title: Whole sprouts 5 cm long, replicate 1

organism: Glycine max

source_name: Whole sprouts_5 cm long

label_protocol: RNA was amplified and labeled with Cy3 using Agilent’s Low Input Quick Amp WT Labeling Kit according to the manufacturer’s instruction.

growth_protocol: Soybean seeds (5g) were soaked in 200 ml of distilled water for 16 h and shaken every 60 min. The hydrated seeds were placed in germination trays where a wet laboratory paper was extended, and were then covered. The trays were introduced into the germination machine, QFR-A801 model (Zhejiang XingDa Co.Ltd) and spray thrower was in contact with the circulating water of the germinator; therefore seeds were always wet by spray. Germination processes were carried out at 25℃, at 99% relative humidity and in darkness. At 0.5 and 5 cm long, the germinated soybean sprouts (whole) were collected and harvested

extract_protocol: Total RNA from whole soybean sprouts about 0.5 cm long and about 5 cm long, respectively, was extracted using Trizol reagent (Invitrogen, Gaithersburg, MD) according to the manufacturer’s instructions.

tag: variety

value: Hebei province (Maoyan black soybean)

value: whole sprouts

tag: sprout length

value: 5 cm long


title: MLL_DX-1

status: Public on Aug 10 2012

type: RNA

city: chicago

first: chunjiang

last: he

state: il

address: 900 east 57th st

country: USA

institute: university of chicago

hyb_protocol: The RNA quality control, cRNA amplification, hybridization, and image scan were conducted in the Functional Genomics Facility of University of Chicago

scan_protocol: Affymetrix Genechip human Exon 1.0 ST

data_processing:
Partek was used to do Robust Multi-array Average (RMA) nomalization, which is a robust algorithm of background-adjustment, quantile normalization, and log-transformation. Probes which cannot annotated with refseq genes are filtered out.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: primary untreated leukemia

growth_protocol: All of the AML patient samples were obtained at the time of diagnosis or relapse and with informed consent at the University of Chicago Hospital (UCH) or other collaborative hospitals, and were approved by the institutional review board of the institutes/hospitals.

tag: sample type

value: MLL-associated samples

tag: karyotype

value: MLL-ENL

tag: abnormality


title: leukemia BM1_Control_P1

scan_protocol: Affymetrix GeneChip Mouse Gene 1.0 ST

data_processing: The quantified signals were normalized using Robust Multi-array Average (RMA), which is a robust algorithm of background-adjustment, quantile normalization, and log-transformation. Partek Genomics Suite (Partek Inc., St. Louis, MI) was used for the analysis of the normalized data. Then mediancentering genes for each array and median-centering each gene across all arrays were also conducted for heatmap illustration

organism: Mus musculus

label_protocol: The RNA quality control, cRNA amplification, hybridization, and image scan were conducted in the Functional Genomics Facility of University of Chicago

treatment_protocol: A total of 24 mouse bone marrow samples including 9 primary (including 3 each of negative control, MLL-AF9, and miR-196b+MLL-AF9) and 15 secondary (including 3 negative control, 6 MLL-AF9, and 6 miR-196b+MLL-AF9) obtained from the in vivo mouse bone marrow

tag: strain background

tag: tissue

value: leukemic bone marrow

tag: tissue type

value: primary_negative control


title: Whole sprouts 5 cm long, replicate 4

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

hyb_protocol: According to the instructions of Agilent Gene Expression Hybridization Kit.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).Agilent GeneSpring GX 11.5 was used for background subtraction and LOWESS normalization.


title: Whole sprouts 5 cm long, replicate 3


title: Whole sprouts 5 cm long, replicate 2


title: MLL_DX-5

extract_protocol: The RNA quality control, cRNA amplification, hybridization, and image scan were conducted in the Functional Genomics Facility of University of Chicago


title: UN_0h_2

city: Heidelberg

first: Doreen

last: Heckmann

country: Germany

institute: DKFZ

description:
replicate 2
UN_0h_2

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes. After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430. Data extraction was done for all beads individually, and outliers are removed when > 2.5 MAD (median absolute deviation). All remaining data points are used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated.

data_processing:
The data were normalised using quantile normalization with JMP Genomics (v.4.0).
quantile normalized (columns 'value' and 'exp'). Data for each sample are shown in five colomns. The first two columns (Value and detection_pval) were originated from Illumina software; the mean and n columns indicate the mean signal and the number of beads; exp shows the log2 transformed product by multiplying mean and n.

label_protocol: Biotin-labeled cRNA samples for hybridization on Illumina Human Sentrix-8 BeadChip arrays (Illumina, Inc.) were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine J. et al., 1992). In brief, 250 ng total RNA was used for complementary DNA (cDNA) synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA according to the MessageAmp II aRNA Amplification kit (Ambion, Inc., Austin, TX). Biotin-16-UTP was purchased from Roche Applied Science, Penzberg, Germany. The cRNA was column purified according to TotalPrep RNA Amplification Kit, and eluted in 60 µl of water. Quality of cRNA was controlled using the RNA Nano Chip Assay on an Agilent 2100 Bioanalyzer and spectrophotometrically quantified (NanoDrop).

growth_protocol: The colon cancer cell line SW480 was grown in RPMI supplemented with 10 % fetal calf serum, penicillin (100 IU/ml) and streptomycin (100 µg/ml) at 37 °C in a humified atmosphere containing 5 % CO2. Lentiviral overexpression of CXCR4 and CXCR7 was established by transduction of SW480 cells and flow cytometric sort as described in Heckmann D. et al., 2011.

extract_protocol: Total RNA was extracted RNeasy Mini Kit, according to the manufacturer’s instructions.

treatment_protocol: SW480Wildtype, SW480CXCR4, SW480CXCR7, and SW480CXCR4/CXCR7 cells were exposed to 100 ng/ml SDF-1α for 3 and 12 h.

tag: gender

value: male

tag: cell line

tag: cell type

value: colon cancer cells

value: tumor

tag: tumor stage

value: Dukes' type B

tag: genotype/variation

value: SW480Wildtype=UN (untransduced)

tag: exposed to

value: PBS


title: t(4;11)_KOCL69

source_name: leukemia cell line


title: MLL_DX-3


title: Whole sprouts 0.5 cm long, replicate 4

source_name: Whole sprouts_0.5 cm long

value: 0.5 cm long


title: UN_0h_1

description:
replicate 1
UN_0h_1


title: Whole sprouts 0.5 cm long, replicate 3


title: Hoolock_poolD

type: genomic

city: Beaverton

first: Lucia

last: Carbone

state: Oregon

address: 505 NW 185th ave

institute: Oregon Health & Science University

hyb_protocol: Test and reference samples were mixed with 120 µg human Cot-1 DNA, co-precipitated and resuspended in 120 µl of a hybridization solution containing 50% formamide, 10% dextran sulfate, 2X SCC, 4% SDS and 10 µg/µl yeast tRNA. Overnight hybridization and post-hybridization washing procedures were performed using a GeneTac Hybridization Station

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4200AL fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.0 analysis software.

data_processing: Analysis and normalization were performed using GenePix 5.0

molecule: genomic DNA

organism: Hoolock leuconedys

source_name: Hoolock_sorted chromosomes

label_protocol: Five hundred nanogram of genomic DNA was labelled by random priming with Cy3-dUTP or Cy5-dUTP

extract_protocol: FACS sorting followed by Degenerate oligonucleotide-primed (DOP)-PCR

tag: dna source

value: FACS sorted chromosomes

tag: molecule subtype

value: DOP amplified DNA

source_name: Human reference DNA

extract_protocol: Reference DNA was isolated from blood obtained from an anonymous healthy male donor and used for all the hybridizations.

value: unidentified human reference


title: Whole sprouts 0.5 cm long, replicate 2

value: Hebei province (Maoyan black soybean)


title: Hoolock_poolC

value: blood obtained from an anonymous healthy male donor


title: E1 vs N1

city: Omaha

first: Parama

last: Dey

state: Nebraska

address: 985870 Nebraska Medical Center

department: Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

description: Biological replicate 1 of 3. Ecd knockdown vector transfected cells versus scrambled control cells

hyb_protocol: Amino Allyl MessageAmp II aRNA Amplification and Hybridization for Phalanx OneArray Slides protocol

scan_protocol: Images were quantified using GenePix software

data_processing: Methods/Results     Normalization of gene expression data was done using BRB ArrayTools developed by Dr. Richard Simon and Amy Peng (1).       Several filters and normalization were applied prior to analysis.       Median background was subtracted.    Intensity filter was applied: if both the red and green channels are below 100 intensity, the spot was set to missing, if only one of the channels was below 100 it was set at the threshold of 100.  Log2 transformation was applied to all ratios.  Normalization was then done to “center” each array using lowess smoother.  Genes were excluded if the percent of spots missing or filtered out exceeded 50%.  Empty spots and control spots have been excluded.  Duplicate spots have not been averaged and are treated as separate genes for analysis.     Random-variance paired t-tests were used to determine which genes are differentially expressed between tumor and the normal samples. The random-variance paired t-test allows sharing information among genes about variation without assuming that all genes have the same variance, which gives a more accurate estimate of the variability when sample sizes are small (2). A significance level of 0.05 combined with a 2-fold change was selected to help limit the false discovery rate due to multiple comparisons.       Results  After filtering and sub-setting the data, 18574 genes were left for analysis.   3574 genes were found to be significantly different between the tumor and normal groups at the 0.05 significance level. Of the 3574 significant genes 227 also had a 2-fold change.  These genes are presented in GSE39988_Analyzed_data_from_three_replicates_with_p-values.xls.gz  The file contains the original ranking by p-value from the 3574 significant genes, the unique ID, the gene symbol, the p-value, the mean expression in the ECD group, the mean expression in the control group (N), and the fold change of the ECD/N.  The genes have been sorted by original ranking of the p-value.    References  1.    BRB-Array Tools v3.1 developed by Dr. Richard Simon and Amy Peng Lam.     2.    Wright G.W. and Simon R. A random variance model for detection of differential gene expression in small microarray experiments. Bioinformatics 19:2448-2455,2003.

source_name: HPAF/CD18 Pancreatic cancer cells

growth_protocol: Generation of stable Ecd knockdown clones in HPAF/CD18 Pancreatic cancer cells : Ecd Scrambled and KD cells were generated by transfection of retroviral vector carrying either Scrambled or Ecd specific shRNA into phoenix cells (packaging cells) using lipofectamine 2000 (Invitrogen) following manufacturer’s protocol. Viral supernatant collected from phoenix cells 48 hours post-transfection was used to infect CD18/HPAF pancreatic cancer cells followed by selection with Puromycin (5μg/ml). Selected cells were maintained in 10% DMEM containing puromycin (3μg/ml). The knockdown of Ecd was verified at mRNA level using quantitative Real-time PCR analysis and protein level by Immunoblotting using monoclonal Ecd antibody.

extract_protocol: Both CD18 Scrambled control and CD18 Ecd KD cells were seeded in triplicate and RNA was isolated using Ambion Kit after 48 hours. The RNA quality was first checked by Nanodrop Spectrophotometer followed by BioAnalyzer. The RNA thus collected was submitted for Microarray analysis, protocol for which is submitted in a separate file.

tag: transfection

value: Ecd knockdown vector

source_name: Total RNA from pooled population of HPAF/CD18 Scr cells

value: Scrambled control


title: Whole sprouts 0.5 cm long, replicate 1

tag: variety

value: whole sprouts


title: Hoolock_poolE


title: E3 vs N3

description: Biological replicate 3 of 3. Ecd knockdown vector transfected cells versus scrambled control cells

label_protocol: Amino Allyl MessageAmp II aRNA Amplification and Hybridization for Phalanx OneArray Slides protocol


title: Hoolock_poolA


title: E2 vs N2

description: Biological replicate 2 of 3. Ecd knockdown vector transfected cells versus scrambled control cells


title: SK-N-MC 50nM rotenone 4week rep3

status: Public on Aug 09 2012

city: Los Angeles

first: Yofre

last: Cabeza-Arvelaiz

state: California

address: 650 Charles E. Young Drive South

department: Pathology and Environmental Health Sciences

institute: University of California, Los Angeles

description: Gene expression data from neuroepithelioma SK-N-MC cells, grown for 4 weeks with 50 nM  rotenone

hyb_protocol: After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip®  HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.

data_processing: The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),

source_name: Neuroepithelioma SK-N-MC cells, exposed to 50 nM rotenone for 4 week

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).

growth_protocol: Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen).  As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.

extract_protocol: Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).

treatment_protocol: Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol).  The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells

value: SK-N-MC

tag: treatment

value: 50nM rotenone

tag: time

value: 4 week


title: Hoolock_poolB

tag: sample type


title: SK-N-MC 5nM rotenone 4week rep3

description: Gene expression data from neuroepithelioma SK-N-MC cells, grown for 4 weeks with 5 nM  rotenone

source_name: Neuroepithelioma SK-N-MC cells, exposed to 5 nM rotenone for 4 week

value: 5nM rotenone


title: SK-N-MC 50nM rotenone 4week rep1


title: SK-N-MC 0nM rotenone 4week rep1

description: Gene expression data from neuroepithelioma SK-N-MC cells, grown for 4 weeks without  rotenone

source_name: Neuroepithelioma SK-N-MC cells, not exposed to rotenone, 4 week

value: 0nM rotenone


title: SK-N-MC 0nM rotenone 4week rep3


title: SK-N-MC 5nM rotenone 4week rep2


title: MLL_DX-6

value: MLL-associated samples

tag: karyotype

tag: abnormality


title: SK-N-MC 5nM rotenone 1week rep2

description: Gene expression data from neuroepithelioma SK-N-MC cells, grown for 1 week with 5 nM rotenone

source_name: Neuroepithelioma SK-N-MC cells, exposed to 5 nM rotenone for 1 week

value: 1 week


title: SK-N-MC 0nM rotenone 4week rep2


title: SK-N-MC 5nM rotenone 1week rep1


title: SK-N-MC 50nM rotenone 4week rep2


title: SK-N-MC 5nM rotenone 1week rep3


title: SK-N-MC 50nM rotenone 1week rep1

description: Gene expression data from neuroepithelioma SK-N-MC cells, grown for 1 week with 50 nM rotenone

source_name: Neuroepithelioma SK-N-MC cells, exposed to 50 nM rotenone for 1 week


title: SK-N-MC 0nM rotenone 1week rep3

description: Gene expression data from neuroepithelioma SK-N-MC cells, grown for 1 week without  rotenone

source_name: Neuroepithelioma SK-N-MC cells, not exposed to rotenone, 1 week


title: SK-N-MC 50nM rotenone 1week rep3


title: SK-N-MC 5nM rotenone 4week rep1


title: SK-N-MC 0nM rotenone 1week rep1


title: SK-N-MC 50nM rotenone 1week rep2


title: Ni deplete  vs. Ni replete  urea cultured bsy89280c0045

city: San Diego

first: Chris

last: Dupont

state: CA

address: 10355 Science Center Drive

institute: J. Craig Venter Institute

hyb_protocol: Slides were pretreated for 2 h at 42°C in a 50-ml solution of 5 × SSC, 0.1% SDS and 1% BSA followed by four washes in MilliQ water, and three washes in isopropanol. Residual isopropanol was removed by brief centrifugation at 2500 g. Dried probes were resupended in 30 µl hybridization buffer (50% formamide, 5× SSC, 0.1% SDS and 100 µg ml−1 salmon sperm DNA). This mixture was heated for 10 min at 95°C and then applied to a pretreated slide under a cover slip. Hybridizations were carried out at 42°C for 16 h in a sealed hybridization chamber (Corning ♯2551), which was humidified with 20 µl of 5× SSC. Microarrays were washed once in ∼ 200 ml 2× SSC/0.1% SDS at 55°C for 10 min, once in 0.1× SSC/0.1% SDS for 10 min at room temperature, three times in 0.1× SSC for 2 min each, and finally in MilliQ water. They were scanned immediately or following storage in a dessicator in the dark.

scan_protocol: Slides were promptly scanned at a 10 μm resolution using an Axon 4000B scanner with GenePix 4.0 software (Molecular Devices, Sunnyvale, CA). Processing of the TIFF images from hybridized arrays was performed using TIGR-Spotfinder and TIGR-MIDAS (http://www.tm4.org).

data_processing: Statistical analysis was performed on log2-transformed signal ratios of the replicate spots using the Significance Analysis of Microarray (SAM) software (http://www-stat.stanford.edu/~tibs/SAM/) (Tusher et al., 2001).

organism: Parasynechococcus marenigrum WH 8102

source_name: Ni deplete cells

label_protocol: ix µg of Random Hexamer Primers (Invitrogen, Carlsbad, CA) were annealed to 2 µg of RNA in a total volume of 18.5 µl by heating the reaction to 70°C for 10 min, followed by quick chilling on ice. To this reaction was added 6 µl of 5× Reverse Transcriptase cDNA reaction buffer (250 mM Tris-HCl, pH 8.3, 375 mM KCl, 15 mM MgCl2), 3 µl 0.1 M DTT (Invitrogen), and 0.6 µl of a dNTP solution containing (25 mM each dATP, dGTP, and dCTP, 8 mM dTTP (Invitrogen) and 17 mM amino allyl-dUTP (Sigma)). Reverse Transcriptase Superscript II (Invitrogen) (400 U in 2 µl) was added and reactions were then incubated at 42°C for three hours to overnight. The RNA template was hydrolysed by adding 10 µl 1 M NaOH and 10 µl 0.5 M EDTA and heating to 65°C for 15 min. The solution was neutralized with 25 µl 1 M Tris pH 7.0 and cDNA was purified over QIAquick PCR purification columns replacing the Tris buffers with phosphate buffers (5 mM KPO4 pH 8, 80% EtOH) and (4 mM KPO4 pH 8) for column washing and cDNA elution respectively. Reactions were dried to completion in a Speed-Vac centrifuge. Aminoallyl-labelled cDNA was resuspended in 4.5 µl 0.1 M Na2HCO3, pH 9.3, plus 4.5 µl containing 63 µg of the appropriate ester dye (Cy3 or Cy5). The coupling reaction proceeded for 2 h at room temperature in the dark. Thirty-five µl 100 mM NaOAc, pH 5.2 was added to coupling reactions which were then purified with QIAquick PCR purification columns, using the supplied buffers. The cDNA probes, Cy3 and Cy5, were combined and dried to completion.

growth_protocol: Exponential growth in synthetic ocean water for the nitrogen source indicated and either total Nickel=5nM (Ni deplete) or total Ni =50 nM (Ni replete)

extract_protocol: Modified trizol protocol (lysis at 60oC for 1 hour) followed by Qiagen Rneasy with Dnase treatment

tag: growth condition

value: urea cultured

value: Ni deplete

source_name: Ni replete cells

value: Ni replete


title: Cultured astrocyte control

city: Tokyo

first: Kazunori

last: Kanemaru

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Pharmacology

country: Japan

institute: Graduate School of Medicine, The University of Tokyo

description: Gene expression data from astrocytes expressing IRES2-RFP, i.e. control

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Rattus norvegicus

source_name: Rat embryo hippocampus

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: Kept at 37C and 5% CO2

extract_protocol: RNeasy was used according to the manufacturer's instructions.

treatment_protocol: Cultured astrocytes were washed with PBS, and RNeasy (Qiagen) was used.

value: astrocyte

tag: genotype

value: normal

tag: age

value: embryonic day 18

value: vector control

tag: genetic background

value: Sprague-Dawley


title: Ni deplete  vs. Ni replete  urea cultured bsy89280d0095


title: Ni deplete  vs. Ni replete  NH4 cultured bsy89280c0070

value: NH4 cultured


title: Ni deplete  vs. Ni replete  urea cultured bsy89280c0053


title: Ni deplete  vs. Ni replete  NH4 cultured bsy89280d0088


title: Ni deplete  vs. Ni replete  urea cultured bsy89280d0094


title: Ni deplete  vs. Ni replete  urea cultured bsy89280c0043


title: Ni deplete  vs. Ni replete  NH4 cultured bsy89280d0089

source_name: Ni Deplete cells


title: Ni deplete  vs. Ni replete  NH4 cultured bsy89280c0071


title: Cultured astrocyte 5ppase

description: Gene expression data from astrocytes expressing 5ppase-IRES2-RFP

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

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

tag: cell type


title: Ni deplete  vs. Ni replete  urea cultured bsy89280c0051


title: WAP-Cre:PTENp53 primary tumor TW53-51

city: Toronto

first: Jeff

last: Liu

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

country: Canada

institute: University Health Network

description:
TW53-51
Gene expression data from primary WAP-Cre:PTENp53 tumor

hyb_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

data_processing: Microarray Data were normalized using RMA method via Partek Genomics Suite (v.5.6) and absolute expression values were obtained

source_name: WAP-Cre:PTENp53 primary tumor

growth_protocol: Samples from independent primary mammary tumors from MMTV-Neu,MMTV-Cre:p53, MMTV-Cre:PTEN, MMTV-Cre:PTEN:p53, WAP-Cre:PTEN, and WAP-Cre:PTEN:p53 models were frozen and kept in -80 degree.

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

treatment_protocol: Total RNA obtained from primary tumors were used for microarray analysis to determine differentially regulated genes among different mouse models.  Cluster analysis and pathway analysis based on gene expression were then performed to determine significant genes/pathways

tag: strain background

value: mixed

tag: tissue

value: primary mammary tumor less than 1.0 cm diameter


title: WAP-Cre:PTENp53 primary tumor TW53-102

description:
TW53-102
Gene expression data from primary WAP-Cre:PTENp53 tumor

scan_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

tag: genotype/variation


title: WAP-Cre:PTENp53 primary tumor TW53-88

description:
TW53-88
Gene expression data from primary WAP-Cre:PTENp53 tumor

label_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)


title: WAP-Cre:PTENp53 primary tumor TW53-104

description:
TW53-104
Gene expression data from primary WAP-Cre:PTENp53 tumor


title: WAP-Cre:PTENp53 primary tumor TW53-63

description:
TW53-63
Gene expression data from primary WAP-Cre:PTENp53 tumor


title: WAP-Cre:PTEN primary tumor PW83

description:
PW83
Gene expression data from primary WAP-Cre:PTEN tumor

source_name: WAP-Cre:PTEN primary tumor


title: WAP-Cre:PTEN primary tumor PW105

description:
PW105
Gene expression data from primary WAP-Cre:PTEN tumor


title: MMTV-Cre:PTENp53 primary tumor RB401

description:
RB401
Gene expression data from primary MMTV-Cre:PTENp53 tumor

source_name: MMTV-Cre:PTENp53 primary tumor


title: MMTV-Cre:PTENp53 primary tumor RB406

description:
RB406
Gene expression data from primary MMTV-Cre:PTENp53 tumor


title: WAP-Cre:PTENp53 primary tumor TW53-105

description:
TW53-105
Gene expression data from primary WAP-Cre:PTENp53 tumor


title: WAP-Cre:PTENp53 primary tumor TW53-80

description:
TW53-80
Gene expression data from primary WAP-Cre:PTENp53 tumor


title: WAP-Cre:PTEN primary tumor PW104

description:
PW104
Gene expression data from primary WAP-Cre:PTEN tumor


title: WAP-Cre:PTEN primary tumor PW96

description:
PW96
Gene expression data from primary WAP-Cre:PTEN tumor


title: WAP-Cre:PTEN primary tumor PW19

description:
PW19
Gene expression data from primary WAP-Cre:PTEN tumor


title: WAP-Cre:PTEN primary tumor PW153

description:
PW153
Gene expression data from primary WAP-Cre:PTEN tumor


title: MMTV-Cre:PTENp53 primary tumor RB407

description:
RB407
Gene expression data from primary MMTV-Cre:PTENp53 tumor


title: MMTV-Cre:PTENp53 primary tumor TC53-90

description:
TC53-90
Gene expression data from primary MMTV-Cre:PTENp53 tumor


title: WAP-Cre:PTEN primary tumor PW3

description:
PW3
Gene expression data from primary WAP-Cre:PTEN tumor


title: MMTV-Cre:PTEN primary tumor TCP96

description:
TCP96
Gene expression data from primary MMTV-Cre:PTEN tumor

source_name: MMTV-Cre:PTEN primary tumor


title: MMTV-Cre:PTENp53 primary tumor RB400

description:
RB400
Gene expression data from primary MMTV-Cre:PTENp53 tumor


title: MMTV-Cre:PTENp53 primary tumor TC53-127

description:
TC53-127
Gene expression data from primary MMTV-Cre:PTENp53 tumor


title: MMTV-Cre:PTENp53 primary tumor TC53-152

description:
TC53-152
Gene expression data from primary MMTV-Cre:PTENp53 tumor


title: WAP-Cre:PTEN primary tumor PW28

description:
PW28
Gene expression data from primary WAP-Cre:PTEN tumor


title: MMTV-Cre:PTENp53 primary tumor TC53-120

description:
TC53-120
Gene expression data from primary MMTV-Cre:PTENp53 tumor


title: MMTV-Cre:PTEN primary tumor CP227

description:
CP227
Gene expression data from primary MMTV-Cre:PTEN tumor


title: WAP-Cre:PTEN primary tumor P196

description:
P196
Gene expression data from primary WAP-Cre:PTEN tumor


title: MMTV-Cre:PTEN primary tumor CP243

description:
CP243
Gene expression data from primary MMTV-Cre:PTEN tumor


title: MMTV-Cre:PTEN primary tumor CP71

description:
CP71
Gene expression data from primary MMTV-Cre:PTEN tumor


title: Macrophages from protectively immunized mice (H99γ) Toll-like receptor PCR array 3

city: San Antonio

first: Sarah

middle: E

last: Hardison

state: Georgia

address: One UTSA Circle

department: Biology

institute: University of Texas at San Antonio

description: test

data_processing: The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php. For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB. Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]. The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR green

source_name: Murine macrophage

label_protocol: PCR assays were performed using the Toll-like Receptor PCR assay panel (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (7300 Real-Time PCR System, Applied Biosystems) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: macrophage

tag: immunization

value: protective immunization with strain H99γ

value: 7 days post-challenge

tag: challenge

value: C. neoformans strain H99

value: Balb/c


title: MMTV-Cre:PTEN primary tumor TCP75

description:
TCP75
Gene expression data from primary MMTV-Cre:PTEN tumor


title: Macrophages from mock-immunized mice (HKCn) Toll-like receptor PCR array 3

description: control

value: mock immunization with heat-killed C. neoformans


title: Macrophages from mock-immunized mice (HKCn) Toll-like receptor PCR array 2

description: control

value: 3 days post-challenge


title: Macrophages from protectively immunized mice (H99γ) Toll-like receptor PCR array 1

description: test

value: 24 hours post-challenge


title: Macrophages from mock-immunized mice (HKCn) Toll-like receptor PCR array 1

description: control


title: Macrophages from protectively immunized mice (H99γ) Toll-like receptor PCR array 2

description: test


title: MMTV-Cre:PTEN primary tumor CP200

description:
CP200
Gene expression data from primary MMTV-Cre:PTEN tumor


title: MMTV-Cre:PTEN primary tumor CP225

description:
CP225
Gene expression data from primary MMTV-Cre:PTEN tumor


title: MMTV-Cre:p53 primary tumor C53-22

description:
C53-22
Gene expression data from primary MMTV-Cre:p53 tumor

source_name: MMTV-Cre:p53 primary tumor


title: MMTV-Cre:p53 primary tumor TC53-33

description:
TC53-33
Gene expression data from primary MMTV-Cre:p53 tumor


title: MMTV-Neu primary tumor N222

description:
N222
Gene expression data from primary MMTV-Neu tumor

source_name: MMTV-Neu primary tumor

value: MMTV-Neu


title: MMTV-Cre:PTEN primary tumor CP221

description:
CP221
Gene expression data from primary MMTV-Cre:PTEN tumor


title: MMTV-Cre:p53 primary tumor C53-1

description:
C53-1
Gene expression data from primary MMTV-Cre:p53 tumor


title: MMTV-Cre:PTEN primary tumor CP207

description:
CP207
Gene expression data from primary MMTV-Cre:PTEN tumor


title: MMTV-Neu primary tumor N240

description:
N240
Gene expression data from primary MMTV-Neu tumor


title: 92-1400

first: Xiao

last: Zheng

address: Liuzi five hao

institute: China CDC

description:
ICDC_31
Mutation mapping 92-1400

hyb_protocol: Labeled genomic DNA was hybridized to arrays in the NimbleGen Hybridization Buffer for 16 hours at 42 ℃ using a MAUI hybridization system (BioMicro Systems, Inc. Salt Lake City, Utah). Labeled genomic DNA (5ug) from the reference strain Streptococcus suis GZ1 and from each test strain were co-hybridized to each array. Arrays were washed with NimbleGen wash buffer, and then were spun dry in a microarray high-speed centrifuge (TeleChem International, Inc., Sunnyvale, CA) and stored until scanned. (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per the manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 CGS data extraction.

organism: Streptococcus suis

label_protocol: Genomic DNA was labeled with a random prime reaction. DNA (1 ug) was mixed with 1 O.D. of 5’-fluorescence dye labeled random nonamer (Cy3 for test strains and Cy5 for reference strain) (TriLink Biotechnologies) in 62.5 mM Tris-HCl, 6.25 mM MgCl2 and 0.0875% ß-mercaptoethanol, denatured at 98°C for 5 min, chilled on ice, and incubated with 100 units Klenow fragment (NEB) and dNTP mix (6 mM each in TE) for 2 h at 37°C. Reactions were terminated with 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water. A fifty-fold amplification was typically achieved. (http://www.nimblegen.com/products/lit/lit.html)

growth_protocol: Cells were cultured in Todd-Hewitt broth (THB; Difco Laboratories, Detroit, MI) medium.

extract_protocol: Genomic DNA was extracted using the QIAGEN Genomic-tip 100/G kit (Qiagen).

tag: strain

tag: serotype

tag: sequence type

tag: site isolated

value: Canada

tag: origin

value: diseased pig

tag: pathogenicity

value: virulent

value: test strain

source_name: Reference GZ1 DNA

value: China

value: patient

value: highly virulent

value: reference strain


title: MMTV-Neu primary tumor N242

description:
N242
Gene expression data from primary MMTV-Neu tumor

value: mixed

value: primary mammary tumor less than 1.0 cm diameter


title: NT77

description:
ICDC_25
Mutation mapping NT77

value: healthy pig

value: unknown

tag: sample type


title: 89-590

description:
ICDC_30
Mutation mapping 89-590


title: 89-3576-3

description:
ICDC_29
Mutation mapping 89-3576-3


title: 2726

description:
ICDC_23
Mutation mapping 2726

value: Denmark


title: SK-N-MC 0nM rotenone 1week rep2

description: Gene expression data from neuroepithelioma SK-N-MC cells, grown for 1 week without  rotenone

tag: cell line

value: SK-N-MC

tag: treatment

value: 0nM rotenone

tag: time

value: 1 week


title: 42A

description:
ICDC_26
Mutation mapping 42A


title: NCTC1046

description:
ICDC_22
Mutation mapping NCTC1046

value: Netherland


title: 93A

description:
ICDC_24
Mutation mapping 93A

value: Canada


title: 14A

description:
ICDC_27
Mutation mapping 14A


title: 10581

description:
ICDC_21
Mutation mapping 10581

value: diseased pig


title: 22083

description:
ICDC_17
Mutation mapping 22083

value: virulent


title: Ni deplete  vs. Ni replete  NH4 cultured bsy89255c0054

tag: growth condition

value: NH4 cultured

value: Ni deplete

value: Ni replete


title: 2651

description:
ICDC_11
Mutation mapping 2651

value: test strain

value: China

value: patient

value: highly virulent


title: 12814

description:
ICDC_19
Mutation mapping 12814

value: reference strain


title: 11611

description:
ICDC_09
Mutation mapping 11611

value: Germany

value: unknown


title: 14636

description:
ICDC_16
Mutation mapping 14636

value: Denmark


title: 89-1591

description:
ICDC_10
Mutation mapping 89-1591


title: 89-2479

description:
ICDC_28
Mutation mapping 89-2479


title: 8830

description:
ICDC_20
Mutation mapping 8830


title: Ni deplete  vs. Ni replete  NH4 cultured bsy89255c0063


title: 6407

description:
ICDC_13
Mutation mapping 6407


title: 4961

description:
ICDC_12
Mutation mapping 4961


title: 2524

description:
ICDC_15
Mutation mapping 2524


title: LeGO-DCR (with differentiation) 3

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: HC11 mammary epithelial cells, with overexpression of PINC isoform lacking the most conserved regions of the gene, and with differentiation-inducing agents

hyb_protocol: Hybridizations were performed using One-colour hybridization on SurePrint G3 Mouse GE 60k Microarray (Agilent)

scan_protocol: Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).

data_processing: quantile normalized, background subtracted data. Agilent and Bioconductor software was used.

source_name: HC11 mammary epithelial cells

label_protocol: standard Agilent protocol

growth_protocol: Cells were grown from HC11 line, a mouse mammary epithelial cell line derived from the Comma-D cell line which were isolated from a mid-pregnant Balb/c mouse

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and quantified using a NanoDrop (ThermoScientific).

treatment_protocol: Lentiviral vectors (LeGO-GFP, LeGO-1.0, LeGO-1.6 or LeGO-DCR) were co-transfected with packaging vectors (pCMV-VSVG, pMDLg/pRRE, pRSV-Rev) into 293-T cells using Fugene 6 (Roche). HC11 cells were transfected with siRNAs (10 nM/well) at 60-80 % confluency in 6 well plates using Lipofectamine RNAiMAX reagent (Invitrogen).  Silencer Select siRNAs (Ambion) were used to target mPINC1.0 (n273107), mPINC1.6 (n254312) and DCR2 (n254314).  The controls included mock tranfection without siRNAs and a siNEG, Silencer Select Negative Control #1 (4390843). Cells were treated with or without the lactogenic hormones hydrocortisone, insulin and prolactin to induce differentiation.

tag: differentiation

value: differentiation-inducing agents lactogenic hormones hydrocortisone, insulin and prolactin


title: 4417

description:
ICDC_18
Mutation mapping 4417


title: Ni deplete  vs. Ni replete  urea cultured bsy89255c0066

value: urea cultured


title: 11538

description:
ICDC_14
Mutation mapping 11538


title: LeGO-1/6 (with differentiation) 3

description: HC11 mammary epithelial cells, with PINC1/6 over-expression, and with differentiation-inducing agents

value: PINC1/6 over-expression


title: 393P cells with Zeb1 overexpression, sample 3

hyb_protocol: Hybridization, washing, staining, imaging and signal extraction were performed according to Affymetrix-recommended procedures, excet that the 20X GeneChip Eikaryotic Hybridization Control cocktail was omitted from the hybridization.

scan_protocol: Affymetrix GeneChip® 3000 7G scanner

data_processing: The signal processing implemented for the Ambion miRCHIP is a multi-step process involving probe specific signal detection calls, background estimate and correction, constant variance stabilization and either array scaling or global normalization. For each probe, an estimated background value is subtracted that is derived from the median signal of a set of G-C matched anti-genomic controls. Arrays within a specific analysis experiment were normalized together according to the variance stabilization methods described by Huber et al. (Huber et al., 2002). Detection calls were based on a Wilcoxon rank-sum test of the miRNA probe signal compared to the distribution of signals from GC-content matched anti-genomic probes. For statistical hypothesis testing, a two-sample t-Test, with assumption of equal variance, was applied. One-way ANOVA was used for experimental designs with more than two experimental groupings or levels of the same factor. These tests define which probes are considered to be significantly differentially expressed, or significant, based on a default p-value of 0.001 and log2 difference > 1.

source_name: Zeb

label_protocol: The 3' ends of the RNA molecules were tailed and biotin-labeled using the mirVana miRNA Labeling Kit (Ambion Inc., Austin, TX). The kit's dNTP mixture in the tailing reaction was replaced with a proprietary nucleotide mixture containing biotin-modified nucleotides (PerkinElmer, Waltham, MA).

growth_protocol: Murine lung cancer cells (393P) were cultured in RPMI 1640 (Mediatech) with 10% FBS (Sigma-Aldrich).

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

treatment_protocol: Zeb1 was inducibly expressed in a low-Zeb1, non-metastatic KP cell line (393P).

tag: cell type

value: lung cancer

value: Zeb1 overexpression


title: 393P cells with Zeb1 overexpression, sample 2


title: 393P cells with control vector, sample 2

source_name: Zeb control

value: control vector


title: LeGO-DCR (with differentiation) 1

value: overexpression of PINC isoform lacking the most conserved regions of the gene


title: LeGO-DCR (with differentiation) 2


title: 393P cells with Zeb1 overexpression, sample 1


title: SC84

description:
ICDC_07
Mutation mapping SC84


title: LeGO-1/6 (with differentiation) 1


title: SC22

description:
ICDC_06
Mutation mapping SC22


title: LeGO-GFP (with differentiation) 2

description: HC11 mammary epithelial cells, with GFP control, and with differentiation-inducing agents

value: GFP control


title: 393P cells with control vector, sample 3


title: 31533

description:
ICDC_05
Mutation mapping 31533

value: France

value: diseased pig


title: 13730

description:
ICDC_08
Mutation mapping 13730

value: Netherland

value: virulent

value: test strain

value: China


title: 393P cells with control vector, sample 1


title: GX1

description:
ICDC_04
Mutation mapping GX1

value: patient

value: highly virulent

value: reference strain


title: LeGO-1/6 (with differentiation) 2

value: differentiation-inducing agents lactogenic hormones hydrocortisone, insulin and prolactin


title: LeGO-GFP (with differentiation) 3


title: siPINC (with differentiation) 3

description: HC11 mammary epithelial cells, with siRNA against PINC, and with differentiation-inducing agents

value: siRNA against PINC


title: siPINC (with differentiation) 2


title: viral fibroblast iPSC line IMR4

city: Baltimore

first: Elias

middle: Thomas

last: Zambidis

state: MD

address: 733 N. Broadway

department: Oncology

institute: Johns Hopkins School of Medicine

description: Individual sample

hyb_protocol: For array assay, 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed. Illumina HumanHT-12 V3.0 expression beadchips were used for all analyses in this series.

scan_protocol: Fluorescent signals were obtained by scanning with the iScan System.

data_processing: Data were extracted with Gene Expression Module 1.0.6 in GenomeStudio 1.0.2 and signal intensities from multiple chips comprising this single series were normalized without background subtraction to obtain non-normalized data. Signals for each gene were then log 2 transformed and mean subtracted across all conditions to obtain processed data.

source_name: viral fibroblast iPSC clone iPS(IMR90)-4

label_protocol: 500 ng total RNA from each sample was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) as described in the instruction manual.

extract_protocol: Total RNA was prepared as described in the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion. RNA quality was assessed by Nanodrp-1000 spectrometer for OD260/280 and OD260/230 ratio and Bioanalyzer (Agilent Technologies).

value: viral fibroblast iPSC line IMR4

value: Obtained from WiCell (Madison, WI). Originally derived in Yu et al. Science 318:1917-1920. 1997.


title: Cord Blood Day +3 +4F, +BMSC, Experiment 3

description: Individual sample

hyb_protocol: For array assay, 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed. Illumina HumanHT-12 V4.0 expression beadchips were used for each assay.

source_name: neonatal cord blood CD34+ cells, treated as described

treatment_protocol: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) on Day zero; co-cultured with BMSC from day zero to +3, then harvested

value: fibroblast


title: LeGO-GFP (with differentiation) 1


title: siPINC (with differentiation) 1


title: GZ2

description:
ICDC_02
Mutation mapping GZ2


title: viral fibroblast iPSC line IMR1

description: Individual sample

source_name: viral fibroblast iPSC clone iPS(IMR90)-1

value: viral fibroblast iPSC line IMR1


title: siPINC1/6 (with differentiation) 3

description: HC11 mammary epithelial cells, with siRNA against major PINC splice forms (PINC1 and PINC6), and with differentiation-inducing agents


title: nonviral Fetal fibroblast iPSC clone 6

description: Individual sample

source_name: nonviral Fetal fibroblast iPSC clone 6, passage 14

tag: pasage

value: nonviral Fetal fibroblast iPSC clone 6

value: non-integrated fetal fibroblast iPSC generated in the Zambidis laboratory


title: Cord Blood Day +3 no 4F, +BMSC, Experiment 3

description: Individual sample

treatment_protocol: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero; co-cultured with BMSC from day zero to +3, then harvested


title: nonviral Fetal fibroblast iPSC clone 1

description: Individual sample

source_name: nonviral Fetal fibroblast iPSC clone 1, passage 14

value: nonviral Fetal fibroblast iPSC clone 1


title: LN1

description:
ICDC_01
Mutation mapping LN1


title: siPINC1/6 (with differentiation) 1

value: siRNA against major PINC splice forms (PINC1 and PINC6)


title: P1/7

description:
ICDC_03
Mutation mapping 1/7

value: England

value: diseased pig


title: nonviral Keratinocyte iPSC clone 1

description: Individual sample

source_name: nonviral Keratinocyte iPSC clone 1, passage 13

value: nonviral Keratinocyte iPSC clone 1

value: non-integrated keratinocyte iPSC generated in the Zambidis laboratory


title: miR34a-overexpressing tumors 2

description: 344SQ cells with miR34a overexpression, sample 2

hyb_protocol: Following fragmentation, cRNA was hybridized on Mouse430A_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: The data were analyzed with dChip version2006 using Affymetrix default analysis settings, PM-MM model, and quantile normalization.

source_name: 344SQ lung cancer cell line

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

growth_protocol: Murine lung cancer cells (344SQ) were cultured in RPMI 1640 (Mediatech) with 10% FBS (Sigma-Aldrich).

extract_protocol: Total RNA was isolated by the Ambion kit. RNA quality and quantity were evaluated on a NanoDrop spectrophotometer and the Agilent 2100 Bioanalyzer.

treatment_protocol: miR-34a was inducibly expressed in a high-Zeb1, metastatic KP cell line (344SQ).

value: 344SQ cells with miR-34a overexpression


title: miR34a-overexpressing tumors 3

description: 344SQ cells with miR34a overexpression, sample 3


title: Cord Blood Day +3 no 4F, no BMSC, Experiment 3

description: Individual sample

treatment_protocol: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero; co-cultured without BMSC from day zero to +3, then harvested

value: +4F +BMSC

value: Day +3


title: Cord Blood Day -3, Experiment 3

description: Individual sample

treatment_protocol: Cord blood CD34+ cells harvested immediately after thawing (day -3)

value: no 4F +BMSC


title: siPINC1/6 (with differentiation) 2

value: differentiation-inducing agents lactogenic hormones hydrocortisone, insulin and prolactin


title: siNegative (with differentiation) 3

description: HC11 mammary epithelial cells, with siRNA negative control, and with differentiation-inducing agents

value: siRNA negative control


title: nonviral Cord Blood iPSC clone 19.11

description: Individual sample

source_name: nonviral Cord Blood iPSC clone 19.11, passage 11

value: nonviral Cord Blood iPSC clone 19.11

value: non-integrated cord blood iPSC generated in the Zambidis laboratory


title: nonviral Cord Blood iPSC clone 6.11

description: Individual sample

source_name: nonviral Cord Blood iPSC clone 6.11, passage 14

value: nonviral Cord Blood iPSC clone 6.11


title: siPINC (no differentiation) 2

description: HC11 mammary epithelial cells, with siRNA against PINC, and with no differentiation-inducing agents

value: siRNA against PINC

value: no differentiation-inducing agents


title: Cord Blood Day +3 +4F, no BMSC, Experiment 3

description: Individual sample

treatment_protocol: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) on Day zero; co-cultured without BMSC from day zero to +3, then harvested

value: fibroblast


title: nonviral Cord Blood iPSC clone 6.2

description: Individual sample

source_name: nonviral Cord Blood iPSC clone 6.2, passage 14

value: nonviral Cord Blood iPSC clone 6.2


title: human Embryonic Stem Cell

description: Individual sample

source_name: Undifferentiated H9 human Embryonic Stem Cells, Passage 51 (NIH Code WA09)

value: human Embryonic Stem Cell


title: siNegative (with differentiation) 2


title: nonviral Cord Blood iPSC clone 6.13

description: Individual sample

source_name: nonviral Cord Blood iPSC clone 6.13, passage 14

value: nonviral Cord Blood iPSC clone 6.13


title: Vector Ctrl 1

description: 344SQ cells with control vector, sample 1

value: 344SQ cells with control vector


title: siPINC (no differentiation) 1


title: Vector Ctrl 2

description: 344SQ cells with control vector, sample 2


title: nonviral Keratinocyte iPSC clone 3

description: Individual sample

source_name: nonviral Keratinocyte iPSC clone 3, passage 13

value: nonviral Keratinocyte iPSC clone 3

value: non-integrated keratinocyte iPSC generated in the Zambidis laboratory


title: siPINC1/6 (no differentiation) 2

description: HC11 mammary epithelial cells, with siRNA against major PINC splice forms (PINC1 and PINC6), and with no differentiation-inducing agents


title: Bone Marrow CD34+ progenitors, adult

description: Individual sample

source_name: Bone Marrow CD34+ progenitors  Day 0

value: Bone Marrow CD34+ progenitors, adult

value: Obtained from ALLCELLS (Emeryville, CA), stimulated with Flt3L, TPO, SCF X 3 days


title: siNegative (with differentiation) 1

source_name: HC11 mammary epithelial cells


title: Cord Blood Day +3 +4F, +BMSC, Experiment 2

description: Individual sample

treatment_protocol: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) on Day zero; co-cultured with BMSC from day zero to +3, then harvested

value: Day +3

tag: tissue

value: cord blood


title: Vector Ctrl 3

description: 344SQ cells with control vector, sample 3


title: mobilized Peripheral Blood CD34+ progenitors, adult

description: Individual sample

source_name: mobilized Peripheral Blood CD34+ progenitors Day 0


title: Cord Blood CD34+ progenitors, neonatal

description: Individual sample

source_name: Cord Blood CD34+ progenitors Day 0

value: Cord Blood CD34+ progenitors, neonatal


title: miR34a-overexpressing tumors 1

description: 344SQ cells with miR34a overexpression, sample 1

value: 344SQ cells with miR-34a overexpression


title: siPINC1/6 (no differentiation) 1

value: siRNA against major PINC splice forms (PINC1 and PINC6)


title: siNegative (no differentiation) 1

description: HC11 mammary epithelial cells, with siRNA negative control, and with no differentiation-inducing agents

value: siRNA negative control


title: Fetal Liver CD34+ progenitors

description: Individual sample

source_name: Fetal Liver CD34+ progenitors Day 0

value: Fetal Liver CD34+ progenitors


title: siNegative (no differentiation) 2

value: no differentiation-inducing agents


title: Cord Blood Day +3 no 4F, no BMSC, Experiment 2

description: Individual sample

source_name: neonatal cord blood CD34+ cells, treated as described

treatment_protocol: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero; co-cultured without BMSC from day zero to +3, then harvested

value: +4F +BMSC


title: Doxycyline withdrawal 72 hrs

first: Lawrence

middle: N

last: Kwong

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

description: iNRAS-475 off dox d3

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

data_processing: Raw image files were converted to probe set data (.cel files) in Microarray Suite (MAS 5.0). The 18 probe set data files were normalized together, and expression values were determined, using the Robust Multi-chip Average (RMA) method as implemented in RMAExpress (Bolstad/Berkeley).

source_name: Melanoma allograft_doxycycline withdrawal_72 hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: The iNRAS-475 mouse melanoma cell line was injected intradermally into nude mice which were fed 2mg/ml doxycycline water. Tumors were allowed to reach 200-500mm3 after 6 weeks. Doxycyline was then withdrawn from the diet for the given time periods.

treatment_protocol: Tumors were harvested from nude mice hosts. Skin was trimmed off of the tumors and a small piece (~50mg) of tumor parenchyma was snap frozen in liquid nitrogen, then stored at -80oC. Samples were later placed into Trizol after minimal thawing and homogenized using a hand-held electric tissue homogenizer.

tag: host strain

value: nude mice

tag: injected with

value: iNRAS-475 mouse melanoma cells

value: Melanoma allograft

value: Doxycycline withdrawal for 72 hours


title: Doxycyline withdrawal 24 hrs

description: iNRAS-475 off dox d1

source_name: Melanoma allograft_doxycycline withdrawal_24 hrs

value: Doxycycline withdrawal for 24 hours


title: Cord Blood Day +3 +4F, no BMSC, Experiment 2

description: Individual sample

treatment_protocol: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) on Day zero; co-cultured without BMSC from day zero to +3, then harvested


title: Cord Blood Day zero, Experiment 2

description: Individual sample

treatment_protocol: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO, and then harvested

value: +4F no BMSC


title: Fetal Fibroblasts

description: Individual sample

source_name: Fetal Fibroblasts

value: fetal fibroblast

value: From Coriell Institute, Cat # GM02340


title: Doxycyline withdrawal 48 hrs

description: iNRAS-475 off dox d2

source_name: Melanoma allograft_doxycycline withdrawal_48 hrs

value: Doxycycline withdrawal for 48 hours


title: 5 month old mouse, Sox1-GFP positive cells, biological rep2

city: San Francisco

first: Robert

middle: Joseph Allen

last: Bell

address: 1253 5th Ave

department: Institute of Human Genetics

institute: UCSF

hyb_protocol: Samples were hybridized to the Affymetrix (Santa Clara, CA, USA) GeneChip Mouse Gene 1.0 ST Array (Gladstone Genomics Core)

scan_protocol: Arrays were scanned with GCS3000 using the standard procedures recommended by Affymetrix

data_processing: Arrays were normalized using Robust Multichip Average (RMA) and the latest probe map to MM9 RefSeq genes (Irizarry et al., 2003; Dai et al., 2005).   The statistical package R was used to perform average linkage hierarchical clustering of the remaining samples.  Significance Analysis of Microarrays (SAM) was performed to determine significant differentially expressed genes between the old and young mice with a False Discovery Rate cutoff of 5% (Tusher et al., 2001).

source_name: Sox1-GFP SGZ neural stem/progenitor cells at 5 months (young mice)

label_protocol: Samples were amplified using the NuGEN FFPE kit (San Carlos, CA, USA) and cDNA was prepared using an oligo(dT)-T7 RNA polymerase primer before biotinylation by in vitro transcription

growth_protocol: All animals were maintained according to institutional regulations.

extract_protocol: RNA was harvested using the Arcturus PicoPure RNA isolation kit (Life Technologies Corp, Carlsbad, CA, USA) and the quality and quantity of each sample was checked using Agilent BioAnalyzer (Santa Clara, CA, USA) and Nanodrop spectrophotometer (Wilmington, DE, USA).

value: papain dissociated hippocampus

tag: genotype

value: Sox1-GFP heterozygotes

tag: age

value: 5 months


title: Cord Blood Day +3 no 4F, +BMSC, Experiment 2

description: Individual sample

treatment_protocol: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero; co-cultured with BMSC from day zero to +3, then harvested

value: Day +3

value: cord blood


title: Cord Blood Day +3 +4F, no BMSC, Experiment 1

description: Individual sample

value: Dayzero

value: Day zero

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) on Day zero; co-cultured without BMSC from day zero to +3, then harvested


title: Cord Blood Day -3, Experiment 2

description: Individual sample

treatment_protocol: Cord blood CD34+ cells harvested immediately after thawing

value: no 4F +BMSC


title: 4 month old mouse, Sox1-GFP positive cells, biological rep3

source_name: Sox1-GFP SGZ neural stem/progenitor cells at 4 months (young mice)

value: 4 months


title: MEKi 4 days, biological rep5

description: iNRAS-475 AZD d4 5

source_name: Melanoma allograft_AZD6244 100mg/kg 4 days

growth_protocol: The iNRAS-475 mouse melanoma cell line was injected intradermally into nude mice which were fed 2mg/ml doxycycline water. Tumors were allowed to reach 200-500mm3 after 6 weeks. Mice were then treated with vehicle or 100mg/kg of the AZD6244 MEK inhibitor, or doxycyline was withdrawn from the diet.

treatment_protocol: Tumors were harvested from nude mice hosts. Skin was trimmed off of the tumors and a small piece (~50mg) of tumor parenchyma was placed into RNA Later preservation reagent, refrigerated overnight at 4C, then stored at -80C. Samples were later placed into Trizol after minimal thawing and homogenized using a hand-held electric tissue homogenizer.

value: nude mice

value: iNRAS-475 mouse melanoma cells

value: Melanoma allograft

tag: treated with

value: AZD6244 MEK inhibitor 100mg/kg for 4 days


title: Control, on doxycycline

description: iNRAS-475 control

value: On doxycycline


title: MEKi 4 days, biological rep4

description: iNRAS-475 AZD d4 4


title: MEKi 4 days, biological rep3

description: iNRAS-475 AZD d4 3


title: 7 month old mouse, Sox1-GFP negative cells, biological rep2

source_name: non-GFP hippocampal cells at 7 months (young mice)

value: 7 months


title: 4 month old mouse, Sox1-GFP negative cells, biological rep3

source_name: non-GFP hippocampal cells at 4 months (young mice)


title: 7 month old mouse, Sox1-GFP positive cells, biological rep1

source_name: Sox1-GFP SGZ neural stem/progenitor cells at 7 months (young mice)


title: Cord Blood Day zero, Experiment 1

description: Individual sample

treatment_protocol: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO, and then harvested

value: +4F no BMSC


title: Cord Blood Day +3 no 4F, no BMSC, Experiment 1

description: Individual sample

treatment_protocol: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero (D0); co-cultured without BMSC from day zero to +3, then harvested

value: +4F +BMSC


title: Cord Blood Day +3 +4F, +BMSC, Experiment 1

description: Individual sample

value: no 4F no BMSC

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) on Day zero; co-cultured with BMSC from day zero to +3, then harvested


title: MEKi 4 days, biological rep6

description: iNRAS-475 AZD d4 6


title: 7 month old mouse, Sox1-GFP negative cells, biological rep1

value: papain dissociated hippocampus

value: Sox1-GFP heterozygotes


title: Cord Blood Day +3 no 4F, +BMSC, Experiment 1

description: Individual sample

treatment_protocol: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero (D0); co-cultured with BMSC from day zero to +3, then harvested

value: Day -3

value: cord blood


title: 1 year 9 month old mouse, Sox1-GFP positive cells, biological rep4

source_name: Sox1-GFP SGZ neural stem/progenitor cells at 1 year 9 months (old mice)

value: 1 year 9 months


title: Cord Blood Day -3, Experiment 1

description: Individual sample

value: no 4F +BMSC

value: Day +3

value: Cord blood CD34+ cells harvested immediately after thawing (day -3)


title: MEKi 4 days, biological rep2

description: iNRAS-475 AZD d4 2

value: nude mice

value: iNRAS-475 mouse melanoma cells


title: Cord Blood Day zero, Experiment 3

description: Individual sample

value: fibroblast

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO, and then harvested


title: Cord Blood Day 23 +4F +BMSC, Experiment 2

description: Individual sample

treatment_protocol: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) episome on Day zero; co-cultured with BMSC from day zero to +3, then maintained on MEF until day 23, and then harvested

value: Day zero


title: 1 year 9 month old mouse, Sox1-GFP positive cells, biological rep2


title: MEKi 4 days, biological rep1

description: iNRAS-475 AZD d4 1

value: Melanoma allograft

value: AZD6244 MEK inhibitor 100mg/kg for 4 days


title: 1 year 9 month old mouse, Sox1-GFP positive cells, biological rep3


title: Macrophages from mock-immunized mice (HKCn) JAK/STAT PCR array 3

description: control

source_name: Murine macrophage

value: macrophage

tag: immunization

value: mock immunization with heat-killed C. neoformans

value: 7 days post-challenge

tag: challenge

value: C. neoformans strain H99

tag: genetic background

value: Balb/c


title: Macrophages from protectively immunized mice (H99γ) JAK/STAT PCR array 3

description: test

value: protective immunization with strain H99γ


title: -NRAS 4 days, biological rep4

description: iNRAS-475 -Dox d4 4

source_name: Melanoma allograft_doxycyline withdrawal 4 days

value: Doxycycline withdrawal 4 days


title: -NRAS 4 days, biological rep2

description: iNRAS-475 -Dox d4 2


title: Cord Blood Day 23 +4F +BMSC, Experiment 3

description: Individual sample

treatment_protocol: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) on Day zero; co-cultured with BMSC from day zero to +3, then maintained on MEF until day 23, and then harvested

value: no 4F no BMSC

value: cord blood

tag: sample type


title: -NRAS 4 days, biological rep6

description: iNRAS-475 -Dox d4 6


title: -NRAS 4 days, biological rep5

description: iNRAS-475 -Dox d4 5


title: Cord Blood Day 23 +4F +BMSC, Experiment 1

description: Individual sample

value: Day -3

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) episome on Day zero; co-cultured with BMSC from day zero to +3, then maintained on MEF until day 23, and then harvested


title: Macrophages from mock-immunized mice (HKCn) JAK/STAT PCR array 2

description: control

value: 3 days post-challenge


title: Macrophages from protectively immunized mice (H99γ) JAK/STAT PCR array 2

description: test


title: H9 p52 hESC

description: Individual sample

source_name: H9 human Embryonic Stem Cells, Passage 52 (NIH Code WA09)

value: +4F +BMSC

value: Day 23

tag: cell line

value: Undifferentiated hESC


title: Macrophages from protectively immunized mice (H99γ) JAK/STAT PCR array 1

description: test

value: 24 hours post-challenge


title: H9 p54 hESC

description: Individual sample

tag: treatment


title: H9 p51 hESC

description: Individual sample

tag: time


title: vehicle, biological rep5

description: iNRAS-475 Veh 5

source_name: Melanoma allograft_vehicle-treated

value: nude mice

value: iNRAS-475 mouse melanoma cells

value: Melanoma allograft

value: vehicle


title: 1 year 9 month old mouse, Sox1-GFP positive cells, biological rep1

value: papain dissociated hippocampus

value: Sox1-GFP heterozygotes

value: 1 year 9 months


title: vehicle, biological rep3

description: iNRAS-475 Veh 3


title: vehicle, biological rep1

description: iNRAS-475 Veh 1


title: Macrophages from mock-immunized mice (HKCn) JAK/STAT PCR array 1

description: control

value: macrophage

value: mock immunization with heat-killed C. neoformans

value: C. neoformans strain H99

value: Balb/c


title: -NRAS 4 days, biological rep1

description: iNRAS-475 -Dox d4 1

value: Doxycycline withdrawal 4 days


title: vehicle, biological rep6

description: iNRAS-475 Veh 6


title: vehicle, biological rep4

description: iNRAS-475 Veh 4


title: vehicle, biological rep2

description: iNRAS-475 Veh 2


title: -NRAS 4 days, biological rep3

description: iNRAS-475 -Dox d4 3


title: Adult keratinocytes

description: Individual sample

source_name: Adult keratinocytes

value: Adult keratinocytes

value: Isolated from hair folicle in Zambidis laboratory, as per Peters et al. Human Embryonic and Induced Pluripotent Stem Cells, Springer Protocols Handbooks, Part 2:202-227 (2011)


title: PUER shRNA undiff repB

status: Public on Aug 08 2012

city: Chicago

first: David

last: Young

state: IL

department: Department of Medicine

institute: University of Chicago

description: PUER cell expressing the Hnrnpa0 shRNA construct prior to differentiation

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 400 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome 4x44K Oligo Microarrays (G4122F) for 17 hours at 65ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were taken down and washed per Agilent protocol.

scan_protocol: Slides were scanned with the GenePix 4000B (Molecular Devices) imaging system.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PUER cell line, hairpin vector, undifferentiated

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

growth_protocol: PUER cells were grown in suspension phenol red-free IMDM, 10% FBS, 2mM L-glutamine and 1x 2-mercaptoethanol, and supplemental IL-3 at 37ºC with 5% CO2. They were infected by spinoculation with retroviral supernatants expressing the indicated construct, sorted for GFP positivity, and then further expanded.

extract_protocol: Total RNA was extracted with STAT-60 (Tel-Test) and cleaned with the RNeasy kit (Qiagen) according to manufacturer protocols

treatment_protocol: Cells in log-phase growth were washed and suspended in growth medium with either vehicle or 2nM 4-hydroxytamoxifen for 24 hours. Undifferentiated cells were harvested prior to 4-OHT exposure to serve as undifferentiated controls.

tag: knockdown

value: Hnrnpa0 shRNA

value: undifferentiated

value: PUER


title: mouse adult liver

city: Kyoto

first: Soo Ki

last: kim

address: Shogoin-Kawaharacho 54, Sakyo-ku

institute: Graduate School of Medicine, Kyoto University

description: Gene expression of mouse adult liver.

hyb_protocol: 1.65microgram of cRNA was fragmented and hybridized to Agilent whole mouse genome oligo microarray

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1). For normalization, We used Agilent GeneSpring GX11.5.1 for data analysis. Per Chip: Normalize to 75 percentile

source_name: adult liver

label_protocol: Sample labeling was done using Agilent’s Quick Amp Labeling Kit (5190-0442: Agilent) following manufacture’s instructions. Amplified cRNAs were quantified using the Agilent 2100 bioanalyzer and RNA 6000 Nano kit.

extract_protocol: Total RNA was extracted from adult mice (12 wk old) liver tissues, bone marrow, and the fetal liver at day 13.5 of gestation using QuickGene RNA Tissue Kit (Fuji, Tokyo, Japan).

tag: strain

value: adult liver


title: mouse fetal liver

description: Gene expression of mouse fetal liver.

source_name: fetal liver

value: fetal liver


title: PUER shRNA diff repA

description: PUER cell expressing the Hnrnpa0 shRNA construct after 24 hours of 4-OHT induced differentiation

source_name: PUER cell line, hairpin vector, differentiated 24 hours

value: 4-OHT induced differentiation


title: PUER shRNA diff repB


title: PUER control diff repC

description: PUER cell expressing the control construct after 24 hours of 4-OHT induced differentiation

source_name: PUER cell line, control vector, differentiated 24 hours

value: control


title: PUER control undiff repA

description: PUER cell expressing the control construct prior to differentiation

source_name: PUER cell line, control vector, undifferentiated


title: mouse bone marrow

description: Gene expression of mouse bone marrow.

source_name: bone marrow

value: bone marrow


title: MMP13ko_granul_14d_rep2

city: Turku

first: Veli-Matti

last: Kähäri

address: Tykistökatu 6A, 4. floor

country: Finland

institute: University of Turku, Turku University Hospital

hyb_protocol: Each sample was hybridized to Mouse Genome 430 2.0 Array at +45°C overnight (18 h) according to Affymetrix GeneChip Expression Analysis Technical Manual (With Specific Protocols for Using the GeneChip Hybridization, Wash and Stain kit). GeneChip® Fluidics Station 450 was used to wash and stain the arrays.

scan_protocol: GeneChip® Scanner 3000 7G with AutoLoader was used to scan the arrays. Affymetrix GeneChip®Command Console® (AGCC) 3.1 was used to control GeneChip® Fluidics Station and Scanner and in generation of the .CEL files. After hybridization the quality was checked with AGCC and Expression ConsoleTM 1.1 and with Chipster v1.4.7 (CSC- IT Center for Science Ltd, Espoo, Finland).

data_processing: The summarized probe set data were generated using Chipster v1.4.7 (CSC- IT Center for Science Ltd, Espoo, Finland) and RMA-algorithm. For sample comparisons, subsets of the data were normalized in pairs (KO vs. WT in a given timepoint) and subjected for linear modelling using grouping and Hybridization_1/2 as main effect factors (Chipster v1.4.7).

source_name: VCS-induced subcutaneous granulation tissue in MMP13-/- -mouse harvested at day 14

label_protocol: Hybridization_1: 2 µg of total RNA was used as starting material. Biotinylated cRNA were prepared according to One-cycle Target Labeling protocol from GeneChip® Expression Analysis Technical Manual (With Specific Protocols for Using the GeneChip Hybridization, Wash and Stain kit). Hybridization_2: 250 ng of total RNA was used as starting material. Biotinylated cRNA were prepared according to Affymetrix GeneChip 3'IVT Express Kit protocol (Part no. 901228). In both, before and after the amplifications the total RNA / cRNA concentrations were checked with Nanodrop ND-1000 and totalRNA / cRNA quality was controlled by BioRad's Experion / Agilent's Bioanalyzer electrophoresis station.

growth_protocol: WT and Mmp13-/- mice (Inada et al.  2004, PNAS, 101: 17192-17197) 5 to 8 weeks of age were used in the study. The mice were fed standard chow and water ad lipitum.

extract_protocol: The mice were sacrificed 7, 14, and 21 days after implantation, and the sponges were removed and cut into four pieces. The ends of the rectangular VCS were frozen in liquid nitrogen for RNA extraction. The total RNA was extracted according to manufacturer's instructions and eluted in sterile water (Qiagen RNeasy kit, Qiagen GmbH, Hilden, Germany).

treatment_protocol: All mouse experiments were performed according to the institutional guidelines (University of Turku, Finland) and with the permission of the animal test review board of the Regional Government of Southern Finland. The establishment of experimental granulation tissue was performed as previously described (Inkinen et al. 2000, APMIS, 108: 318-328 ;Laato et al. 1987,  Biochem J, 247: 385-388). The mice were anesthetized with Hypnorm-Dormicum solution. A single vertical incision was made to dorsal skin under aseptic conditions, a sterile rectangular viscose cellulose sponge (VCS; Cellomeda Oy, Turku, Finland) of size 5x5x10 mm was implanted horizontally under the skin at cranial location, and the wound was closed with continuous monofilament 4-0 suture (Prolene; Ethicon, Norderstedt, Germany).

value: C57BL/6 x 129 mixed

tag: time point

value: day 14


title: PUER shRNA undiff repA


title: MMP13ko_granul_7d_rep3

source_name: VCS-induced subcutaneous granulation tissue in MMP13-/- -mouse harvested at day 7

value: day 7


title: MMP13ko_granul_14d_rep1


title: MMP13ko_granul_7d_rep1


title: MMP13ko_granul_14d_rep3


title: PUER control undiff repC


title: PUER shRNA undiff repC


title: MMP13ko_granul_21d_rep2

source_name: VCS-induced subcutaneous granulation tissue in MMP13-/- -mouse harvested at day 21

value: day 21


title: MMP13ko_granul_21d_rep3


title: MMP13ko_granul_7d_rep2


title: WT_granul_21d_rep3

source_name: VCS-induced subcutaneous granulation tissue in WT-mouse harvested at day 21

value: WT


title: WT_granul_21d_rep4


title: WT_granul_21d_rep2


title: MMP13ko_granul_21d_rep4


title: MMP13ko_granul_21d_rep1


title: MMP13ko_granul_14d_rep4


title: PUER control diff repB


title: PUER control undiff repB


title: WT_granul_14d_rep4

source_name: VCS-induced subcutaneous granulation tissue in WT-mouse harvested at day 14


title: Day 4, rep 3

city: Bangi

first: Abdul Munir

last: Abdul Murad

state: Selangor

address: Jalan Universiti

department: Faculty of Science & Technology

country: Malaysia

institute: Universiti Kebangsaan Malaysia

description: Biological replicate 3 of 3 day 4 post infection.

hyb_protocol: Prehybridization of slides was according to Hegde et al. (2000). A Concise Guide to cDNA Microarray Analysis-II. Biotechniques 29(3):548-562. Labelled cDNA were hybridized to the L. calcarifer array and put inside an incubation chamber (Genetix, UK). The incubation chamber was placed in a water bath for 18 h at 42 °C. Arrays then were washed according to Corning® GAPS II  slide (USA) instructions.

scan_protocol: Arrays were scanned immediately with a GenePix 4100A (Axon Instruments, USA) scanner, software GenePixTM Pro 6.0.

data_processing: The GenePix results (.gpr) file was further analyzed by GeneSpring GX 7.3.1, which applied intensity-dependent LOWESS normalization to the results and calculated normalized Cy5 to Cy3 ratios.

organism: Lates calcarifer

source_name: Liver tissue, Control, Day 4 post infection

label_protocol: 10 μg total RNA were converted to cDNA and labeled with either a Cy3 or Cy5 dye using the Post labelling CyscribeTM kit (Amersham Biosciences, USA) as per manufacturerss instructions. Samples were purified using the CyScribeTM GFXTM purification kit (Amersham Biosciences, USA) before hybridization.

extract_protocol: Snaped frozen liver's tissue were homogenized with mortar and pestle, and total RNA was extracted using TRIREAGENT® (Molecular Research Center, USA) following the manufacturer’s instructions. The quality and quantity of the total RNA were determinate by NanoDrop Spectrophotometer ND-1000 (Nanodrop Technologies, USA) and Agilent 2100 Bioanalyzer (Agilent, USA).

treatment_protocol: Fish were screened for ectoparasites via body and gill smears, acclimatized for 2 weeks and later randomly separated into infected and control groups. Every fish in the infected group was challenged with 4,000-8,000 therons individually.

value: liver

tag: developmental stage

value: juvenile

tag: condition

tag: time post-infection

value: day 4

source_name: Liver tissue, Infected, Day 4 post infection

value: infected


title: Day 4 swap, rep 3

description: Biological replicate (dye-swap) 3 of 3 Day 4 post infection.

tag: tissue


title: Day 4 swap, rep 2

description: Biological replicate (dye-swap) 2 of 3 day 4 post infection.


title: Day 4, rep 2

description: Biological replicate 2 of 3 day 4 post infection.


title: Day 4, rep 1

description: Biological replicate 1 of 3 day 4 post infection.


title: Day 3 swap, rep 3

description: Biological replicate (dye-swap) 3 of 3 day 3 post infection.

source_name: Liver tissue, Infected, Day 3 post infection

value: day 3

source_name: Liver tissue, Control, Day 3 post infection


title: Day 4 swap, rep 1

description: Biological replicate (dye-swap) 1 of 3 day 4 post infection.


title: WT_granul_14d_rep3

tag: genotype


title: Day 3, rep 3

description: Biological replicate 3 of 3 day 3 post infection.


title: Day 3 swap, rep 2

description: Biological replicate (dye-swap) 2 of 3 day 3 post infection.


title: Day 3 swap, rep 1

description: Biological replicate (dye-swap) 1 of 3 day 3 post infection.


title: Day 3, rep 2

description: Biological replicate 2 of 3 day 3 post infection.


title: WT_granul_7d_rep3

source_name: VCS-induced subcutaneous granulation tissue in WT-mouse harvested at day 7


title: WT_granul_21d_rep1


title: Day 2 swap, rep 3

description: Biological replicate (dye-swap) 3 of 3 day 2 post infection.

source_name: Liver tissue, Infected, Day 2 post infection

value: day 2

source_name: Liver tissue, Control, Day 2 post infection


title: WT_granul_14d_rep1


title: Day 2 swap, rep 2

description: Biological replicate (dye-swap) 2 of 3 day 2 post infection.


title: WT_granul_7d_rep2


title: Day 2 swap, rep 1

description: Biological replicate (dye-swap) 1 of 3 day 2 post infection.


title: WT_granul_14d_rep2


title: Female lung, biological replicate 7

city: Hannover

first: Thomas

last: Krüwel

address: Nikolai-Fuchs-Str. 1

institute: Fraunhofer Institute for Toxicology and Experimental Medicine

description: lung tissue of a non-transgenic C57BL/6 mouse

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

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

data_processing: Data were normalized with the Probe Logarithmic Intensity Error (PLIER) algorithm. Following experimental normalization a Welch's t-Test was performed. Genes with p<0.01 and a Fold Change >2 were considered as differentially expressed.

source_name: non-transgenic lung tissue

label_protocol: Total RNA (200 ng) was used to generate biotin-labelled cRNA (10 µg) by means of GeneChip 3' IVT Express Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing; Agilent Technologies, Böblingen, Germany).

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; PAA, Cölbe, Germany) supplemented with 10% foetal calf serum, 2 mmol/l L-glutamine, 100 units/ml streptomycin and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37°C. Cells were plated in 96well microtiter plates at a density of 5000 cells/well 24 h prior treatment.

extract_protocol: RNA-extraction was done with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.

treatment_protocol: Cells were treated with a monoclonal anti-mouse EpCAM antibody at concentrations of 100 µg/ml for 48 h. Subsequently, 10^6 cells/ml were resuspended in warm DMEM containing 2% FCS and 10 mmol/l HEPES buffer (Sigma-Aldrich, Munich, Germany). Hoechst 33342 dye was added to a final concentration of 5 µg/ml in the presence or absence of reserpine (50 µmol/l; Sigma-Aldrich, Munich, Germany) and incubated at 37°C for 90 min with gentle shaking. Afterwards, the cells were centrifuged at 4°C and resuspended in ice-cold Hank's balanced salt solution (HBSS, Invitrogen, Karlsruhe, Germany) containing 2% FCS and 10 mmol/l HEPES. Viable cells were visualized by propidium iodide staining (Invitrogen, Karlsruhe, Germany) and was added to a final concentration of 2 µg/ml. The cells were filtered by a 40 µm cell strainer to obtain a single cell suspension before sorting. Analyses and sorting were carried out on a FACSAria cytometer (Becton Dickinson, Heidelberg, Germany). Emissions of Hoechst 33342 (Hoechst-red and Hoechst-blue) were detected using 695/40 nm band-pass and 450/40 nm band-pass filters, respectively.

tag: background strain

tag: gender

value: female


title: Day 2, rep 1

description: Biological replicate 1 of 3 day 2 post infection.


title: Day 3, rep 1

description: Biological replicate 1 of 3 day 3 post infection.


title: Day 2, rep 2

description: Biological replicate 2 of 3 day 2 post infection.


title: Female lung, biological replicate 8


title: WT_granul_7d_rep1


title: Day 1 swap, rep 2

description: Biological replicate (dye-swap) 2 of 3 day 1 post infection.

source_name: Liver tissue, Infected, Day 1 post infection

value: day 1

source_name: Liver tissue, Control, Day 1 post infection


title: Day 1 swap, rep 3

description: Biological replicate (dye-swap) 3 of 3 day 1 post infection.


title: Female lung, biological replicate 5


title: Female lung, biological replicate 4


title: Female lung, biological replicate 3


title: Female lung, biological replicate 6


title: Female lung, biological replicate 2


title: Day 1 swap, rep 1

description: Biological replicate (dye-swap) 1 of 3 day 1 post infection.


title: Male lung, biological replicate 8

value: male


title: Day 2, rep 3

description: Biological replicate 3 of 3 day 2 post infection.


title: Female lung, biological replicate 1


title: Day 1, rep 2

description: Biological replicate 2 of 3 day 1 post infection.


title: Male lung, biological replicate 6


title: Day 1, rep 3

description: Biological replicate 3 of 3 day 1 post infection.


title: Day 1, rep 1

description: Biological replicate 1 of 3 day 1 post infection.


title: Male lung, biological replicate 7


title: Male lung, biological replicate 5


title: #14-43MM

city: Vienna

first: Harald

last: Scheuch

state: Vienna

address: Dr. Bohrgasse 7

department: Core Facilities

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

hyb_protocol: Probe- Prehybridisation (TECAN HS4800) Protocol for 40 domain chips:  Combine: 50µl Labeled DNA, 29µl    20x SSPE, 4µl 50x Denhardts solution, 50µl Form amid, 1.5µl   mouse block, 3.5µl 20% SDS (last component to be added), Incubate at 94°C for 2 min; Prehybridise probe for at least 1 hour at 50°C, start prehybridization of the slides, After prehyb of the samples and the slides pipette 135 µl onto each slide.  If you have duplicates then pool and use 135µl per slide, split and pipette 140 µl onto each slide, Continue with hybridization on TECAN HS4800  for 12hours 45°C.

scan_protocol: Scanner: GenePix 4000B

data_processing: Image Analysis: GenPix Pro 6.0,  R (v.2.5.0) with Library Limma. RGbkg <- backgroundCorrect(RG, method=rma), MA <- normalizeWithinArrays(RGbkg), fit <- lmFit(MA, design), Replicates are averaged.

source_name: afc2-3/4-14 liver DEN 48hrs

label_protocol: Labeling with a Reactive Fluorescent Dye/ Molecular probes (Alexa 555, 647); Thoroughly dissolve the amine-modified 4µg DNA in 5µl  nuclease free H2O (warming to 42°C for 5 min if necessary), Add 3µl  Labeling buffer (Just before use dissolve one vial of reactive dye in 10-20µl DMSO or use aliquots from –80°C), Add 2µl  reactive dye to the samples, vortex briefly to mix (do not spin), Incubate for 1 hour in the dark at room temperature.

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

tag: strain background

value: mixed C57Bl/6; 129Sv

tag: age

value: 4 weeks

tag: genotype/variation

value: Alfp-cre-/c-jun f/f

tag: treated with

value: diethylnitrosamine 100mg/kg body weight

value: 48hours after DEN treament

tag: hybridization chip

source_name: a mix from all samples

value: equal parts of each sample pooled


title: Male lung, biological replicate 4


title: #18-43MM

source_name: Afc4-18 liver DEN 0hrs

value: Alfp-cre+/c-junf/f

value: before DEN treatment

tag: sample type


title: Male lung, biological replicate 3


title: #19-43MM

source_name: Afc4-19 liver DEN 0hrs

value: liver


title: A2C12 anti-EpCAM treated SP cells biological replicate 3

description: lung tumour cell line from a c-myc/c-raf double transgenic mouse model (background C57BL/6)

source_name: A2C12 anti-EpCAM treated SP cells

tag: cell line

tag: cell fraction

value: SP


title: #12-43MM

source_name: afc2-3/4-12 liver DEN 48hrs


title: Male lung, biological replicate 1


title: PUER control diff repA

description: PUER cell expressing the control construct after 24 hours of 4-OHT induced differentiation

source_name: PUER cell line, control vector, differentiated 24 hours

tag: knockdown

value: control

tag: treatment

value: 4-OHT induced differentiation

value: PUER


title: #13-43MM

source_name: afc2-3/4-13 liver DEN 48hrs

tag: time point


title: Male lung, biological replicate 2


title: B cell of TG mouse 2

city: CHONGQING

first: qiuye

last: guo

address: GAO TAN YAN

institute: The military medical university

scan_protocol: reference to the manual of Affymetrix (GeneAtlas™ 3’ IVT Express Kit), follow the manuscipts of GeneAtlas Workstation.

data_processing: Command Console CHP file version 1, affymetrix-algorithm-name = rma, affymetrix-algorithm-version = 1.0, affymetrix-array-type = HT_MG-430_PM

source_name: B cells of transgenic mice

extract_protocol: B cells were isolated from lymph nodes with untouched magnetic separated assay, and dead cells were depleted with Dead Cell Removal Kit (Miltenyi Biotec). Cells were lysated with TRIzol reagent (Invitrogen). Transfer upper phase containing the RNA (final ethanol concentration of 35%) to a RNeasy spin cartridge and follow the manufacture’s guide (Qiangen).

tag: genetic background

value: Balb/C

tag: cell type

value: B cell from lymph nodes

value: miR-146a transgenic


title: #19-41MM

value: male

tag: tissue


title: #11-43MM

source_name: afc2-3/4-11 liver DEN 48hrs

value: mixed C57Bl/6; 129Sv


title: B cell of WT mouse 2

hyb_protocol: reference to the manual of Affymetrix (GeneAtlas™ 3’ IVT Express Kit)

source_name: B cells of wild type mouse

tag: genotype

value: wild type


title: B cell of TG mouse 1

label_protocol: reference to the manual of Affymetrix (GeneAtlas™ 3’ IVT Express Kit)


title: #18-41MM

value: 4 weeks


title: A2C12 anti-EpCAM treated SP cells biological replicate 2

tag: background strain


title: #13-41MM

tag: gender

value: diethylnitrosamine 100mg/kg body weight


title: #19-40MM

tag: strain background

value: Alfp-cre-/c-jun f/f


title: A2C12 anti-EpCAM treated SP cells biological replicate 1


title: #14-41MM

tag: age

value: 48hours after DEN treament

value: equal parts of each sample pooled


title: nemacIL4_3 signal

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

description: raw data: slide6.txt (rows 1 to 20820)

hyb_protocol: The arrays were incubated at 60°C for 16 hours in a hybridisation oven.

scan_protocol: After hybridisation the slides were manually washed for 2 minutes in Buffer A at 60oC, rinsed in Buffer B followed by a 2-minute wash in buffer B at RT and 2 minutes in Buffer C at RT. All buffers were supplied by EXIQON. After washing the slides were dried by centrifugation for 2 minutes at 1000rpm. The slides were immediately scanned using an Agilent G2565BA scanner with a spot size of 10um and 100% PMT gain.

data_processing: Each slide contains two arrays. Two samples were run per slide in separate hybridisation chmabers. Rows 1 to 20820 represent signals for one biological sample and rows 20821 to  41557 represent signals for the second biological sample on the slide. QuantArray software was used to quantify the signals from the Agilent scanner using the fixed circle approach. Background subtracted signal intensities were normalized in R using quantile normalization.

source_name: Nematode (Brugia malayi) elicited peritoneal macrophages from IL4 receptor KO BALB/c mice

label_protocol: Samples were labelled using Exiqon’s miRCURY LNA array labelling kit (Vedbæk, Denmark): 1ug total RNA was incubated with labelling buffer, the Hy3 dye, labelling enzyme and spike-in microRNAs for 1 hour at 37°C. The enzyme was then heat-inactivated at 65°C for 15 minutes, followed by addition of 2 x hybridisation buffer. The samples were incubated at 95°C for 5 minutes while protected from light. The samples were then briefly spun down and filtered through a 0.45-micron durapore filter (Millipore), and 40 ul sample was loaded to the arrays by capillary force using a cover slip (Erie Scientific).

growth_protocol: Peritoneal macrophages were elicited 3 days after intraperitoneal thioglycollate injection or 21 days after peritoneal implant of the nematode Brugia malayi. These latter macrophages are termed nematode elicited macrophages (NeMacs).

extract_protocol: Total RNA was isolated from macrophages lysed in Qiazol using the miRNEasy-kit (Qiagen) according to the manufacturers instructions. Briefly the RNA from lysed cells was precipitated using Phenol-Chloroform-extraction and the aequeous supernatant purified over a spin-column. RNA-content was determined using a NanoDrop (Thermo Scientific).

treatment_protocol: Peritoneal exudate cells were seeded at 5x10^6 cells per well to 6-well cell-culture plates (NUNC) in RPMI, 5% FCS, 2 mM L-glutamine, 0.25 U/mL penicillin and 100 mg/mL streptomycin. After 4 hours incubation at 37oC / 5% CO2 non-adherent cells were washed off and the adherent MΦs detached using a rubber-policeman. Detached cells were > 80% pure as assessed by flow-cytometry (FACS) analysis of their F4/80 and CD11b surface expression.

value: IL4 receptor ko peritoneal macrophages

tag: mouse strain

value: BALB/c

tag: activation status

value: Nematode (Brugia malayi) elicited


title: nemacIL4_4 signal

description: raw data: slide6.txt (rows 20821 to 41557)


title: PUER shRNA diff repC

description: PUER cell expressing the Hnrnpa0 shRNA construct after 24 hours of 4-OHT induced differentiation

source_name: PUER cell line, hairpin vector, differentiated 24 hours

value: Hnrnpa0 shRNA


title: nemacIL4_2 signal

description: raw data: slide15.txt (rows 20821 to 41557)


title: #12-41MM

tag: genotype/variation

value: Alfp-cre+/c-junf/f

tag: treated with

value: liver

tag: hybridization chip


title: #18-40MM

value: before DEN treatment

tag: sample type


title: B cell of WT mouse 1

source_name: B CELLS

value: Balb/C

value: B cell from lymph nodes


title: nemacIL4_1 signal

description: raw data: slide15.txt (rows 1 to 20821)


title: #14-40MM

value: male


title: A2C12 SP cells biological replicate 2

source_name: A2C12 SP cells

tag: cell line

tag: cell fraction

value: SP


title: A2C12 SP cells biological replicate 1


title: #13-40MM

value: mixed C57Bl/6; 129Sv

tag: time point


title: #12-40MM

value: 4 weeks


title: nemacWT_4 signal

description: raw data: slide7.txt (rows 20821 to 41557)

source_name: Nematode (Brugia malayi) elicited peritoneal macrophages from wild type BALB/c mice

value: WT peritoneal macrophages


title: #11-41MM

value: Alfp-cre-/c-jun f/f

value: diethylnitrosamine 100mg/kg body weight


title: nemacWT_3 signal

description: raw data: slide7.txt (rows 1 to 20821)


title: #19-35MM

data_processing: Image Analysis: GenPix Pro 6.0,  R (v. 2.5.0) with Library Limma. RGbkg <- backgroundCorrect(RG, method=rma), MA <- normalizeWithinArrays(RGbkg), fit <- lmFit(MA, design), Replicates are averaged.

value: equal parts of each sample pooled


title: #11-40MM

value: 48hours after DEN treament


title: #18-35MM


title: nemacWT_2 signal

description: raw data: slide9.txt (rows 20821 to 41557)

value: BALB/c


title: A2C12 SP cells biological replicate 3


description: lung tumour cell line from a c-myc/c-raf double transgenic mouse model

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

data_processing: Data were normalized with the Robust Microarray Averaging (RMA) algorithm. Following experimental normalization signals < 50 were defined as background. Expression values were calculated as the ratio of non-stimulated (control) and anti-EpCAM stimulated SP vs. non-SP signals. Gene expression that was at least 25% increased or decreased in replicate experiments was considered as differentially expressed.

tag: treatment

value: anti-EpCAM


title: nemacWT_1 signal

description: raw data: slide9.txt (rows 1 to 20821)

value: Nematode (Brugia malayi) elicited


title: thioIL4_2 signal

description: raw data: slide14.txt (rows 1 to 20821)

source_name: Thioglycollate elicited peritoneal macrophages from IL4 receptor KO BALB/c mice

value: IL4 receptor ko peritoneal macrophages

value: Thioglycollate elicited


title: thioIL4_3 signal

description: raw data: slide14.txt (rows 20821 to 41557)


title: A2C12 SP cells biological replicate 2


title: #12-35MM

value: Alfp-cre+/c-junf/f

value: liver


title: #13-35MM


title: thioIL4_1 signal

description: raw data: slide12.txt (rows 1 to 20821)


title: #14-35MM

source_name: afc2-3/4-14 liver DEN 48hrs


title: A2C12 SP cells biological replicate 3


title: wt_rep4

city: Milan

first: Francesca

middle: R.

last: Santoni de Sio

address: via Olgettina 58

department: SR-TIGET

country: Italy

institute: San Raffaele Scientific Institute

hyb_protocol: Hybridization on Mouse WG 6 v2 expression arrays (Illumina) was carried out according to the manufacturer’s instructions

scan_protocol: Scanning was carried out according to the manufacturer’s instructions

data_processing:
Data were normalized and analyzed using Illumina Beadstudio 3.1.3 (background correction and quantile normalization)
Expression profiles of each sample were imported into GeneSpringGX 7.3.1 (Agilent Technologies, USA).
In addition to expression values, Illumina BeadStudio software computes a detection p-value. Based on this, each probe was assigned a detection flag (P (present): p < 0.045; M (Marginal): p between 0.050 and 0.045, A (Absent): p>0.05). Expression values below a defined threshold (i.e. 20) are set to the threshold in order to remove negative values after background correction. To identify dysregulated genes in KO mice, t-test and/or ANOVA and additional steps of filtering were carried out.

source_name: Thymus

label_protocol: 100 ng of RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit (Ambion)

extract_protocol: 8-12 weeks old mouse lymphocytes from 3 KO and 3 littermate control C57/bl6-129sv mice were mechanically extracted from thymus. Total RNA was extracted by MirVana kit (Ambion) and treated with DNAse (Turbo DNA free kit, Ambion), following manufacturer instructions. Quality control for RNA integrity was performed by capillary electrophoresis on Agilent 2100 Bioanalyzer,

value: 8-12 weeks

tag: strain

value: WT


title: A2C12 anti-EpCAM treated non-SP cells biological replicate 2

source_name: A2C12 anti-EpCAM treated non-SP cells

value: non-SP


title: wt_rep6


title: A549 anti-EpCAM treated SP cells biological replicate 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome-U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: A549 anti-EpCAM treated SP cells

tag: cell type

value: lung adenocarcinoma

value: SP


title: #11-35MM

value: mixed C57Bl/6; 129Sv

value: male

value: 4 weeks

tag: genotype

tag: tissue

source_name: a mix from all samples


title: wt_rep5


title: KO_rep2

value: KAP1 KO


title: A2C12 anti-EpCAM treated non-SP cells biological replicate 3

tag: background strain


title: A549 anti-EpCAM treated SP cells biological replicate 3


title: A549 anti-EpCAM treated SP cells biological replicate 1


title: KO_rep3


title: thiowt_3 signal

description: raw data: slide12.txt (rows 20821 to 41557)

source_name: Thioglycollate peritoneal elicited macrophages from wild type BALB/c mice

value: WT peritoneal macrophages


title: thiowt_1 signal

description: raw data: slide10.txt (rows 1 to 20821)

value: BALB/c