title: Liver_KO_P0_4

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done under R (www.r-project.org) using packages from Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot):  myfunw<-function(x)  {okType<-x$ControlType==0  okFoundGreen<-x$gIsFound==1  okPos=x$gIsPosAndSignif==1  okWellAbove<- x$gIsWellAboveBG==1  as.numeric(okType & okFoundGreen & okPos & okWellAbove)}  We selected the spots with a weight of 1 for at least 12 out of 15 microarrays or with a weight of 1 in 2 microarrays from at least one experimental group. Additionally, we replaced by NA all values which were flagged with gFeatNonUniOL==1. The filtered data were then stored as an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 35951 rows each corresponding to a unique ProbeName.

source_name: Liver, KO, P0, replicate 4

treatment_protocol: Breeding was performed overnight. Female breeders positive for copulation plugs in the morning were considered embryonic day 0.5 (E0.5). Animals were obtained from cesarean performed at E19.5 or by natural delivery.


title: Liver_KO_P0_5

status: Public on Aug 22 2014

type: RNA

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarrays (8x60K) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarray chambers were disassembled in Wash Buffer 1 and the slides were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on an Agilent High Resolution C Scanner (G2565CA)

molecule: total RNA

organism: Mus musculus

source_name: Liver, KO, P0, replicate 5

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions,  followed by RNeasy column purification (QIAGEN, Courtaboeuf, France).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice with a maternally-inherited deletion of the miR-379/miR-410 cluster and wild-type littermates on a C57BL/6J genetic background were housed at room temperature on a 12h light/dark cycle (lights on at 8:00 am) and had free access to food (standard rodent chow) and tap water.

extract_protocol: Immediately following euthanasia, liver was removed, snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction. Total RNA was extracted from frozen liver samples with Tri-reagent (Euromedex) following  manufacturer's instructions. Total RNA samples were controlled for integrity on an Agilent 2100 Bioanalyzer (Agilent Technologies) and assayed at 260nm on a Nanodrop ND-1000 spectrophotometer (Thermo Scientific).

tag: strain

tag: age

tag: tissue

value: liver


title: 36_Lund_AS_sample Primary

city: Lund

first: Emelie

last: Styring

address: Skanes University Hospital

department: Dept of Orthopedics

country: Sweden

institute: Lund University

description: Primary

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina iScan N240 scanning protocol.

data_processing: Gene expression data were uploaded and processed in the GenomeStudio software (Illumina, San Diego, CA). Data were normalized using background correction and the cubic spline method.

organism: Homo sapiens

source_name: FFPE tumor tissue

label_protocol: Standard Illumina labeling protocol (Ligated products were PCR-amplified and labeled with a universal Cy3-coupled primer, after which single-stranded labeled products were precipitated and then hybridized to WG gene expression BeadChips as previously described (Kuhn et al. 2004).)

extract_protocol: Non-necrotic tumor areas were macro-dissected from FFPE blocks and RNA extraction was performed from three 10-µm sections using the High Pure RNA Paraffin Kit (Roche, Castle Hill, Australia) according to the manufacturer's instructions.

tag: Sex

value: m

tag: year of birth

tag: year of breast cancer

value: Not applicable

tag: year of angiosarcoma

tag: previous radiotherapy to tumor area

value: No


title: 35_Lund_AS_sample Secondary

description: Secondary

value: f

value: Yes


title: lc_129

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the NanoString nCounter Assay System Manual

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

label: biotin

extract_protocol: RNA was isolated with TRIzol LS reagent (Invitrogen) according to manufacturer’s protocol.

treatment_protocol: FFPE tissue sections (10 micron-thick) sliced from FFPE blocks

tag: disease state

value: hepatitis C virus (HCV)-related liver cirrhosis

tag: prognostic prediction

value: Poor


title: lc_121

scan_protocol: Refer to the NanoString nCounter Assay System Manual


title: 34_Lund_AS_sample Secondary

description: Secondary


title: lc_205

label_protocol: Refer to the NanoString nCounter Assay System Manual

value: Good


title: Liver_KO_P0_1

source_name: Liver, KO, P0, replicate 1


title: lc_110


title: CCSK11

first: Jenny

last: Karlsson

address: BMC C13

department: Clinical genetics

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing: Data was normalized with the quantile normalisation algorithm in the BeadStudio (Illumina) software

label: Biotin

source_name: Tumour tissue

label_protocol: Illumina Totalprep-96RNA Amplification kit 4397949 RevB, (Modification of Amplification kit v1.1)

extract_protocol:
Total RNA was extracted with the RNeasy Lipid Tissue Mini Kit (Qiagen) followed by On-column DNase Digestion (Qiagen) according to the manufacturers´ instructions. Quality control was performed with Agilent Bioanalyzer.
Total RNA was extracted with the RNeasy Lipid Tissue Mini Kit (Qiagen) followed by On-column DNase Digestion (Qiagen) according to the manufacturers´ instructions. Quality control was performed with Agilent Bioanalyzer.

value: Clear cell sarcoma of the kidney

tag: gender

value: M

value: 10 months


title: Liver_KO_P0_3

source_name: Liver, KO, P0, replicate 3


title: Liver_KO_P0_2

source_name: Liver, KO, P0, replicate 2


title: 32_Lund_AS_sample Primary

description: Primary


title: 31_Lund_AS_sample

value: Unknown

tag: replicate

value: Techn repl (sample 31 :sample 10)


title: CCSK15

value: F

value: 1 year


title: Liver_WildType_P0_3

source_name: Liver, Wild-type, P0, replicate 3


title: CCSK2


title: CCSK7

value: 8 months


title: lc_097

value: liver

value: Intermediate


title: lc_096


title: 33_Lund_AS_sample Secondary

description: Secondary


title: CCSK5

value: 5 years


title: CCSK9

value: 2 years


title: lc_094


title: Liver_WildType_P0_2

source_name: Liver, Wild-type, P0, replicate 2


title: 30_Lund_AS_sample Secondary

description: Secondary

value: f

value: Biol repl A2


title: Liver_WildType_P0_4

source_name: Liver, Wild-type, P0, replicate 4


title: lc_085

value: hepatitis C virus (HCV)-related liver cirrhosis


title: lc_093


title: lc_076

value: Poor


title: Liver_KO_E19_3

source_name: Liver, KO, E19.5, replicate 3


title: lc_075


title: 29_Lund_AS_sample Secondary

description: Secondary

value: Yes


title: lc_068


title: Liver_KO_E19_2

source_name: Liver, KO, E19.5, replicate 2


title: lc_063


title: Liver_WildType_E19_3

source_name: Liver, Wild-type, E19.5, replicate 3


title: 23_Lund_AS_sample Primary

description: Primary

value: m

value: Not applicable

value: No


title: Liver_KO_E19_1

source_name: Liver, KO, E19.5, replicate 1


title: Liver_WildType_E19_2

source_name: Liver, Wild-type, E19.5, replicate 2


title: CCSK1

value: Clear cell sarcoma of the kidney

value: M

value: 9 years


title: 26_Lund_AS_sample Secondary

description: Secondary

value: Biol repl A1


title: 22_Lund_AS_sample Primary

description: Primary


title: 24_Lund_AS_sample Primary

description: Primary


title: 25_Lund_AS_sample Primary

description: Primary


title: 28_Lund_AS_sample Primary

description: Primary


title: 27_Lund_AS_sample Primary

description: Primary

value: Techn repl (sample 14 :sample 27)


title: lc_062

value: liver

value: Good


title: Liver_KO_rep3

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done under R (www.r-project.org) using packages from Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot):  myfunw<-function(x)  {okType<-x$ControlType==0  okFoundGreen<-x$gIsFound==1  okPos=x$gIsPosAndSignif==1  okWellAbove<- x$gIsWellAboveBG==1  as.numeric(okType & okFoundGreen & okPos & okWellAbove)}  We selected the spots with a weight of 1 for at least 6 out of 8 microarrays or with a weight of 1 for 4 microarrays from at least one experimental group. The filtered data were then stored as an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 27084 rows each corresponding to a unique ProbeName.

source_name: Liver, KO, E19.5+4h, replicate 3

extract_protocol: Immediately following euthanasia, liver was removed, dissected (~100 mg fragments from the large lobe), snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction. Total RNA was extracted from frozen liver samples with Tri-reagent (Euromedex) following  manufacturer's instructions. Total RNA samples were controlled for integrity on an Agilent 2100 Bioanalyzer (Agilent Technologies) and assayed at 260 nm on a Nanodrop ND-1000 spectrophotometer (Thermo Scientific).

treatment_protocol: Breeding was performed overnight. Female breeders positive for copulation plugs in the morning were considered embryonic day 0.5 (E0.5). Animals were obtained from cesarean performed at E19.5. Pups were immediately expelled and put in a warm and moist box placed in a 37°C water bath. Pups’ mouth and nostrils were gently cleaned with cotton swabs, which were also used also to stimulate breathing and motion by gentle massage. Pups were continuously monitored during the course of the experiment and sacrificed by decapitation 4h following the caesarean.


title: lc_055


title: lc_057


title: Liver_KO_rep4

source_name: Liver, KO, E19.5+4h, replicate 4


title: lc_010

value: Intermediate


title: Liver_WildType_E19_1

source_name: Liver, Wild-type, E19.5, replicate 1


title: Liver_WildType_rep3

source_name: Liver, Wild-type, E19.5+4h, replicate 3


title: lc_004


title: Liver_WildType_rep4

source_name: Liver, Wild-type, E19.5+4h, replicate 4


title: 21_Lund_AS_sample Secondary

description: Secondary

source_name: FFPE tumor tissue


title: 20_Lund_AS_sample Primary

description: Primary


title: lc_024


title: Liver_KO_rep1

source_name: Liver, KO, E19.5+4h, replicate 1


title: Liver_WildType_rep1

source_name: Liver, Wild-type, E19.5+4h, replicate 1


title: lc_030


title: 18_Lund_AS_sample Secondary

description: Secondary


title: 14_Lund_AS_sample Primary

description: Primary

value: Biol rep C1 AND techn repl (sample 14:sample 27)


title: 16_Lund_AS_sample Secondary

description: Secondary

value: f


title: 72hrs_pBabe_Rep3

city: Newcastle Upon Tyne

first: Gary

last: Beale

state: Tyne and Wear

address: Framlington place

department: NICR

country: United Kingdom

institute: Newcastle University

description: Total RNA was converted to cRNA and hybridised to the whole genome chip expression levels were compared between KLF6 overexpressing and control infected HepG2 cells

hyb_protocol: Biotin labelled cRNA was hybridised to the arrays overnight at 16oC, washed and then stained with streptavidin Cy5

scan_protocol: Slides were scanned on the Genepix 4000B array scanner using GE Healthcare guidelines for whole genome microarray scanning (http://www.fda.gov/downloads/ScienceResearch/BioinformaticsTools/MicroarrayQualityControlProject/UCM132984.pdf

data_processing: TIFF files from the Axon scanner were converted to Axon text files using their own programm to normalise expression values

label_protocol: Total RNA (1ug) was converted to biotin labelled cRNA via cDNA and in vitro transcription

growth_protocol: HepG2 cells were grown in DMEM containing 10% FCS

extract_protocol: RNA was extracted from Hep G2 cells using the Qiagen RNAeasy mini kit under the manufacturers recommended conditions

treatment_protocol: Early passage HepG2 cells were transformed with a rettovirus containing KLF6

value: Liver

tag: cell line


title: 72hrs_pBabe_Rep2


title: Liver_KO_rep2

source_name: Liver, KO, E19.5+4h, replicate 2


title: Liver_WildType_rep2

source_name: Liver, Wild-type, E19.5+4h, replicate 2


title: 17_Lund_AS_sample Secondary

description: Secondary


title: FL Btg1-/-+ETV6-RUNX1

city: Nijmegen

first: Frank

middle: N

last: van Leeuwen

address: PO BOX 9101 route 412

department: Pediatrics

country: Netherlands

institute: Radboudumc

hyb_protocol: Standard Illumina direct hybridization protocol

scan_protocol: Standard Illumina direct hybridization scanning protocol

data_processing: The data were normalised using RMA normalisation with arraystar

source_name: FL Btg1-/-+ETV6-RUNX1

label_protocol: Biotinylated cRNA were prepared using the Illumina Ambion Total Prep-96 Kit

growth_protocol: Transduced wild-type and Btg1-/- FL-HPCs (1x105 cells/well) were cultured in IMDM medium supplemented with 10% FBS, 1% Penicillin-Streptomycin and 55µM 2-ME in the presence of 10ng/ml FLT-3L, 20ng/ml IL-7 and 100ng/ml SCF (standard expansion medium) in a 24 well TC plate. The cells were cultured for 12 days and every 3-4 days the cells were splitted to a concentration of 1x105 cells/well.

extract_protocol: Primitive fetal liver progenitor cells (FL-HPCs) were purified as c-Kit+ Ter119- cells from fetal livers of embryonic day 13.5 (E13.5) of C57Bl6/J wild-type and Btg1-/- mice by MACS sort using Ter119 and cKit (CD117) beads.

treatment_protocol: Wild-type and Btg1-/- FL-HPCs were expanded in standard expansion medium (see growth protocol) for 24 hours. The cells were infected with retrovirus by spinoculation for 45 min at 700xg (25°C) in the presence of 5µg/ml polybrene and cultured in the same expansion medium for 48 hours

tag: genotype/variation


title: FL Btg1-/-+Ctrl

source_name: FL Btg1-/-+Ctrl


title: alaninescan S. enterica 2 rep

type: protein

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

description:
alanine scan of peptides derived from KPN_00459 and KPN_00363
raw data file: 11.txt
11_2

hyb_protocol: Slides were blocked using SuperBlock (Pierce) for 2 h at room temperature with mild shaking. Incubation with primary antibody (rabbit polyclonal to K. pneumoniae, E. coli or S. enterica) was performed overnight at 4°C with mild shaking in a humidity chamber. Secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) was incubated for 1.5 h with mild shaking at room temperature in the dark. After each incubation step, the slides were washed three times with PBSI (PBS + 0.05% IGEPAL). Slides were dried with nitrogen and scanned afterwards.

scan_protocol: Fluorescent array images were collected for Cy3 with a Genepix 4300 fluorescent scanner and a PMT gain of 400 and 40% laser power. Image intensity data were extracted and analyzed using Origin Pro 8G.

data_processing: From the raw data the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. RFI resulting in negative values were set to 0.This was done for all the samples except the positive control Rabbit IgG, as the secondary antibody (Goat antibody to Rabbit IgG) is supposed to bind at this site. This acknowledges the presence of non-specific interaction of the secondary antibody to the samples.

molecule: protein

organism: Klebsiella pneumoniae

source_name: KPN_00363 and KPN_00459 protein

extract_protocol: N/A; The microarrays carrying the peptides were synthesized by JPT Peptides Technology and upon arrival processed. Thus, no cell lysis and extraction was performed.


title: alaninescan S. enterica 2

description:
alanine scan of peptides derived from KPN_00459 and KPN_00363
raw data file: 11.txt
11_1


title: 72hrs_KLF6_Rep3


title: FL WT+ETV6-RUNX1

source_name: FL WT+ETV6-RUNX1

value: WT


title: 72hrs_pBabe_Rep1


title: alaninescan S. enterica 1 rep

description:
alanine scan of peptides derived from KPN_00459 and KPN_00363
raw data file: 10.txt
10_2


title: 15_Lund_AS_sample Primary

description: Primary


title: 12_Lund_AS_sample Secondary

description: Secondary

value: Biol repl H2


title: alaninescan S. enterica 1

description:
alanine scan of peptides derived from KPN_00459 and KPN_00363
raw data file: 10.txt
10_1


title: alaninescan E. coli 2 rep

description:
alanine scan of peptides derived from KPN_00459 and KPN_00363
raw data file: 8.txt
8_2


title: 11_Lund_AS_sample Primary

description: Primary


title: 10_Lund_AS_sample Secondary

description: Secondary

value: Unknown

value: Techn repl (sample 31 :sample 10)


title: alaninescan E. coli 1 rep

description:
alanine scan of peptides derived from KPN_00459 and KPN_00363
raw data file: 7.txt
7_2


title: alaninescan E. coli 2

description:
alanine scan of peptides derived from KPN_00459 and KPN_00363
raw data file: 8.txt
8_1


title: 72hrs_KLF6_Rep1


title: 19_Lund_AS_sample Secondary

description: Secondary

value: Biol repl E2

value: Yes


title: 48hrs_pBabe_Rep3


title: FL WT+Ctrl

description: Control

source_name: FL WT+Ctrl


title: 9_Lund_AS_sample Primary

description: Primary

value: Not applicable

value: No


title: 8_Lund_AS_sample Primary

description: Primary

value: m


title: alaninescan E. coli 1

description:
alanine scan of peptides derived from KPN_00459 and KPN_00363
raw data file: 7.txt
7_1


title: 7_Lund_AS_sample Secondary

description: Secondary

value: Biol repl D1


title: 48hrs_pBabe_Rep1


title: alaninescan K. pneumoniae 2

description:
alanine scan of peptides derived from KPN_00459 and KPN_00363
raw data file: 6.txt
6_1


title: 48hrs_pBabe_Rep2


title: alaninescan K. pneumoniae 1 rep

description:
alanine scan of peptides derived from KPN_00459 and KPN_00363
raw data file: 5.txt
5_2


title: 4_Lund_AS_sample Secondary

description: Secondary


title: 48hrs_KLF6_Rep2


title: 5_Lund_AS_sample Secondary

description: Secondary


title: alaninescan K. pneumoniae 2 rep

description:
alanine scan of peptides derived from KPN_00459 and KPN_00363
raw data file: 6.txt
6_2


title: 6_Lund_AS_sample Primary

description: Primary


title: Burkitt's lymphoma, clone AB7, doxycycline, t=96 hours

city: Leicester

first: Simon

middle: David

last: Wagner

address: Lancaster Road

department: CSMM

institute: University of Leicester

hyb_protocol: Labelled sample (10 µg) was hybridisedfor 16 hours at 45˚C to Human GeneChip 1.0 ST Array, Affymetrix.

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

data_processing: In background correction, intensity values of each individual array are corrected for non-specific binding by subtracting the average signal intensity of the area between spots from each probe set. Normalisation is required so multiple chips can be compared to each other. Quantile normalisation adjusts the distribution of probe intensity of each array analysed and so that the distribution of probe intensities for each array in a set of arrays is the same. Probe summarisation refers to the conversion of probe level values (there are approximately 26 probes per gene on each GeneChip®) to a single probe set expression value. Variance stabilisation of 16 refers to the addition of the value 16 to the expression values. By increasing the expression value, the variance of the data set is reduced and the distribution (defined by its mean and its variance) is stabilised.

label: Phycoerythrin

source_name: Clone AB7

label_protocol: Double stranded cDNA was synthesised from total RNA using random hexamers that are tagged with a T7 promoter sequence. Linear amplification of the resulting cDNA by in vitro transcription by T7 RNA polymerase produced antisense cRNA, which was subsequently purified and used as template for a repeated round of cDNA synthesis. Synthesis of single-stranded cDNA in sense orientation used random primers and a dUTP + dNTP mix. Following RNA hydrolysis, sense cDNA was fragmented. In this step uracil-DNA glycosylase (UDG) removed the uracil residues from the single stranded cDNA molecule and apurinic/apyrimidinic endonuclease 1 (APE 1) cleaved the phosphodiester backbone where the base is missing and thereby generates fragments of approximately 40-70 nucleotides. cDNA fragments are labelled by terminal deoxynucleotidyl transferase (TdT) with biotin allonamide triphosphate and were hybridised to the array. For final scanning, probes were visualised by staining with streptavidin-phycoerythrin (SAPE), biotin-anti-streptavidin and SAPE again.

growth_protocol: Cells were cultured in RPMI 1640.

extract_protocol: Cells were harvested and lysed using Rneasy minipreps (Qiagen)

treatment_protocol: Bcl6-/-;tetBCL6-HA cells (clone AB7) were either grown without doxycycline (control) or with 1 μg/ml doxycycline for 16, 48 or 96 hours.

tag: clone

tag: doxycycline

value: 1ug for 96 hours


title: Burkitt's lymphoma, clone AB7, doxycycline, t=16 hours

value: 1ug for 16 hours


title: 3_Lund_AS_sample Primary

description: Primary

value: Biol repl C2


title: 48hrs_KLF6_Rep1


title: Burkitt's lymphoma, clone AB7, doxycycline, t=48 hours

value: 1ug for 48 hours


title: alaninescan K. pneumoniae 1

description:
alanine scan of peptides derived from KPN_00459 and KPN_00363
raw data file: 5.txt
5_1


title: MDM(co-culture+LPS)_day6_donor4

status: Public on Aug 21 2014

city: Iowa City

first: Joel

last: Graff

state: IA

address: 400 EMRB

department: Internal Medicine

institute: University of Iowa

description: Test

data_processing:
Fluidigm Real-Time PCR Analysis software version 4.1.2
Non-normalized = Ct; Normalized (in data table and on series record) = Target Ct - Endogenous Control (TBP) Ct; The Fold Change data file contains 2^-deltadeltaCt values for the indicated sample relative to the control sample for each donor and TBP was used as the housekeeping gene.

label: FAM (TaqMan Assay)

source_name: Human monocytic cells

label_protocol: Integrated fluidic circuit (IFC)-based RT-qPCR was performed using the Bio-Mark System for Genetic Analysis (Fluidigm).  First, RNA was reverse transcribed using random hexamer-primer reactions with SuperScript III RT.  Next, pre-amplification of the RT product was performed using a pool of 48 Individual TaqMan Gene Expression Assays with TaqMan PreAmp MasterMix according to recommendations by Fluidigm.  Finally, gene expression was monitored by real time PCR on 48.48 Dynamic Array IFCs.

growth_protocol: Monocytic cells were isolated from blood samples using two standard protocols.  Each method started with peripheral blood mononuclear cells (PBMCs) isolated using Ficoll-Paque Plus (GE Healthcare) density gradients.  In the first method, monocytes were isolated on the day of blood donation directly from PBMCs using CD14 MicroBeads (Miltenyi Biotec).  Monocyte samples were collected at the time of sorting to provide a reference/control sample.  The remaining purified monocytes were then cultured in tissue culture plates at 1e6 cells/ml in RP-10 supplemented with M-CSF (50 ng/ml).  Adherent monocytic cells lysates were collected after incubation for the indicated number of days. The second method, selects MDMs from total PBMC cultures based on adherence.  Briefly, PBMCs were cultured in Petri dishes at a density of 5e6 cells/ml in RP-10 (RPMI 1640 (Gibco) with FBS (10% v/v; Gibco) and L-glutamine (2mM; Gibco)) supplemented with M-CSF (5ng/ml; eBioscience).  After 4 days of culture, Petri plates were washed extensively with HBSS lacking divalent cations (Gibco) to remove nonadherent cells.  The adherent MDMs were trypsinized and pelleted.  Upon resuspension at 1e6 cells/ml in RP-10 with M-CSF (5ng/ml), the MDMs were incubated one additional.

extract_protocol: Total RNA purified using TRIzol Reagent

treatment_protocol: Where indicated as LPS treated, cells were stimulated with LPS (10ng/ml) on day 5 and samples were collected on day 6.

tag: cell type

value: monocyte

tag: cd14 microbead purification?

tag: monocytes co-cultured with nonmonocytic pbmcs?

tag: number of days cultured in vitro

tag: non-monocytic cells removed on day 5?


title: MDM(PBMCculture)_day5_donor1

description: Test


title: MDM(PBMCculture)_day5_donor3

description: Test


title: MDM(PBMCculture)_day5_donor2

description: Test


title: MDM(PBMCculture)_day5_donor4

description: Test


title: MDM(PBMCculture+LPS)_day6_donor4

description: Test


title: MDM(PBMCculture)_day6_donor3

description: Test


title: MDM(PBMCculture)_day6_donor2

description: Test


title: MDM(co-culture+LPS)_day6_donor3

description: Test


title: MDM(PBMCculture)_day6_donor1

description: Test


title: Burkitt's lymphoma, clone AB7, no doxycycline, t=0


title: 48hrs_KLF6_Rep3

tag: tissue


title: MDM(PBMCculture+LPS)_day6_donor2

description: Test


title: MDM(PBMCculture)_day6_donor4

description: Test


title: MDM(PBMCculture+LPS)_day6_donor1

description: Test


title: MDM(co-culture+LPS)_day6_donor2

description: Test


title: Liver_WildType_P0_1

source_name: Liver, Wild-type, P0, replicate 1

tag: strain

tag: age

value: liver


title: MDM(PBMCculture+LPS)_day6_donor3

description: Test


title: MDM(co-culture+LPS)_day6_donor1

description: Test


title: MDM(co-culture)_day6_donor4

description: Test


title: KYSE520 miR203 transfectant

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: A stable cell line with induced expresion of mir-203

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

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

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: KYSE520 Mock②

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

growth_protocol: Cells were cultured in Ham's F12/RPMI 1640 with 2% FCS

extract_protocol: Total RNA was extracted from cells using the TRIzol Reagent (Invitrogen, Carlsbad, CA) method.

treatment_protocol: Cells were cultured with medium containing 400 micro g/ml of G418.

value: transfected with mock vector

source_name: KYSE520 miR203⑥

value: transfected with mir-203 expression vector


title: MDM(co-culture)_day6_donor3

description: Test


title: 2_Lund_AS_sample Secondary

description: Secondary

tag: Sex

value: f

tag: year of birth

tag: year of breast cancer

tag: year of angiosarcoma

tag: previous radiotherapy to tumor area


title: MDM(co-culture)_day6_donor1

description: Test


title: MDM(co-culture)_day6_donor2

description: Test


title: MDM(co-culture)_day5_donor4

description: Test


title: MDM(co-culture)_day5_donor3

description: Test


title: Monocyte_day6_donor4

description: Test


title: MDM(co-culture)_day5_donor1

description: Test


title: MDM(co-culture)_day5_donor2

description: Test


title: Monocyte_day6_donor3

description: Test


title: Monocyte(LPS)_day6_donor1

description: Test


title: Monocyte(LPS)_day6_donor4

description: Test


title: Monocyte(LPS)_day6_donor2

description: Test


title: Monocyte_day6_donor2

description: Test


title: Monocyte_day1_donor4

description: Test


title: Monocyte_day6_donor1

description: Test


title: Monocyte_day3_donor4

description: Test


title: Monocyte_day5_donor1

description: Test


title: Monocyte_day5_donor2

description: Test


title: Monocyte_day5_donor3

description: Test


title: Monocyte_day3_donor1

description: Test


title: Monocyte_day3_donor2

description: Test


title: Monocyte_day5_donor4

description: Test


title: Monocyte_day1_donor2

description: Test


title: Monocyte_day1_donor3

description: Test


title: Monocyte_day1_donor1

description: Test


title: Monocyte_day0_donor4

description: Control


title: Monocyte_day0_donor2

description: Control


title: Monocyte(LPS)_day6_donor3

description: Test


title: Monocyte_day3_donor3

description: Test


title: Monocyte_day0_donor1

description: Control


title: Monocyte_day0_donor3

description: Control


title: young pulp-2

city: Seoul

first: Seong-Oh

last: Kim

address: 250 Seongsanno, Seodaemun-gu

department: Pediatric dentistry

country: South Korea

institute: Yonsei University College of Dentistry

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 1.0 ST Array. The 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: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: young pulp

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: Pulp samples were obtained from permanent premolar (n=6; aged 11-14 years) and deciduous teeth (n=6; aged 11-14 years).

extract_protocol: Pulp tissues were homogenized using a homogenizer. The Rneasy Fibrous Mini kit (Qiagen) was then used to extract total RNA from the pulp tissues, according to the manufacturer's instructions.

treatment_protocol: Pulp samples were obtained from healthy permanent premolars extracted for orthodontic reasons and from deciduous teeth from pulp extirpation due to vital pulp exposure. Pulp tissues were immediately frozen and stored in liquid nitrogen.

tag: subject age range

value: 11-14 years

tag: tissue source

value: deciduous teeth

value: milk tooth pulp


title: adult tooth PDL tissue-3

source_name: adult tooth PDL

growth_protocol: PDL samples were obtained from permanent premolars (n=11; from 1 males and 4 females, aged 11-19 years) and dental follicles were obtained from children (n=4;from 3 males and 1 female, aged 6-7 years).

extract_protocol: The PDL and dental follicle tissues were homogenized using a homogenizer. The Rneasy Fibrous Mini kit (Qiagen) was then used to extract total RNA from the PDL tissues, according to the manufacturer's instruction.

treatment_protocol: PDL samples were obtained from healthy permanent premolars extracted for orthodontic reasons. And dental follicles were obtained from children during extraction of supernumerary teeth. The extracted teeth and dental folicles were immediately frozen and stored in liquid nitrogen. The PDL tissues were obtained carefully using sterile curettes from the middle-third.

value: adult tooth PDL


title: excess tooth follicle-3

source_name: excees tooth follicle

value: excess tooth follicle


title: adult pulp-2

source_name: adult pulp

value: permanent premolars

value: adult tooth pulp


title: 72hrs_KLF6_Rep2

value: Liver

tag: cell line


title: adult pulp-3


title: A549Home sapiensppp5RNA_h245645570045_K

city: Port Saint Lucie

first: John

last: Hiscott

state: Florida

address: 9801 SW Discovery Way

department: Infectious Diseases

institute: Vaccine and Gene Institute-Florida

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

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

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

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

growth_protocol: A549 cells were cultured as per ATCC recommendations.

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.

treatment_protocol: Cells were either transfected with 5'pppRNA (10ng/mL) using RNAiMax and collected at 1h, 2h, 4h, 6h, 8h, 12h, 24h or 48h post-treatment, or left non-treated and collected at 6h

value: human  lung epithelial cells

tag: treated with

tag: time point

value: 24 hrs


title: A549Home sapiensNT_h488118927032_B

tag: cell type

value: NT

value: 48 hrs


title: adult pulp-1


title: A549Home sapiensppp5RNA_h25645692042_A

value: 2 hrs


title: A549Home sapiensppp5RNA_h485645692042_D


title: A549Home sapiensppp5RNA_h65645692042_B

value: 6 hrs


title: A549Home sapiensNT_h488118927032_I


title: A549Home sapiensppp5RNA_h85645570045_J

value: 8 hrs


title: excess tooth follicle-2


title: A549Home sapiensppp5RNA_h45645570045_I

value: 4 hrs


title: adult tooth PDL tissue-2


title: excess tooth follicle-1


title: young pulp-3


title: A549Home sapiensppp5RNA_h15645570045_H

value: 1 hr


title: adult tooth PDL tissue-4


title: A549Home sapiensppp5RNA_h125645692042_C

value: 12 hrs


title: A549Home sapiensppp5RNA_6H8118927045_J

treatment_protocol: Cells were either non-treated and collected at 6h, mock treated with RNAiMax and collected at 6h, transfected with 5'pppRNA (10ng/mL) using RNAiMax and collected at 6h or 24h, or treated with IFNa-2b (100 or 1000IU/mL) and collected at 6h or 24h.


title: A549Home sapiensIFN_2b_100_6H8118927045_F


title: young pulp-1

value: 11-14 years

value: deciduous teeth


title: A549Home sapiensNT_h488118927030_E


title: A549Home sapiensIFN_2b_100_24H8118927045_G


title: A549Home sapiensIFN_2b_1000_6H8118927045_E


title: A549Home sapiensIFN_2b_1000_6H8118927045_L


title: A549Home sapiensRNAiMax8118927045_D

value: RNAiMax


title: A. tumefaciens_visR_WT_Rep2

city: Bloomington

first: Jason

middle: Eugene

last: Heindl

state: IN

address: 1001 E. 3rd St., Jordan Hall 142

department: Biology

institute: Indiana University

description: Biological replicate 2 of 3

hyb_protocol: Hybridization reactions were performed using Agilent in situ Hybridization Kit Plus, boiled 5 min 95 C, applied to Agilent custom arrays for A. tumefaciens C58, and hybridized overnight at 65 C.  Hybridized arrays were washed with Agilent Wash Solutions 1 and 2, rinsed with acetonitrile, and incubated in Agilent Stabilization and Drying Solution immediately prior to scanning the arrays

scan_protocol: Scanned on an GenePix 4200A 01 scanner. Images were quantified using GenePix Pro (version 6.0.1.25.)

data_processing: Limma Software (version 3.6.9) from Bioconductor (version 2.7) was used for background subtraction, Loess within arrays normalization  and Quantile between arrays normalization.

label: Alexa Fluor 647

organism: Agrobacterium tumefaciens

source_name: Whloe cell_lab culture, visR

label_protocol: Labeled cDNA with Invitrogen SuperScript Indirect Labeling Kit, cDNA was purified on Qiagen QIAQuick columns.  cDNA was labeled with AlexaFluor 555 and 647 dyes using Invitrogen SuperScript cDNA Labeling Kit

growth_protocol: Grown w/shaking in ATGN minimal medium, 28 °C, mid-log phase cultures

extract_protocol: 11 mL of cultures at OD600~0.6. Cells lysed with lysozyme and RNA extracted using Qiagen RNease Kit.

tag: genotype

value: visR

label: Alexa Fluor 555

source_name: Whole cell_lab culture, WT

value: WT


title: A. tumefaciens_visR_WT_Rep3

description: Biological replicate 3 of 3

source_name: Whloe cell_lab culture, WT

source_name: Whole cell_lab culture, visR


title: A549Home sapiensRNAiMax8118927030_K


title: A549Home sapiensppp5RNA_24H8118927032_H


title: A549Home sapiensIFN_2b_100_6H8118927045_A


title: A549Home sapiensppp5RNA_24H8118927032_J


title: A549Home sapiensppp5RNA_24H8118927032_E


title: A549Home sapiensIFN_2b_100_24H8118927032_A


title: A. tumefaciens_visR_WT_Rep1

description: Biological replicate 1 of 3


title: Control cell 4

city: Galveston

first: QiQi

last: Zhou

address: 301 University Blvd

institute: UTMB

description: sle liver

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: Control Col

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 1 µg total RNA sample and the RNA was 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

growth_protocol: Standard mouse liver cell culture protocol

extract_protocol: Standard RNA Trizol extraction protocol

treatment_protocol: 0.5 mg TN-CF / 100000 T-C cell  / dish per 24 hrs and control

tag: gender

value: Male


title: Control cell 3

description: sle liver


title: Control cell 5

description: sle liver


title: Control cell 1

description: sle liver


title: A549Home sapiensIFN_2b_1000_6H8118927032_L


title: Control cell 2

description: sle liver


title: A549Home sapiensNon_Treated8118927032_B

value: none (media)


title: A549Home sapiensNon_Treated8118927032_I

value: human  lung epithelial cells


title: A549Home sapiensIFN_2b_100_6H8118927030_I


title: Irradiated 4

city: Daejeon

first: Bu-Yeo

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

institute: Korea Institute of Oriental Medicine

description: Irradiated left lung tissue

hyb_protocol: The labelled RNA were hybridized to a microarray (Agilent Rat whole genome 44K, Agilent Technologies, USA) containing approximately 44,000 probes (~26,600 unique genes) in accordance with the manufacturer's instructions.

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner.

data_processing: Signal intensities of genes were normalized by the quantile method.

source_name: Lung

label_protocol: The pooled RNA was amplified and labeled using Agilent’s Low RNA Input Linear Amplification kit PLUS (Agilent Technologies, USA).

growth_protocol: The mice were housed in a room with the temperature controlled at 24±1 °C at a relative humidity of 50±10%, with a 12h dark/light cycle. Food and water were provided ad libitum throughout the experiment.

extract_protocol: Total RNA from mouse lung tissues was prepared using the Easy-SpinTM total RNA extraction kit according to the manufacturer’s instructions (iNtRON Biotechnology, Seoul, Republic of Korea).

treatment_protocol: During irradiation, the mice were anesthetized with an intraperitoneally administered mixture of 30 mg/kg of zoletil and 10 mg/kg of rompun.

value: Ten-week-old

value: male


title: A549Home sapiensIFN_2b_1000_24H8118927032_C

value: 24 hrs


title: Irradiated 2

description: Irradiated left lung tissue


title: A549Home sapiensppp5RNA_6H8118927045_B


title: T-C cell 5

description: sle liver

source_name: Col -/-


title: A549Home sapiensppp5RNA_6H8118927030_G


title: T-C cell 4

description: sle liver


title: Irradiated 1

description: Irradiated left lung tissue


title: A549Home sapiensIFN_2b_1000_24H8118927030_D


title: Irradiated 3

description: Irradiated left lung tissue


title: A549Home sapiensIFN_2b_1000_24H8118927032_D


title: T-C cell 3

description: sle liver


title: A549Home sapiensNon_Treated_media_h68118927030_E


title: T-C cell 1

description: sle liver

source_name: Col-/-


title: T-C cell 2

description: sle liver


title: Irradiated 5

description: Irradiated left lung tissue


title: Control 4

description: Control


title: A549Home sapiensRNAiMax_h68118927030_C


title: Control 1

description: Control


title: shTUSC4_3

city: Houston

first: Yang

last: Peng

state: TEXAS

address: 7435 Fannin Street

department: Systems Biology

institute: MD Anderson Cancer Center

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

value: Sarcoma cancer cells

tag: genotype/variation

value: TUSC4 stable knockdown cells


title: sh-SIRT1 RA 6

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from E14 mESC stably expressing SIRT1 shRNA in lentivirus vector, treated with 20 nM RA for 2 days.

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: E14 mESC stably expressing SIRT1 shRNA in lentivirus vector, treated with 20 nM RA for 2 days, rep6

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: All cells were cultured in the M10 ES cell medium (DMEM, 10% ES cell FBS, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 10 μM 2-mercaptoethanol, and 500 units/ml leukocyte inhibitory factor).

extract_protocol: Qiagen RNA easy mini kit with on-column DNAseI treatment

treatment_protocol: Cells were treated with vehicle ethanol or with 20 nM RA in the M10 medium for 2 days.

value: E14 mESCs

tag: lentivirus vector

value: SIRT1 shRNA

tag: treatment

value: 20 nM RA


title: Control 2

description: Control

tag: age

tag: strain


title: sh-SIRT1 RA 4

source_name: E14 mESC stably expressing SIRT1 shRNA in lentivirus vector, treated with 20 nM RA for 2 days, rep4


title: sh-Control RA 4

description: Gene expression from E14 mESC stably expressing control shRNA in lentivirus vector, treated with 20 nM RA for 2 days.

source_name: E14 mESC stably expressing control shRNA in lentivirus vector, treated with 20 nM RA for 2 days, rep4

value: control shRNA


title: sh-SIRT1 RA 1

source_name: E14 mESC stably expressing SIRT1 shRNA in lentivirus vector, treated with 20 nM RA for 2 days, rep1


title: Control 3

description: Control


title: RT4_Mock_2b

city: Vancouver

first: Peter

last: Black

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression 8x60K v2 Microarray (AMDID 039494) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately with a 1min acetonitrile rinse.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) at a 3um scan resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended green processed signal intensities.

label_protocol: Samples were prepared following the procedures of Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.6.  100ng of total RNA was used as input for each sample.

growth_protocol: Cell lines were cultured in MEM medium, supplemented with 10%FBS, 1% non-essential amino acids, 1% L-glutamine and 1% sodium pyruvate (all purchased from Invitrogen, Grand Island, NY). Cell lines were routinely grown and passaged at 37oC in a humidified atmosphere of 5% CO2.

extract_protocol: RNA was extracted from cells using a RNEasy mini kit (Qiagen) according to manufacturer’s instructions

treatment_protocol: The cDNA construct containing the Notch2 intracellular domain (ICD) was obtained by amplifying Notch2 from nucleotide 5115 to the stop codon, and cloning into pLenti4-To-V5 using the Gateway system (Life Technologies).  Notch2 ICD entry clones were verified by sequencing (UBC NAPS Unit, Vancouver, BC) prior to the LR clonase reaction into the destination vector.  Notch2 ICD lentivirus was generated in HEK293T cells using the Profection Mammalian Transfection System (Promega) and Virapower Lentiviral Expression plasmids (Life Technologies).  Resultant virus was used to infect RT4V6 with 6μg/mL polybrene (Sigma) for 24 hours.  Overexpressing cells were selected in 200μg/mL Zeocin (Life Technologies).

tag: tissue

value: bladder

value: carcinoma


title: shCtrl_3

value: Parental cells


title: sh-SIRT1 RA 3

source_name: E14 mESC stably expressing SIRT1 shRNA in lentivirus vector, treated with 20 nM RA for 2 days, rep3


title: sh-Control RA 2

source_name: E14 mESC stably expressing control shRNA in lentivirus vector, treated with 20 nM RA for 2 days, rep2


title: shTUSC4_1


title: sh-Control RA 1

source_name: E14 mESC stably expressing control shRNA in lentivirus vector, treated with 20 nM RA for 2 days, rep1


title: sh-Control RA 3

source_name: E14 mESC stably expressing control shRNA in lentivirus vector, treated with 20 nM RA for 2 days, rep3


title: shTUSC4_2


title: sh-SIRT1 RA 2

source_name: E14 mESC stably expressing SIRT1 shRNA in lentivirus vector, treated with 20 nM RA for 2 days, rep2


title: sh-SIRT1 RA 5

source_name: E14 mESC stably expressing SIRT1 shRNA in lentivirus vector, treated with 20 nM RA for 2 days, rep5


title: RT4_Mock_6


title: RT4_Mock_2a


title: shCtrl_1


title: sh-SIRT1 ethanol 2

description: Gene expression from E14 mESC stably expressing SIRT1 shRNA in lentivirus vector, treated with vehicle ethanol for 2 days.

source_name: E14 mESC stably expressing SIRT1 shRNA in lentivirus vector, treated with vehicle ethanol for 2 days, rep2

value: vehicle ethanol


title: shCtrl_2


title: A549Home sapiensIFN_2b_100_24H8118927030_B


title: RT4_N2_2


title: sh-SIRT1 ethanol 3

source_name: E14 mESC stably expressing SIRT1 shRNA in lentivirus vector, treated with vehicle ethanol for 2 days, rep3


title: sh-SIRT1 ethanol 1

source_name: E14 mESC stably expressing SIRT1 shRNA in lentivirus vector, treated with vehicle ethanol for 2 days, rep1


title: sh-Control ethanol 2

description: Gene expression from E14 mESC stably expressing control shRNA in lentivirus vector, treated with vehicle ethanol for 2 days.

source_name: E14 mESC stably expressing control shRNA in lentivirus vector, treated with vehicle ethanol for 2 days, rep2


title: sh-Control ethanol 3

source_name: E14 mESC stably expressing control shRNA in lentivirus vector, treated with vehicle ethanol for 2 days, rep3


title: RT4_N2_3


title: C393

status: Public on Aug 20 2014

city: New York

first: Rebecca

last: Haeusler

state: NY

address: 1150 Saint Nicholas Ave Room 303A

department: Pathology and Cell Biology

institute: Columbia University

hyb_protocol: Hybridization was performed by Columbia University microarray core facility. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning was performed by Columbia University microarray core facility. GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: RMA by software Partek

source_name: WT-refed

label_protocol: Labeled cRNA were prepared according to the standard Nugen protocol.

growth_protocol: All animal studies were approved by the Columbia Animal Care and Use Committee.

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

treatment_protocol: Mice were maintained in a pathogen-free facility, with 4–5 animals  per cage in a temperature-controlled room with a 12-h light/dark cycle and access to food  and water ad libitum. Age and sex matched littermate cohorts were used for all the  experiments to account for potential strain differences.

value: WT

value: refed

value: liver

tag: genetic background

value: mixed background of C57BL/6J and 129


title: C343


title: C503


title: I305


title: I106_2


title: sh-Control ethanol 1

source_name: E14 mESC stably expressing control shRNA in lentivirus vector, treated with vehicle ethanol for 2 days, rep1


title: I169

value: fasted


title: C345

source_name: WT-fasted


title: I307


title: I103


title: RT4_N2_1


title: I306


title: Lumi Venus Hi

city: Singapore

first: Alexandra

last: Pietersen

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Centre Singapore

hyb_protocol: Following fragmentation, 12.5ug of cRNA was hybridized on GeneChip Mouse Genome 430 2.0 Arrays for 16 hours at 45 degrees celsius

scan_protocol: GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix) and scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0). Sport filtering: treshold intensity was set at the minimum value 10 if the intensity was below the minimum. A log base 2 transformation was applied to the data before the array was normalized. Normalization and centering all genes for each sample was performed by BRB Array software. Annotation: 2011.07.22 BRB Array software website.

source_name: Luminal mammary epithelial cells

label_protocol: Biotinylated cRNA was prepared from 250ng of total RNA according to the Affymetrix protocol (GeneChip 3' IVT Express Kit User Manual, 2008, Affymetrix)

growth_protocol: three 5-month old adult virgin mice (Tbx3-Venus-KI, so heterozygote for Tbx3 & Tbx3 promoter driving Venus expression)

extract_protocol: Cell pellets were lysed in Trizol and total RNA was isolated according to the manufacturer (with the addition of GlycoBlue to the aqeous phase to facilitate RNA precipitation). Quality of RNA was tested on an Agilent Bioanalyzer and both samples had RIN > 9.4.

treatment_protocol: Mammary epithelial cells were processed to single cells and after exclusion of dead cells, CD45+ lymphocytes and stromal cells, luminal cells were identified based on expression of CD24-PEcy5 and CD49f-PEcy7, according to DOI 10.1186/bcr3381. Cells were sorted into L15 medium with 6% FCS (200,000 luminal cells with high Venus expression and 200,000 luminal cells with low/negative for Venus expression). Purity was confirmed by post-sort analysis.

tag: tbx3 promoter activity

value: High


title: Lumi Venus Lo

value: Low


title: ros1 dml2 dml3-triple mutant_rep1

city: Canberra

first: Ming-Bo

last: Wang

state: ACT

address: Clunies Ross Street

department: Agriculture Flagship

country: Australia

institute: CSIRO

description: This sample is of Arabidopsis thaliana ros1 dml2 dml3 triple mutant. It is the first of two biological replicates used in this experiment, each from separate plates.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
Statistical testing between samples was performed using the LIMMA package in Bioconductor and probes displaying ≥ 2 fold expression changes significant at the P ≤ 0.01 level were chosen for further analyses.

organism: Arabidopsis thaliana

source_name: ros1 dml2 dml3 triple mutant

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Seeds were sown on Murashige and Skoog (MS) agar plates supplemented with 3% sucrose and incubated at 4oC for three days. Seedlings were transferred to fresh MS plates one week after germination and grown under 16h light/8h dark photoperiod at 28oC for three weeks.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at CSIRO Plant Industry (Black Mountain, Canberra, Australia).

treatment_protocol: Whole plant tissues of three week-old A. thaliana plants grown on MS agar were collected and snap frozen in liquid N2.

value: seedling

value: ros1 dml2 dml3 triple mutant

tag: phenotype

value: Extreme susceptibility to Fusarium oxysporum


title: C391


title: nrpd1_mutant_rep2

description: This sample is of Arabidopsis thaliana nrpd1 mutant. It is the second of two biological replicates used in this experiment, each from separate plates.

source_name: nrpd1 mutant

value: nrpd1 mutant

value: Resistance to Fusarium oxysporum


title: nrpe1_mutant_rep2

description: This sample is of Arabidopsis thaliana nrpe1 mutant. It is the second of two biological replicates used in this experiment, each from separate plates.

source_name: nrpe1 mutant

value: nrpe1 mutant

value: Moderate susceptibility to Fusarium oxysporum


title: ros1 dml2 dml3-triple mutant_rep2

description: This sample is of Arabidopsis thaliana ros1 dml2 dml3 triple mutant. It is the second of two biological replicates used in this experiment, each from separate plates.


title: #6 R+KO

city: NEW YORK

first: Domenico

last: Accili

address: 1150 St. Nicholas Ave

data_processing: RMA by  Expression Console

source_name: b-FoxO triple KO

tag: backgroud strain

value: 129 x FVBn x C57BL/6

value: pancreatic islets


title: nrpe1_mutant_rep1

description: This sample is of Arabidopsis thaliana nrpe1 mutant. It is the first of two biological replicates used in this experiment, each from separate plates.


title: C344


title: Col-0_wild-type_rep3

description: This sample is of wild-type Arabidopsis thaliana Col-0. It is the third of three wild-type biological replicates used in this experiment, each from separate plates.

value: wt

value: Normal


title: #4 WT

source_name: WT


title: #5 R+KO


title: #7 R+KO


title: Footpad skin E15.5 wild type embryo replication 1

city: Baltimore

first: Chang-Yi

last: Cui

state: MD

address: 251 Bayview Blvd Suite 100, 10C222

department: NIA

institute: NIH

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol, Product # G4140-90050, Version 5.0.1)

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1).

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 14 arrays in the series: AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr (adjust to UMR)
(4) Remove outliers. Each cell/treatment type (CTT) is characterized by 2 replications, all are log-transformed (log10). Here we check if any of these values is an outlier.  First we estimate the average square difference (ASD) between replication pairs:  ASD = SUM[(x(i,1)-x(i,2))^2]/N/2
where x(i,j) is logintensities for i-th CTT and replication j, N = number of CTT. Then we estimate z-value for each CTT: z = (x(i,1)-x(i,2))/sqrt(ASD). If abs(z) > 4 then one of the replications is an outlier. The value that is farther away from the median expression value is considered an outlier and it is replaced with the value from another replication.
The result is used as the normalized VALUE.

source_name: Footpad skin E15.5 embryo wildtype replication 1

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol:
Cy3 RNAs were extracted from frozen footpad skin with Trizol. RNAs were reprecipitaed with LiCl.
Universal Reference RNA (Cy5) was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

value: footpad skin

source_name: Universal Mouse Reference 129ES Cell

tag: reference

value: 129ES Cell


title: #2 WT


title: Footpad skin E17.5 embryo beta-catenin wild type replication 2

description: Footpad skin E17.5 embryo wild type replication 2

source_name: Footpad skin E17.5 embryo wildtype replication 2

extract_protocol:
Cy3 sample RNAs were extracted from frozen footpad skin with Trizol. RNAs were reprecipitaed with LiCl.
Universal Reference RNA (Cy5) was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube


title: Footpad skin E15.5 wild type embryo replication 2

source_name: Footpad skin E15.5 embryo wildtype replication 2


title: Footpad skin E16.5 wild type embryo replication 2

source_name: Footpad skin E16.5 embryo wildtype replication 2


title: Footpad skin E17.5 embryo beta-catenin Knockout replication 2

description: Footpad skin E17.5 embryo Knockout replication 2


title: sorted spleenic MyD88-/- CD4+ T cells rep2

first: Bernardo

last: Reis

address: 1234 York Avenue

institute: Rockefeller University

description: MyD88-/- sample2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Myd88-/- CD4+ (CD45.2) T cells

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

value: B6 mixed bone marrow chimera

value: 12 months

value: spleen

value: MyD88-/- CD4+ T cells


title: Footpad skin E17.5 embryo beta-catenin wild type replication 1

description: Footpad skin E17.5 embryo wild type replication 1

source_name: Footpad skin E17.5 embryo wildtype replication 1


title: #3 WT


title: Col-0_wild-type_rep1

description: This sample is of wild-type Arabidopsis thaliana Col-0. It is the first of three wild-type biological replicates used in this experiment, each from separate plates.

value: seedling


title: Col-0_wild-type_rep2

description: This sample is of wild-type Arabidopsis thaliana Col-0. It is the second of three wild-type biological replicates used in this experiment, each from separate plates.


title: Footpad skin E16.5 embryo beta-catenin wild type replication 2

description: Footpad skin E16.5 embryo wild type replication 2


title: Footpad skin E16.5 embryo beta-catenin wild type replication 1

description: Footpad skin E16.5 embryo wild type replication 1

source_name: Footpad skin E16.5 embryo wildtype replication 1


title: nrpd1_mutant_rep1

description: This sample is of Arabidopsis thaliana nrpd1 mutant. It is the first of two biological replicates used in this experiment, each from separate plates.


title: Footpad skin E16.5 Transgenic embryo replication 2

source_name: Footpad skin E16.5 Dkk4 transgenic embryo replication 2


title: Footpad skin E16.5 wild type embryo replication 1


title: sorted spleenic MyD88-/- CD4+ T cells rep1

description: MyD88-/- sample1


title: Footpad skin E16.5 Transgenic embryo replication 1

source_name: Footpad skin E16.5 Dkk4 transgenic embryo replication 1


title: sorted spleenic WT CD4+ T cells rep1

description: WT sample1

source_name: WT CD4+ (CD45.1) T cells

value: WT CD4+ T cells


title: Footpad skin E16.5 embryo beta-catenin Knockout replication 2

description: Footpad skin E16.5 embryo Knockout replication 2


title: Footpad skin E15.5 Transgenic embryo replication 2

source_name: Footpad skin E15.5 Dkk4 transgenic embryo replication 2


title: #1 WT


title: Footpad skin E17.5 embryo beta-catenin Knockout replication 1

description: Footpad skin E17.5 embryo Knockout replication 1


title: Footpad skin E16.5 embryo beta-catenin Knockout replication 1

description: Footpad skin E16.5 embryo Knockout replication 1


title: sorted spleenic WT CD4+ T cells rep2

description: WT sample2


title: Footpad skin E15.5 Transgenic embryo replication 1

source_name: Footpad skin E15.5 Dkk4 transgenic embryo replication 1


title: Footpad skin E15.5 embryo beta-catenin wild type replication 1

description: Footpad skin E15.5 embryo wild type replication 1


title: Footpad skin E15.5 embryo beta-catenin wild type replication 2

description: Footpad skin E15.5 embryo wild type replication 2


title: IL-15 24h_4

city: Sacramento

first: Dennis

middle: Jay

last: Montoya

state: CA

address: 2700 Stockton Blvd #2354

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

hyb_protocol: Performed by UCLA Clinical Microarray Core on GPL570

data_processing: Dchip analysis and RMA normalization using DNA-Chip Analyzer (Build date: Feb 21 2010, www.dchip.org)

label_protocol: Performed by UCLA Clinical Microarray Core using Ambion Labeling kit

extract_protocol: Trizol protocol for RNA isolation followed by purification of RNA by Qiagen Rneasy kit

treatment_protocol: Adherent peripheral blood monuclear cells from four healthy donors were stimulated with IL-10, IL-15 (R&D Systems), or IL-4 in RPMI 1640 supplemented with 10% fetal-calf serum. Cells were harvested at 6 h or 24 h after stimulation and monocytes purified by CD14 microbeads (Miltenyi Biotec).

value: peripheral blood monuclear cells

tag: donor id

value: Healthy donor 4


title: IL-4 24h_4

scan_protocol: Performed by UCLA Clinical Microarray Core


title: Footpad skin E15.5 embryo beta-catenin Knockout replication 1

description: Footpad skin E15.5 embryo Knockout replication 1


title: Footpad skin E15.5 embryo beta-catenin Knockout replication 2

description: Footpad skin E15.5 embryo Knockout replication 2


title: IL-10 24h_4


title: Wild-type Liver, replicate3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430A 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: R version 2.11.1 (x86_64-pc-linux-gnu), affyPLM_1.24.1, preprocessCore_1.10.0, gcrma_2.20.0, affy_1.26.1, Biobase_2.8.0

source_name: Mouse Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA according to the Affymetrix Expression Analysis Technical Manual.

growth_protocol: Liver Samples Disected from wild-type and SIRT7 knock-out mice

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was DNAseI treated and further purified using the QIAgen Rneasy mini columns

treatment_protocol: All samples were subjected to the same treatment conditions

tag: sirt7 allele

value: wild-type


title: IL-4 6h_4

source_name: IL-4 6h


title: SIRT7 Knockout Liver, replicate2

value: knock-out


title: SIRT7 Knockout Liver, replicate3


title: IL-15 24h_3

value: Healthy donor 3


title: Media 24h_4

source_name: Media 24h


title: IL-15 6h_3


title: Media 6h_3

source_name: Media 6h


title: SIRT7 Knockout Liver, replicate1


title: Media 6h_4


title: IL-4 24h_3


title: IL-15 6h_4


title: IL-4 24h_2

value: Healthy donor 2


title: IL-10 6h_4


title: IL-10 24h_3


title: Media 24h_3


title: IL-4 6h_3


title: Wild-type Liver, replicate1


title: IL-10 6h_3


title: Media 24h_2


title: Wild-type Liver, replicate2


title: IL-15 24h_2


title: IL-10 24h_2


title: IL-10 6h_2


title: IL-15 6h_2


title: IL-4 6h_2


title: Human gastric cancerous tissue10

status: Public on Aug 19 2014

city: Shanghai

first: Ye

last: Hu

address: 145 Middle Shandong Rd

country: China

institute: Division of Gastroenterology and Hepatology, Shanghai Jiao-Tong University School of Medicine Renji Hospital

description: Gene expression of gastric cancerous tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v2.0 (8 x 60K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies)

source_name: Human gastric cancerous tissue

label_protocol: 1 µg of total RNA were primed with 1.2 μL of T7 Promoter Primer at 65°C for 10 min, then prepare labeling reaction at 40°C for 2 h in the presence of 8.5 μL of cDNA Master Mix, Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting. Incubate samples at 40°C for 2 hours. And then purify the labeled/amplified RNA and labeled cRNA QC, finally do the hybridaztion.

growth_protocol: the samples were stored in -80 degrees prior to extract preparation

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre)

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

value: male

value: gastric cancerous tissue


title: IL-4 24h_1

value: Healthy donor 1


title: Human gastric cancerous tissue8


title: Human gastric cancerous tissue9


title: Media 6h_2


title: Human gastric noncancerous tissue8

description: Gene expression of gastric noncancerous tissue

source_name: Human gastric noncancerous tissue

value: gastric noncancerous tissue


title: Human gastric cancerous tissue6


title: Human gastric cancerous tissue7


title: Media 24h_1


title: Human gastric noncancerous tissue7


title: Human gastric noncancerous tissue4

value: female


title: Human gastric noncancerous tissue5


title: IL-10 24h_1


title: IL-15 24h_1


title: IL-4 6h_1


title: IL-10 6h_1


title: IL-15 6h_1


title: Human gastric noncancerous tissue9


title: Human gastric cancerous tissue5


title: Human gastric cancerous tissue3


title: Human gastric noncancerous tissue2


title: Human gastric noncancerous tissue3


title: Empty vector transfected T47D-rep 2

city: Augusta

first: yong

last: teng

address: 1120 15th Street

institute: Medical College of Georgia

hyb_protocol: All samples passing this quality control were hybridized to a GeneChip miRNA Array (Affymetrix, CA), which provides the most sensitive, accurate, and complete measurement of small non-coding RNA transcripts involved in gene regulation. Following hybridization, the array is washed and stained according to the Affymetrix protocols.

scan_protocol: The stained arrays are scanned at 532 nm using an Affymetrix GeneChip Scanner 3000, generating CEL files for each array.

data_processing: miRNA alterations were determined using PARTEK Genomics Suite. The CEL files are imported from the Affymetrix Expression Console and background corrected, quantile normalized and probe summarization are performed using RMA. Principle component (PCA) analysis will be performed to examine whether clusters could be explained by the first few principle components. PCA is used for dimensionality reduction by retaining the characteristics of the data that contribute most to its variance.

source_name: Empty vector transfected T47D

label_protocol: FlashTag RNA Labeling Procedure

growth_protocol: T47D cells were purchased from the American Type Culture Collection (Rockville, MD) and maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA including small RNA was extracted using  Qiagen miRNeasy Mini kit (Qiagen, CA) according to manufacturer’s instructions and then evaluated using an Agilent® 2100 Bioanalyzer.

treatment_protocol: To generate WASF3 overexpressing stable T47D cells, the pCDH-CMV-MCS-EF1-PURO (System Biosciences, Mountain View, CA, USA)  lentiviral vector containing a full length of WASF3  gene was used for transfection and infection. In this assay the empty lentiviral vector was used as a control. Virally infected cells were selected in a medium containing 1.0 μg/ml puromycin (Sigma, NY) for 2 weeks and the small RNAs were exacted from the cell population, respectively.

tag: cell line

tag: passage

value: 2, puromycin resistant

tag: vector

value: empty lentiviral


title: Media 6h_1

tag: cell type


title: Human gastric cancerous tissue1

tag: gender


title: Human gastric noncancerous tissue6


title: MEF-UBFwt/wt 48h post 4-HT

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

description:
MEFc2_TMS018
MEF UBFwt/wt-ErCre+/+

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Data analysis was performed using the Affymetrix Power tools version 1.14.4 and R (www.r-project.org) version 2.14.0. Firstly, data were normalized using RMA-sketch. Ubfwt/wt/Er-cre+/+ normalized gene expression was then subtracted from the corresponding Ubffl/fl/Er-cre+/+ timepoint before all the expressions were placed relative to time T0. We required a gene to be detected in at least one time point using a cutoff of 0.001 on the detection p-values obtained from the DABG algorithm (Affymetrix Power tools) to be used in the analysis.

source_name: MEF control inactivation 48 hours

label_protocol: Standard Affymetrix protocol

growth_protocol: Primary mouse embryo fibroblasts (MEFs) from E14.5 Ubffl/fl/Er-cre+/+ and isogenetic Ubfwt/wtEr-cre+/+ embryos were prepared as previously described (Giroux et al., 1999). They were cultured in Dulbecco’s modified Eagle medium (DMEM)-high glucose (Invitrogen), supplemented with 10% fetal calf serum (Wisent), L-glutamine (Invitrogen) and Antibiotic/Antimycotic (Wisent). MEFs were immortalized by the introduction of the SV40 Tt antigens via transfection using the pBSV0.3T/t, a modification of the pBSV-early vector (Schaffner, 1980) kindly provided by E. W. Khandjian

extract_protocol: RNA for expression microarray analysis was extracted by the acid phenol/guanidinium thiocyanate method (Chomczynski and Sacchi, 1987), and subsequently purified using the RNeasy Plus Mini kit (QIAGEN).

treatment_protocol: Cells were grown in 6 cm petri dishes (0.8x106 cells each) for 18 hours in DMEM, high glucose, 10% fetal bovine serum. To activate ER-Cre, 4-hydroxytamoxifen (4-HT) was added to a final concentration of 50nM, and after 4 hr incubation the medium replaced with fresh medium without 4-HT and cells harvested for analysis at various time points.

value: MEF

tag: protocol

value: control

tag: time

value: 48 hours

tag: genotype/variation

value: MEF UBFwt/wt-ErCre+/+


title: MEF-UBFwt/wt 72h post 4-HT

description:
MEFc3_TMS019
MEF UBFwt/wt-ErCre+/+

source_name: MEF control inactivation 72 hours

value: 72 hours


title: MEF-UBFwt/wt 0h post 4-HT

description:
MEFc0_TMS016
MEF UBFwt/wt-ErCre+/+

source_name: MEF control 0 hours

value: 0 hours


title: WASF3 overexpressing T47D-rep 1

source_name: WASF3 overexpressing stable T47D

value: pCDH-CMV-MCS-EF1-PURO lentiviral


title: Empty vector transfected T47D-rep 1


title: WASF3 overexpressing T47D-rep 2


title: MEF-UBFwt/wt 24h post 4-HT

description:
MEFc1_TMS017
MEF UBFwt/wt-ErCre+/+

source_name: MEF control inactivation 24 hours

value: 24 hours


title: iMEF-UBFwt/wt 72h post 4-HT

description:
IMFc3_TMS009
iMEF UBFwt/wt-ErCre+/+

source_name: Immortalized MEF control inactivation 72 hours

value: Immortalized MEF

value: iMEF UBFwt/wt-ErCre+/+


title: MEF-UBFfl/fl 0h post 4-HT

description:
MEFko0_TMS011
MEF UBFfl/fl-ErCre+/+

source_name: MEF Ubf inactivation 0 hours

value: Ubf inactivation

value: MEF UBFfl/fl-ErCre+/+


title: Human gastric cancerous tissue2

value: male

tag: age

value: gastric cancerous tissue


title: Human gastric noncancerous tissue10

tag: tissue

value: gastric noncancerous tissue


title: iMEF-UBFwt/wt 96h post 4-HT

description:
IMFc4_TMS010
iMEF UBFwt/wt-ErCre+/+

source_name: Immortalized MEF control inactivation 96 hours

value: 96 hours


title: MEF-UBFfl/fl 96h post 4-HT

description:
MEFko4_TMS015
MEF UBFfl/fl-ErCre+/+

source_name: MEF Ubf inactivation 96 hours


title: MEF-UBFwt/wt 96h post 4-HT

description:
MEFc4_TMS020
MEF UBFwt/wt-ErCre+/+

source_name: MEF control inactivation 96 hours


title: Human gastric noncancerous tissue1


title: MEF-UBFfl/fl 24h post 4-HT

description:
MEFko1_TMS012
MEF UBFfl/fl-ErCre+/+

source_name: MEF Ubf inactivation 24 hours


title: iMEF-UBFwt/wt 24h post 4-HT

description:
IMFc1_TMS007
iMEF UBFwt/wt-ErCre+/+

source_name: Immortalized MEF control inactivation 24 hours


title: iMEF-UBFwt/wt 48h post 4-HT

description:
IMFc2_TMS008
iMEF UBFwt/wt-ErCre+/+

source_name: Immortalized MEF control inactivation 48 hours


title: MEF-UBFfl/fl 48h post 4-HT

description:
MEFko2_TMS013
MEF UBFfl/fl-ErCre+/+

source_name: MEF Ubf inactivation 48 hours


title: iMEF-UBFfl/fl 96h post 4-HT

description:
IMFko4_TMS005
iMEF UBFfl/fl-ErCre+/+

source_name: Immortalized MEF Ubf inactivation 96 hours

value: iMEF UBFfl/fl-ErCre+/+


title: iMEF-UBFfl/fl 48h post 4-HT

description:
IMFko2_TMS003
iMEF UBFfl/fl-ErCre+/+

source_name: Immortalized MEF Ubf inactivation 48 hours


title: iMEF-UBFfl/fl 72h post 4-HT

description:
IMFko3_TMS004
iMEF UBFfl/fl-ErCre+/+

source_name: Immortalized MEF Ubf inactivation 72 hours


title: MA-10_1.5h forskolin treatment_rep2

city: Quebec

first: Jacques

middle: J

last: Tremblay

state: Quebec

address: 2705, boulevard Laurier

department: Department of Obstetrics, Gynecology, and Reproduction

institute: Centre de recherche du CHU

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. The cDNAss hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven. After 17±1 h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix-recommended protocol.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G and Gene-Chip Operating Software (Affymetrix, Santa Clara, CA), to produce the intensity files.

data_processing: Analysis was performed using Partek® software, version 6.6 (Partek Inc., St. Louis, MO). Robust Multiarray Analysis (RMA) background correction and a logarithmic transformation were applied to data arrays.

source_name: MA-10 Leydig cells

label_protocol: Affymetrix GeneChip® WT cDNA Synthesis and Amplification Kit protocol

growth_protocol: Cells were grown in DMEM-F12 supplemented with 15% horse serum and penicillin/streptomycin (P/S) at 37°C, 5% CO2 prior to treatment. During the treatment, the cells were cultured in serum-free DMEM-F12 supplemented with P/S only for 1.5 h at at 37°C, 5% CO2.

extract_protocol: Total RNA was extracted using the TRIZOL reagent, as per the manufacturer's instructions.

treatment_protocol: Cells were treated with either DMSO (control), 10 uM forskolin or forskolin+1 mM AICAR for 1.5 h.

value: MA-10 Leydig cells

tag: treatment

value: 10 uM forskolin


title: iMEF-UBFfl/fl 24h post 4-HT

description:
IMFko1_TMS002
iMEF UBFfl/fl-ErCre+/+

source_name: Immortalized MEF Ubf inactivation 24 hours


title: MA-10_1.5h forskolin treatment_rep3


title: control human gastric cancer cell line biological rep1

description: Gene expression data from control MGC803

hyb_protocol: Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip cartridge arrays.

scan_protocol: GeneChips were scanned using the GeneChip® HT Scanner (Affymetrix 00-0172).

data_processing: Affymetrix®Microarray Suite 5.0 statistical algorithm.

source_name: control human gastric cancer cell line 1

label_protocol: Total RNA is first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. The cDNA is converted into double-stranded cDNA template during second strand cDNA synthesis. In vitro transcription synthesizes aRNA that is biotin incorporated and purified.

growth_protocol: MGC803 cells were maintained at 37 °C in an atmosphere of 5% CO2 in RPMI-1640 medium (Invitrogen) supplemented with 10% fetal bovine serum, penicillin and streptomycin (Invitrogen) in 25-ml culture flasks

extract_protocol: High-quality total RNA was isolated using the RNeasy® Mini Kit from QIAGEN

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

value: control


title: iMEF-UBFwt/wt 0h post 4-HT

description:
IMFc0_TMS006
iMEF UBFwt/wt-ErCre+/+

source_name: Immortalized MEF control 0 hours


title: MA-10_1.5h forskolin+Aicar treatment_rep2

value: 10 uM forskolin and 1mM Aicar


title: MA-10_control no treatment_rep1

value: DMSO


title: iMEF-UBFfl/fl 0h post 4-HT

description:
IMFko0_TMS001
iMEF UBFfl/fl-ErCre+/+

source_name: Immortalized MEF Ubf inactivation 0 hours

value: 0 hours


title: MA-10_1.5h forskolin treatment_rep1


title: control human gastric cancer cell line biological rep2

source_name: control human gastric cancer cell line 2


title: MA-10_1.5h forskolin+Aicar treatment_rep1


title: MA-10_1.5h forskolin+Aicar treatment_rep3


title: MA-10_control no treatment_rep2


title: Rapamycin 5

status: Public on Aug 18 2014

city: Saint Louis

first: Wilson

middle: Chun Yim

last: Fok

state: MO

address: 660 S Euclid Ave

department: Hematology

institute: Washington University in St. Louis

data_processing: Data was processed in R by log2 transformation and z-normalization

source_name: Mouse epididymal fat

label_protocol: Biotinylated cRNA were prepared using Ambion kit- Illumina TotalPrep RNA Amplification Kit

extract_protocol: Total RNA was extracted from 25 mg of liver in each sample using Qiagen Rneasy kit following manufacturer’s protocol.  RNA quantity was assessed by Nanodrop and RNA quality was assessed by Agilent Bioanalyzer.

tag: strain

value: 8 months

value: Liver

tag: Sex

value: Male

value: 14 ppm Rapamycin


title: Rapamycin 8


title: Rapamycin 2


title: MEF-UBFfl/fl 72h post 4-HT

description:
MEFko3_TMS014
MEF UBFfl/fl-ErCre+/+

source_name: MEF Ubf inactivation 72 hours

value: MEF

value: Ubf inactivation

value: 72 hours


title: Rapamycin 7


title: control human gastric cancer cell line biological rep3

source_name: control human gastric cancer cell line 3


title: Rapamycin 3


title: Rapamycin 4


title: MA-10_control no treatment_rep3


title: Dietary Restriction 8

value: 40% Dietary Restriction


title: Dietary Restriction 7


title: Rapamycin 6


title: Rapamycin 1


title: Dietary Restriction 6


title: Dietary Restriction 2


title: Dietary Restriction 1


title: Dietary Restriction 4


title: Dietary Restriction 5


title: Human gastric cancerous tissue4

source_name: Human gastric cancerous tissue

value: female

value: gastric cancerous tissue


title: Ad Libitum 5

value: Ad Libitum


title: Ad Libitum 4


title: Dietary Restriction 3


title: Ad Libitum 7


title: Ad Libitum 6


title: Ad Libitum 3


title: Ad Libitum 1


title: Ad Libitum 8


title: Ad Libitum 2


title: 12h_induced_rep2

city: tokyo

first: Kyoko

last: Ohashi-Ito

address: 7-3-1 hongo bunkyo-ku

department: biological sciences

institute: the university of tokyo

description: Estrogen-inducible LHW/T5L1-GFP transformed cells treated with estrogen for 12h

hyb_protocol: Hybridization, washing, staining procedures were run on Fluidics Station 450 (Affymetrix) with GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

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

data_processing: Data procession was performed with Expression Console Version 1.3 (Affymetrix).

source_name: LHW-T5L1 culture cell, 12h

label_protocol: Sense-strand DNA target preparation was performed in combination with Ambion WT Expression Kit (Affymetrix) and GeneChip WT Terminal Labeling Kit and Controls Kit (Affymetrix)

growth_protocol: Cell suspension was cultured on a rotary shaker at 124 rpm at 23°C in the dark.

extract_protocol: Total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN)

treatment_protocol: Cultured cells were treated with/without 5 μM estrogen for 0h and 12h

value: culture cell, Alex

tag: genetic background

value: Col-O


title: 12h_uninduced_rep3

description: Estrogen-inducible LHW/T5L1-GFP transformed cells treated without estrogen for 12h


title: 12h_induced_rep3

value: Estrogen-inducible LHW/T5L1-GFP transformed cells treated with estrogen for 12h


title: 0h_rep1

description: Estrogen-inducible LHW/T5L1-GFP transformed cells treated with estrogen for 0h

source_name: LHW-T5L1 culture cell, 0h

value: 0 h


title: 12h_uninduced_rep2

value: Estrogen-inducible LHW/T5L1-GFP transformed cells treated without estrogen for 12h


title: 0h_rep2

value: Estrogen-inducible LHW/T5L1-GFP transformed cells treated with estrogen for 0h


title: 12h_induced_rep1


title: X5901414040_L.AVG_Signal

city: New Haven

first: Fabio

last: Parisi

address: 462 Humphrey Street

institute: Yale School of Medicine

hyb_protocol: Standard Illumina hybridization protocol: 58 C overnight.

scan_protocol: BeadChips were imaged using the Illumina iScan Reader

data_processing: The software package to extract raw data was Genomestudio. The raw microarray data was initially sorted by intensity values greater or equal to a pre-set baseline intensity value and then quantile normalized.

label_protocol: RNA was labeled using Cy3 dye form the WG-DASL kit from Illumina.

extract_protocol: Total RNA from FFPE was extracted by Ambion (tm) 'Recover all Nucleic Acid RNA Isolation Kit'. Quality control was performed by NanoDrop ND-1000.

value: metastatic melanoma

tag: histology

value: LN (lymph node)

tag: cerebrotropic status

tag: ajcc m stage

tag: mutational status

value: 1, BRAF V600K/WT

tag: location of primary melanoma

value: unknown

tag: presence of lung metastases 1=yes; 0=no


title: 12h_uninduced_rep1

tag: cell type


title: 0h_rep3


title: X5901414042_I.AVG_Signal

value: Trunk


title: X5901414040_H.AVG_Signal

value: 0, wild type

value: Extremities


title: X5901414042_D.AVG_Signal


title: X5901414040_K.AVG_Signal

value: ST (soft tissue)

value: 2, NRAS Q61R/WT (CGA/CAA)


title: X5901414040_F.AVG_Signal

value: R plantar foot


title: X5901414040_C.AVG_Signal

value: 1, BRAF N581T

value: Head&Neck


title: X5901414020_K.AVG_Signal

value: 2, NRAS G12DG-V


title: X5901414020_G.AVG_Signal

value: SK (skin)

value: 1, BRAF V600E (GAG/GAG)


title: X5901414020_B.AVG_Signal

value: 1, BRAF V600E/WT


title: X5901414020_E.AVG_Signal


title: X5901414012_L.AVG_Signal


title: X5901414012_G.AVG_Signal

value: 2, NRAS Q61L


title: X5901414012_H.AVG_Signal

value: metastatic melanoma


title: X5901414012_A.AVG_Signal


title: X5901414020_F.AVG_Signal


title: X5901414020_D.AVG_Signal

value: 1, BRAF P75L


title: X5901414010_J.AVG_Signal

value: 2, NRAS Q61K/WT


title: X5901414012_I.AVG_Signal


title: X5901414010_G.AVG_Signal

value: unknown


title: X5901414010_E.AVG_Signal

value: LN (lymph node)

value: Ocular


title: X5901414010_A.AVG_Signal

value: 0, wild type

value: Extremities


title: X5901414042_K.AVG_Signal

value: ST (soft tissue)


title: X5901414010_H.AVG_Signal


title: X5901414041_B.AVG_Signal

value: 1, BRAF V600E/WT (GTG/GAG)

value: Trunk


title: X5901414041_C.AVG_Signal


title: X5901414010_D.AVG_Signal


title: X5901414041_F.AVG_Signal


title: X5901414042_E.AVG_Signal

value: 1, BRAF V600E/WT (GAG/GTG)


title: X5901414010_C.AVG_Signal


title: X5901414041_I.AVG_Signal


title: X5901414042_B.AVG_Signal


title: X5901414042_F.AVG_Signal


title: X5901414041_E.AVG_Signal

value: R thumb nailbed


title: X5901414041_G.AVG_Signal

value: 1, BRAF V600K/WT

value: Head&Neck


title: X5901414020_J.AVG_Signal

value: 1, BRAF V600E/E


title: X5901414012_F.AVG_Signal

value: SK (skin)

value: 1, BRAF V600E/WT


title: intestinal metaplasia rep4

city: Yufu

first: Katsuhiro

last: Hanada

state: Oita

address: 1-1 Idaigaoka, Hasama-machi

department: Faculty of Medicine

institute: Oita University

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Human Genome Microarray Kit v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: human stomach biopsy, intestinal metaplasia

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: gastric mucosa


title: X5901414040_E.AVG_Signal

value: metastatic melanoma


title: X5901414020_H.AVG_Signal

value: 1, BRAFV600E/WT(GAG/GTG)


title: intestinal metaplasia rep1


title: intestinal metaplasia rep2


title: X5901414012_E.AVG_Signal

value: 1, BRAF V600K


title: X5901414010_I.AVG_Signal

value: LN (lymph node)


title: severe gastritis rep4

source_name: human stomach biopsy, severe gastritis


title: intestinal metaplasia rep3


title: X5901414020_L.AVG_Signal

value: unknown

value: 2, NRAS Q61R/WT


title: severe gastritis rep3


title: mild gastritis rep1

source_name: human stomach biopsy, mild gastritis


title: control rep4

source_name: human stomach biopsy, control


title: mild gastritis rep3


title: mild gastritis rep4


title: control rep1


title: Ramos control, rep 1

city: Porto

first: Rune

last: Matthiesen

address: Rua Dr. Roberto Frias s/n

country: Portugal

institute: IPATIMUP

description: Ramos control, replica 1

hyb_protocol: 3.5 µg of end-labeled, fragmented cDNA was used in a 150-µl  hybridization cocktail containing added hybridization controls  (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips,  Affymetrix), of which 120 ul were hybridized on array strips for 20 h at  48°C. Standard post hybridization wash and double-stain protocols  (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips,  Affymetrix) were used on an Affymetrix GeneAtlas system.

scan_protocol: Array strips were scanned on an Affymetrix GeneAtlas system using standard settings.

data_processing: AFFYLMGUI

source_name: Ramos control

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA)  human HuGENE-1_1-st-v1 Array Strips by using the Ambion WT Expression  Kit (Life Technologies, CA, USA) and Affymetrix GeneChip WT Terminal  Labeling Kit, according to the manufacturer’s protocols. Briefly, 100 ng  of total RNA containing spiked in Poly-A RNA controls (GeneChip  Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was  used in a reverse transcription reaction (Ambion WT Expression Kit) to  generate first-strand cDNA. After second-strand synthesis,  double-stranded cDNA was used in an in vitro transcription (IVT)  reaction to generate cRNA (Ambion WT Expression Kit). 15 ug of this cRNA  was used for a second cycle of first-strand cDNA synthesis (Ambion WT  Expression Kit). 5.5 ug of single stranded cDNA was fragmented and  end-labeled (GeneChip WT Terminal Labeling Kit; Affymetrix). Size  distribution of the fragmented and end-labeled cDNA, respectively, was  assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: All cell lines were cultured in Gibco RPMI medium 1640 GlutaMAX™ (Invitrogen) supplemented with 10% heat-inactivated FBS and penicillin/streptomycin in a humid environment of 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated from the various cell lines and cellular clones using the RNeasy Plus Mini Kit (QIAGEN, Stanford, CA) according to the manufacturer’s protocol.

treatment_protocol: 24 hours glucosamine treatment

tag: cell line

value: Ramos

value: lymphocyte


title: severe gastritis rep2


title: control rep2


title: KMH2 control, rep 2

description: KMH2 control, replica 2

source_name: KMH2 control


title: KMH2 24h glucosamine, rep 1

description: KMH2 24h glucosamine, replica 1

source_name: KMH2 24h glucosamine


title: KMH2 24h glucosamine, rep 2

description: KMH2 24h glucosamine, replica 2


title: severe gastritis rep1


title: KMH2 control, rep 3

description: KMH2 control, replica 3


title: control rep3


title: KMH2 24h glucosamine, rep 3

description: KMH2 24h glucosamine, replica 3


title: KMH2 control, rep 1

description: KMH2 control, replica 1