title: LSK BL6 Msi2Gt rep2

source_name: Sorted LSK cells from Msi2 null animals

value: LSK


title: LSK BL6 Msi2Gt rep3

status: Public on May 21 2011

type: RNA

city: Barcelona

first: Eric

middle: M.

last: Kallin

state: Barcelona

address: C/ Dr. Aiguader, 88

department: Differentiation and Cancer

country: Spain

institute: Center for Genomic Regulation

hyb_protocol: The labelled cRNA was hybridized to the Agilent Whole Mouse Genome 4x44k 60-mer oligo microarray using stnadard Agilent protocol.

scan_protocol: The arrays were scanned on an Agilent G2565CA microarray scanner at 110% PMT and 5 μm resolution.

data_processing: Intensity data was extracted using the Feature Extraction v 10.7.3.1 software (Agilent) and corrected for background noise using the normexp method [Ritchie ME etal. 2007. Bioinformatics]. To assure comparability across samples we use quantile normalization [Bolstad, B. (2001). Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf].

molecule: total RNA

organism: Mus musculus

label_protocol: cDNA from 25 ng of RNA was transcribed with T7 RNA polymerase in the presence of Cy3-CTP to produce labelled cRNA using the standard Agilent labelling protocol.

growth_protocol: BM cells were pooled from 4 Msi2Gt/Gt females (aged 6-7 weeks) or 4 C57/Bl6 females (aged 6-7 weeks) and subjected to lineage depletion. Cells from each pool were stained with fluorochrome-labelled anti-c-Kit and anti-Sca-1 monoclonal antibodies to mark LSK cells (defined as Lineage- Sca-1+ c-kit+) and Kit+ (defined as Lineage-, Sca-1-, c-kit+) and sorted by FACS into PBS+5%FBS.

extract_protocol: Cells were pelleted and RNA was extracted using the RNeasy Mini Kit (Qiagen) by the manufacturer's instructions.

tag: marker phenotype

tag: marker phenotype short name

tag: genotype

tag: cell type

tag: genetic background


title: array4: Human fetal lung fibroblasts transduced with HPV-E6

city: Stanford

first: Tiffany

last: Hung

state: CA

address: 371 SERRA MALL

country: USA

institute: Stanford University

hyb_protocol: standard Nimblegen protocol

scan_protocol: standard Nimblegen protocol

data_processing: RMA normalized raw signals followed by peak calling analysis

organism: Homo sapiens

label_protocol: RT to cDNA, standard Nimblegen protocol

growth_protocol: dmem 10% FBS

extract_protocol: Trizol extraction

tag: cell line

value: fetal lung fibroblasts


title: KIT BL6 WT rep1

source_name: Sorted KIT+ cells from WT animals

value: KIT+

value: KIT


title: LSK BL6 Msi2Gt rep1


title: array12: HeLa synchronized by double thymidine block: 12 hr

value: HeLa


title: array4: Human fetal lung fibroblasts transduced with HPV-E6 (control)

treatment_protocol: empty vector


title: array3: Human fetal lung fibroblasts transduced with HPV-E7


title: array7: HeLa synchronized by double thymidine block: 2 hr (control)

source_name: HeLa asynchronous

value: hela


title: LSK BL6 WT rep3

source_name: Sorted LSK cells from WT animals


title: LSK BL6 WT rep1


title: 3t2m-4

city: Chicago

first: Xinan

middle: Holly

last: Yang

state: IL

address: 900 East 57th Street, KCBD Room 5121

department: Pediatrics

institute: universty of Chicago

description:
human tumor xenograft in mouse
cDNA synthesis: Ten μL of each triplicate were combined and 3 μL of this pooled sample were used to obtain a total of 30 ng of total RNA.  Single stranded cDNA synthesis was performed using Megaplex RT Primers, Human Pool Set v2.1 and TaqMan MicroRNA Reverse Transcription kit (Applied Biosystems) according to the manufacturer’s protocol.
real time qPCR: Pre-amplification of specific cDNA targets was performed using Megaplex PreAmp Primers and TaqMan PreAmp Master Mix (Applied Biosystems).  Real-time qPCR was performed using the 7900HT Fast Real-Time PCR System, TaqMan Universal PCR Master Mix and Taqman MicroRNA Array A Card v2.0 (Applied Biosystems) according to the manufacturer’s protocol.

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
The qPCR data were processed and outputed by Sequence Dectection System (SDS) Software (Applied Biosystems); the undetermined data were set to the Ct value of 40. The raw Ct values were scrutinized to identify and remove technical sample outliers (3t2m-4) with exceptionally higher portion of undetermined miRNAs. The Ct values were then normalized by rank invariant normalization using R package HTqPCR with default parameters.

This Sample does not have processed data since the data were removed due to poor quality.

label: not applicable

source_name: lung metastases

label_protocol: not applicable

extract_protocol: Total RNA from four lungs of oligometastatic animals’ tail-vein injected with L1 MDA-MB-435-GFP cells, or of polymetastatic animals receiving L1Mic MDA-MB-435-GFP cells were extracted and purified using TRIzol (Gibco/BRL) according to manufacturer’s instructions. Lung tissues were snap frozen immediately in liquid nitrogen upon resection and stored at -80 degree C.

tag: classifier

value: oligometastasis

tag: tissue

value: lung metastases


title: mic7t2m-1

data_processing: The qPCR data were processed and outputed by Sequence Dectection System (SDS) Software (Applied Biosystems); the undetermined data were set to the Ct value of 40. The raw Ct values were scrutinized to identify and remove technical sample outliers (3t2m-4) with exceptionally higher portion of undetermined miRNAs. The Ct values were then normalized by rank invariant normalization using R package HTqPCR with default parameters.

value: polymetastasis


title: array9: HeLa synchronized by double thymidine block: 6 hr (control)


title: mic2t2m-1


title: mic8t2m-1


title: 8t2m-3


title: LSK BL6 WT rep2


title: 4t2m-5


title: array2: Serum starvation

source_name: Serum starvation

growth_protocol: Dmem .01% FBS

treatment_protocol: 24 hrs


title: SCC4-Sal B treated

city: Shanghai

first: Ya

address: 639 Zhi Zao Ju Road

department: General Dentistry

country: China

institute: Ninth People's Hospital, School of Stomatology

hyb_protocol: Hybridization was performed at 60°C overnight in a rolling bottle. The arrays were washed twice with 2X SSC and 0.5 % SDS at 60°C for 30 min; followed by two stringent washes with 0.5X SSC, 0.5% SDS at the same temperature and for the same length of time. Finally, damp arrays were sealed in plastic wrap and exposed to imaging plates  for 24 hours, which were then scanned with a HP GeneArray Scanner

scan_protocol: scanned with a HP GeneArray Scanner

data_processing: All raw signal intensities were corrected for background by subtracting the minimum value to avoid the appearance of negative numbers. All signal intensities were normalized to that of a housekeeping gene. These corrected, normalized signals can then be used to estimate the relative abundance of particular transcripts.

label: biotin

source_name: tongue squamous cell carcinoma cells

label_protocol: RNAs were denatured at 70°C for 10 min and cDNAs were synthesized at 42°C by oligo-dT priming in a final volume of 30 μl. The labelled cDNAs were purified by spin column chromatography.

growth_protocol: CAL27 cells were cultured in DMEM with 10% fetal bovine. SCC4 cells were cultured in DMEM/F12 with 10% FBS. All cells were maintained in a humidified atmosphere.

extract_protocol: Total RNA was isolated from cell culture flasks with RNAbee, purified with chloroform, precipitated with cold isopropano, washing with 75% ethanol.

treatment_protocol: Cells were treated with different doses of Sal B (50,100,200) ug/ml for 24, 48 and 72 hours.

value: oral squamous cell carcinoma


title: 12t2m-2


title: SCC4-untreated


title: CAL27-untreated


title: CAL27-Sal B treated


title: Activin for day5, biological rep3

first: Si Wan

last: Kim

address: 300 Pasteur Drive M313

department: Genetics

description: Activin-treated cells for day5

hyb_protocol: Samples were hybridized using Affymetrix GeneChip Hybridization, Wash and Stain Kit. • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes and centrifuge at max speed for 1 minute. • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm. • Fluidics washing is FS450_0001.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G

data_processing:
Exon array data were processed using GeneBASE (Kapur et al., 2007, Genome Biol 8, R82). Probe intensities were corrected using background probes. Probes were selected and summarized for gene level expression. Gene expression profiles were pooled for quantile-normalization.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.na24.hg18.probeset.csv

source_name: Activin-treated cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Sense Target Labeling Assay Kit (Affymetrix)

growth_protocol: Differentiation was performed in RPMI-1640 medium supplemented with glutamax, 100 ng/ml recombinant human Activin A (R&D Systems), penicillin/streptomycin, and defined fetal bovine serum (FBS; HyClone) at sequentially increasing concentrations (0, 0.2 to 2%). 2% FBS was maintained afterwards in cultures over the duration of differentiation.

extract_protocol: Cells were harvested and used for total RNA preparation using Trizol (Invitrogen). Samples were then treated with the RiobMinus rRNA reduction kit (Invitrogen). cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: not applicable

value: ESC-derived cells

tag: passage

tag: treatment

value: activin

tag: time

value: 5 d


title: array1: Dox DNA damage

source_name: Human fetal lung fibroblasts treated with doxorubicin (200ng/ul) for 24 hours

treatment_protocol: (200ng/ul) for 24 hours


title: Activin for day5, biological rep2

description: Activin-treated cells for day5


title: Activin for day5, biological rep4 technical rep1

description: Activin-treated cells for day5


title: Activin for day5, biological rep1

description: Activin-treated cells for day5


title: Activin for day5, biological rep4 technical rep2

description: Activin-treated cells for day5


title: Activin for day1, biological rep2

description: Activin-treated cells for day1

value: 1 d


title: Activin for day3, biological rep2

description: Activin-treated cells for day3

value: 3 d


title: Activin for day3, biological rep1

description: Activin-treated cells for day3


title: Lucidea array 5

city: Umeå

first: Mattias

last: Landfors

address: Umeå University

department: Clinical bacteriology

country: Sweden

institute: Umeå University

description: Self-Self hybridization of total RNA from Mus Musculus with added Lucidea spike mix

hyb_protocol: The arrays were hybridized overnight at 37°C. Washing was performed in a Genetac hybridization station (Genomic olutions) at 50°C in 0.1 × SSC, 0.1% SDS, followed by 0.1 × SSC at 20°C.

scan_protocol: Each array was scanned using a ScanArray 4000XL (PerkinElmer) at 80/80 laser/PMT settings, where the numbers are percentage of maximum voltages. The Images were analyzed in ScanArrayExpress 2.0, using adaptive circle with nominal diameter 150 μm.

data_processing:
In the 80.I.1 normalization, all spots flagged as not found during image analysis considered missing values (complete filtration). Print-tip MA-loess dye normalization based on the calibration clones was applied to the raw data and the B-statistic was calculated.
In the 80.II.1 normalization, all spots flagged as not found during image analysis considered missing values (complete filtration). Local background correction was applied and all spots with negative values were excluded. Print-tip MA-loess dye normalization based on the calibration clones was applied to the background corrected data and the B-statistic was calculated.
In the 80.II.64 normalization, all spots flagged as not found during image analysis considered missing values (complete filtration). Local background correction was applied, negative values were excluded and all spots with a value below 64 were set to 64 (censored). Print-tip MA-loess dye normalization based on the calibration clones was applied to the background corrected data and the B-statistic was calculated.
In the 80.V.1 normalization, The intensities of all spots flagged not found were treated as missing values during normalization, but prior to calculating test-statistics the spot's log-ratios were set to zero. In the special case when all arrays generated not-found spots, the gene was removed from the experiment (Partial filtration). Local background correction was applied and all negative values were considered missing values. Print-tip MA-loess dye normalization based on the calibration clones was applied to the background corrected data and the B-statistic was calculated.

source_name: Amersham Lucidea Universal ScoreCard spike mix

label_protocol: The fluorophores Cy3 and Cy5 (Amersham Biosciences) were coupled to the aminoallyl group in the test and reference reactions respectively. The labeled cDNA was purified, and cDNA from test and reference reactions were mixed and dissolved in DIG Easy Hyb (Roche) supplemented with tRNA (Sigma) and fish sperm DNA (Sigma).

extract_protocol: First strand cDNA-synthesis was performed using Superscript II (Invitrogen) incorporating aminoallyl-dUTP (Amersham Biosciences). Five μl of the Lucidea Universal ScoreCard reference and test spike mix RNA, together with 25 μg of total RNA from murine cell line J774.1.

tag: strain

tag: spiked with

value: Amersham Lucidea Universal ScoreCard test mix

value: Amersham Lucidea Universal ScoreCard reference mix


title: Lucidea array 8


title: Lucidea array 7


title: Lucidea array 3


title: Lucidea array 4


title: Activin for day3, biological rep3

description: Activin-treated cells for day3


title: Lucidea array 2


title: Lucidea array 1


title: array2: Serum starvation (control)


title: Lucidea array 6


title: Activin for day1, biological rep1

description: Activin-treated cells for day1


title: Activin for day1, biological rep3

description: Activin-treated cells for day1


title: hESCs, biological rep4 technical rep1

description: undifferentiated human embryonic stem cells

source_name: human embryonic stem cells

growth_protocol: Undifferentiated H9 hESCs were maintained on mouse embryonic fibroblast (MEF) feeder layers or on Matrigel (1:20 dilution; BD Biosciences) in mouse embryonic fibroblast-conditioned medium (CM). CM was produced by conditioning of MEFs for at least 24 hours in Dulbecco's modified Eagle's medium/Ham's F-12 medium (DMEM/F12) supplemented with 20% knockout serum replacement (Gibco), 1 mM L-glutamine, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol and 8 ng/ml recombinant human fibroblast growth factor-basic (bFGF; Peprotech). Cultures were routinely passed with 200 U/ml type IV collagenase (Gibco) in 1:4 ratio every 4–5 days.

value: embryonic stem cells


title: hESCs, biological rep2


title: hESCs, biological rep1


title: hESCs, biological rep3


title: hESCs, biological rep4 technical rep2


title: MCF7_untreated_rep1

status: Public on May 20 2011

city: Zurich

first: Leah

middle: N

last: Cueni

address: Wolfgang Pauli-Str. 10

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

description: Replicate 1 of 2.

hyb_protocol: Array hybridization, array processing, chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (PN 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer according to the manufacturer’s protocol.

scan_protocol: Scanning was performed according to the Chemiluminescent Detection Kit (PN 4339627) and Chemiluminescent Microarray Analyzer User Guide (PN 4338852).

data_processing:
The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation. The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values. The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values. The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement. An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise. In situations where the probe showed S/N < 1, the signal measurement is replaced with a 1 SDEV upper limit based on its probe signal SDEV.
Quantile normalization of the raw signals was performed using R software version 2.3.1 (The R Foundation for Statistical Computing).

label: Digoxigenin-UTP

source_name: MCF7 breast carcinoma cells, untreated

label_protocol: Digoxigenin-UTP labeled cRNA was generated from 1 µg of total RNA for each sample using Applied Biosystems NanoAmp RT-IVT Labeling Kit (PN 4365715) according to the manufacturer’s protocol.

growth_protocol: Cells were cultured in DMEM, containing 10% fetal bovine serum, 100 U/ml penicillin, 100 μg/ml streptomycin and selection antibiotics (150 µg/ml G418 and 60 µg/ml hygromycin B) for 12 days prior to extraction of total RNA.

extract_protocol: Approx. 60% confluent cells in a 10cm-cell culture dish were washed twice with cold PBS, before total cellular RNA was extracted using 1 ml Trizol reagent (Invitrogen), according to the manufacturer's instructions. The air-dried RNA pellet was dissolved in 50 µl RNAse/DNAse-free water.

treatment_protocol: Cells were grown for 12 days in their normal growth medium.

tag: MCF7 human breast carcinoma cells, stably transfected with the pTet-Off-regulator plasmid and the pTRE2hyg response plasmid (Clontech).

tag: Cell clone 1.


title: MCF7_untreated_rep2

description: Replicate 2 of 2.

tag: Cell clone 2.


title: MCF7_doxycycline_12d_rep1

description: Replicate 1 of 2.

source_name: MCF7 breast carcinoma cells, treated with doxycycline

growth_protocol: Cells were cultured in DMEM, containing 10% fetal bovine serum, 100 U/ml penicillin, 100 μg/ml streptomycin and selection antibiotics (150 µg/ml G418 and 60 µg/ml hygromycin B). 80 ng/ml doxycycline (Clontech) was added for 12 days prior to extraction of total RNA.

treatment_protocol: Cells were grown for 12 days in their normal growth medium with the addition of 80 ng/ml doxycycline (Clontech).


title: MCF7_doxycycline_12d_rep2

description: Replicate 2 of 2.


title: TRAMP_serum_advancedDiseased_rep1

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description: miRNA data from TRAMP serum

hyb_protocol: cRNA were hybridized for 16 hr at 48C on GeneChip miRNA Arrays and then washed and stained with a Steptavidin-PE solution prior to imaging.

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

data_processing: Data were background corrected and statistically analysed using Partek Genomics Suite (Partek Inc.) using the subset of mouse probes on the array. Raw data was processed using RMA background correction and Partek’s own GC content correction with mean probe summarization.

source_name: Serum from TRAMP mice with advanced disease

label_protocol: Approximately 800ng of RNA was labelled using the FlashTag HSR Biotin RNA Labelling Kit (Genisphere), according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted twice with phenol:chloroform and precipitated using ethanol.

value: serum

value: C57BL/6 TRAMP x FVB

tag: genotype/variation

value: TRAMP

tag: age

value: mixed


title: TRAMP_serum_advancedDiseased_rep2

description: miRNA data from TRAMP serum


title: 14090008 - colD 1 vs col1h 1

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

country: France

institute: INRA

description: Role of histone UbH2B in the regulation of gene expression in response to light

hyb_protocol: col1h 1 Cy5 / colD 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias using R version 2.8.1 (2008-12-22) (ISBN 3-900051-07-0). Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: col1h 1

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seedling - Media: MS 1/2   hygrometry: 60%  Temperature:19°C for 8h / 23°C for 16h  Light: 100µEinstein

extract_protocol: col1h 1:4ug. using RNeasy Kit of Qiagen

treatment_protocol: Name:5 days of darkness and 1h of light exposure - time course study - light,light:quantity 100uE time 1hour .

tag: ecotype

value: columbia

value: wild type

tag: developmental stage (boyes et al. plant cell 2001)

value: boyes 0.70

source_name: colD 1

extract_protocol: colD 1:4ug. using RNeasy Kit of Qiagen

treatment_protocol: Name:5 days of darkness and no light exposure - time course study - light,light:quantity 100uE time 0hour .


title: 14092653 - col6h 1 vs colD 1

hyb_protocol: colD 1 Cy5 / col6h 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col6h 1

extract_protocol: col6h 1:4ug. using RNeasy Kit of Qiagen

treatment_protocol: Name:5 days of darkness and 6h of light exposure - time course study - light,light:quantity 100uE time 6hour .


title: WT_serum_rep2

description: miRNA data from WT serum

source_name: Serum from wild-type littermate control mice

value: C57BL/6 x FVB


title: 14092656 - colD 1 vs col6h 1

hyb_protocol: col6h 1 Cy5 / colD 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: mic3t2m-2

value: polymetastasis

value: lung metastases


title: U266N

type: genomic

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description: U266 cell line without CD34 cells

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. The WACA algorithm (F Lepretre et al., NAR 2010) was finally used for CGH waves correction for fine and reliable genomics comparisons.

molecule: genomic DNA

source_name: U266 cell line without CD34 cells

label_protocol: manufacturer's instructions

extract_protocol: manufacturer's instructions

treatment_protocol: Total DNA extracted using manufacturer's instructions

source_name: Promega male control DNA

tag: reference

value: Promega male control DNA


title: U266P

description: U266 cell line with CD34 cells

source_name: U266 cell line with CD34 cells


title: WT_serum_rep3

description: miRNA data from WT serum


title: HL60P

description: HL60 cell line with CD34 cells

source_name: HL60 cell line with CD34 cells


title: 14090011 - col1h 2 vs colD 2

hyb_protocol: colD 2 Cy5 / col1h 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: colD 2

extract_protocol: colD 2:4ug. using RNeasy Kit of Qiagen

source_name: col1h 2

extract_protocol: col1h 2:4ug. using RNeasy Kit of Qiagen


title: array1: Dox DNA damage (control)


title: 14090003 - hub1h 2 vs hubD 2

hyb_protocol: hubD 2 Cy5 / hub1h 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: hubD 2

extract_protocol: hubD 2:4ug. using RNeasy Kit of Qiagen

value: mutant (hub1-3)

source_name: hub1h 2

extract_protocol: hub1h 2:4ug. using RNeasy Kit of Qiagen


title: 14090010 - colD 2 vs col1h 2

hyb_protocol: col1h 2 Cy5 / colD 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HepG2 APRIL 2h

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

department: Medicine

country: Greece

institute: University of Crete

hyb_protocol: RNA was hybridized according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual), on HGU133A plus 2 chips.

scan_protocol: Signals were detected by an Affymetrix microarray chip reader.

data_processing: Normalization and analysis was performed with the raw data using Genespring GX V11.0 (Agilent, Foster City, CA). RMA algorithm used with baseline set to the median of all.

source_name: HepG2 cells, treated for 2 hours with 200ng/ml APRIL

label_protocol: RNA was labeled according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual)

growth_protocol: The human hepatocyte-derived cancer cell line HepG2 was obtained from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal bovine serum, at 37 °C, 5% CO2.

extract_protocol: Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer’s instructions.

treatment_protocol: HepG2 cells were incubated with or without APRIL (200ng/ml) for 2, 6 and 12 hours after overnight serum starvation.

tag: cell type

value: hepatocyte derived cancer


title: 14090009 - col1h 1 vs colD 1

hyb_protocol: colD 1 Cy5 / col1h 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14090006 - hubD 2 vs hub6h 2

hyb_protocol: hub6h 2 Cy5 / hubD 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: hub6h 2

extract_protocol: hub6h 2:4ug. using RNeasy Kit of Qiagen


title: 14090015 - hub6h 2 vs hubD 2

hyb_protocol: hubD 2 Cy5 / hub6h 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14090004 - hubD 1 vs hub6h 1

hyb_protocol: hub6h 1 Cy5 / hubD 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: hub6h 1

extract_protocol: hub6h 1:4ug. using RNeasy Kit of Qiagen

source_name: hubD 1

extract_protocol: hubD 1:4ug. using RNeasy Kit of Qiagen


title: 14090005 - hub6h 1 vs hubD 1

hyb_protocol: hubD 1 Cy5 / hub6h 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14089998 - hubD 1 vs hub1h 1

hyb_protocol: hub1h 1 Cy5 / hubD 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: hub1h 1

extract_protocol: hub1h 1:4ug. using RNeasy Kit of Qiagen


title: 14090000 - hub1h 1 vs hubD 1

hyb_protocol: hubD 1 Cy5 / hub1h 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HepG2 APRIL 6h

source_name: HepG2 cells, treated for 6 hours with 200ng/ml APRIL

tag: cell line


title: HL60N

description: HL60 cell line without CD34 cells

source_name: HL60 cell line without CD34 cells


title: 14089997 - col6h 2 vs colD 2

hyb_protocol: colD 2 Cy5 / col6h 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col6h 2

extract_protocol: col6h 2:4ug. using RNeasy Kit of Qiagen


title: WT_serum_rep1

description: miRNA data from WT serum

hyb_protocol: cRNA were hybridized for 16 hr at 48C on GeneChip miRNA Arrays and then washed and stained with a Steptavidin-PE solution prior to imaging.

source_name: Serum from wild-type littermate control mice


title: 14089996 - colD 2 vs col6h 2

hyb_protocol: col6h 2 Cy5 / colD 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: no_cancer_45

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

state: NY

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

description: Hy3 and Hy5 are Cy3- and Cy5-like dyes, respectively.

hyb_protocol: Hybridization of the mix of Hy3-labeled sample and Hy5-labeled reference RNAs to the arrays at 56 ºC for 16 hours followed by washing was performed by Exiqon® (Vedbaek, Denmark) on an HS Pro instrument (Tecan®, Männedorf, Switzerland). The 5th generation miRCURY LNA microRNA arrays (Exiqon®, Vedbaek,Denmark) that were used have approx. 1891 locked nucleic acid oligonucleotide probes on quadruplicate 105 µM-sized probe-spots to detect 74%, 72% and 68% of the 1223, 1055 and 680 human, mouse and rat microRNAs, respectively, of miRbase v.16.

scan_protocol: Arrays were scanned, after hybridization and washing, using the G2505B scanning system (Agilent®, Santa Clara, CA, USA) by Exiqon® (Vedbaek, Denmark).

data_processing: Data processing was done in R (version 2.12.1) using the limma (version 3.4.5) Bioconductor package. The 'normexp' method with offset=10 was used for background-correction, and followed with within-array global 'loess' normalization, with span=1/3 and values from probe-spots with flag-values >1 ignored, and then, between-array 'Rquantile' normalization. For probe-set summarization, the median of the values from multiple spots was used when the ratio of the maximum and minimum values was > 1.5; else, the mean was used. The ratios of the summarized normalized Hy3/Hy5 (test/reference) signal-intensities were log2-transformed.

source_name: No cancer control ID 45

label_protocol: RNA was labeled by Exiqon®, Vedbaek, Denmark using the miRCURY LNA microRNA Power labeling kit. Five hundred ng of RNA, as quantified using Bioanalyzer (Agilent®, Santa Clara, CA, USA), was used per labeling reaction with the Hy3 dye. A human universal reference RNA, made by pooling contents of FirstChoice total RNA panel (Ambion®, Austin, TX, USA; catalog no. AM6000), was similarly labeled with the Hy5 dye. Synthetic small RNAs were spiked-in to the RNA samples before labeling as per the kit protocol.

extract_protocol: Total RNA was isolated from blood collected and stored in PAXgene Blood RNA tubes using a PAXgene Blood RNA isolation kit at the University of Pennsylvania as per the protocol suggested by the manufacturer (Qiagen®, Valencia, CA, USA). The human universal reference RNA was made by pooling contents of FirstChoice total RNA panel that is made of RNA from different tissues of multiple individuals (Ambion®, Austin, TX, USA; catalog no. AM6000.

tag: gender

value: Male

value: Normal lung

tag: disease

value: No cancer

source_name: Human universal reference RNA from Ambion®

tag: sample type

value: universal reference RNA was made by pooling contents of FirstChoice total RNA panel that is made of RNA from different tissues of multiple individuals,  Ambion, Austin, TX, USA; catalog no. AM6000

value: Mixed


title: no_cancer_46

source_name: No cancer control ID 46

tag: tissue


title: no_cancer_48

source_name: No cancer control ID 48


title: no_cancer_49

source_name: No cancer control ID 49


title: HepG2 APRIL 0h

source_name: HepG2 cells, untreated


title: 14090001 - hubD 2 vs hub1h 2

hyb_protocol: hub1h 2 Cy5 / hubD 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: hubD 2


title: TRAMP_serum_advancedDiseased_rep3

description: miRNA data from TRAMP serum

source_name: Serum from TRAMP mice with advanced disease

value: serum

value: C57BL/6 TRAMP x FVB


title: 14089832 - colD 2 vs hubD 2

hyb_protocol: hubD 2 Cy5 / colD 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: colD 2


title: 14089831 - hubD 1 vs colD 1

hyb_protocol: colD 1 Cy5 / hubD 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: colD 1


title: 14090007 - hubD 2 vs colD 2

hyb_protocol: colD 2 Cy5 / hubD 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: no_cancer_44

source_name: No cancer control ID 44

value: Female


title: MDS3e strain, biological rep1

city: Mississauga

first: Lucas

last: Parreiras

state: Ontario

address: 3359 Mississauga Road N.

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

description: Gene expression data for haploid S. cerevisiae strain carrying an evolved allele of the gene MDS3.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on GeneChip Yeast Genome 2.0 arrays following standard manufacturer protocols.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 following standard manufacturer protocols.

data_processing: The data were analyzed using Affymetrix expression console.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells undergoing logarithmic growth

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ug total RNA (Affymetrix 3’IVT Express Kit).

growth_protocol: Yeast cells were removed from archive and grown overnight in liquid yeast peptone dextrose (YPD: 1% yeast extract, 2% peptone, 2% dextrose). Each culture was used to inoculate a set volume of defined low glucose medium (LGM: 0.67% yeast nitrogen base without amino acids, 0.25% dextrose, 0.02 mg ml-1 of uracil). These cultures were incubated and allowed to grow until reaching an OD600 of approximately 0.2 (≈17 hrs).

extract_protocol: Total RNA was isolated using RNeasy Mini Kits (Qiagen). Manufacturer protocols were followed.

treatment_protocol: Aliquots from each LGM culture were added to tubes containing cold methanol (stored at -80°C), mixed and centrifuged.  The cells were then washed with DEPC treated water, centrifuged and re-suspended in RNAlater (Ambion).

tag: genotype

tag: growth condition

value: low glucose

tag: genetic background


title: no_cancer_47

source_name: No cancer control ID 47


title: MKT1e strain, biological rep1

description: Gene expression data for haploid S. cerevisiae strain carrying an evolved allele of the gene MKT1.


title: HepG2 APRIL 12h

hyb_protocol: RNA was hybridized according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual), on HGU133A plus 2 chips.

source_name: HepG2 cells, treated for 12 hours with 200ng/ml APRIL


title: 14089830 - colD 1 vs hubD 1

hyb_protocol: hubD 1 Cy5 / colD 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: hubD 1

value: columbia

value: wild type


title: no_cancer_43

source_name: No cancer control ID 43


title: no_cancer_41

source_name: No cancer control ID 41


title: no_cancer_42

source_name: No cancer control ID 42


title: MDS3e MKT1e strain, biological rep1

description: Gene expression data for haploid S. cerevisiae strain carrying evolved alleles of the genes MDS3 and MKT1.

value: MDS3e MKT1e


title: MDS3e MKT1e strain, biological rep2


title: no_cancer_40

source_name: No cancer control ID 40

source_name: Human universal reference RNA from Ambion®


title: MDS3e strain, biological rep2


title: no_cancer_39

source_name: No cancer control ID 39


title: non-cancerous_lung-nodule_38

source_name: No cancer control ID 38


title: MKT1e strain, biological rep2


title: Progenitor strain, biological rep2

description: Gene expression data for haploid S. cerevisiae strain carrying no evolved alleles.

value: Ancestral


title: Progenitor strain, biological rep1


title: PMA1e MKT1e strain, biological rep2

description: Gene expression data for haploid S. cerevisiae strain carrying evolved alleles of the genes PMA1 and MKT1.

value: PMA1e MKT1e


title: macrophage, untreated, biological rep 4

city: San Diego

first: Christine

last: Esau

address: 3545 John Hopkins Court

institute: Regulus Therapeutics

description: Gene expression data from plaque macrophages treated with saline

hyb_protocol: Hybridize fragmented, biotin-labeled cRNA to the Affymetrix GeneChip® Array overnight at 45oC for 16 to 18 hours (GeneChip Hybridization Oven 640) according to the manufacturer’s recommendations.

scan_protocol: Stain, wash (GeneChip Fluidics Station 450, EukGE-WS2v5_450 script) and scan (GCS 3000 7G with the GeneChip® AutoLoader) performed according to the manufacturer’s recommendations.

data_processing: The data were analyzed with Array Studio version 4.1 using Affymetrix default analysis settings and RMA as normalization method. The normalized signals were log-2 transformed.

source_name: plaque macrophage untreated

label_protocol: Starting with 1 ug total RNA, produce amplified biotin-labeled cRNA targets using the Enzo Target Labeling method.

growth_protocol: Ldlr-/- mice were weaned at 4 weeks of age and placed on a high fat diet (21% (wt/wt) fat, 0.3% cholesterol; Research Diets) for 14 weeks, at which point mice were switched to chow diet for 4 weeks and anti-miR treatment began.

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

treatment_protocol: Mice received 2 injections of 10 mg/kg anti-miR or control (or an equivalent volume of PBS) the first week, spaced two days apart, and weekly injections of 10 mg/kg anti-miR (or PBS) thereafter for 4 weeks.

tag: strain

value: male

value: macrophage

value: LDLR knockout


title: no_cancer_37

source_name: No cancer control ID 37


title: non-cancerous_lung-nodule_36

source_name: No cancer control ID 36

value: Granuloma of lung


title: non-cancerous_lung-nodule_30

source_name: No cancer control ID 30

value: Male

value: Amyloid nodule of lung


title: non-cancerous_lung-nodule_31

source_name: No cancer control ID 31

value: No cancer

value: universal reference RNA was made by pooling contents of FirstChoice total RNA panel that is made of RNA from different tissues of multiple individuals,  Ambion, Austin, TX, USA; catalog no. AM6000


title: non-cancerous_lung-nodule_32

source_name: No cancer control ID 32

value: Mixed


title: non-cancerous_lung-nodule_35

source_name: No cancer control ID 35


title: macrophage, control anti-miR, biological rep 4

description: Gene expression data from plaque macrophages treated with control anti-miR

source_name: plaque macrophage control anti-miR


title: macrophage, untreated, biological rep 3


title: macrophage, untreated, biological rep 1


title: macrophage, control anti-miR, biological rep 3


title: macrophage, untreated, biological rep 2


title: macrophage, control anti-miR, biological rep 1


title: non-cancerous_lung-nodule_28

source_name: No cancer control ID 28

value: Benign nodule of lung


title: PMA1e MKT1e strain, biological rep1

source_name: Saccharomyces cerevisiae cells undergoing logarithmic growth


title: non-cancerous_lung-nodule_27

source_name: No cancer control ID 27


title: macrophage, anti-miR-33 treated, biological rep 3

description: Gene expression data from plaque macrophages treated with anti-miR-33

source_name: plaque macrophage anti-miR-33 treated


title: non-cancerous_lung-nodule_33

source_name: No cancer control ID 33


title: macrophage, control anti-miR, biological rep 2


title: macrophage, anti-miR-33 treated, biological rep 1


title: non-cancerous_lung-nodule_29

source_name: No cancer control ID 29

value: Female

value: Hamartoma of lung


title: non-cancerous_lung-nodule_26

source_name: No cancer control ID 26

source_name: Human universal reference RNA from Ambion®


title: macrophage, anti-miR-33 treated, biological rep 4


title: lung_adenocarcinoma_25

source_name: Lung adenocarcinoma case ID 25

value: Lung adenocarcinoma


title: Mouse_ear_skin_LEC_inflamed_rep4

first: benjamin

last: vigl

address: W.-Pauli-Str. 10, HCI, G490

description: Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single stranded cDNA

hyb_protocol: Biotin-labeled cDNAs were mixed in 220 μl of Hybridization Mix (Affymetrix Inc.) containing hybridization controls and control oligonucleotide B2 (Affymetrix Inc.). Samples were hybridized to GeneChip Mouse Genome 430 2.0 arrays for 18h at 45°C. Arrays were washed using an Affymetrix Fluidics Station 450 FS450 0004 protocol.

scan_protocol: Fluorescence intensity of the arrays was measured on an Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as implemented in the BioConductor simpleaffy package - with default parameters, in particular the trimmed mean target intensity of each array was set to 100. The chip description file used for summarization was standard Affymetrix Mouse430_2 CDF file.

source_name: Mouse, ear skin, lymphatic endothelial cells, inflamed

label_protocol: Single-stranded cDNA (5 μg) was fragmented and biotin-labeled, using the FL-Ovation cDNA Biotin Module V2 kit (NuGEN Technologies), following the manufacturer’s instructions.

growth_protocol: Mice were maintained under conventional conditions (SPF)

extract_protocol: Sorted cells in RNAprotect Cell Protect reagent were kept at 4°C until further processing. Cells were lyzed by vortexing for 1 min. Total RNA was extracted in parallel from one control and one inflamed sample (LECs extracted from the ears of 3 mice - sorted on the same day), using RNeasy plus micro kit (Qiagen). Note: gDNA eliminator column was used to eliminate genomic DNA. The Whole Transcriptome-OvationTM Pico RNA amplification kit from Nugen Technologies (San Carlos, CA) and QIAQuick PCR purification kit (Quiagen) was used for cDNA synthesis and a single round of isothermal amplification (SPIA amplification, i.e. a linear isothermal DNA amplification process, was used to prepare single-stranded cDNA in the antisense direction of the mRNA starting material), typically yielding more than 5 μg of amplified cDNA. The quantity and quality of amplified cDNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies) and a Bioanalyzer 2100 (Agilent). Amplified cDNA gave a peak length of 300 - 900 nt.

treatment_protocol: Mice were sensitized by topical application of 2% oxazolone (4 ethoxymethylene 2 phenyl 2 oxazoline 5 one; Sigma) in acetone/olive oil (4:1 vol/vol) on the shaved abdomen (50 μl) and on each paw (5 μl). 5 days later mice were challenged with oxazolone 1% in acetone: olive oil (10 μl) applied topically to each side of the ears). 24 hours after induction of skin inflammation (CHS challenge), mice (3 per group) were sacrificed and the ears were cut off at the basis of the pinna. Ear halves were separated by tearing along the cartilage and cut into small pieces with forceps and a scalpel. The tissue was briefly digested by incubation for 13 min at 37° C in PBS containing 10 mg/ml of collagenase IV (Invitrogen). The tissue was passed twice through a 40 μm cell strainer (BD Biosciences) and incubated for additional 8 minutes. All subsequent steps were performed on ice. Resulting single cell suspensions were rapidly stained by incubation with the following antibodies: APC rat anti mouse CD31; PerCP labeled anti mouse CD45 (both from BD Biosciences); hamster anti mouse podoplanin (clone 8.1.1; Developmental Studies Hybridoma Bank, University of Iowa) and anti-hamster PE (CALTAG, Invitrogen). Isolation of LECs (identified as CD45-CD31+podoplanin+) was performed on a FACSAria Cell Sorter and the FACSDiva software (both BD Biosciences). Cells were directly sorted into RNAprotect Cell Protect reagent (Qiagen). Sample processing (i.e. from the start of the ear digest to the end of the sorting) was optimized to last less than 2.5 hours.

value: FVB

tag: Sex

value: female

value: 10 weeks

value: ear skin

value: lymphatic endothelial cells

tag: condition

value: healthy, CHS inflamed

tag: cell isolation method

value: FACS


title: Mouse_ear_skin_LEC_untreated_rep4

source_name: Mouse, ear skin, lymphatic endothelial cells, untreated

tag: age

value: healthy, untreated


title: DKO replicate 3

city: Cleveland

first: Angela

last: Ting

state: Ohio

address: 9500 Euclid Ave/NE50

department: Genomic Medicine

institute: Cleveland Clinic

description:
DKO-3
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was quantile normalized and analyzed using the Illumina GenomeStudio v2009.1.

source_name: DKO cells

growth_protocol: Both HCT116 and DKO cells were cultured in McCoy's 5A medium supplemented with 10% fetal bovine serum at 37oC, 5% CO2.

extract_protocol: Total RNA was extracted with Trizol reagent, followed by DNase I treatment.  RNA quality and concentration was measure using the nanodrop spectrophtometer.

treatment_protocol: No treatments were given to the cells.

value: cancer cell line HCT116

tag: genotype/variation

value: DMNT-1 and 3B double knock out (DKO)


title: macrophage, anti-miR-33 treated, biological rep 2

value: male

value: macrophage

value: LDLR knockout


title: lung_adenocarcinoma_20

source_name: Lung adenocarcinoma case ID 20

value: Male

value: universal reference RNA was made by pooling contents of FirstChoice total RNA panel that is made of RNA from different tissues of multiple individuals,  Ambion, Austin, TX, USA; catalog no. AM6000

value: Mixed


title: lung_adenocarcinoma_21

source_name: Lung adenocarcinoma case ID 21

value: Female

value: Lung adenocarcinoma


title: lung_adenocarcinoma_23

source_name: Lung adenocarcinoma case ID 23


title: lung_adenocarcinoma_24

source_name: Lung adenocarcinoma case ID 24


title: lung_adenocarcinoma_22

source_name: Lung adenocarcinoma case ID 22


title: DKO replicate 1

description:
DKO-1
replicate 1

label_protocol: Standard Illumina hybridization protocol


title: HCT116 replicate 3

description:
HCT116-3
replicate 3

source_name: HCT116 cells

value: control


title: HCT116 replicate 2

description:
HCT116-2
replicate 2


title: Mouse_ear_skin_LEC_inflamed_rep2

value: FVB

value: female

value: 8 weeks


title: HCT116 replicate 1

description:
HCT116-1
replicate 1


title: lung_adenocarcinoma_16

source_name: Lung adenocarcinoma case ID 16


title: lung_adenocarcinoma_14

source_name: Lung adenocarcinoma case ID 14


title: DKO replicate 2

description:
DKO-2
replicate 2


title: Mouse_ear_skin_LEC_untreated_rep3

value: ear skin

value: lymphatic endothelial cells


title: lung_adenocarcinoma_17

source_name: Lung adenocarcinoma case ID 17


title: lung_adenocarcinoma_12

source_name: Lung adenocarcinoma case ID 12


title: Mouse_ear_skin_LEC_inflamed_rep3

value: healthy, CHS inflamed

value: FACS


title: Mouse_ear_skin_LEC_untreated_rep2

value: healthy, untreated


title: lung_adenocarcinoma_18

source_name: Lung adenocarcinoma case ID 18


title: Mouse_ear_skin_LEC_inflamed_rep1

value: 9 weeks


title: lung_adenocarcinoma_10

source_name: Lung adenocarcinoma case ID 10


title: lung_adenocarcinoma_8

source_name: Lung adenocarcinoma case ID 8

source_name: Human universal reference RNA from Ambion®


title: Mouse_ear_skin_LEC_untreated_rep1


title: lung_adenocarcinoma_13

source_name: Lung adenocarcinoma case ID 13


title: DON treated stationary phase rep1

type: mixed

city: Norwich

first: Neil

last: Shearer

state: Norfolk

address: Colney Lane

department: Gut Health and Food Safety

country: United Kingdom

institute: Institute of Food Research

hyb_protocol: see Kelly et al. Microbiology 2004

scan_protocol: Axon GenePix4000A 10 µm resolution scan and see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

data_processing: Intensity ratios of channel 1 (cDNA) divided bu channel 2 (reference gDNA) signals are calculated usiong BlueFuse 3.01 (BlueGnome, Cambridge, UK). Data centering was subsequently performed using the block median

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: S. Typhimurium DON treated stationary phase

label_protocol: see Kelly et al. Microbiology 2004

growth_protocol: Stationary phase cultures were obtained by aerated, overnight culture at 37 °C in 5 mL LB in 50 mL flasks. To obtain highly invasive late logarithmic culture, 2 µL of a stationary phase culture was inoculated in 5 mL LB and grown for 5 hours at 37 °C without aeration

extract_protocol: see Kelly et al. Microbiology 2004

treatment_protocol: DON treated cultures contain 0.250 µg/mL of Deoxynivalenol

tag: growth phase

value: stationary

tag: treatment

value: Deoxynivalenol

source_name: S. typhimurium genomic DNA


title: DON treated stationary phase rep2


title: lung_adenocarcinoma_7

source_name: Lung adenocarcinoma case ID 7

value: Male


title: DON treated stationary phase rep3


title: lung_adenocarcinoma_6

source_name: Lung adenocarcinoma case ID 6

value: universal reference RNA was made by pooling contents of FirstChoice total RNA panel that is made of RNA from different tissues of multiple individuals,  Ambion, Austin, TX, USA; catalog no. AM6000


title: Untreated stationary phase rep3

source_name: S. Typhimurium untreated stationary phase

value: untreated


title: lung_adenocarcinoma_4

source_name: Lung adenocarcinoma case ID 4

value: Mixed


title: Untreated stationary phase rep2


title: DON Treated log phase rep2

source_name: S. Typhimurium DON treated log phase

value: log


title: Untreated stationary phase rep1


title: DON Treated log phase rep3


title: DON Treated log phase rep1


title: lung_adenocarcinoma_5

source_name: Lung adenocarcinoma case ID 5

value: Lung adenocarcinoma


title: lung_adenocarcinoma_3

source_name: Lung adenocarcinoma case ID 3


title: lung_adenocarcinoma_2

source_name: Lung adenocarcinoma case ID 2


title: lung_adenocarcinoma_1

source_name: Lung adenocarcinoma case ID 1

value: Female


title: Untreated log phase rep3

source_name: S. Typhimurium untreated log phase


title: Lsh+/+ (WT) Set38

status: Public on May 19 2011

city: Frederick

first: Jigui

last: Shan

address: 430 Miller Dr

institute: NCI-Frederick

description: CHIP_ID: 10453602

hyb_protocol: Pool and hybridize the samples to the array using a NimbleGen Hybridization Kit and NimbleGen Hybridization System 4 or 12.

scan_protocol: Scan the array using the 2-μm, high-resolution NimbleGen MS 200 Microarray Scanner

data_processing:
Analyze the data using NimbleScan software and visualize your MeDIP-chip results using SignalMap software.

Analysis on chromosomes X, Y, M is incomplete (GFF data not supplied for this sample).

source_name: Lsh+/+ test sample

label_protocol: Label the immunoprecipitated (IP) and Input DNA samples with Cy3 and Cy5 respectively, using the NimbleGen Dual-Color DNA Labeling Kit.

growth_protocol: Lsh+/+ mouse embryonic fibroblast cell lines were grown in DMEM (Invitrogen/GIBCO) supplemented with 10% fetal bovine serum, 2 mM L-glutamine and antibiotics (Invitrogen/GIBCO).

extract_protocol: Methylated DNA was extracted with MeDIP  followed by hybridization to NimbleGen Arrays.Genomic DNA of WT (Lsh+/+) or Lsh−/− MEFs (32) was sonicated into fragments (300–1,000 bp), precipitated with anti-5-methylcytidine (Eurogentec), as previously described (12, 26), and DNA pooled for whole genome array hybridization (NimbleGen Service Laboratory). The murine whole-genomic array contains about 13 × 106 probes with a resolution of one 50-mer probe for every 100-bp region. Data were extracted from scanned images by using NimbleScan 2.3 extraction

treatment_protocol: Genomic DNA of WT (Lsh+/+) MEFs (32) was sonicated into fragments (300–1,000 bp), precipitated with anti-5-methylcytidine (Eurogentec), as previously described (12, 26), and DNA pooled for whole genome array hybridization (NimbleGen Service Laboratory). The murine whole-genomic array contains about 13 × 106 probes with a resolution of one 50-mer probe for every 100-bp region. Data were extracted from scanned images by using NimbleScan 2.3 extraction software. Cytosine methylation enrichment was evaluated using normalized log2 ratio intensity values (the ratio of the MeDIP to the input sample) and then −log10 P values from one-sided Kolmogorov-Smirnov tests performed to determine if probes displayed a significantly more positive distribution over the rest of the array. For details of the MM8 tiling array and calculation of data, please refer to www.nimblegen.com. Data calculation and detailed methods are found in SI Materials and Methods.

tag: cell type

value: Mouse embryonic fibroblast

tag: antibody

value: anti-5-methylcytidine (Eurogentec)

source_name: Lsh+/+ reference sample

value: none (input)


title: Untreated log phase rep2


title: B6 BMM infected with PA7 MOI4

city: Cambridge

first: Kenneth

last: Hu

state: MA

address: 31 Ames Street

department: Biology

institute: Massachusetts Institute of Technology

description:
PA7-MOI4_AA440
Gene expression data from B6 bone marrow-derived macrophages infected with MOI4 PA7 for 18 hrs.

hyb_protocol: Followed Affymetrix instructions.

scan_protocol: Scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. We normalized such that the median intensity value was 500. We then set the minimum intensity to be 50.

source_name: B6 BMM infected with PA7 for 18hrs at MOI4

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

growth_protocol: BMMs were plated at 3x10^6 cells per well in 6-well plates. They were incubated 6-7 days after harvesting.

treatment_protocol: BMMs were infected with parasite strains at the indicated Multiplicity of Infection (MOI) for 18 hours before RNA harvesting.

value: bone marrow-derived macrophages

value: PA7 infection

tag: moi

tag: treatment duration

value: 18 hrs


title: B6 BMM uninfected

description:
uninfected B6_AA439
Gene expression data from uninfected B6 bone marrow-derived macrophages.

source_name: Uninfected B6 BMM

value: uninfected


title: Lsh-/- (KO) Set38

description: CHIP_ID: 10441702

source_name: Lsh-/- test sample

growth_protocol: Lsh-/- mouse embryonic fibroblast cell lines were grown in DMEM (Invitrogen/GIBCO) supplemented with 10% fetal bovine serum, 2 mM L-glutamine and antibiotics (Invitrogen/GIBCO).

treatment_protocol: Genomic DNA of WT Lsh−/− MEFs (32) was sonicated into fragments (300–1,000 bp), precipitated with anti-5-methylcytidine (Eurogentec), as previously described (12, 26), and DNA pooled for whole genome array hybridization (NimbleGen Service Laboratory). The murine whole-genomic array contains about 13 × 106 probes with a resolution of one 50-mer probe for every 100-bp region. Data were extracted from scanned images by using NimbleScan 2.3 extraction software. Cytosine methylation enrichment was evaluated using normalized log2 ratio intensity values (the ratio of the MeDIP to the input sample) and then −log10 P values from one-sided Kolmogorov-Smirnov tests performed to determine if probes displayed a significantly more positive distribution over the rest of the array. For details of the MM8 tiling array and calculation of data, please refer to www.nimblegen.com. Data calculation and detailed methods are found in SI Materials and Methods.

source_name: Lsh-/- reference sample


title: Untreated log phase rep1

source_name: S. typhimurium genomic DNA


title: B6 BMM infected with PA7 Δgra15 MOI2

description:
PA7-JLP2KO MOI2_AA443
Gene expression data from B6 bone marrow-derived macrophages infected with MOI2 PA7 with gra15 KO for 18 hrs.

source_name: B6 BMM infected with PA7 Δgra15 for 18hrs at MOI2

value: PA7 Δgra15 infection


title: B6 BMM infected with PA7 Δgra15 + ROP16I MOI4

description:
PA7JLP2KO+ROP16I MOI4_AA442
Gene expression data from B6 bone marrow-derived macrophages infected with MOI4 PA7 with gra15 KO and type I ROP16 for 18 hrs.

source_name: B6 BMM infected with PA7 Δgra15+ROP16I for 18hrs at MOI4

value: PA7 Δgra15 + ROP16I infection


title: B6 BMM infected with PA7+ROP16I MOI4

description:
PA7+ROP16I MOI4_AA441
Gene expression data from B6 bone marrow-derived macrophages infected with MOI4 PA7+type I ROP16 gene for 18 hrs.

source_name: B6 BMM infected with PA7+ROP16I for 18hrs at MOI4

value: PA7+ROP16I infection


title: Lsh+/+ (WT) Set37

description: CHIP_ID: 10428102

data_processing:
Analyze the data using NimbleScan software and visualize your MeDIP-chip results using SignalMap software.

Analysis on chromosomes X, Y, M is incomplete (GFF data is partial).


title: lung_adenocarcinoma_11

source_name: Lung adenocarcinoma case ID 11

tag: gender

tag: disease

source_name: Human universal reference RNA from Ambion®

tag: sample type


title: Lsh-/- (KO) Set37

description: CHIP_ID: 11003402


title: Highly bone metastatic subline of HARA

city: Fukuoka

first: Soichi

last: Takiguchi

address: 3-1-1 Notame, Minami-ku

country: Japan

institute: National Kyushu Cancer Center

description: Gene expression data from a highly bone metastatic subline, HARA-B4

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Affymetrix GeneChip Command Console and normalized with Affymetrix Expression Console.

source_name: bone-seeking squamous lung cancer cell line (HARA-B4)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: HARA and HARA-B4 were cultured in RPMI 1640 medium (Invitrogen, Carlsbad, CA) supplemented with 10% FBS and 50 units/ml of penicillin and streptomycin in humidified atmosphere under 5% CO2 at 37˚C.

extract_protocol: Total RNA was extracted from HARA and HARA-B4 cells using the Qiagen RNeasy kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s protocol.

tag: cell line

tag: tissue

value: squamous cell lung cancer


title: Lsh-/- (KO) Set35

description: CHIP_ID: 10441402

data_processing: Analyze the data using NimbleScan software and visualize your MeDIP-chip results using SignalMap software.


title: Lsh-/- (KO) Set17

description: CHIP_ID: 10404902


title: Parental HARA

description: Gene expression data from human squamous cell lung cancer cell line, HARA

source_name: squamous cell lung cancer cell line (HARA)

value: HARA


title: Lsh-/- (KO) Set15

description: CHIP_ID: 10604102


title: Lsh-/- (KO) Set24

description: CHIP_ID: 11194002


title: Lsh+/+ (WT) Set31

description: CHIP_ID: 10447702


title: Lsh+/+ (WT) Set36

description: CHIP_ID: 10452802


title: Lsh-/- (KO) Set36

description: CHIP_ID: 10429502


title: Lsh-/- (KO) Set33

description: CHIP_ID: 10446502


title: Lsh-/- (KO) Set13

description: CHIP_ID: 10427702


title: Lsh+/+ (WT) Set24

description: CHIP_ID: 10434502


title: Lsh-/- (KO) Set22

description: CHIP_ID: 10627202


title: Lsh-/- (KO) Set20

description: CHIP_ID: 10404702


title: Lsh+/+ (WT) Set33

description: CHIP_ID: 10446602


title: Lsh+/+ (WT) Set06

description: CHIP_ID: 11037102


title: Lsh+/+ (WT) Set17

description: CHIP_ID: 10644102


title: Lsh-/- (KO) Set21

description: CHIP_ID: 10432502


title: Lsh-/- (KO) Set06

description: CHIP_ID: 10381102


title: Lsh+/+ (WT) Set34

description: CHIP_ID: 10434702


title: Lsh-/- (KO) Set31

description: CHIP_ID: 11051802


title: Lsh+/+ (WT) Set22

description: CHIP_ID: 10691702


title: Lsh+/+ (WT) Set13

description: CHIP_ID: 10988802


title: Lsh+/+ (WT) Set21

description: CHIP_ID: 10434802


title: Lsh+/+ (WT) Set20

description: CHIP_ID: 10441102


title: Lsh+/+ (WT) Set35

description: CHIP_ID: 10991302


title: Lsh-/- (KO) Set34

description: CHIP_ID: 10452602


title: Lsh+/+ (WT) Set15

description: CHIP_ID: 10994302


title: Lsh-/- (KO) Set08

description: CHIP_ID: 10430402


title: Lsh+/+ (WT) Set08

description: CHIP_ID: 10442802


title: Lsh-/- (KO) Set19

description: CHIP_ID: 10427302


title: Lsh-/- (KO) Set18

description: CHIP_ID: 6013702


title: Lsh-/- MEF

description: Gene expression data from Lsh-/- MEF cells.

hyb_protocol: Pool and hybridize the samples to the array using the mouse genome 430 2.0 array (Affymetrix, Inc.),

data_processing: Data were analyzed using the robust multiarray average using a custom chip definition file (v14) mapping to RefSeq genes.

source_name: Lsh-/- (KO)

label_protocol: Complementary DNA generated from Lsh−/− and WT MEF cell lines was hybridized on the mouse  genome 430 2.0 array (Affymetrix, Inc.), which consists of more than 39,000 probes.

growth_protocol: Lsh-/- and Lsh+/+ mouse embryonic fibroblasts (MEF) were generated as described previously (Fan et al, 2003) and grown in DMEM (Invitrogen/GIBCO) supplemented with 10% fetal bovine serum, 2 mM L-glutamine and antibiotics (Invitrogen/GIBCO).

treatment_protocol: Total RNA was extracted from  WT (Lsh+/+) or Lsh−/− MEFs cells and converted into cDNA with reverse transcription.


title: Lsh-/- (KO) Set02

description: CHIP_ID: 10426802


title: Lsh+/+ (WT) Set18

description: CHIP_ID: 10648502


title: Lsh+/+ (WT) Set19

description: CHIP_ID: 10452402


title: Lsh+/+ MEF

description: Gene expression data from Lsh+/+ MEF cells.

source_name: Lsh+/+ (WT)


title: Lsh-/- (KO) Set01

description: CHIP_ID: 10429402


title: Lsh-/- (KO) Set28

description: CHIP_ID: 10430002


title: Lsh-/- (KO) Set03

description: CHIP_ID: 10366902


title: Lsh+/+ (WT) Set02

description: CHIP_ID: 10436802


title: Lsh+/+ (WT) Set10

description: CHIP_ID: 10988602


title: Lsh-/- (KO) Set09

description: CHIP_ID: 10981302


title: Lsh+/+ (WT) Set04

description: CHIP_ID: 10434302


title: Lsh+/+ (WT) Set03

description: CHIP_ID: 10671702


title: Lsh-/- (KO) Set27

description: CHIP_ID: 10434102


title: Lsh+/+ (WT) Set01

description: CHIP_ID: 10444902


title: Lsh+/+ (WT) Set29

description: CHIP_ID: 10418602


title: Lsh-/- (KO) Set11

description: CHIP_ID: 11193402


title: Lsh-/- (KO) Set29

description: CHIP_ID: 10637402


title: Lsh-/- (KO) Set10

description: CHIP_ID: 10980702


title: Lsh+/+ (WT) Set28

description: CHIP_ID: 10474802


title: Lsh-/- (KO) Set16

description: CHIP_ID: 10636302


title: Lsh+/+ (WT) Set11

description: CHIP_ID: 10980402


title: Lsh+/+ (WT) Set26

description: CHIP_ID: 10644402


title: Lsh-/- (KO) Set12

description: CHIP_ID: 10451902


title: Lsh-/- (KO) Set26

description: CHIP_ID: 10434202


title: Lsh+/+ (WT) Set27

description: CHIP_ID: 10981102


title: Lsh+/+ (WT) Set14

description: CHIP_ID: 10980602


title: Lsh+/+ (WT) Set09

description: CHIP_ID: 10447902


title: CNP-hEGFR SVZ tissue

city: Washington

first: Vittorio

last: Gallo

state: DC

address: 111 Michigan Av. NW

department: Center for Neuroscience

institute: CNMC

hyb_protocol: 1ug of cRNA was used for hybridization with the Genearray. Incubation was performed for 12hrs at 60C shaking at 500rpm.

scan_protocol: The arrays were exposed at different time points starting for 1 min and maximum of 10 min to have the largest possible dynamic range for the individual signals and images acquire using x-ray film.  X-ray film were scanned and save as TIFF file format.

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities and ratios of CNP-hEGFR vs. WT were calculated after values were normalizing for each gene.

label: Biotin UTP

source_name: CNP-hEGFR SVZ tissue

growth_protocol: RNA was isolated from 300um fresh brain sections at the level of the SVZ and SVZ was microdissected and used for RNA extraction using Trizol (Invitrogen).

extract_protocol: 1ug of total RNA was reverse-transcribed using oligo-dT primers (Superarray) and reverse transcriptase (Superarray) to perform cDNA. Then cRNA synthesis was performed using the total cDNA reaction in the presence of 10 mM of Biotinylated-UTP (Perlin Elmer) and RNA polymerase according to the instructions for the Gene

value: brain subventricular zone (SVZ)

value: CNP-hEGFR

value: Post natal day 8


title: Lsh+/+ (WT) Set12

description: CHIP_ID: 10447802

source_name: Lsh+/+ test sample


title: Lsh-/- (KO) Set07

description: CHIP_ID: 10396302


title: WT SVZ tissue

source_name: WT SVZ tissue

label_protocol: cRNA synthesis was performed using the total cDNA reaction in the presence of 10 mM of Biotinylated-UTP (Perlin Elmer) and RNA polymerase according to the instructions for the Gene

value: wild-type


title: Mac-1(+) monocytes/macrophages, biological replicate 2

city: Tokyo

first: Hitoshi

last: Ichikawa

address: 5-1-1 Tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

description: Mac-1(+) monocytes/macrophages purified by cell sorting

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45˚C on GeneChip Mouse Genome 430 2.0 Array (Affymetrix). Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Softwere version 1.4 (GCOS1.4, Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: Mac-1(+) monocytes/macrophages

label_protocol: Biotinylated cRNA were prepared from the purified total RNA equivalent to 3,000 cells with a Two-Cycle cDNA Synthesis Kit and 3'-Amplification Reagents for IVT Labeling (Affymetrix).

extract_protocol: Total RNA was isolated using an ISOGEN reagent (Nippon Gene).

value: Mac-1(+) monocytes/macrophages

tag: genetic background


title: Lsh-/- (KO) Set14

description: CHIP_ID: 10427002

value: Mouse embryonic fibroblast


title: Gr-1(+) neutrophils, biological replicate 2

description: Gr-1(+) neutrophils purified by cell sorting

source_name: Gr-1(+) neutrophils

value: Gr-1(+) neutrophils


title: Ter119(+) erythroblasts, biological replicate 2

description: Ter119(+) erythroblasts purified by cell sorting

source_name: Ter119(+) erythroblasts

value: Ter119(+) erythroblasts


title: Lsh+/+ (WT) Set07

description: CHIP_ID: 10436902

value: anti-5-methylcytidine (Eurogentec)

source_name: Lsh+/+ reference sample

value: none (input)


title: Lsh-/- (KO) Set05

description: CHIP_ID: 10433802

source_name: Lsh-/- test sample

source_name: Lsh-/- reference sample


title: Gr-1(+) neutrophils, biological replicate 1


title: Mac-1(+) monocytes/macrophages, biological replicate 1


title: NK1.1+ NK cells, biological replicate 2

description: NK1.1+ NK cells purified by cell sorting

source_name: NK1.1+ NK cells

value: NK1.1+ NK cells


title: Lsh+/+ (WT) Set05

description: CHIP_ID: 10452502


title: NK1.1+ NK cells, biological replicate 1


title: Lsh+/+ (WT) Set25

description: CHIP_ID: 10437002


title: Lsh+/+ (WT) Set32

description: CHIP_ID: 10431402


title: Lsh+/+ (WT) Set30

description: CHIP_ID: 10448202


title: CD3ε(+)NK1.1(+) NKT cells, biological replicate 2

description: CD3ε(+)NK1.1(+) NKT cells purified by cell sorting

source_name: CD3ε(+)NK1.1(+) NKT cells

value: CD3ε(+)NK1.1(+) NKT cells


title: Ter119(+) erythroblasts, biological replicate 1


title: Lsh-/- (KO) Set30

description: CHIP_ID: 10985302


title: Lsh-/- (KO) Set32

description: CHIP_ID: 10994702


title: Lsh-/- (KO) Set04

description: CHIP_ID: 10434602


title: CD3ε(+)NK1.1(+) NKT cells, biological replicate 1


title: CD8(+) T lymphocytes, biological replicate 1

description: CD8(+) T lymphocytes purified by cell sorting

source_name: CD8(+) T lymphocytes

value: CD8(+) T lymphocytes


title: Lsh-/- (KO) Set25

description: CHIP_ID: 10429702


title: CD8(+) T lymphocytes, biological replicate 2


title: CD4(+) T lymphocytes, biological replicate 2

description: CD4(+) T lymphocytes purified by cell sorting

source_name: CD4(+) T lymphocytes

value: CD4(+) T lymphocytes


title: CD4(+) T lymphocytes, biological replicate 1


title: B220(+) B lymphocytes, biological replicate 1

description: B220(+) B lymphocytes purified by cell sorting

source_name: B220(+) B lymphocytes

value: B220(+) B lymphocytes


title: B220(+) B lymphocytes, biological replicate 2


title: 90

city: New York

first: Yupu

last: Liang

address: 1230 York Avenue

institute: The Rockefeller University

description: Gene expression data from MPM tumors.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Human U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data is normalized through the RMA method with default parameters using Bioconductor.

source_name: Mesothelioma tumor, epi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

extract_protocol: RNA was extracted using the Qiagen RNeasy plus mini kit according to the manufacturer's instructions.

value: malignant pleural mesothelioma (MPM)

tag: subtype

value: epi


title: 89

description: Gene expression data from MPM tumors.


title: 91

description: Gene expression data from MPM tumors.


title: 92

description: Gene expression data from MPM tumors.

source_name: Mesothelioma tumor, biphasic

value: biphasic


title: Lsh-/- (KO) Set23

description: CHIP_ID: 10410502


title: 97

description: Gene expression data from MPM tumors.

source_name: Mesothelioma tumor, sarc

value: sarc


title: 8

description: Gene expression data from MPM tumors.


title: Lsh+/+ (WT) Set23

description: CHIP_ID: 10452902


title: KSL cells, biological replicate 2

description: KSL cells purified by cell sorting

source_name: KSL cells

value: KSL cells


title: 99

description: Gene expression data from MPM tumors.


title: KSL cells, biological replicate 1

description: KSL cells purified by cell sorting


title: Lineage marker(-) cells, biological replicate 2

description: Lineage marker(-) cells purified by cell sorting

source_name: Lineage marker(-) cells

value: Lineage marker(-) cells


title: Lineage marker(-) cells, biological replicate 1


title: Lsh+/+ (WT) Set16

description: CHIP_ID: 10455602

source_name: Lsh+/+ test sample


title: CD34(+)KSL multipotent progenitors, biological replicate 1

description: CD34(+)KSL multipotent progenitors purified by cell sorting

source_name: CD34(+)KSL multipotent progenitors

value: CD34(+)KSL multipotent progenitors


title: CD34(+)KSL multipotent progenitors, biological replicate 2


title: 71

description: Gene expression data from MPM tumors.


title: CD34(-)KSL hematopoietic stem cells, biological replicate 2

description: CD34(-)KSL hematopoietic stem cells purified by cell sorting

source_name: CD34(-)KSL hematopoietic stem cells

value: CD34(-)KSL hematopoietic stem cells


title: 76

description: Gene expression data from MPM tumors.


title: 73

description: Gene expression data from MPM tumors.


title: CD34(-)KSL hematopoietic stem cells, biological replicate 1


title: 79

description: Gene expression data from MPM tumors.


title: Rad21 esiRNA, biological rep3

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

country: Germany

institute: Technische Universität Dresden

description: Gene expression data from mouse ESC after 48h RNAi against Rad21

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Mouse 430 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were normalized with GC-RMA method using Partek Genomics Suite 6.4 (6.09.0129). Properties: quantile normalizytion, GCRMA background correction, median polish probe set summarization

source_name: R1/E ESC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNeasy Mini Kit protocol including DNaseI digest

treatment_protocol: R1/E ES cells were reversely transfected in a 12well plate using 800ng esiRNA and 2ul Lipofectamine2000 (Invitrogen) and 80000cells/well. Procedure according to manufacture's protocol

value: R1/E ESC

tag: RNAi


title: Rad21 esiRNA, biological rep4


title: 69

description: Gene expression data from MPM tumors.


title: 7

description: Gene expression data from MPM tumors.


title: Rad21 esiRNA, biological rep1


title: 78

description: Gene expression data from MPM tumors.


title: Luc control esiRNA, biological rep4

description: Gene expression data from mouse ESC after 48h RNAi against Luciferase

value: Luciferase


title: 59

description: Gene expression data from MPM tumors.


title: 53

description: Gene expression data from MPM tumors.


title: 58

description: Gene expression data from MPM tumors.


title: 6

description: Gene expression data from MPM tumors.


title: 62

description: Gene expression data from MPM tumors.


title: 61

description: Gene expression data from MPM tumors.


title: Rad21 esiRNA, biological rep2


title: Gr1/Mac1_rep2

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

institute: University of Gothenburg

description: All arrays were performed at British Columbia Genome Sciences Centre, Vancouver, BC, Canada.

hyb_protocol: Hybridization was done on the Affymetrix GeneChip Mouse430 2.0 microarray according to manufacturer’s instructions. Protocol EukGE-WS2v5 Wash A1 Recovery Mixes 0 Wash A1 Temperature (C) 30 Number of Wash A1 Cycles 10 Mixes per Wash A1 Cycle 2 Wash B Recovery Mixes 0 Wash B Temperature (C) 50 Number of Wash B Cycles 6 Mixes per Wash B Cycle 15 Stain Temperature (C) 35 First Stain Time (seconds) 300 Wash A2 Recovery Mixes 0 Wash A2 Temperature (C) 30 Number of Wash A2 Cycles 10 Mixes per Wash A2 Cycle 4 Second Stain Time (seconds) 300 Third Stain Time (seconds) 300 Wash A3 Recovery Mixes 0 Wash A3 Temperature (C) 35 Number of Wash A3 Cycles 15 Mixes per Wash A3 Cycle 4 Holding Temperature (C) 25

scan_protocol: Pixel Size 1.56 Filter 570 Scan Temperature Scanner ID 50206370 Number of Scans 1 Scanner Type M10

data_processing: Data were processed using MAS5 with default setting with GCOS 1.3.0.

source_name: Bone marrow

label_protocol: The labeling was done according to the manufacturer instructions.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen), and RNA quality was assessed using the Bioanalyzer 2100 (Agilent Technologies, Mississauga, ON).

treatment_protocol: Bone marrow cells were harvested from mice treated with 150 mg of 5-fluorouracil/kg 4 days before harvest  and stimulated for 48 hours in Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL of human interleukin-6 (hIL-6), 6 ng/mL of murine interleukin-3 (mIL-3), and 20 ng/mL of murine stem cell factor (mSCF; all from StemCell Technologies Inc., Vancouver, Canada). MN1 was introduced into bone marrow cells by cocultivation with irradiated (4,000 cGy) GP+ E86 viral producer cells in the presence of 5 µg/mL protamine sulfate (Sigma-Aldrich, Oakville, Canada). Cells were then sorted for GFP expression and maintained in 6 ng/ml mIL-3, 10 ng/ml hIL-6, and 20 ng/ml mSCF. The transduced bone marrow cells from C57BL/6J mice were then injected into the tail vein of lethally irradiated syngeneic recipient mice that were exposed to a single dose of 750 cGy total-body irradiation accompanied by a life-sparing dose of 1 x 105 freshly isolated bone marrow cells from syngeneic mice. Donor chimerism was monitored by tail vein bleeds and FACS analysis of GFP expressing cells every four weeks. We have showed at the single cell level that CMPs, but not GMPs, are susceptible to MN1-induced transformation. To identify transcriptional differences between CMPs and GMPs that may explain this difference in susceptibilities to MN1 transformation we produced gene expression profiles of bone marrow cells from MN1 leukemic mice and mature myeloid bone marrow cells (Gr1+/CD11b+) from healthy mice and compared those to already published gene expression profiles of CMPs and GMPs (Krivtsov, A.V., et al. (2006). Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9. Nature 442, 818-822).

value: Bone marrow

tag: strain

tag: location

value: bred and maintained in the animal research center of the British Columbia Cancer Agency, Vancouver, BC, Canada


title: Luc control esiRNA, biological rep2

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


title: Luc control esiRNA, biological rep3


title: Luc control esiRNA, biological rep1


title: MN1 leukemic_rep2

value: MN1 leukemic


title: Gr1/Mac1_rep1


title: 46

description: Gene expression data from MPM tumors.


title: 44

description: Gene expression data from MPM tumors.


title: 4

description: Gene expression data from MPM tumors.


title: 49

description: Gene expression data from MPM tumors.