


title: 9 hr sample from LB growth, rep1


title: 7 hr sample from LB growth, rep2


title: WG0041907-DNA_E12_RM1245


title: WG0041907-DNA_E10_RM4267


title: 12 hr sample from LB growth, rep1


title: 7 hr sample from LB growth, rep1


title: Filtered Air Control (Cy5)_Ozone lifetime (Cy3)_Pooled Takanari Seed 2

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description: DYE-SWAP

hyb_protocol: Agilent: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent Microarray scanner G2565BA

data_processing: Agilent Feature Extraction software (version 9.5.3.1)

organism: Oryza sativa

label_protocol: Manual: Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Plants were grown in controlled greenhouse, small open top chamber (sOTC)

extract_protocol: Modified CTAB protocol plus QIAGEN, Rneasy Mini

treatment_protocol: non-filtered air, O3, 37.2 ppb

tag: cultivar

value: L. indica cv. Takanari

tag: ozone sensitivity

value: ozone-sensitive cultivar

value: dry mature rice seeds

source_name: Takanari_control_filtered air

treatment_protocol: control, filtered air


title: WG0041907-DNA_E09_RM3524


title: 6 hr sample from LB growth, rep2


title: Filtered Air Control (Cy3)_Ozone lifetime (Cy5)_Pooled Takanari Seed 1


title: WG0041907-DNA_E08_RM1208


title: Filtered Air Control (Cy5)_Ozone lifetime (Cy3)_Pooled Koshihiraki Seed 2

description: DYE-SWAP

value: L. japonica cv. Koshihikari

value: ozone-tolerant cultivar

source_name: Koshihikari_control_filtered air


title: 6 hr sample from LB growth, rep1

value: Wild type strain


title: WG0041907-DNA_E05_RM3614

value: Passed QC


title: WG0041907-DNA_E02_RX0735

value: Failed QC

value: Unknown


title: WG0041907-DNA_E03_RM1150

value: AD


title: Parathyroid - Prolactin 24 h - Replicate 4

city: Stockholm

first: Felix

last: Haglund

address: Karolinska Universitetssjukhuset Solna, CMM L8:01

department: MMK

country: Sweden

institute: Karolinska Institutet

description: Gene expression of parathyroid adenoma

hyb_protocol: Hybridization to Affymetrix Human Gene 1.1 ST Array plates was performed using GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates.

scan_protocol: Array plates were scanned using Affymetrix GeneChip HT Array Plate Scanner according to standard protocols (Affymetrix Inc., Santa Clara, CA).

data_processing: Preprocessing was performed in Affymetrix Expression Console (v. 1.1) using the following methods: Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.

source_name: Parathyroid_200 mg/L Prolactin_24h

label_protocol: Total RNA was converted to sense strand cDNA using Ambion WT Expression kit. For fragmentation and labeling WT GeneChip WT target Labeling kit was used.

extract_protocol: Parathyroid adenoma samples for culturing and functional studies were obtained at surgery. Up to one third of the tumour was collected from each sample, while the majority of the tissue was sent to routine histopathological diagnostics. Fresh tissue samples were quickly transferred in cold culturing media to the nearby laboratory, and then isolated and cultured using previously described methods. All experiments were performed within 72 hours after isolation.

treatment_protocol: Expression profiling was done in parathyroid adenomas subjected to prolactin treatment in culture. In addition, corresponding paraffin sections were obtained for verification of PRLr expression by immunohistochemistry. 200 mg/L prolactin (recombinant human prolactin, Cat. No. JM-4687-50, MBL Woburn, MA) was added to 1× 10^6 attached parathyroid tumour cells. Cells were harvested using RNAlater (QIAGEN) and homogenized with QIAshredder for RNA extraction after 3 h and 24 h in culture, respectively. Negative controls were collected in parallel with each case at the same time points. RNA was extracted using QIA Cube, and quality assessed with Bioanalyser and Nanodrop.

value: Parthyroid Adenoma


title: WG0041907-DNA_E06_RX1208


title: 5.5 hr sample from LB growth, rep1

value: nutritionally rich LB medium


title: Parathyroid - Control 24 h - Replicate 4

description: Gene expression of parathyroid adenoma


title: 5.5 hr sample from LB growth, rep2


title: WG0041907-DNA_E04_RM1166


title: WG0041907-DNA_E01_RM1116


title: Rapamycin-exposed vs. vehicle-exposed primary undifferentiated spermatogonia

city: Chicago

first: Christopher

middle: J.

last: Payne

address: 2430 N. Halsted St.

institute: Northwestern University Feinberg School of Medicine

description: MACS-sorted cells enriched from total testis germ cells obtained from 5 littermate rapamycin-treated males (RM) and from 5 littermate vehicle-treated males (VEH) - pooled samples used for analysis

hyb_protocol: Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit. Cy3- and Cy5-labeled cRNA samples were combined and hybridized overnight (17 hours at 65 degrees c) to Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Rapamycin-exposed primary undifferentiated spermatogonia (postnatal day 26)

label_protocol: For the linear T7-based amplification step, 25 ng of each total RNA sample was used. To produce Cy3- and Cy5-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies). For RM sample (Cy3-labeled), cRNA yield was 1.26 ug. For VEH sample (Cy5-labeled), cRNA yield was 1.80 ug.

growth_protocol: Male FVB strain mice aged 12-days-old through 26-days-old were administered daily intraperitoneal injections of rapamycin (4mg/kg body weight) or control vehicle (5% Tween-80, 5% PEG-400), beginning at postnatal day (P)12. Mice were euthanized at P26 and their testes were isolated for germ cell enrichment.

extract_protocol: Total RNA extracted using the Rneasy Micro Kit (Qiagen) following the manufacturer's protocol.

value: FVB

tag: gender

value: male

tag: age

value: day 26

value: MACS-enriched primary undifferentiated spermatogonia

tag: tissue origin

value: testes

source_name: Vehicle-exposed primary undifferentiated spermatogonia (postnatal day 26)


title: Tumor DNA from skin tumor epithelium 4.2

city: Epalinges

first: Bing

last: Hu

address: Chemin des Boveresses 155

department: Department of Biochemistry

institute: University of Lausanne

hyb_protocol: Arrays contained 2.1 million probes across the whole genome based on the MM9 genome build. CGH was according to Nimblegen protocols

scan_protocol: Scanning with an Agilent G2565BA Microarray Scanner was followed by image

data_processing: Data were processed using Nimblescan software v.2.5.

source_name: Tumor DNA from skin tumor epithelium

label_protocol: Tumor DNA samples were labelled with Cy3 and hybridized to Nimblegen mouse CGH arrays together with Cy5-labelled normal brain DNA extracted from the same mice.

extract_protocol: Excised skin tumors were minced into small pieces and digested in 1% Collagenase I (Sigma; 37oC for 1 hour) for removal of stromal tissue. The resulting suspension was filtered through a 40mm mesh and epithelial fragments were used for DNA extraction, using a Wizard® Genomic DNA Purification Kit (Promega).

tag: tissue type

value: Skin tumor

source_name: Brain

value: Brain


title: Filtered Air Control (Cy3)_Ozone lifetime (Cy5)_Pooled Koshihikari Seed 1

value: dry mature rice seeds


title: Tumor DNA from skin tumor epithelium 4.1


title: Tumor DNA from skin tumor epithelium 5.1


title: Parathyroid - Prolactin 3 h - Replicate 4

description: Gene expression of parathyroid adenoma

source_name: Parathyroid_200 mg/L Prolactin_3h


title: Bladder DD CT20 rep1

city: Kyoto

first: Hiromitsu

last: Negoro

state: Kyoto

address: 54 Shogoin-Kawara-cho, Sakyo-ku

department: Urology

institute: Kyoto University, Graduate School of Medicine

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.

data_processing:
R statistical software (version 2.8.1, 2008-12-22) with BioConductor (version 2.3) was used.
The eliminating genes are “bad spots”, which were filtered by performing program as following options (refer to Agi4x44PreProcess package (version 1.2.0) for the content of options).
1.	Setting of filtering:
Filtering setting was as follows:
       control=TRUE,
       wellaboveBG=TRUE,
       isfound=TRUE,
       wellaboveNEG=TRUE,
       sat=TRUE,
       PopnOL=TRUE,
       NonUnifOL=TRUE,
       nas=TRUE,
       limWellAbove=75,
       limISF=75,
       limNEG=75,
       limSAT=75,
       limPopnOL=75,
       limNonUnifOL=75,
       limNAS=100,
2.	Setting of normalization
Quantile normalization was applied by following setting.
       ,BGmethod="half"
       ,NORMmethod="quantile"
       ,foreground="MeanSignal"
       ,background="BGMedianSignal"
       ,offset=50

source_name: Urinary bladder, DD, CT20

label_protocol: Agilent one-color Quick Amp Labeling Kit labeling protocol

extract_protocol: Total RNA was extracted using RNeasy Plus Mini Kit following to the protocol.

treatment_protocol: Sacrificed at Circadian Time (CT) 20 in constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions

tag: time

value: female

value: 10 weeks

value: Urinary bladder


title: WG0041907-DNA_D08_RM1046

city: Toronto

first: Ekaterina

last: Rogaeva

address: 6 Queen’s Park Crescent West

institute: Tanz Centre for Neurodegenerative Diseases

hyb_protocol: Samples were applied to beadchips and the loaded beadchips were incubated overnight in the Illumina Hybridization oven. Unhybridized and non-specifically hybridized DNA was washed away, and beadchips were prepared for staining and extension.

scan_protocol: The beadchips were scanned on the Illumina BeadArray Reader using default settings.

data_processing:
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%.
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.

label_protocol: 750ng of DNA was denatured and neutralized before amplification. The denatured DNA was isothermally amplified in an overnight step, and the amplified product was them enzymatically fragmented (i.e. End-point fragmentation), precipitated with isopropanol, collected by centrifugation at 4 degrees celciums, and resuspended in hybridization buffer. C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled.

extract_protocol: DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.

tag: qc status

value: Passed QC

tag: cell type

value: Blood

tag: disease status

value: Unaffected


title: 5 hr sample from LB growth, rep2

tag: strain

value: Wild type strain

tag: growth medium

tag: growth time


title: Parathyroid - Control 3 h - Replicate 4

description: Gene expression of parathyroid adenoma

tag: tissue

value: Parthyroid Adenoma


title: 5 hr sample from LB growth, rep1

value: nutritionally rich LB medium


title: Bladder DD CT16 rep2

source_name: Urinary bladder, DD, CT16

treatment_protocol: Sacrificed at Circadian Time (CT) 16 in constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions


title: WG0041907-DNA_D10_RX0400

value: AD


title: WG0041907-DNA_D12_RX1223


title: Tumor DNA from skin tumor epithelium 5.2


title: WG0041907-DNA_D09_RX1033


title: WG0041907-DNA_D06_RX1200


title: Parathyroid - Control 24 h - Replicate 3

description: Gene expression of parathyroid adenoma


title: WG0041907-DNA_D11_RM1109


title: Parathyroid - Prolactin 24 h - Replicate 3

description: Gene expression of parathyroid adenoma


title: Bladder DD CT16 rep1


title: Bladder DD CT20 rep2


title: Tumor DNA from skin tumor epithelium 3.1


title: 4.5 hr sample from LB growth, rep1


title: Tumor DNA from skin tumor epithelium 3.2


title: Tumor DNA from skin tumor epithelium 2.2


title: Parathyroid - Prolactin 3 h - Replicate 3

description: Gene expression of parathyroid adenoma


title: Bladder DD CT12 rep1

source_name: Urinary bladder, DD, CT12

treatment_protocol: Sacrificed at Circadian Time (CT) 12 in constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions


title: Parathyroid - Control 3 h - Replicate 3

description: Gene expression of parathyroid adenoma


title: 4 hr sample from LB growth, rep2


title: Bladder DD CT12 rep2


title: 4.5 sample from LB growth, rep2


title: WG0041907-DNA_D05_RM8242


title: Bladder DD CT8 rep2

source_name: Urinary bladder, DD, CT8

treatment_protocol: Sacrificed at Circadian Time (CT) 8 in constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions


title: WG0041907-DNA_D07_RM1045


title: WG0041907-DNA_D04_RM1011


title: 4 hr sample from LB growth, rep1


title: Bladder DD CT8 rep1


title: 3.5 hr sample from LB growth, rep2


title: Parathyroid - Prolactin 24 h - Replicate 2

description: Gene expression of parathyroid adenoma


title: WG0041907-DNA_D03_RX0530


title: 3.5 hr sample from LB growth, rep1


title: Tumor DNA from skin tumor epithelium 2.1


title: 3 hr sample from LB growth, rep2


title: Parathyroid - Control 24 h - Replicate 2

description: Gene expression of parathyroid adenoma


title: Tumor DNA from skin tumor epithelium 1.1


title: Bladder DD CT4 rep2

source_name: Urinary bladder, DD, CT4

extract_protocol: Total RNA was extracted using RNeasy Plus Mini Kit following the protocol.

treatment_protocol: Sacrificed at Circadian Time (CT) 4 in constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions


title: Parathyroid - Prolactin 3 h - Replicate 2

description: Gene expression of parathyroid adenoma


title: 3 hr sample from LB growth, rep1


title: Bladder DD CT0 rep1

source_name: Urinary bladder, DD, CT0

treatment_protocol: Sacrificed at Circadian Time (CT) 0 in constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions


title: Parathyroid - Control 3 h - Replicate 2

description: Gene expression of parathyroid adenoma


title: Bladder DD CT4 rep1


title: Parathyroid - Prolactin 24 h - Replicate 1

description: Gene expression of parathyroid adenoma


title: Bladder DD CT0 rep2


title: 2.5 hr sample from LB growth, rep1


title: Parathyroid - Control 24 h - Replicate 1

description: Gene expression of parathyroid adenoma


title: Parathyroid - Prolactin 3 h - Replicate 1

description: Gene expression of parathyroid adenoma


title: 2 hr sample from LB growth, rep2


title: BW001-7WT-8h-RNA4 vs. BW001-7WT-8h-DOX-RNA4

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing: genes, no bg corr

label_protocol: robot amplification and labeling v1.0

extract_protocol: RNA extraction cellLine

tag: cell line

value: T-REx HeLa


title: BW001-7WT-8h-RNA2 vs. BW001-7WT-8h-DOX-RNA2


title: Parathyroid - Control 3 h - Replicate 1

description: Gene expression of parathyroid adenoma


title: 2 hr sample from LB growth, rep1


title: WG0041907-DNA_E07_RM8285

source_name: Blood


title: 1.5 hr sample from LB growth, rep2

source_name: Cells from batch growth in nutritionally rich LB medium


title: BW001-7WT-8h-DOX-RNA3 vs. BW001-7WT-8h-RNA3


title: WG0041907-DNA_C12_RM3582


title: BW001-7WT-8h-DOX-RNA1 vs. BW001-7WT-8h-RNA1


title: PA5511 rep2

city: Aurora

first: Michael

middle: J

last: Schurr

state: CO

department: Microbiology

institute: University of Colorado School of Medicine

description: SAMPLE 5

hyb_protocol: Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.

data_processing:
Gene expression signal-level data were computed with the robust GeneChip multi-array average method (GCRMA) (Wu and Irizarry, 2004) using default settings, log-transformed, and normalized to total intensities with GeneSpring® GX 10.0.1 using a guided workflow. To test for differential expression between the different strains grown in a biofilm, the Bayesian adjusted t-statistics was used as implemented in the GeneSpring package. P-values were corrected for multiple testing using the Benjamini and Hochberg's method to control the false discovery rate (Benjamini and Hochberg, 1995). Only fold change ratios with adjusted P-values below 0.05 were included as statistically significant. Microarray analysis was performed on all three biological replicates.
Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate – a practical and powerful approach to multiple testing. J Royal Statistical Soc Series B-Methodological 57: 289–300.
Wu Z, Irizarry RA: Preprocessing of oligonucleotide array data. Nat Biotechnol 2004, 22(6):656-658.

organism: Pseudomonas aeruginosa

source_name: mifR (PA5511) deletant_flow-through bioflm on minimal medium with 10 mM glutamate_6 days

label_protocol: Ten micrograms of total RNA was used for cDNA synthesis, fragmentation, and labeling according to the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol (end labeled with biotin-ddUTP with use of the Enzo BioArray Terminal Labeling kit (Affymetrix))

growth_protocol: For biofilm growth experiments, three independent replicates of P. aeruginosa strains PAO1 and ΔmifR were grown as biofilms in a flow-through system using a once-through continuous flow tube reactor system for biofilm sample collection and in flow cells (BioSurface Technologies) for the analysis of biofilm architecture as previously described (Sauer et al., 2002, Sauer et al., 2004, Petrova & Sauer, 2009).

extract_protocol: Cells were treated with RNAprotect (Qiagen) and total RNA was extracted using an RNeasy mini purification kit (Qiagen) per the manufacturer’s instructions.  RNA quality and the presence of residual DNA were checked on an Agilent Bioanalyzer 2100 electrophoretic system pre- and post-DNase treatment.

tag: strain background

tag: genotype/variation

value: mifR (PA5511) deletant


title: WG0041907-DNA_D02_RM0994


title: WG0041907-DNA_D01_RX1107


title: PA5511 rep1

description: SAMPLE 4

scan_protocol: Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.


title: 1.5 hr sample from LB growth, rep1


title: 50 hr sample from Lactate growth, rep2

source_name: Cells from batch growth in lactate minimal medium

value: lactate minimal medium


title: 2.5 hr sample from LB growth, rep2


title: PA5511 rep3

description: SAMPLE 6


title: WG0041907-DNA_C11_RX0569


title: Methyl deficient diet mouse colon 4 sample 1

city: West Haven

first: Petr

last: Protiva

address: 950 Campbell Avenue

institute: Yale University and VA CT Healthcare System

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using 75th percentile shift in Genespring GX

source_name: MDD

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

extract_protocol: Colon 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.

treatment_protocol:
ApcMin mice were fed methyl deficient diets (MDD) or methyl sufficient diet  MSD (CONTROL)  for 11 weeks and normal colons were harvested for expression profiling, duplicate samples were taken from each animal
2 control animals and 4 methyl deficient animals were used for expression profiling

value: ApcMin

value: colon


title: 50 hr sample from Lactate growth, rep1


title: IL17RC+ THP1 Cells rep2

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

hyb_protocol: Starndard Affymetrix protocol

scan_protocol: Starndard Affymetrix protocol

data_processing: RMA normalization was used to summarize the signal using GeneSpring GX 11.0

source_name: IL17RC+ THP1

label_protocol: according to the MessageAmp™ II-Biotin Enhanced Kit protocol (Ambion).

growth_protocol: THP1 cells (ATCC, VA) were cultured in RPMI-1640 medium supplemented with 10% FBS, 2 mM L-glutamine, and 1X penicillin-streptomycin antibiotics (Invitrogen, CA) for two days

extract_protocol: The total RNA was extracted from cultured cells with mirVana RNA isolation kit (Ambion).

treatment_protocol: THP1 cells (ATCC, VA) were stimulated with 100 ng/ml IL-17A (R&D, MN) for two days. Cell surface IL17RC was stained by anti-IL17RC-APC antibody (R&D, MD) and sorted for IL17RC+ vs IL17RC- cells by FACS sorter (JSAN, Japan).

value: Human acute monocytic leukemia cells

tag: stimulated with

value: 100 ng/ml IL-17A


title: 48 hr sample from Lactate growth, rep2


title: WG0041907-DNA_C10_RM4313


title: IL17RC+ THP1 Cells rep1


title: Methyl deficient diet mouse colon 3 sample 2


title: Methyl deficient diet mouse colon 4 sample 2


title: 48 hr sample from Lactate growth, rep1


title: Methyl deficient diet mouse colon 3 sample 1


title: IL17RC- THP1 Cells rep2

source_name: IL17RC- THP1


title: IL17RC- THP1 Cells rep1


title: Methyl deficient diet mouse colon 2 sample 2


title: 36 hr sample from Lactate growth, rep1


title: 35 hr sample from Lactate growth, rep2


title: 36 hr sample from Lactate growth, rep2


title: RMG2-control-rep10

first: TAKAKO

last: OKAMOTO

address: 54 Kawahara-cho, shogoin,sakyo-ku,

institute: Kyoto University

description:
Cont_10
Gene expression data as non-silencing control

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were normalized by Robust Multichip Average (RMA) using R with Bioconductor Affy package.

label: Biotin

source_name: RMG2_non-silencing control

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

growth_protocol: RMG2 cells were cultured in RPMI (Nikken, Kyoto, Japan) supplemented with 10% FBS in a humidified atmosphere containing 5% CO2 at 37C.

extract_protocol: Total RNA was extracted by Qiagen RNEasy kit according to the manufacturer's instructions.

treatment_protocol: RMG2 cells transfected with ｔwo HNF1β-targeting shRNA clones (clone IDs: V2LHS_204881 and V2LHS_196459) and a non-silencing control (clone ID: RHS4348) (Thermo Fisher Scientific, Huntsville, AL, USA), using a standard protocol with lentiviruses.

value: Human ovarian clear cell carcinoma (OCCC) cells

tag: transfected with

value: non-silencing control


title: Methyl deficient diet mouse colon 1 sample 2


title: Methyl deficient diet mouse colon 1 sample 1


title: WG0041907-DNA_C09_NY0979

value: Failed QC


title: Methyl deficient diet mouse colon 2 sample 1


title: RMG2-control-rep9

description:
Cont_9
Gene expression data as non-silencing control


title: WG0041907-DNA_C06_RM0961

value: Passed QC


title: WG0041907-DNA_C08_RM3865

value: Blood


title: RMG2-control-rep8

description:
Cont_8
Gene expression data as non-silencing control


title: WG0041907-DNA_C07_RM0962

value: Unaffected


title: 35 hr sample from Lactate growth, rep1

value: Wild type strain


title: 34 hr sample from Lactate growth, rep2


title: Methyl sufficient diet mouse colon 3 sample 2

source_name: CONTROL


title: RMG2-control-rep7

description:
Cont_7
Gene expression data as non-silencing control


title: Methyl sufficient diet mouse colon 3 sample 1


title: WG0041907-DNA_C02_RM2167


title: Methyl sufficient diet mouse colon 1 sample 2


title: 33 hr sample from Lactate growth, rep2


title: RMG2-control-rep5

description:
Cont_5
Gene expression data as non-silencing control


title: Methyl sufficient diet mouse colon 1 sample 1


title: WG0041907-DNA_C04_RX1188


title: WG0041907-DNA_C05_RM0949


title: 33 hr sample from Lactate growth, rep1


title: 32 hr sample from Lactate growth, rep2


title: 34 hr sample from Lactate growth, rep1


title: WG0041907-DNA_B12_RM3665


title: 32 hr sample from Lactate growth, rep1


title: RMG2-control-rep6

description:
Cont_6
Gene expression data as non-silencing control


title: RMG2-control-rep3

description:
Cont_3
Gene expression data as non-silencing control


title: RMG2-control-rep2

description:
Cont_2
Gene expression data as non-silencing control


title: 31 hr sample from Lactate growth, rep1

description: Gene expression data from wild-type S. oneidensis MR-1


title: RMG2-control-rep4

description:
Cont_4
Gene expression data as non-silencing control


title: 31 hr sample from Lactate growth, rep2


title: WG0041907-DNA_B09_RM4137

description: C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled


title: RMG2-control-rep1

description:
Cont_1
Gene expression data as non-silencing control


title: RMG2-HNF1b-sh1-rep4

description:
Sh1_4
Gene expression data from HNF1b gene supressed cells

source_name: RMG2_HNF1b knockdown

value: HNF1b-targeting shRNA (clones V2LHS_204881)


title: 30 hr sample from Lactate growth, rep2


title: RMG2-HNF1b-sh1-rep2

description:
Sh1_2
Gene expression data from HNF1b gene supressed cells


title: WG0041907-DNA_C03_RM0937


title: 30 hr sample from Lactate growth, rep1


title: RMG2-HNF1b-sh1-rep3

description:
Sh1_3
Gene expression data from HNF1b gene supressed cells


title: 29 hr sample from Lactate growth, rep2


title: WG0041907-DNA_B06_RM4020


title: WG0041907-DNA_C01_RX0294


title: WG0041907-DNA_B10_RX0939


title: RMG2-HNF1b-sh2-rep5

description:
Sh2_5
Gene expression data from HNF1b gene supressed cells

value: HNF1b-targeting shRNA (clones V2LHS_196459)


title: WG0041907-DNA_B08_RM4226

value: AD


title: WG0041907-DNA_B11_RM3759


title: 29 hr sample from Lactate growth, rep1


title: RMG2-HNF1b-sh1-rep1

description:
Sh1_1
Gene expression data from HNF1b gene supressed cells


title: WG0041907-DNA_B07_RM4034


title: 28 hr sample from Lactate growth, rep2


title: 28 hr sample from Lactate growth, rep1


title: RMG2-HNF1b-sh2-rep4

description:
Sh2_4
Gene expression data from HNF1b gene supressed cells


title: RMG2-HNF1b-sh2-rep3

description:
Sh2_3
Gene expression data from HNF1b gene supressed cells


title: 27hr sample from Lactate growth, rep2


title: RMG2-HNF1b-sh2-rep2

description:
Sh2_2
Gene expression data from HNF1b gene supressed cells


title: RMG2-HNF1b-sh1-rep5

description:
Sh1_5
Gene expression data from HNF1b gene supressed cells


title: WG0041907-DNA_B02_RM3678


title: WG0041907-DNA_B05_RM3506


title: 27 hr sample from Lactate growth, rep1


title: WG0041907-DNA_B04_RM0821


title: 26 hr sample from Lactate growth, rep2


title: 26 hr sample from Lactate growth, rep1


title: A549-treated with DAMTC rep2

city: Delhi

first: Neeru

last: Saini

address: Mall Road

department: FGU

country: India

institute: IGIB

hyb_protocol: Refer to the Illumina Gene Expression System Manual

data_processing: Average Normalization using Illumina Beadstudio

source_name: Human lung adenocarcinoma cell line treated with DAMTC

label_protocol: As described in the illumina Human-6 chip processing protocol. Briefly, generation of biotin labelled cRNA from the product of RT cDNA synthesis and 2nd strand cDNA synthesis.

extract_protocol: The total RNA was extracted using TRIzol reagent (Invitrogen Corporation) according to the manufacturer's protocol.The RNA was resuspended in diethyl pyrocarbonate-treated water, quantified by UV absorbance at 260/280 nm and immediately used for RNA amplification and labeling by Illumina TotalPrep RNA amplification kit

value: human lung adenocarcinoma cell line


title: WG0041907-DNA_B01_RM2139


title: A549-treated with DAMTC rep3

scan_protocol: Refer to the Illumina Gene Expression System Manual


title: WG0041907-DNA_A10_RM0796


title: WG0041907-DNA_A11_RM3830


title: Hs578T_3DC

city: Fukuoka

first: Fusanori

last: Yotsumoto

address: 7-45-1, Nanakuma, Jonan-ku

department: Department of Biochemistry, School of Medicine

institute: Fukuoka University

hyb_protocol: Biotinylated cRNAs were fragmented and hybridized to Affymetrix GeneChip Human Genome U133Plus2.0 arrays.

scan_protocol: The arrays were washed and scanned on a GeneChip Fluidics Station 450 and GeneChip Scanner Model 3000 controlled by a GeneChip Operating System v1.4 (GCOS) (Affymetrix) according to standard Affymetrix protocols.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as normalization method, using GeneSpring ver. 11.5.1 (Agilent Technologies).

source_name: Hs578T, 3DC for 48 hours

label_protocol: Biotinylated antisense cRNA was prepared using GeneChip Expression 30-Amplification One-Cycle cDNA Synthesis kit and GeneChip Expression 30-Amplification Reagent (Affymetrix) according to the manufacturer’s protocol.

growth_protocol: Two TNBC cell lines, MDA-MB-231 and Hs578T, were used in this study. For the 2DC, 1×10^5 cells were seeded in 6-well plates and incubated for 72 hours. For the 3DC, 1×10^5 cells were plated in 6-well plates precoated with Matrigel (Biocoat Cellware; Becton Dickinson, Franklin Lakes, NJ). Cells were incubated overnight and medium was removed and replaced with fresh medium. After incubation for 48 hours, cells from 3DC were retrieved from colonies using BD Cell Recovery Solution (Biocoat Cellware). For the tumor xenograft models, 5×10^6 cells were subcutaneously inoculated into 4-week old non-obese diabetic/severe combined immunodeficiency (NOD/SCID) mice (Charles River Laboratories Japan Inc., Yokohama, Japan). Tumors were resected when individual tumor volumes reached approximately 100 mm^3, and were frozen and fractured with liquid nitrogen.

extract_protocol: RNA extraction was performed using TRIzol (Invitrogen Corp., Carlsbad, CA) according to the manufacturer’s protocols.

tag: gender

value: female

value: mammary gland

value: TNBC cell line Hs578T

tag: disease state

value: breast carcinoma

tag: growth condition

value: 3D cultures (3DC)


title: WG0041907-DNA_A08_RM8272


title: A549-treated with DAMTC rep1


title: 24 hr sample from Lactate growth, rep2

last: Beg

institute: Boston University

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on a high-density Shewanella custom microarray manufactured by Affymetrix. The arrays were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000

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

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA easy kit (Qiagen)

value: lactate minimal medium


title: Hs578T_2DC

source_name: Hs578T, 2DC for 72 hours

value: control two-dimensional cultures (2DC)


title: 24 hr sample from Lactate growth, rep1


title: Hs578T_tumor xenograft models

source_name: Hs578T, a tumor volume of approximately 100 mm^3

value: tumor xenograft model


title: 22 hr sample from Lactate growth, rep2


title: A549-control rep2

source_name: human lung adenocarcinoma cell line control


title: A549-control rep3


title: WG0041907-DNA_A09_RM2084


title: 20 hr sample from Lactate growth, rep2


title: RMG2-HNF1b-sh2-rep1

description:
Sh2_1
Gene expression data from HNF1b gene supressed cells

value: Human ovarian clear cell carcinoma (OCCC) cells


title: 22 hr sample from Lactate growth, rep1


title: A549-control rep1


title: WG0041907-DNA_A06_RM3864

value: Failed QC


title: MDA-MB-231_2DC

source_name: MDA-MB-231, 2DC for 72 hours

value: TNBC cell line MDA-MB-231

value: breast adenocarcinoma (derived from metastatic site:pleural effusion)


title: MDA-MB-231_3DC

source_name: MDA-MB-231, 3DC for 48 hours


title: MDA-MB-231_tumor xenograft models

source_name: MDA-MB-231, a tumor volume of approximately 100 mm^3


title: treated neuro-ectodermal cell line rep6

first: Floor

last: Duijkers

address: Dr. Molewaterplein 50-60 Ee15-02

department: Pediatric Oncology-Hematology

institute: Erasmus MC

hyb_protocol: Oligoarray control targets and hybridization buffer (the Oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially according to the Agilent protocol.

scan_protocol: Scanned on an Agilent G2565AA scanner. Scanned at 100% intensity

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Agilent Feature Extraction Software (v 8.5.1.1) was used for data extraction. The R and Bioconductor statistical environment (version 2.7) were used for quality control and weighted P-spline normalization (package Turbotrend, described in this article). No background correction was performed.

source_name: tumor cell line

label_protocol: Using the BioPrime Array-CGH Genomic Labeling kit (Invitrogen, Carlsbad, USA), amino-allyl dUTPs were incorporated into 500ng of the methylated amplicons (generated by DMH) , allowing the amplicons to be labeled with the fluorescent dyes Cy5 (cell line samples) and Cy3 (common reference samples).

growth_protocol: All neuro-ectodermal cell lines were kept in DMEM with glutamax, Non-essential amminoacids, penicilin, streptomycin, fungizone and 10% FCS added

extract_protocol: Total DNA was extracted using Trizol protocol according to manufactors protocol

value: PNET

tag: treatment

value: 30 nM Decitabine (72 hour) and 25 nM trichostatin A (48 hour)

tag: sample type

value: DNA, methylation enriched fragments by DMH

source_name: Blood pool 2 male and 2 female adults

tag: source

value: Blood pool 2 male and 2 female adults

value: blood


title: 20 hr sample from Lactate growth, rep1

first: Qasim

source_name: Cells from batch growth in lactate minimal medium

value: Wild type strain


title: WG0041907-DNA_A05_RX0266

source_name: Blood

tag: qc status

value: Passed QC

tag: cell type

value: Blood

value: Unaffected


title: WG0041907-DNA_A04_RM0763

tag: disease status

value: AD


title: WG0041907-DNA_A07_RM2170


title: Patient 10: healthy control

city: Hangzhou

first: Yulian

last: Wu

state: Zhejiang

address: 88 Jiefang Road

department: surgey

country: China

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

description: peripheral blood samples from pantient with pancreatic cancer and diabetes mellitus,

hyb_protocol: Resulting biotin-labeled cRNA was recovered and purified with the RNeasy mini kit (Qiagen, Hilden, Germany), then hybridized to the human genome U133 plus 2.0 chips at 45℃ overnight.

scan_protocol: arrays were scanned using GeneChip Scanner 3000 according to the manufacture’s protocol.

data_processing: The hybridization data were analyzed using GeneChip Operating software (GCOS 1.4). A variance stabilization normalization (VSN) was performed to normalize the different arrays using dChip software. Genes assigned in the GCOS software as “Absent” call in all samples were removed before further analysis. For comparison analysis, a two class unpaired method in the Significant Analysis of Microarray software (SAM) was applied to identify significantly differentially expressed genes between the two selected groups.

source_name: peripheral blood samples from healthy control

label_protocol: Biotinylated cRNA were prepared from 2 microg total RNA using the MessageAmpTM II aRNA Amplification Kit (Ambion, Huntingdon, UK).

extract_protocol: 6-8 ml of blood samples were drawn into EDTA vacutainer tubes (Becton Dickinson, Franklin Lakes, NJ) by routine venipuncture, put immediately on ice and transferred to the laboratory within 4 hours for blood processing. Total RNA from nucleated blood cells was following lysis of erythrocytes and removal of cell debris. RNA was then purified with RNeasy mini kit (Qiagen, Hilden, Germany). The quality of purified total RNA was assessed by using the RNA 6000 Nano LabChip kit on a 2100 bioanalyzer (Agilent, Palo Alto, CA) and quantity was assessed by A260/280 absorbance ratios.

tag: identifier

tag: sex

value: female

tag: age

value: 72 years


title: 18 hr sample from Lactate growth, rep2

city: Boston

address: 44 Cummington St

tag: strain

tag: growth medium

value: lactate minimal medium

tag: growth time


title: WG0041907-DNA_A02_RM0732


title: WG0041906-DNA_H10_RX0249


title: WG0041907-DNA_A03_RM0762


title: 18 hr sample from Lactate growth, rep1


title: treated neuro-ectodermal cell line rep5

tag: cell line

tag: tissue


title: WG0041906-DNA_H12_RM8371


title: Patient 9: healthy control

value: male

value: 80 years


title: 16 hr sample from Lactate growth, rep2


title: Patient 8: healthy control

value: 70 years


title: 16 hr sample from Lactate growth, rep1


title: Patient 7: healthy control

value: 75 years


title: Patient 6: healthy control

value: 58 years


title: WG0041906-DNA_H07_RM4104

value: Failed QC


title: WG0041906-DNA_H05_RM0661


title: treated neuro-ectodermal cell line rep2

value: PNET

value: 30 nM Decitabine (72 hour) and 25 nM trichostatin A (48 hour)

value: DNA, methylation enriched fragments by DMH


title: WG0041906-DNA_H08_RM2141


title: treated neuro-ectodermal cell line rep3

value: Blood pool 2 male and 2 female adults

value: blood


title: treated neuro-ectodermal cell line rep4


title: WG0041906-DNA_H09_RM0702

value: Passed QC

value: Blood


title: WG0041906-DNA_H11_RM4024

value: Unaffected


title: 15 hr sample from Lactate growth, rep1

value: Wild type strain


title: Patient D4: healthy control

value: 62 years


title: Patient C10-2: patient with pancreatic cancer but without diabetes mellitus

source_name: peripheral blood samples from patient with pancreatic cancer without diabetes mellitus

tag: patient identifier

value: female

tag: age of patient

value: 51 years

tag: fbs

value: 102 mg/dl

tag: diagnosis

value: pancreatic adenocarcinoma


title: untreated neuro-ectodermal cell line rep6

tag: treatment

value: untreated

tag: sample type


title: 15 hr sample from Lactate growth, rep2

value: lactate minimal medium


title: untreated neuro-ectodermal cell line rep4

tag: source


title: Patient D2: healthy control

value: male

value: 77 years


title: Patient C9: patient with pancreatic cancer but without diabetes mellitus


title: Patient D3: healthy control

value: 45 years


title: untreated neuro-ectodermal cell line rep3

value: PNET

value: DNA, methylation enriched fragments by DMH


title: treated neuro-ectodermal cell line rep1

value: 30 nM Decitabine (72 hour) and 25 nM trichostatin A (48 hour)

value: Blood pool 2 male and 2 female adults

value: blood


title: WG0041906-DNA_H06_RM3803

tag: qc status

value: Passed QC

tag: cell type

value: Blood

value: AD


title: untreated neuro-ectodermal cell line rep5


title: untreated neuro-ectodermal cell line rep2


title: wildtype-reproductive-organ4

first: Sidi

last: Chen

institute: MIT

description:
US80900103_251897210234_S01_GE2_107_Sep09_1_1.txt
Technical replicate

hyb_protocol: Tecan HS 4800 Pro Hybridization Station

scan_protocol: Agilent Technologies Scanner G2505C US80900103

data_processing: Agilent Feature Extraction Software, Bioconductor package marray function backgroundCorrect with method option  normexp for background subtraction; function normalizewithArrays with method  option loess for within array normalization ; function  normalizebetweenArrays with method option Aquantile for between array normalization, All FLAG data points treated as NA (null).

label_protocol: two-color Quick Amp labeling Kit

extract_protocol: Trizol-Qiagen

treatment_protocol: RNAi

value: reproductive organ

tag: genotype/variation

value: wildtype


title: WG0041906-DNA_H02_RM0616

tag: disease status


title: Patient C8: patient with pancreatic cancer but without diabetes mellitus

tag: sex

value: 64 years

value: 94 mg/dl


title: WG0041906-DNA_H04_RM0658

value: Unaffected


title: Zeus-RNAi-reproductive-organ3

description:
US80900103_251897210154_S01_GE2_105_Dec08_1_3.txt
Biological replicate

value: Zeus


title: Patient C6: patient with pancreatic cancer but without diabetes mellitus

value: female

value: 58 years

value: 102 mg/dl

value: pancreatic adenocarcinoma


title: Patient C5: patient with pancreatic cancer but without diabetes mellitus

value: male

value: 71 years

value: 104 mg/dl


title: Patient C3: patient with pancreatic cancer but without diabetes mellitus

value: 59 years

value: 89 mg/dl


title: wildtype-reproductive-organ3


title: Zeus-RNAi-reproductive-organ4


title: WG0041906-DNA_H01_RM0605

value: Passed QC

value: Blood


title: WG0041906-DNA_H03_RX0475

value: AD


title: Zeus-RNAi-reproductive-organ2

description:
US80900103_251897210154_S01_GE2_105_Dec08_1_4.txt
Biological replicate

value: reproductive organ


title: WG0041906-DNA_G12_RM0601


title: Patient C1: patient with pancreatic cancer but without diabetes mellitus

value: 60 years

value: 88 mg/dl


title: Patient C2: patient with pancreatic cancer but without diabetes mellitus

value: 65 years


title: WG0041906-DNA_G11_RM3593

value: Unaffected


title: Patient B10: patient with diabetes mellitus

source_name: peripheral blood samples from patient with diabetes mellitus

value: diabetes mellitus>5 years


title: untreated neuro-ectodermal cell line rep1

value: PNET

value: untreated

value: DNA, methylation enriched fragments by DMH

value: Blood pool 2 male and 2 female adults

value: blood


title: wildtype-wholebody2

description:
US80900103_251897210153_S01_GE2_105_Dec08_1_3.txt
Biological replicate

value: wholebody

value: wildtype


title: wildtype-reproductive-organ1

description:
US80900103_251897210153_S01_GE2_105_Dec08_1_1.txt
Biological replicate


title: Zeus-RNAi-reproductive-organ1

value: Zeus


title: wildtype-reproductive-organ2


title: Patient B8: patient with diabetes mellitus

value: female

value: 75 years

value: diabetes mellitus 5 years


title: WG0041906-DNA_G08_RM2184

description: C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled

value: Passed QC

value: Blood

value: AD


title: wildtype-wholebody1

description:
US80900103_251897210153_S01_GE2_105_Dec08_1_4.txt
Biological replicate


title: Patient B7: patient with diabetes mellitus

value: male

value: 85 years

value: diabetes mellitus 8 years


title: WG0041906-DNA_G10_RM3969


title: Patient B6-2: patient with diabetes mellitus

value: 72 years

value: diabetes mellitus 21 years


title: WG0041906-DNA_G06_RM0574


title: WG0041906-DNA_G09_RM3847

value: Unaffected


title: WG0041906-DNA_G04_RM4241

value: Failed QC


title: Zeus-RNAi-wholebody1


title: WG0041906-DNA_G05_RM3632


title: Caf40-RNAi-whiteprepupae4

description:
US80900103_251897210233_S01_GE2_107_Sep09_1_4.txt
Biological replicate

value: white prepupa


title: Zeus-RNAi-wholebody2

value: wholebody


title: Zeus-RNAi-wholebody3

description:
US80900103_251897210153_S01_GE2_105_Dec08_1_2.txt
Biological replicate


title: Patient A10: patient with pancreatic cancer and diabetes mellitus

source_name: peripheral blood samples from pantient with pancreatic cancer and diabetes mellitus

value: 47 years

value: 181 mg/dl

value: pancreatic adenocarcinoma


title: Patient B2: patient with diabetes mellitus

value: diabetes mellitus>5 years


title: WG0041906-DNA_G01_RM0540


title: Patient B1: patient with diabetes mellitus

source_name: peripheral blood samples from pantient with diabetes mellitus

value: diabetes mellitus>10 years


title: Patient B3: patient with diabetes mellitus

value: 68 years

value: diabetes mellitus 6 years


title: WG0041906-DNA_G07_RM2127

value: Passed QC

value: Blood

value: AD


title: WG0041906-DNA_F12_RM4179


title: WG0041906-DNA_G02_RX0311


title: WG0041906-DNA_G03_RM8185


title: Caf40-RNAi-whiteprepupae3

description:
US80900103_251897210234_S01_GE2_107_Sep09_1_4.txt
Biological replicate


title: wildtype-whiteprepupae2

description:
US80900103_251897210233_S01_GE2_107_Sep09_1_3.txt
Biological replicate

value: wildtype


title: Patient A9: patient with pancreatic cancer and diabetes mellitus

value: female

value: 137 mg/dl


title: wildtype-whiteprepupae1

description:
US80900103_251897210234_S01_GE2_107_Sep09_1_3.txt
Biological replicate


title: wildtype-wholebody3


title: WG0041906-DNA_F11_RM4103


title: wildtype-whiteprepupae4


title: Ws_root_2h_KCl_rep1

city: Santiago

first: Elena

middle: A

last: Vidal

address: Avenida Libertador Bernardo O'Higgins 340

department: Genetica Molecular y Microbiologia

country: Chile

institute: Pontificia Universidad Catolica de Chile

description: Ws wild-type seedlings, treated with 5 mM KCl for 2 hours. Roots were cut and total RNA was extracted using TriZol.

hyb_protocol: ATH1 chips were hybridized using the GeneChip Hybridization, Wash and Stain kit from Affymetrix

scan_protocol: Chips were scanned using the Affymetrix GeneChip Scanner 3000 7G and the Affymetrix GeneChip Command Console Scan Control 1.1.0.845 software

data_processing: The summarized probe set data was generated using R/bioconductor (affy library). Normalization of the data was performed using rma. Normalized data was subjected to a two-way ANOVA analysis with a false discovery rate of 5 %.

organism: Arabidopsis thaliana

source_name: Ws roots, treated with 5 mM KCl for 2 hours

label_protocol: Bioitinylated cRNA was prepared using the GeneChip 3'IVT kit from Affymetrix

growth_protocol: Arabidopsis seedlings of the Ws and afb3-1 genotypes were grown on hydroponic medium containing 1X MS salts without Nitrogen, supplemented with 0.5 mM ammonium succinate as Nitrogen source and 3 mM sucrose on a Percival chamber under a photoperiod of 16 hours of light (100 μE/m2/sec) and 8 hours of dark at 22°C for 14 days.

extract_protocol: Total RNA was extracted using the TriZol reagent as indicated by the manufacturer.

treatment_protocol: Plants were treated at the onset of the light period on day 15 with 5 mM KNO3 or 5 mM KCl as control for 2 hours. Roots were cut and frozen on liquid nitrogen.

value: Arabidopsis root

tag: genotype

value: Ws

tag: age

value: 15-day old seedling

value: 2 hours of 5 mM KCl


title: Patient A5: patient with pancreatic cancer and diabetes mellitus

value: male

value: 58 years

value: 145 mg/dl


title: wildtype-whiteprepupae3

value: white prepupa


title: Patient A7: patient with pancreatic cancer and diabetes mellitus

value: 66 years

value: 130 mg/dl

value: pancreatic adenocarcinoma


title: WG0041906-DNA_F10_RX0263

value: Passed QC

value: Unaffected


title: WG0041906-DNA_F08_RM1159

value: Blood


title: Patient B4: patient with diabetes mellitus

value: 69 years

value: diabetes mellitus 7 years


title: Patient A3: patient with pancreatic cancer and diabetes mellitus

hyb_protocol: Resulting biotin-labeled cRNA was recovered and purified with the RNeasy mini kit (Qiagen, Hilden, Germany), then hybridized to the human genome U133 plus 2.0  chips at 45℃ overnight.

value: 70 years

value: 190 mg/dl


title: WG0041906-DNA_F07_RM4260

value: AD


title: Caf40-RNAi-whiteprepupae1


title: afb3-1_root_2h_KNO3_rep1

description: Auxin receptor AFB3 mutant seedlings (afb3-1), treated with 5 mM KNO3 for 2 hours. Roots were cut and total RNA was extracted using TriZol.

source_name: afb3-1 roots, treated with 5 mM KNO3 for 2 hours

value: Arabidopsis root

value: afb3-1 mutant

value: 15-day old seedling

value: 2 hours of 5 mM KNO3


title: Caf40-RNAi-whiteprepupae2


title: Patient A1: patient with pancreatic cancer and diabetes mellitus

value: female

value: 63 years


title: SUM159PT-transfected with LNA-antimiR-control

city: Portland

first: Laura

middle: M.

last: Heiser

state: OR

address: 3181 SW Sam Jackson Park Rd.

institute: OHSU

description: Cell line derived from breast carcinoma

hyb_protocol: RNA was hybridized using the Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: The GenePattern suite of tools was employed to visualize the arrays and mask any visible smudges. Probe set based gene expression measurements were normalized using the RMA algorithm in Genepattern (http://www.broad.mit.edu/cancer/software/genepattern/).

label_protocol: Samples were prepared according to the standard Affymetrix protocol from 3 ug total RNA

growth_protocol: Ham's F12 + 5 % FBS + Insulin (5 ug/ml) + Hydrocortisone (1 ug/ml) + HEPES (10 mM)

extract_protocol: Total RNA was harvested 24 h post-transfection using RNeasy mini kit (Qiagen, Valencia, CA,   USA).

treatment_protocol: Cells transfected with LNA-antimiR-control at final concentration of 50nM with Lipofectamine 2000.

value: Breast

tag: group

value: Control

tag: transfection

value: LNA-antimiR-control


title: WG0041906-DNA_F05_RM0517

value: Passed QC


title: afb3-1_root_2h_KCl_rep3

description: Auxin receptor AFB3 mutant seedlings (afb3-1), treated with 5 mM KCl for 2 hours. Roots were cut and total RNA was extracted using TriZol.

source_name: afb3-1 roots, treated with 5 mM KCl for 2 hours

tag: tissue

value: 2 hours of 5 mM KCl