title: B33

status: Public on Apr 14 2015

city: Paris

first: Hélène

last: LAPILLONNE

address: 27 Rue de Chaligny

department: UMR_S938 CDR Saint-Antoine

country: France

institute: UPMC Univ Paris 06

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.5.1.1 ) was used to read out and process the microarray image files.

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

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

tag: sample type

value: hESC-H1-EB20-Day18 erythroid cells

tag: cell type

value: erythroid cells


title: b5_40_0_t=24h

status: Public on Apr 15 2015

type: RNA

city: Cambridge

first: Sallie

middle: W

last: Chisholm

state: MA

address: 15 Vassar St., Bldg. 48-419

country: USA

institute: MIT

description: Gene expression of MED4 after resuspension in CO2- and O2-limited medium

hyb_protocol: Hybridization and staining were performed by the MIT BioMicro Center.  All reagents were supplied by Affymetrix.  12.5 μg aRNA was hybridized to the MD4-9313 custom Affymetrix array in aqueous hybridization mix during a 16-h incubation at 45°C with rotation at 60 rpm in a GeneChip Hybridization Oven 640.  Hybridized arrays were washed with buffers A (non-stringent) and B (stringent), stained with streptavidin in stain buffer, and washed again with buffer A according to protocol ProkGE_WS2_450 in a GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G.

data_processing: Data processing was performed in R.  Chip images were processed using the package Harshlight prior to robust multi-chip average (RMA) normalization using the package affy.  The Affymetrix chip-definition file used (MD4-9313a520062.2014-06-27.cdf) was updated in June 2014 to reflect recently discovered non-coding RNAs.  Following RMA normalization, the dataset was filtered include only strain-specific probes and to exclude intergenic regions.

label: biotin

molecule: total RNA

organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

source_name: MED4 culture 24 h after resuspension in medium bubbled with 0.004% CO2 and 0% O2, biological rep 1

label_protocol: RNA amplification and biotin labeling were performed by the MIT BioMicro Center using the MessageAmp II - Bacteria kit (Ambion) according to the manufacturer's protocol, using 200 ng input RNA.

growth_protocol: Axenic Prochlorococcus MED4 was grown in Sargasso seawater-based Pro99 medium [Moore et al., 2007] amended with 20-mM Na-HEPES pH 8.1.  Cultures were grown in 25-mm glass tubes at 21 degrees C with continuous illumination at ~60 micromol photons per m^2 per s for >30 generations prior to inoculation of experimental cultures.  1.2-L experimental cultures were grown to mid-log phase in clear 2-L bottles sparged with air.

extract_protocol: Cell suspensions were thawed in small batches and processed with the Zymo Research Mini RNA Isolation II kit.  The manufacturer's protocol was followed except that cell lysis was allowed to continue for 20 min on ice.  DNA was removed by treating 1 µg total nucleic acids with 2 µL Turbo DNAfree (Ambion) in a 50-µL reaction for 1 h, followed by DNase inactivation according to the manufacturer’s protocol.  RNA was concentrated by ethanol precipitation and yields were quantified with Ribogreen (Molecular Probes).

treatment_protocol: Experimental cultures were pelleted and resuspended.  Suspensions were split among four 500-mL bottles, each containing medium pre-equilibrated with a different gas (40_0: 0.004% CO2, 0% O2, balance N2; 40_21: 0.004% CO2, 21% O2, balance N2; 360_0: 0.036% CO2, 0% O2, balance N2; air (control): ambient air) by vigorous sparging for 24 h.  Bottles were swirled to mix and immediately sampled for the t = 0 timepoint.  Sparging continued throughout the 24-h timecourse.  At each timepoint, 20-mL samples were collected and pelleted (12500 rpm, 10 minutes, 4 degrees C, JA-25.50 rotor).  Supernatants were immediately discarded and each pellet resuspended in 500 µL resuspension buffer (200 mM sucrose, 10 mM NaOAc pH 5.2, 5 mM EDTA).  Cell suspensions were transferred to 1.5-mL tubes and flash-frozen in liquid nitrogen.  Sampling for each timepoint was completed within 20 min (from withdrawal of samples to flash-freezing).

tag: genbank synonym

value: Prochlorococcus marinus MED4

tag: time


title: ESC T0 2

type: genomic

city: Boston

first: Adam

middle: C

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description:
Sample name: H9 T0
Gene methylation data from the H9 embryonic stem cell line profiled at T0.

hyb_protocol: Overnight hybridization to BeadChip arrays.

scan_protocol: Next day staining of hybridized arrays produced methylation-dependent differential fluorescence that was detected via an Illumina iScan array scanner.

data_processing: Arrays were visualized and processed using the GenomeStudio software package, which produced IDAT files that were read into a MethyLumiSet using the methylumIDAT function in the methylumi R package (version 2.4.0).  This object was then coerced to a MethyLumiM object and quantile-normalized by sequentially applying the lumiMethyC and lumiMethyN functions from the lumi R package (version 2.10.0).  All methylation analyses were performed using the R environment for statistical computing (version 2.15.1).

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: H9 embryonic stem cell line

label_protocol: 500ng gDNA underwent bisulfite conversion of unmethylated cytosine bases to uracil, and bisulfite converted DNA was then amplified and purified

growth_protocol: iPSC and ESC lines were maintained in “hiPSC Media” composed of DMEM/F12 (Sigma-Aldrich, www.sigma.com) with 20% KnockOut Serum Replacement (Invitrogen, www.invitrogen.com), 1mM nonanimal  L-glutamine (Sigma-Aldrich), 0.1mM Β-mercaptoethanol, and 10 ng/ml FGF2 (R&D Systems, Minneapolis, MN) on 0.1% gelatin (Sigma-Aldrich) coated plates preseeded with mitomycin C-inactivated or irradiated mouse embryonic fibroblast (MEF) feeder cells.  Cells were maintained in a 5% CO2 air environment. For endodermal differentiation, cells were passed onto matrigel-coated dishes at 80% confluency.  On the following day, designated “T0”, differentiation was induced by culture in media containing growth factors listed below.  From T0-T6, differentiation media included 2mM l-glutamine, and 4.5x10-4 M monothioglycerol (MTG).  Cells were grown in T0 media, consisting of RPMI-based serum-free medium with Chir 99021 (2ug/ml) and Activin A (100 ng/ml), for one day. On days “T1-2”, medium was changed to RPMI with BMP4 (0.5 ng/ml), FGF2 (10ng/ml), Activin A (100 ng/ml), and VEGF (10 ng/ml).  On days “T3-4”, cells were cultured in SFD media(Gouon-Evans et al., 2006) with BMP4 (0.5 ng/ml), FGF2 (10ng/ml), Activin A (100 ng/ml), and VEGF (10 ng/ml). For hepatic differentiation, PSCs were differentiated as monolayer cultures as outlined above to generate definitive endoderm and then further differentiated for an additional 3 weeks in SFD-based media with ascorbic acid (50mcg/ml), monothioglycerol (4.5x10-4 M ), and the following supplements: T7-12: BMP4 (50 ng/ml), FGF2 (10 ng/ml), VEGF (10 ng/ml), EGF (10ng/ml), TGFa (20 ng/ml), HGF (100 ng/ml), and 0.1 uM Dexamethasone; T13-18: FGF2 (10 ng/ml), VEGF (10 ng/ml), EGF (10 ng/ml), HGF (100 ng/ml), Oncostatin M (20 ng/ml), Vitamin K (6 ug/ml), 1.5 uM gamma secretase inhibitor, 0.1 uM Dexamethasone, and 1% DMSO; T19-24: HGF (100 ng/ml), Oncostatin M (20 ng/ml), Vitamin K (6 ug/ml), and 0.1 uM Dexamethasone. Differentiating human PSCs were maintained in a 5% CO2, 5% O2, 90% N2 environment.

extract_protocol: According to Illumina protocol

treatment_protocol: Aside from differentiation and sorting as described above, cells were not treated in any specific manner prior to DNA/RNA extraction.

tag: cell line

value: ESC H9

tag: Stage

tag: group

value: ESC


title: B23


title: B31


title: B21

value: hESC-H1-EB9-Day18 erythroid cells


title: B13


title: B11


title: Cic-L-/- rep 4

city: Daegue

first: Jieon

last: Lee

address: 333. Techno Jungang-daero Hyeongpung-myeon, Dalseong-gun

department: Chemical Engineering

country: South Korea

institute: POSTECH

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization

organism: Mus musculus

source_name: Mouse liver

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNA was isolated with Qiagen RNeasy Mini Kit in accordance with prescribed protocal provided with kit. Quality control was performed with Agilent 2100 Bioanalyzer

tag: strain

tag: age

value: 18 day

tag: tissue

value: liver

tag: genotype

value: Cic-L-/-


title: gDNA-7E-vs-VMA7

city: Albuquerque

first: Ulfar

last: Bergthorsson

state: New Mexico

address: 219 Yale Blvd NE

department: Biology

institute: University of New Mexico

hyb_protocol: The sample was rehydrated in 40 μl of NimbleGen Hybridization Buffer (NimbleGen Systems, Inc.), denatured at 95 °C for 5 min, and then cooled to 42 °C. Hybridizations were carried out for 18 hr at 42 °C in the NimbleGen Service Laboratory. The arrays were washed using a NimbleGen Wash Buffer System (NimbleGen Systems, Inc.) and immediately dried down by centrifugation. See Selzer,R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44:305-319 (PMID 16075461).

scan_protocol: The scanner used was an Axon Scanner (Model # 40008). See Selzer,R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44:305-319 (PMID 16075461).

data_processing: The raw log2 intensity ratios were normalized with the LOESS regression.

organism: Caenorhabditis elegans

source_name: VMA7 gDNA from populations

label_protocol: Cy3/Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 μl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 μl/ml β-Mercaptoethanol. 1 μg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 °C and then chilled on ice in 0.2 ml PCR tubes. 10 μl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP, and dTTP), 8 μl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixede well with a pipet. Samples were centrifuged and incubated at 37 °C for 2 hours. 10 μl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precpitated by adding 11.5 μl 0.5 M NaCl and 110 μl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrfuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 μl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 μl DI water. DNA concentration was measured using a spectrophotometer. See Maydan JS, Lorch A, Edgley ML, Flibotte S, and Moerman DG. 2010. Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans. BMC Genomics Jan 25;11:62 (PMID: 20100350)

growth_protocol: Large populations maintained on agar plates and fed E coli bacteria prior to freezing and DNA extraction.

extract_protocol: DNA was prepared either by standard phenol-chloroform extraction followed by ethanol precipitation, or with the Puregene DNA Purification Kit (D-7000A, Gentra Systems) using solid tissue protocol.

treatment_protocol: Mutation accumulation via Msh-2 knockdown and population bottlenecking

tag: subline

value: VMA7 ancestral

source_name: 7E gDNA from populations.

treatment_protocol: Fitness recovery from mutation accumulation in large populations.


title: gDNA-7D-vs-VMA7

source_name: 7D gDNA from populations.


title: A31

value: embryoid body cells


title: A33


title: gDNA-7A_2-vs-VMA7

source_name: 7A gDNA from populations.


title: A21

value: hESC-H1 EB9-Day0


title: A11


title: A23


title: gDNA-7A-vs-VMA7


title: gDNA-7B-vs-VMA7

source_name: 7B gDNA from populations.


title: ESC T0 1

description:
Sample name: H1 T0
Gene methylation data from the H1 embryonic stem cell line profiled at T0.

source_name: H1 embryonic stem cell line

value: ESC H1


title: Tesa_PFC-8

city: Austin

first: Laura

last: Ferguson

state: TX

address: 1601 Trinity St Bldg. B, Rm 5.222

department: Waggoner Center for Alcohol and Addiction Research

institute: Dell Medical School, University of Texas at Austin

hyb_protocol: aliquots of labeled cRNA were sent to the Yale Center for Genome Analysis (West Haven, CT) where they were hybridized to Illumina® MouseWG-6 v2 Expression BeadChips (Illumina, Inc., San Diego, CA). Each beadchip contains six independent arrays. Samples were counterbalanced to avoid batch effects.

scan_protocol: The amount of each transcript for each animal was measured by fluorescent intensity after scanning.

data_processing: Microarray data were analyzed using R and Microsoft Excel. Each tissue was analyzed separately. Quality assessment of the data using Bioconductor arrayQualityMetrics package resulted in the removal of 8 outliers: amygdala 3 (saline-treated), 16 (feno-treated) and 31 (beza-treated), PFC 6 (tesa-treated) and 36 (feno-treated) and liver 11 (beza-treated), 27 (tesa-treated) and 36 (feno-treated). Liver 11 and 36, amygdala 16 and 31, and PFC 6 and 36 were on a faulty beadchip. Variance stabilization transformation and quantile normalization were used to pre-process the data using the Bioconductor Lumi package. Please note that in the normalized data provided, all samples of one tissue were normalized together after the removal of the previously mentioned outliers.  Also note that the probes that are not reliably expressed have not been removed or the Grubb's test performed in the normalized data file provided. For differential expression analysis, groups being compared were normalized together, i.e., saline and beza, saline and tesa, and saline and feno. Lastly, outlier values for each gene within a group were removed using Grubbs’ test (p-value<0.05).

source_name: mouse prefrontal cortex

label_protocol: RNA was amplified and biotin-labeled using the Illumina® TotalPrepTM RNA Amplification kit (Ambion, Austin, TX)

extract_protocol: We extracted RNA using the MagMAX-96 Total RNA Isolation Kit (Life Technologies, Grand Island, NY). Total RNA was quantified on a NanoDrop 8000 spectrophotometer (Thermo Fisher Scientific Inc., Rockford, IL) and assessed for quality using the Agilent TapeStation (Agilent Technologies, Inc., Santa Clara, CA). All samples passed quality control measures.

treatment_protocol: PPARα agonist fenofibrate (feno) (Sigma-Aldrich, St. Louis, MO), pan-PPAR agonist bezafibrate (beza) (Sigma-Aldrich, St. Louis, MO) and dual PPARα-PPARγ agonist tesaglitazar (tesa) (Tocris Bioscience, Minneapolis, MN) were freshly prepared as a suspensions in saline with 4-5 drops of Tween-80 and injected in volume 0.05 ml/10 g of body weight. Doses of drugs and routes for administration were based on published biological activity, in vivo.  We administered (p.o.) PPAR agonist or saline at 9 am for eight days at 150 mg/kg, 75 mg/kg, and 1.5 mg/kg of feno, beza, and tesa, respectively.

tag: Sex

value: male

value: mouse prefrontal cortex


title: Tesa_PFC-28


title: A13


title: Tesa_PFC-9


title: Tesa_PFC-7


title: Tesa_PFC-29


title: Tesa_PFC-30


title: Tesa_PFC-26


title: Tesa_PFC-10


title: Tesa_PFC-27


title: Saline_PFC-4


title: Saline_PFC-5


title: Saline_PFC-24


title: Saline_PFC-21


title: Feno_PFC-39


title: Feno_PFC-38


title: Feno_PFC-20


title: Saline_PFC-2


title: Feno_PFC-40


title: Saline_PFC-25


title: Saline_PFC-1


title: Saline_PFC-22


title: Saline_PFC-3


title: Feno_PFC-19


title: Feno_PFC-37


title: Beza_PFC-35


title: Beza_PFC-33


title: Beza_PFC-34


title: Feno_PFC-17


title: Feno_PFC-18


title: Feno_PFC-16


title: gDNA-7C-vs-VMA7

source_name: 7C gDNA from populations.


title: Tesa_LIVER-29

source_name: mouse liver

value: mouse liver


title: Tesa_LIVER-26


title: Saline_PFC-23


title: Saline_LIVER-1


title: Tesa_LIVER-6


title: Beza_PFC-15


title: Beza_PFC-11


title: Beza_PFC-13


title: Tesa_LIVER-9


title: Saline_LIVER-3


title: Beza_PFC-14


title: Saline_LIVER-5


title: Saline_LIVER-23


title: Saline_LIVER-24


title: Tesa_LIVER-7


title: Beza_PFC-12


title: Saline_LIVER-21


title: Beza_PFC-31


title: Tesa_LIVER-8


title: Saline_LIVER-25


title: Saline_LIVER-22


title: Saline_LIVER-4


title: Saline_LIVER-2


title: Feno_LIVER-40


title: Tesa_LIVER-28


title: Tesa_LIVER-10


title: Feno_LIVER-19


title: Feno_LIVER-38


title: Tesa_LIVER-30


title: Feno_LIVER-39


title: Feno_LIVER-37


title: Beza_LIVER-15


title: Feno_LIVER-18


title: Feno_LIVER-20


title: Beza_LIVER-31


title: Beza_LIVER-14


title: Feno_LIVER-16


title: Beza_LIVER-34


title: Beza_LIVER-12


title: Beza_LIVER-33


title: Feno_LIVER-17


title: Tesa_AMY-9

source_name: mouse amygdala

value: mouse amygdala


title: Tesa_AMY-8


title: Beza_LIVER-35


title: Beza_LIVER-32


title: Beza_LIVER-13


title: Tesa_AMY-7


title: Tesa_AMY-30


title: Tesa_AMY-28


title: Beza_PFC-32


title: Tesa_AMY-26


title: Saline_AMY-5


title: Saline_AMY-23


title: Saline_AMY-25


title: Tesa_AMY-6


title: Saline_AMY-1


title: Feno_AMY-38


title: Saline_AMY-21


title: Tesa_AMY-29


title: Beza_AMY-35


title: Feno_AMY-17


title: Beza_AMY-34


title: Beza_AMY-32


title: Beza_AMY-12


title: Tesa_AMY-10


title: Feno_AMY-36


title: Saline_AMY-4


title: Feno_AMY-18


title: Feno_AMY-37


title: Beza_AMY-33


title: Beza_AMY-15


title: Saline_AMY-24


title: Feno_AMY-40


title: Beza_AMY-13


title: Feno_AMY-20


title: Saline_AMY-22


title: Feno_AMY-19


title: Feno_AMY-39


title: Tesa_AMY-27


title: Beza_AMY-14


title: Saline_AMY-2


title: Beza_AMY-11


title: GFP NB4

city: Hong Kong

first: Cheuk Him

last: Man

address: L816, LAB BLK, FMB, HKU

country: Hong Kong

institute: HKU

description: Gene Expression data of NB4 with GFP overexpression by lenti-viral transduction

hyb_protocol: Procedures were prepared according to the standard Affymetrix protocol

data_processing: Data was analysed using GeneSpring GX default analysis

source_name: GFP overexpression in NB4

growth_protocol: Cell lines were cultured in optimum media

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

treatment_protocol: Lentivirus was applied to infect the cells and cells were harvested


title: GFP-SOX7 ML2

description: Gene Expression data of ML2 with GFP-SOX7 overexpression by lenti-viral transduction

scan_protocol: Procedures were prepared according to the standard Affymetrix protocol

source_name: GFP-SOX7 overexpression in ML2


title: GFP ML2

description: Gene Expression data of ML2 with GFP overexpression by lenti-viral transduction

source_name: GFP overexpression in ML2

label_protocol: Procedures were prepared according to the standard Affymetrix protocol


title: IL7_8

city: Hamburg

first: Christian

last: Schulze

address: Falkenried 94

country: Germany

institute: ZMNH

description: Gene expression data from CD4+ T cell fraction

data_processing: Intensity data were processed with R and Bioconductor packages to obtain quantile-normalized (robust multi-array average, RMA) intensity values.

label: Biotin

source_name: human CD4+ T cells, untouched

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol

growth_protocol: ex vivo isolated cells

extract_protocol: Total RNA was isolated by total RNA purification using selective binding columns (RNeasy Mini Kit, Qiagen), according to the manufacturer’s protocol.

treatment_protocol: peripheral blood was collected by venipuncture in heparinezed tubes and further processed by Ficoll gradient. CD4+ T cells were purified by magnetic beads (untouched). All samples have been processed within 3 hours after sampling. IL7 stimulation was done at 10 ng/ml for 6 h.

tag: disease state

value: multiple sclerosis

tag: patient

value: CD4+ T cell

tag: il7r haplotype

value: Risk

tag: effect on susceptibility to develop ms

value: positive effect

tag: treatment protocol

value: IL7 stimulation


title: untreated_6

hyb_protocol: according to the standard Affymetrix protocol

tag: cell type

value: Prot

value: neutral effect

value: unstimulated


title: IL7_4

scan_protocol: according to the standard Affymetrix protocol


title: untreated_8


title: IL7_6


title: IL7_2


title: untreated_9


title: IL7_7


title: untreated_7


title: untreated_4


title: CD45dim CD11b+ microglia_MFP2 knockout_rep1

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of purified and fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix Mouse Gene 1.0 ST arrays followed by staining and washing in a GeneChip® fluidics station 450  (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were processed with RMA (as implemented in the XPS v1.18.1 package of Bioconductor). Reported values are on log2-scale.

source_name: Whole brain microglia, MFP2 knockout

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 5.775 ng of total RNA was amplified and converted to single-stranded antisense cDNA using the NuGEN WT-Ovation Pico RNA Amplification System v1.0. Subsequently, the anti-sense cDNA was converted to the sense orientation using the NuGEN WT-Ovation Exon Module. cDNA was fragmented  and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module v2. All steps were carried out according to the manufacturers protocol (NuGEN).

extract_protocol: Total RNA was isolated from FACS sorted microglia by using the RNeasy Micro kit (Qiagen). The quality of the RNA samples was determined with an Agilent 2100 Bioanalyzer (Agilent Technologies, California, USA). Only samples with RIN values (RNA Integrity Number) higher or equal to 8 were used.

treatment_protocol: Mfp2 knockout mice and control mice were sacrificied at 17 weeks. After transcardiac perfusion with ice-cold PBS, brains were quickly dissected and mechanically homogenized with a tissue homogenizer in ice-cold HBSS containing 15mM HEPES and 0.5 % glucose (De Haas et al., 2007). Cells were filtered over a 70 μm strainer and pelleted at 220 g for 10 min at 4 °C. Contaminating myelin was removed by resuspending the pellet in 25 ml ice-cold 22% Percoll buffer, overlaying with  5 mL ice-cold PBS followed by centrifugation in a swinging bucket rotor at 950 g for 25 min at 4 °C (modified from (Yang et al., 2014)). The cells were incubated with mouse anti-CD45-FITC (eBiosciences 11-0451; 1:40) and mouse anti-CD11b-APC (eBiosciences 17-0112; 1:100) for 30 minutes at 4 °C in the dark. CD11bhigh/CD45mid cells were isolated using an Aria I fluorescence-activated cell sorter (FACS) (BD Biosciences) equipped with a 488 nm and 633 nm laser. Cells with low forward/sideward scatter profile were excluded from the isolation. Microglia yield ranged between 1 x 105 to 3 x 105 cells/mouse brain. Cells were collected in RNA lysis buffer provided with the RNeasy microkit (Qiagen, 74004).  Data from FACS sorting of CD11bhigh/CD45mid myeloid cells were analyzed using BD FACsuite software (BD Biosciences).

value: Swiss Webster

value: MFP2 knockout

tag: gender

value: female

value: 17 weeks

value: brain

value: microglia


title: IL7_3


title: Uninfected-FS140

city: Philadelphia

first: Minal

last: Caliskan

state: PA

address: 415 Curie Blvd., Room 540

department: Genetics

institute: University of Pennsylvania

data_processing: The process of quality-control checks (probes that mapped to unique Ensembl gene IDs, probes that did not contain any HapMap SNPs with minor allele frequency> 0.01 in the CEU population) resulted in retention of 26,440 probes. Among those, 13,881 autosomal probes that were detected as expressed in PBMCs (any probe with a detection P value<0.05 in at least 25% of the samples) were used in subsequent analyses. Probe intensity estimates were log2-transformed and rank-invariate normalized using scripts developed in-house by Russell Bainer ("Matrix normalized"). The effects of potential covariates (gender, virus batch, processing day, chip number, PBMC count, age, ancestry fractions)  on genome-wide gene expression levels were explored and the effects of a significant covariate, processing day was regressed out of the gene expression data ("GSE53543_Matrix_final").

label_protocol: Standard Illumina label protocol

growth_protocol: Peripheral blood mononuclear cells were isolated from whole blood samples by Ficoll-Paque separation.

extract_protocol: Total RNA was extracted using the Rneasy Plus Mini Kit

treatment_protocol: From each subject, 4 million cells were treated with media alone for 24 hours and 4 million cells were treated with media containing rhinovirus (RV16) for 24 hours

tag: subject id

value: Male

tag: sample group

value: Uninfected

value: peripheral blood mononuclear cells

tag: treated with

value: media alone for 24 hours


title: untreated_2

value: multiple sclerosis

value: CD4+ T cell


title: Uninfected-FS121


title: Uninfected-FS95

value: Female


title: IL7_9

value: Risk

value: positive effect

value: IL7 stimulation


title: CD45dim CD11b+ microglia_control_rep3

source_name: Whole brain microglia, control

value: wild type


title: Uninfected-FS125


title: CD45dim CD11b+ microglia_control_rep2

value: Swiss Webster


title: CD45dim CD11b+ microglia_MFP2 knockout_rep4

value: MFP2 knockout


title: CD45dim CD11b+ microglia_MFP2 knockout_rep2

value: female


title: CD45dim CD11b+ microglia_control_rep4

value: 17 weeks


title: untreated_3

value: neutral effect

value: unstimulated


title: RV_infected-FS104

value: Male

value: media containing rhinovirus (RV16) for 24 hrs


title: GFP-SOX7 K562

description: Gene Expression data of K562 with GFP-SOX7 overexpression by lenti-viral transduction

source_name: GFP-SOX7 overexpression in K562

tag: cell line


title: CD45dim CD11b+ microglia_MFP2 knockout_rep3

tag: strain

value: brain

value: microglia


title: CD45dim CD11b+ microglia_control_rep1

tag: age


title: RV_infected-FS105

value: peripheral blood mononuclear cells


title: Uninfected-FS101

value: Uninfected

value: media alone for 24 hours


title: RV_infected-FS133

value: Female


title: GFP-SOX7 NB4

description: Gene Expression data of NB4 with GFP-SOX7 overexpression by lenti-viral transduction

source_name: GFP-SOX7 overexpression in NB4


title: Uninfected-FS89


title: RV_infected-FS138


title: Uninfected-FS92


title: Uninfected-FS149


title: RV_infected-FS158


title: RV_infected-FS154


title: RV_infected-FS119


title: Uninfected-FS66


title: RV_infected-FS147


title: RV_infected-FS92


title: Uninfected-FS150


title: RV_infected-FS111


title: RV_infected-FS114


title: Uninfected-FS117


title: RV_infected-FS130


title: Uninfected-FS124


title: Uninfected-FS104


title: RV_infected-FS112


title: RV_infected-FS75


title: Uninfected-FS91


title: RV_infected-FS63


title: Uninfected-FS122


title: Uninfected-FS158


title: RV_infected-FS126


title: Uninfected-FS153


title: Uninfected-FS54


title: RV_infected-FS129


title: RV_infected-FS131


title: RV_infected-FS132


title: GFP K562

description: Gene Expression data of K562 with GFP overexpression by lenti-viral transduction

source_name: GFP overexpression in K562


title: Uninfected-FS141


title: RV_infected-FS80


title: RV_infected-FS109


title: Uninfected-FS74


title: Uninfected-FS88


title: Uninfected-FS161


title: RV_infected-FS60


title: Uninfected-FS136


title: RV_infected-FS61


title: RV_infected-FS122


title: RV_infected-FS135


title: RV_infected-FS157


title: RV_infected-FS85


title: Uninfected-FS80


title: Uninfected-FS147


title: Uninfected-FS75


title: RV_infected-FS81


title: RV_infected-FS54


title: Uninfected-FS84


title: RV_infected-FS82


title: Uninfected-FS77


title: Uninfected-FS160


title: RV_infected-FS155


title: RV_infected-FS66


title: Uninfected-FS145


title: Uninfected-FS97


title: Uninfected-FS129


title: RV_infected-FS99


title: RV_infected-FS100


title: Uninfected-FS132


title: Uninfected-FS138


title: Uninfected-FS94


title: Uninfected-FS70


title: Uninfected-FS87


title: Uninfected-FS139


title: RV_infected-FS70


title: RV_infected-FS58


title: Uninfected-FS78


title: RV_infected-FS89


title: Uninfected-FS52


title: RV_infected-FS106


title: RV_infected-FS121


title: Uninfected-FS143


title: Uninfected-FS85


title: RV_infected-FS159


title: RV_infected-FS56


title: Uninfected-FS63


title: RV_infected-FS153


title: Uninfected-FS96


title: Uninfected-FS81


title: RV_infected-FS107


title: RV_infected-FS91


title: Uninfected-FS112


title: RV_infected-FS87


title: Uninfected-FS135


title: RV_infected-FS108


title: RV_infected-FS124


title: RV_infected-FS123


title: Uninfected-FS76


title: RV_infected-FS117


title: RV_infected-FS102


title: RV_infected-FS93


title: RV_infected-FS149


title: RV_infected-FS97


title: Uninfected-FS86


title: Uninfected-FS126


title: Uninfected-FS58


title: RV_infected-FS86


title: Uninfected-FS109


title: Uninfected-FS99


title: RV_infected-FS65


title: Uninfected-FS103


title: RV_infected-FS77


title: RV_infected-FS115


title: RV_infected-FS143


title: RV_infected-FS145


title: Uninfected-FS137


title: RV_infected-FS160


title: RV_infected-FS71


title: Uninfected-FS60


title: Uninfected-FS53


title: Uninfected-FS157


title: Uninfected-FS123


title: RV_infected-FS139


title: RV_infected-FS59


title: RV_infected-FS144


title: Uninfected-FS131


title: Uninfected-FS134


title: RV_infected-FS78


title: RV_infected-FS103


title: Uninfected-FS146


title: RV_infected-FS116


title: RV_infected-FS94


title: Uninfected-FS100


title: Uninfected-FS98


title: Uninfected-FS71


title: RV_infected-FS118


title: Uninfected-FS93


title: Uninfected-FS59


title: RV_infected-FS55


title: Uninfected-FS111


title: Uninfected-FS55


title: RV_infected-FS150


title: Uninfected-FS61


title: Uninfected-FS83


title: Uninfected-FS90


title: Uninfected-FS155


title: Uninfected-FS154


title: Uninfected-FS130


title: Uninfected-FS116


title: RV_infected-FS96


title: Uninfected-FS73


title: RV_infected-FS146


title: RV_infected-FS74


title: Uninfected-FS105


title: RV_infected-FS136


title: RV_infected-FS125


title: RV_infected-FS53


title: RV_infected-FS137


title: Uninfected-FS56


title: Uninfected-FS102


title: RV_infected-FS90


title: Uninfected-FS62


title: Uninfected-FS67


title: RV_infected-FS140


title: RV_infected-FS62


title: RV_infected-FS156


title: RV_infected-FS76


title: Uninfected-FS110


title: RV_infected-FS84


title: RV_infected-FS161


title: RV_infected-FS134


title: Uninfected-FS107


title: Uninfected-FS108


title: RV_infected-FS101


title: Uninfected-FS159


title: RV_infected-FS88


title: Uninfected-FS106


title: Uninfected-FS115


title: Uninfected-FS133


title: Uninfected-FS65


title: RV_infected-FS142


title: Uninfected-FS118


title: RV_infected-FS110


title: RV_infected-FS83


title: RV_infected-FS95


title: Uninfected-FS144


title: Uninfected-FS142


title: Uninfected-FS156


title: RV_infected-FS67


title: RV_infected-FS52


title: RV_infected-FS64


title: Uninfected-FS82


title: RV_infected-FS73


title: RV_infected-FS98


title: Uninfected-FS119


title: Uninfected-FS114


title: RV_infected-FS141


title: KO_MN_rep1

city: Taipei

first: Jun-An

last: Chen

address: 128 Academia Road, Section 2

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description:
Gene expression in mir-17~92-/-;Hb9::GFP+ MN
7551_252800518173_A3_1_3

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4858A-028005) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: e12.5 FACS-sorted mir-17~92-/-;Hb9::GFP+ MN

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Sorted cells were harvested for total RNA isolation by mirVana kit (Life Technology), DNase treated by TURBO DNA-free Kit (Life Technology), and checked with Bioanalyzer 2100 (Agilent) for RIN > 9.

treatment_protocol: Freshly dissected spinal cord from WT and mir-17~92 -/- ; Hb9::GFP embryos at E12.5 were trypsinized, and were subjected to FACS to isolate GFP+ motor neurons and GFP- non motor rneurons .

tag: tissue

value: sorted spinal cord

value: N/D


title: Non-irradiated unsorted intestinal epithelial cells rep 7

city: Chapel Hill

first: P. Kay

last: Lund

state: NC

address: 6336 MBRB CB 7545 111 Mason Farm Road

department: Cell and Molecular Physiology

institute: UNC at Chapel Hill

description:
Biological replicate 7/8; unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 71

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit (5188-5242, Santa Clara, CA) and the Agilent Microarray Hybridization Chamber Kit (G2534A, Santa Clara, CA)

scan_protocol: Slides were scanned using Agilent Microarray Scanner and Agilent Scan Control software (Santa Clara, CA)

data_processing: Scanned images were analyzed, data were processed and LogRatio analysis was perfomed using Agilent Feature Extraction Software version 10.7.3.1 (Santa Clara, CA)

source_name: Unsorted intestinal epithelial cells

label_protocol: 0.1-1µg ot total RNA was amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit, Two-Color (5190-2306, Santa Clara, CA) - Cy5 for samples and Cy3 for reference

growth_protocol: Sox9-EGFP BAC transgenic mice used between 6-10 weeks old

extract_protocol: Total RNA was extracted using Qiagen Rneasy mini kit (Qiagen, Venlo, The Netherlands) following manufacturer's instructions

treatment_protocol: Sox9-EGFP transgenic mice were given a single dose of 14Gy abdominal irradiation using an XRAD320 (Precision X-Ray, East Haven, CT - Filter: 2mm, Al; 47cm ; 320kV/s, 10mA; 2.8Gy/min). Immediately following radiation, mice were implanted mini pumps (Alzet, Cupertino, CA, model 1007D, subcutaneously) filled with either vehicle (NaCl 0.9%) or IGF1 (Genentech, 10mg/ml). Mice were euthanized 5 days after radiation/mini-pump implantation, jejunum was collected and processed for single cell dissociation. Cells expressing either Negative, Sublow, Low or HIgh levels of the Sox9-EGFP transgene were isolated by FACS. Non-irradiated control mice were included in the same run of FACS and gating was defined using EGFP intensity profile of the non-irradiated controls.

tag: developmental stage

value: adult

value: male

value: small intestine - jejunum

tag: mouse model

value: Sox9-EGFP BAC transgenic mice

tag: level of expression of the sox9-egfp reporter gene

value: non-applicable (unsorted)

tag: treatment

value: non-irradiated - vehicle (control)

source_name: Pool of non-sorted intestinal epithelial cells from non-irradiated mice


title: KO_MN_rep2

description:
Gene expression in mir-17~92-/-;Hb9::GFP+ MN
7551_252800518173_B1_1_4

tag: genotype


title: Non-irradiated unsorted intestinal epithelial cells rep 5

description:
Biological replicate 5/8; unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 69


title: WT_MN_rep1

description:
Gene expression in mir-17~92+/+;Hb9::GFP+ MN
7551_252800518173_B4_2_1

source_name: e12.5 FACS-sorted mir-17~92+/+;Hb9::GFP+ MN

value: WT ; Hb9::GFP


title: PC9 gefitinib resistant_2

city: Waltham

first: Aleksandra

last: Markovets

state: Massachusetts

address: 35 Gatehouse Dr.

department: Oncology, iMED

institute: AstraZeneca

description: Populations of PC9 cells resistant to gefitinib (1.5 uM)

hyb_protocol: The hybridization master mix was prepared by mixing 25 μl of Cot-1 (1mg/ml), 26 μl or Agilent 1-x Blocking Agent and 130 μl of Aligent 2x HiRPM Hybridization Buffer. The master mix was mixed with labeled experimental and control DNA and hybridized to the Agilent Human Genome CGH 2x400k Miscoarray (Agilent Technologies, Santa Clara, CA).  The arrays were incubated for 40 hours at 65°C in a rotating oven at 20 rpm. After hybridization slides were washed as stated in the protocol.

scan_protocol: All hybridized arrays were scanned on an Agilent G2505B scanner.

data_processing: Images were analized using Agilent Feature Extraction Software (version 10.7.3.1). Nexus Copy Number software v7.0 was used for data processing and visualization. Log2 ratio for each gene was calculated as mean of log2 values of all probes mapped to a particular gene.

source_name: PC9 cell line resistant to gefitinib

label_protocol: Genomic DNA extracted from experimental (cell lines) and normal control female gDNA (Promega, Madison, WI) samples was labeled using CytoSure HT Genomic DNA Labelling Kit (Oxford Gene Technology, Oxfordshire, UK)  following the OGT protocol for aCGH analysis with an adjustment to the post purification step. After labelled targets were combined in one tube, an additional 2 μl of water was added and directly proceeded to hybridization.

growth_protocol: Resistant cell populations were cultured in RPMI, 10% FCS, 2mM L-glutamine supplemented with the indicated EGFR inhibitor. Parental cells were cultured in RPMI, 10% FCS, 2mM L-glutamine.

extract_protocol: Genomic DNA was prepared from the cell pellets using the Allprep DNA/RNA/miRNA Universal kit (Qiagen, Valencia, CA)

treatment_protocol: Cells were harvested when they had grown to 80% confluency. The cells were washed once in 10mls of PBS and then pelleted at 1000rpm for 5 minutes. The supernatant was removed and the cell pellet frozen at -80oC until DNA preparation was performed.

tag: population

value: resistant to gefitinib

value: Gefitinib (1.5 uM), dose escalation

source_name: normal female gDNA, Promega

value: female

tag: phenotype

value: normal


title: Non-irradiated unsorted intestinal epithelial cells rep 3

description:
Biological replicate 3/8; unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 67


title: Pooled non-sorted intestinal epithelial cells from non-irradiated mice

description:
Biological replicate 8/8; pool of unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 72


title: WT_MN_rep2

description:
Gene expression in mir-17~92+/+;Hb9::GFP+ MN
7551_252800518173_A6_2_2


title: KO_nonMN_rep1

description:
Gene expression in mir-17~92-/-;Hb9::GFP- nonMN
7551_252800518173_A3-_2_3

source_name: e12.5 FACS-sorted mir-17~92-/-;Hb9::GFP- non-MN


title: WT_nonMN_rep1

description:
Gene expression in mir-17~92+/+;Hb9::GFP- nonMN
7551_252800518173_B4-_2_4

source_name: e12.5 FACS-sorted mir-17~92+/+;Hb9::GFP- non-MN


title: Non-irradiated unsorted intestinal epithelial cells rep 2

description:
Biological replicate 2/8; unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 66


title: Non-irradiated unsorted intestinal epithelial cells rep 4

description:
Biological replicate 4/8; unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 68


title: Non-irradiated unsorted intestinal epithelial cells rep 6

description:
Biological replicate 6/8; unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 70


title: PC9 WZ4002 resistant_1

description: Populations of PC9 cells resistant to WZ4002 (1.5 uM)

source_name: PC9 cell line resistant to WZ4002

value: resistant to WZ4002

value: WZ4002 (1.5 uM), dose escalation


title: Irradiated/IGF1 Sox9-EGFP High rep 3

description:
Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 64

source_name: Sorted intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene

value: High

value: irradiated - IGF1


title: PC9

description: Parental PC9 cell line

source_name: PC9 parental cell line

value: parental line

value: Parental cell line


title: Non-irradiated unsorted intestinal epithelial cells rep 1

description:
Biological replicate 1/8; unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 65

value: adult


title: PC9 AZD9291 resistant_2

description: Populations of PC9 cells resistant to AZD9291 (160 nM)

source_name: PC9 cell line resistant to AZD9291

value: resistant to AZD9291

value: AZD9291 (160nM), dose escalation


title: PC9 AZD9291 resistant_3


title: PC9 gefitinib resistant_1


title: PC9 afatinib resistant_1

description: Populations of PC9 cells resistant to afatinib (1.5 uM)

source_name: PC9 cell line resistant to afatinib

value: resistant to afatinib

value: Afatinib (1.5 uM), dose escalation


title: PC9 WZ4002 resistant_3


title: PC9 gefitinib resistant_6


title: PC9 afatinib resistant_6


title: PC9 AZD9291 resistant_4


title: PC9 AZD9291 resistant_1


title: Uninfected-FS64

value: Male

value: Uninfected

value: peripheral blood mononuclear cells

value: media alone for 24 hours


title: PC9 gefitinib resistant_8

value: resistant to gefitinib

value: Gefitinib (1.5 uM), dose escalation

value: female


title: PC9 AZD9291 resistant_5

value: AZD9291 (160nM), single dose

value: normal


title: Irradiated/IGF1 Sox9-EGFP Low rep 1

description:
Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 59

source_name: Sorted intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene

value: male

value: small intestine - jejunum

value: Sox9-EGFP BAC transgenic mice

value: Low

value: irradiated - IGF1

value: non-applicable (unsorted)

value: non-irradiated - vehicle (control)


title: Irradiated/IGF1 Sox9-EGFP High rep 1

description:
Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 62

value: adult

value: High


title: Non-irradiated/IGF1 Sox9-EGFP High rep 1

description:
Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 50

value: non-irradiated - IGF1


title: Irradiated/IGF1 Sox9-EGFP Negative rep 1

description:
Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 53

source_name: Sorted intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene

value: Negative


title: Non-irradiated/IGF1 Sox9-EGFP Low rep 1

description:
Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 47


title: Non-irradiated/IGF1 Sox9-EGFP Sublow rep 1

description:
Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 44

source_name: Sorted intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene

value: Sublow


title: Irradiated/vehicle Sox9-EGFP High rep 1

description:
Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 38

value: irradiated - vehicle


title: Irradiated/IGF1 Sox9-EGFP Sublow rep 1

description:
Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 56


title: Non-irradiated/IGF1 Sox9-EGFP Low rep 3

description:
Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 49


title: Non-irradiated/IGF1 Sox9-EGFP High rep 3

description:
Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 52


title: Irradiated/vehicle Sox9-EGFP High rep 3

description:
Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 40


title: Irradiated/vehicle Sox9-EGFP Low rep 3

description:
Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 37


title: Irradiated/IGF1 Sox9-EGFP Sublow rep 2

description:
Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 57


title: Irradiated/IGF1 Sox9-EGFP Low rep 2

description:
Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 60


title: Non-irradiated/IGF1 Sox9-EGFP Negative rep 3

description:
Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 43


title: Non-irradiated/IGF1 Sox9-EGFP Negative rep 1

description:
Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 41


title: Irradiated/IGF1 Sox9-EGFP Negative rep 3

description:
Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 55


title: Non-irradiated/IGF1 Sox9-EGFP Sublow rep 2

description:
Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 45


title: Irradiated/vehicle Sox9-EGFP Low rep 2

description:
Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 36


title: Irradiated/IGF1 Sox9-EGFP Low rep 3

description:
Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 61


title: Non-irradiated/IGF1 Sox9-EGFP Low rep 2

description:
Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 48


title: Non-irradiated/IGF1 Sox9-EGFP Sublow rep 3

description:
Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 46


title: Non-irradiated/IGF1 Sox9-EGFP High rep 2

description:
Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 51


title: Non-irradiated/IGF1 Sox9-EGFP Negative rep 2

description:
Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 42


title: Irradiated/IGF1 Sox9-EGFP Negative rep 2

description:
Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 54


title: Irradiated/IGF1 Sox9-EGFP High rep 2

description:
Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 63


title: Irradiated/vehicle Sox9-EGFP High rep 2

description:
Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 39


title: Irradiated/vehicle Sox9-EGFP Low rep 1

description:
Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 35


title: Irradiated/vehicle Sox9-EGFP Sublow rep 3

description:
Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 34


title: Irradiated/vehicle Sox9-EGFP Sublow rep 1

description:
Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 32


title: Irradiated/vehicle Sox9-EGFP Negative rep 2

description:
Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 30


title: Irradiated/vehicle Sox9-EGFP Sublow rep 2

description:
Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 33


title: Irradiated/vehicle Sox9-EGFP Negative rep 3

description:
Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 31


title: Non-irradiated/vehicle Sox9-EGFP Low rep 6

description:
Biological replicate 6/7; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 20


title: Non-irradiated/vehicle Sox9-EGFP Low rep 1

description:
Biological replicate 1/7; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 15


title: Non-irradiated/vehicle Sox9-EGFP Low rep 3

description:
Biological replicate 3/7; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 17


title: Non-irradiated/vehicle Sox9-EGFP Sublow rep 7

description:
Biological replicate 7/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 14


title: Non-irradiated/vehicle Sox9-EGFP Sublow rep 2

description:
Biological replicate 2/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 9


title: Irradiated/IGF1 Sox9-EGFP Sublow rep 3

description:
Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with IGF1 (mini-pump Alzet 1007D, subcutaneous, 10mg/ml).
Sample 58


title: Non-irradiated/vehicle Sox9-EGFP Low rep 4

description:
Biological replicate 4/7; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 18


title: Non-irradiated/vehicle Sox9-EGFP Low rep 7

description:
Biological replicate 7/7; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 21


title: Non-irradiated/vehicle Sox9-EGFP High rep 6

description:
Biological replicate 6/7; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 27


title: Irradiated/vehicle Sox9-EGFP Negative rep 1

description:
Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 29


title: Non-irradiated/vehicle Sox9-EGFP Negative rep 5

description:
Biological replicate 5/7; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 5


title: Non-irradiated/vehicle Sox9-EGFP High rep 1

description:
Biological replicate 1/7; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 22


title: Non-irradiated/vehicle Sox9-EGFP High rep 3

description:
Biological replicate 3/7; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 24


title: Non-irradiated/vehicle Sox9-EGFP Low rep 5

description:
Biological replicate 5/7; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 19


title: Non-irradiated/vehicle Sox9-EGFP High rep 7

description:
Biological replicate 7/7; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 28


title: Non-irradiated/vehicle Sox9-EGFP Sublow rep 4

description:
Biological replicate 4/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 11


title: Non-irradiated/vehicle Sox9-EGFP High rep 5

description:
Biological replicate 5/7; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 26


title: Non-irradiated/vehicle Sox9-EGFP Sublow rep 1

description:
Biological replicate 1/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 8


title: Non-irradiated/vehicle Sox9-EGFP High rep 2

description:
Biological replicate 2/7; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 23


title: Non-irradiated/vehicle Sox9-EGFP Sublow rep 5

description:
Biological replicate 5/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 12


title: Non-irradiated/vehicle Sox9-EGFP Negative rep 7

description:
Biological replicate 7/7; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 7


title: Non-irradiated/vehicle Sox9-EGFP Sublow rep 6

description:
Biological replicate 6/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 13


title: Non-irradiated/vehicle Sox9-EGFP Sublow rep 3

description:
Biological replicate 3/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 10


title: Non-irradiated/vehicle Sox9-EGFP Low rep 2

description:
Biological replicate 2/7; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 16


title: Non-irradiated/vehicle Sox9-EGFP Negative rep 6

description:
Biological replicate 6/7; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 6


title: Non-irradiated/vehicle Sox9-EGFP High rep 4

description:
Biological replicate 4/7; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 25


title: Non-irradiated/vehicle Sox9-EGFP Negative rep 3

description:
Biological replicate 3/7; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 3


title: Non-irradiated/vehicle Sox9-EGFP Negative rep 4

description:
Biological replicate 4/7; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 4


title: CEN.PK113-7D Aerobic glucose-limited chemostat pH3.5 (EH5)

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description: S. cerevisiae CEN.PK113-7D aerobic glucose-limited chemostat with a dilution rate of 0.1h-1.

hyb_protocol: Acquisition and quantification of array images were performed using Affymetrix GeneChip Operating Software (GCOS version 1.2). Before comparison, all arrays were globally scaled to a target value of 100 using the average signal from all gene features. To the 9,383 transcript features on the arrays, a filter was applied to extract 6,385 yeast probesets. To represent the variation in replicated measurements, the coefficient of variation (S.D. divided by the mean) was calculated. When the genes were ranked according to increasing average intensity, the average coefficient of variation showed a sharp increase for the genes with the lowest expression. Therefore, all genes in which the average expression in all conditions was below 12 were removed from the dataset. Subsequently all remaining values below 12 were set to a value of 12. To assess differential expression, the Significance Analysis of Microarrays (SAM version 1.21) add-in to MicrosoftTM Excel was used for comparisons of replicate array experiments. SAM identifies genes with statistically significant changes in expression by assimilating a set of gene-specific t tests. Each gene is assigned a score on the basis of its change in gene expression relative to the standard deviation of repeated measurements for that gene. Genes with scores greater than a threshold are deemed potentially significant. The percentage of such genes identified by chance is the false discovery rate (FDR). To estimate the FDR, nonsense genes are identified by analyzing permutations of the measurements. The threshold can be adjusted to identify smaller or larger sets of genes, and FDRs are calculated for each set. Here internal SAM parameters for fold-change threshold and the false discovery rate values were set at 2 and 1% respectively.   The genes with significantly changed expression in one of the comparisons were arranged in groups via overlapping them in MicrosoftTM Excel.

scan_protocol: Scanning of the Affymetrix Genechip® microarrays was performed with The Affymetrix scanner 3000 following Affymetrix instructions

data_processing: Data were processed with the GeneChip® Operating Software version 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each

organism: Saccharomyces cerevisiae

source_name: CEN.PK113-7D Glucose-limited chemostat culture -0.1H-1

label_protocol: Double stranded cDNA synthesis was carried out using 10 µg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labelling using the GeneChip IVT labeling Kit (Affymetrix). Finally, labelled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridised to Affymetrix Saccharomyces cerevisiaeYG98S GeneChip® microarrays  at 40ºC for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.

growth_protocol: Chemostat cultivation of S.cerevisiae CEN.PK113-7D was carried out at 30°C and at a dilution rate of 0.10 h-1 in 2 litre bioreactors (Applikon, Schiedam, the Netherlands) with a working volume of 1.0 litre and Physiology of Saccharomyces cerevisiae in anaerobic glucose-limited chemostat cultures. J Gen Microbiol 136, 395-403. equipped with an electronic level sensor to maintain a constant volume. For aerobic cultures, synthetic medium (Verduyn et al. 1990) with 7.5 g∙l-1 glucose was used. Dissolved oxygen concentrations in the cultures were monitored with an autoclavable oxygen electrode (Applisens, Schiedam, the Netherlands). Anaerobic cultures were fed with synthetic medium supplemented with 25 g∙l-1 glucose and the anaerobic growth factors ergosterol (0.01 g∙l-1) and Tween 80 (0.42 g∙l-1). Silicone antifoam was used to prevent foaming. To minimize oxygen diffusion, bioreactors were equipped with Norprene tubing (Cole-Parmer Instrument Company, Vernon Hills, IL) and Viton O-rings and the medium vessel was sparged with N2. Galacturonic acid (Carbosynth, Compton (Berkshire), UK) fed to cultures was filter-sterilised separately and added to the autoclaved medium. The pH of the cultures was kept at 3.5 by the automatic addition of 2M KOH. Cultures were stirred at 800 rpm and sparged with 0.5 l∙min-1 air or N2 (<10 ppm oxygen). Chemostat cultures were assumed to be in steady state when, after at least 5 volume changes, the culture dry weight and specific carbon dioxide production rate changed by less than 3% over 2 consecutive volume changes. Steady-state samples were taken between 10 and 14 volume changes after inoculation to minimize evolutionary adaptation. Aerobic glucose-limited chemostat cultures at pH 3.5, supplemented with 0.23 g∙l-1 galactose were run similarly.

extract_protocol: 60 mL of culture broth was sampled and immediatly quenched in liquid nitrogen and stored at -80ºC until further use. For total RNA extraction, half of the pellet was grounded by mortar and pestle under constant cooling with liquid nitrogen. The powder was dissolved in 5 mL of Trizol reagent (Invitrogen) and 1 mL chloroform (Sigma) and mixed well. The two phases were separated by centrifugation (4600 g, 15 min). Total RNA was isolated using a phenol-chloroform extraction method, which consisted of two extraction steps in acid-phenol/chloroform/isoamyl alcohol (5:1, pH 4.8, Ambion, Foster City, USA), followed by a chloroform extraction step. Each time the phases were separated by centrifugation (4600 g, 15 min). Total RNA was precipitated for 30 min at -20ºC in 96% ethanol and 0.3 M sodium acetate. The RNA was collected by centrifugation at 23000 g for 15 min and dissolved in RNAse free H2O.

value: glucose


title: Non-irradiated/vehicle Sox9-EGFP Negative rep 2

description:
Biological replicate 2/7; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 2


title: CEN.PK113-7D Aerobic glucose-limited chemostat 10g/l GalU pH3.5 (EH3)

description: S. cerevisiae CEN.PK113-7D  aerobic glucose-limited chemostat with a dilution rate of 0.1h-1 with 10 g/l galacturonic acid.

source_name: CEN.PK113-7D Glucose-limited 10g/l GalU chemostat culture -0.1H-2

growth_protocol: Chemostat cultivation of S.cerevisiae CEN.PK113-7D  was carried out at 30°C and at a dilution rate of 0.10 h-1 in 2 litre bioreactors (Applikon, Schiedam, the Netherlands) with a working volume of 1.0 litre and Physiology of Saccharomyces cerevisiae in anaerobic glucose-limited chemostat cultures. J Gen Microbiol 136, 395-403. equipped with an electronic level sensor to maintain a constant volume. For aerobic cultures, synthetic medium (Verduyn et al. 1990) with 7.5 g∙l-1 glucose was used. Dissolved oxygen concentrations in the cultures were monitored with an autoclavable oxygen electrode (Applisens, Schiedam, the Netherlands). Anaerobic cultures were fed with synthetic medium supplemented with 25 g∙l-1 glucose and the anaerobic growth factors ergosterol (0.01 g∙l-1) and Tween 80 (0.42 g∙l-1). Silicone antifoam was used to prevent foaming. To minimize oxygen diffusion, bioreactors were equipped with Norprene tubing (Cole-Parmer Instrument Company, Vernon Hills, IL) and Viton O-rings and the medium vessel was sparged with N2. Galacturonic acid (Carbosynth, Compton (Berkshire), UK) fed to cultures was filter-sterilised separately and added to the autoclaved medium. The pH of the cultures was kept at 3.5 by the automatic addition of 2M KOH. Cultures were stirred at 800 rpm and sparged with 0.5 l∙min-1 air or N2 (<10 ppm oxygen). Chemostat cultures were assumed to be in steady state when, after at least 5 volume changes, the culture dry weight and specific carbon dioxide production rate changed by less than 3% over 2 consecutive volume changes. Steady-state samples were taken between 10 and 14 volume changes after inoculation to minimize evolutionary adaptation. Aerobic glucose-limited chemostat cultures at pH 3.5, supplemented with 0.23 g∙l-1 galactose were run similarly.

treatment_protocol: 60 mL of culture broth was sampled and immediatly quenched in liquid nitrogen and stored at -80ºC until further use. For total RNA extraction, half of the pellet was grounded by mortar and pestle under constant cooling with liquid nitrogen. The powder was dissolved in 5 mL of Trizol reagent (Invitrogen) and 1 mL chloroform (Sigma) and mixed well. The two phases were separated by centrifugation (4600 g, 15 min). Total RNA was isolated using a phenol-chloroform extraction method, which consisted of two extraction steps in acid-phenol/chloroform/isoamyl alcohol (5:1, pH 4.8, Ambion, Foster City, USA), followed by a chloroform extraction step. Each time the phases were separated by centrifugation (4600 g, 15 min). Total RNA was precipitated for 30 min at -20ºC in 96% ethanol and 0.3 M sodium acetate. The RNA was collected by centrifugation at 23000 g for 15 min and dissolved in RNAse free H2O.

value: glucose + 10g/l galacturonic acid


title: CEN.PK113-7D Aerobic glucose-limited chemostat pH3.5 0.23g/l galactose (MA185R2)

description: S. cerevisiae CEN.PK113-7D aerobic glucose-limited chemostat with a dilution rate of 0.1h-1 with 0.23 g/l galactose

source_name: CEN.PK113-7D Glucose-limited 0.23g/l GalU chemostat culture -0.1H-1

value: glucose + 0.23 g/l galactose


title: Non-irradiated/vehicle Sox9-EGFP Negative rep 1

description:
Biological replicate 1/7; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice treated for 5 days with vehicle (mini-pump Alzet 1007D, subcutaneous).
Sample 1

source_name: Pool of non-sorted intestinal epithelial cells from non-irradiated mice


title: CEN.PK113-7D Aerobic glucose-limited chemostat 10g/l GalU pH3.5 (EH4)

description: S. cerevisiae CEN.PK113-7D aerobic glucose-limited chemostat with a dilution rate of 0.1h-1 with 10 g/l galacturonic acid.

source_name: CEN.PK113-7D Glucose-limited 10g/l GalU chemostat culture -0.1H-1


title: CEN.PK113-7D Aerobic glucose-limited chemostat pH3.5 (EH6)


title: CEN.PK113-7D Aerobic glucose-limited chemostat pH3.5 0.23g/l galactose (MA186R2)

description: S. cerevisiae CEN.PK113-7D  aerobic glucose-limited chemostat with a dilution rate of 0.1h-1 with 0.23 g/l galactose

source_name: CEN.PK113-7D Glucose-limited 0.23g/l GalU chemostat culture -0.1H-2


title: CEN.PK113-7D Aerobic glucose-limited chemostat pH3.5 (EH7)


title: 18T1

city: Stockholm

first: John

last: Lövrot

address: Cancer Center Karolinska

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

description: Ultrasound/CT guided fine needle aspiration biopsy from selected metastasis

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Probe intensities were extracted, background corrected, normalized and summarized to probeset expression using the rma function in the R/Bioconductor package affy with the default settings

source_name: Breast cancer metastasis to bone

label_protocol: Two-cycle cDNA synthesis with Affymetrix IVT protocol

extract_protocol: RNA extraction was performed using the RNeasy mini kit (Qiagen, Hilden, Germany) according to a standard protocol. In brief, biopsies preserved in RNAlater were centrifuged and the pellets were transferred into test tubes with RLT buffer (RNeasy Lysis Buffer, Qiagen, Hilden, Germany). Proteinase K was then added and the samples were treated for 10 min at 55°C according to Egyházi et al. (2004). Total RNA was then isolated using Qiagen's microspin technology. DNase was also added to the samples to further increase the RNA quality.

tag: arraycd

tag: subjid

tag: tptcd

tag: tpt

value: Baseline

tag: armcd

value: A

tag: arm

value: SU+DOC

tag: bioploc

value: bone


title: 17T2

value: Day 14

value: B

value: DOC


title: liver of Pemt+/+, HFHS 4W

city: Okayama

first: Jun

last: Wada

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Nephrology, Rheumatology, Endocrinology and Metabolism

country: Japan

institute: Okayama University

description: gene expression data from liver of Pemt+/+ mice fed HFHS for 4 weeks

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on GeneChip Mouse Genome 430 2.0 Array using Hybridization, Wash and Stain Kit, accoding to GeneChip 3'IVT Express Kit user Manual.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Affymetrix GeneChip Command Console Software (AGCC) for CEL file, and Affymetrix Expression Console Software (Expression Console) for the other files.

source_name: liver tissue of Pemt+/+ mouse fed with HFHS for 4 weeks

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

extract_protocol: Total RNAs were purified using RNeasy Midi kit (QIAGEN) according to manufacture's instructions.

tag: genotype/variation

value: Pemt WT

value: liver

tag: diet

value: HFHS diet

tag: time

value: 4 weeks


title: 16T1

source_name: Breast cancer metastasis to liver


title: 18T2


title: 15T1

source_name: Breast cancer metastasis to lymph node

value: lymph node


title: 14T1


title: 13T1


title: liver of Pemt-/-, HFHS 3W

description: gene expression data from liver of Pemt-/- mice fed HFHS for 3 weeks

source_name: liver tissue of Pemt-/- mouse fed with HFHS for 3 weeks

value: Pemt KO

tag: tissue

value: 3 weeks


title: liver of Pemt+/+, HFHS 1W

description: gene expression data from liver of Pemt+/+ mice fed HFHS for 1 week

source_name: liver tissue of Pemt+/+ mouse fed with HFHS for 1 week

value: 1 week


title: 12T1


title: liver of Pemt+/+, HFHS 2W

description: gene expression data from liver of Pemt+/+ mice fed HFHS for 2 weeks

source_name: liver tissue of Pemt+/+ mouse fed with HFHS for 2 weeks

value: 2 weeks


title: liver of Pemt+/+, HFHS 3W

description: gene expression data from liver of Pemt+/+ mice fed HFHS for 3 weeks

source_name: liver tissue of Pemt+/+ mouse fed with HFHS for 3 weeks


title: liver of Pemt-/-, HFHS 4W

description: gene expression data from liver of Pemt-/- mice fed HFHS for 4 weeks

source_name: liver tissue of Pemt-/- mouse fed with HFHS for 4 weeks


title: liver of Pemt-/-, HFHS 1W

description: gene expression data from liver of Pemt-/- mice fed HFHS for 1 week

source_name: liver tissue of Pemt-/- mouse fed with HFHS for 1 week


title: 14T2


title: 15T2


title: 17T1


title: 13T2


title: liver of Pemt-/-, HFHS 2W

description: gene expression data from liver of Pemt-/- mice fed HFHS for 2 weeks

source_name: liver tissue of Pemt-/- mouse fed with HFHS for 2 weeks


title: 07T2


title: 07T1


title: 12T2


title: 10T1


title: 11T2


title: RootstockLeaf2

city: Mohali

first: Sudhir

middle: P

last: Singh

state: Punjab

address: NABI, C127, Indus Area, Phase8

country: India

institute: National Agri-Food Biotechnology Institu

hyb_protocol: Hybridization of arrays were performed according to Affymetrix protocol described in technical manual.

scan_protocol: The hybridized chips were washed, stained and scanned using GeneChip scanner to generate the CEL files.

data_processing: The intensities of probe arrays were normalized by using GeneSpring software. The Robust Multi-array normalization algorithm (RMA) values of probe sets were used for further statistical analysis. One-way ANOVA analysis was carried out in GeneSpring software with ‘Asymptotic’ p value computation and the Benjamini-Hochberg false discovery rate (FDR) for multiple test correction (at p < 0.05).

organism: Arabidopsis thaliana

source_name: Rootstock Leaf

label_protocol: Double stranded cDNA synthesis, In vitro transcription to synthesize biotin labeled cRNA, purification and fragmentation of cRNA were performed according to Affymetrix protocol described in technical manual.

growth_protocol: The Arabidopsis thaliana var. Columbia-0 (Col-0) plants were used in the grafting experiments.  The dried seeds were sterilized following the standard procedures, and were sown on the Soilrite bed in the pots. The pots were kept at 4oC in the dark for 2 days for stratification of seeds to synchronize the germination. After stratification, pots were shifted to PGC 20 growth chamber (Conviron, Canada) under long-day conditions (16-h light/8-h dark at 150 µmol m-2 s-1 irradiance) at 22°C ± 1°C and 65% humidity.

extract_protocol: Total RNA was extracted from the leaf and flower bud samples using the Spectrum Plant Total RNA kit (Sigma-Aldrich, USA), following the manufacturer’s instructions. On-column DNase (Sigma-Aldrich, USA) treatment was performed as instructed in the manual.

tag: ecotype

value: Rootstock Leaf


title: RootstockLeaf1


title: 08T2


title: 10T2


title: 11T1

value: Baseline


title: 05T2

value: A


title: ScionLeaf3

source_name: Scion Leaf

value: Scion Leaf


title: 04T2

value: bone


title: B23

city: Paris

first: Hélène

last: LAPILLONNE

address: 27 Rue de Chaligny

institute: UPMC Univ Paris 06

hyb_protocol: The fluorescently labeled samples were hybridized overnight to miRXplore TM Microarrays using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized miRXplore (TM) microarrays were done with the Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA) and ImaGene software Version 9.0 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned miRXplore TM microarrays was done using ImaGene software Version 9.0 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Cy5/Cy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed. The mean ratios were normalised using the calibration oligos. Within-array normalization occured by quantile normalization.

organism: synthetic construct

source_name: Universal Reference provided by Miltenyi Biotec GmbH

label_protocol: 2 µg of respective total RNA as well as 2 fmol of the Universal Reference were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The total RNA and Universal Reference mix was hybridized in a dual colour approach to microarrays.

extract_protocol: Total RNA was extracted with Trizol according to the manufacturer’s instructions.

tag: sample type

value: syntethic miRNA pool of 954 miRNA sequences from human, mouse, rat, and virus

value: hESC-H1-EB20-Day18 erythroid cells

tag: cell type

value: erythroid cells

tag: cell line


title: B33


title: RootstockLeaf3


title: 08T1

value: B

value: DOC


title: RootstockFlowerBud2

source_name: Rootstock Flower Bud

value: Rootstock Flower Bud


title: RootstockFlowerBud3


title: RootstockFlowerBud1


title: A23

value: hESC-H1-EB9-Day18 erythroid cells


title: Adipose Derived Stem Cells  Replicate 2

city: Atlanta

first: Dong

last: Liu

state: GA

address: 720 Westview Drive, SW

department: Cardiovascular Research Institute

institute: Morehouse School of Medicine

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using Applied Biosystems RQ Manager 1.2 software and exported into a Microsoft Excel file.
For the normalization it used the expression levels of Mammalian U6.
Target gene signals normalized to Mammalian U6; Delta Ct, where deltaCt = (Ct_Target − Ct_MU6)

source_name: Adipose Derived Stem Cells

growth_protocol: hASCs were maintained in hASCs growth medium; hASCs were reseeded in 100mm dish (3x10^5 cells per dish) and cultured in endothelial differentiation medium (EDM) containing endothelial basal medium (EBM) supplemented with endothelial growth factors and 50ng/ml VEGF for 4 days; medium changed once during preconditioning period

treatment_protocol: Endothelial Differentiation Medium (EDM) preconditioning; ASC were kept in an undifferentiated, pluripotent state by using MesenPro RS Medium (Life Technologies, 12747-010)

value: Adipose Derived Stem Cells

tag: passage


title: 02T2

source_name: Breast cancer metastasis to subcutaneous site

value: Day 14

value: SU+DOC

value: subcutaneous


title: Adipose Derived Stem Cells  Replicate 1

description: Test


title: 01T2

value: liver


title: ScionLeaf1


title: B31

value: embryoid body cells


title: ScionFlowerBud3

source_name: Scion Flower Bud

value: Scion Flower Bud


title: ScionLeaf2


title: 05T1

value: Baseline

value: A

value: lymph node


title: LD-2

city: Wuhan

first: Rui

last: Zhou

state: Hubei

address: 湖北省武汉市江汉区唐家墩156号

department: Cancer Center

country: China

institute: Wuhan Union Hospital

description:
miRNAs expression before treatment
041

hyb_protocol: Follow miRNA Complete Labeling and Hyb Kit  (Agilent) protocol.

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Agilent Feature Extraction(v10.7)was used for background subtraction and Agilent GeneSpring was used to normalization.

source_name: serum form LD SCLC patient

label_protocol: 200ng of total RNA were used to fellow expriment follow miRNA Complete Labeling and Hyb Kit (Agilent) protocol.

growth_protocol: Patients' blood were collected and seperated in 4hours.

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

treatment_protocol: All serum was collected before any treatment

tag: gender

value: male

tag: age

tag: subject status

value: small cell lung cancer (SCLC) patient

tag: Stage

value: limited-stage

value: patient's serum


title: 04T1

source_name: Breast cancer metastasis to bone

tag: arraycd

tag: subjid

tag: tptcd

tag: tpt

value: B

value: DOC

value: bone


title: 02T1

tag: armcd

tag: arm

tag: bioploc


title: 01T1

source_name: Breast cancer metastasis to liver


title: LD-3

address: 湖北省武汉市江汉区唐家墩156号

description:
miRNAs expression before treatment
050

tag: tissue


title: B21

value: syntethic miRNA pool of 954 miRNA sequences from human, mouse, rat, and virus


title: B13

value: hESC-H1-EB20-Day18 erythroid cells

value: erythroid cells


title: B11


title: LD-1

address: 湖北省武汉市江汉区唐家墩156号

description:
miRNAs expression before treatment
045


title: A33

value: hESC-H1-EB9-Day18 erythroid cells


title: ScionFlowerBud2

tag: ecotype


title: ScionFlowerBud1


title: A13

tag: sample type


title: A31

value: hESC-H1 EB9-Day0

tag: cell type


title: A21

value: embryoid body cells

tag: cell line


title: A11


title: ED-2

address: 湖北省武汉市江汉区唐家墩156号

description:
miRNAs expression before treatment
WXL1&WXC1

source_name: serum form ED SCLC patient

value: female

value: extensive-stage


title: ED-3

address: 湖北省武汉市江汉区唐家墩156号

description:
miRNAs expression before treatment
012019-1&019


title: pLX3607 vector vs. pLX3805 mrpJ, replicate 3

status: Public on Apr 13 2015

city: Ann Arbor

first: Melanie

middle: M

last: Pearson

state: MI

address: 1150 W Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan Medical School

description: vector vs. pmrpJ#3

hyb_protocol: Labeled cDNA was mixed and hybridized to an array slide by using TIGR SOP no. M008.

scan_protocol: The microarray was scanned using a ScanArray Express microarray scanner (Perkin Elmer) at 10 um resolution and quantified using the ScanArray Express software.

data_processing:
Data were normalized using MIDAS and analyzed using MeV software (v. 4.7.4, TIGR).
The supplementary *.xlsx file shows the normalized median value for each probe set. MedA and MedB are median values for each channel, and IA and IB are integrated values. The fold changes listed in the table match the fold changes in the Sample data table.

organism: Proteus mirabilis HI4320

label_protocol: RNA was used as a cDNA template and labeled with either Cyanine 3 or Cyanine 5 dye according to TIGR protocol 007.

growth_protocol: To measure MrpJ-regulated gene transcription, HI4320, HI4320ΔmrpJ, vector control HI4320(pLX3607), or mrpJ in vivo mimic HI4320(pLX3805) were cultured to logarithmic phase with aeration (OD600 = 0.7-0.9).

extract_protocol: RNA was stabilized with RNAprotect (Qiagen) and isolated from cultures using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s directions, with the exception of treating stabilized bacteria with 3 mg/ml lysozyme in TE buffer for 15 min.

tag: strain/background

tag: genotype/variation

value: vector

value: mrpJ plasmid


title: pLX3607 vector vs. pLX3805 mrpJ, replicate 4

description: vector vs. pmrpJ#4


title: pLX3607 vector vs. pLX3805 mrpJ, replicate 2

description: vector vs. pmrpJ#2


title: HI4320 vs. ΔmrpJ, replicate 3

description: wt vs. mrpJ#3

source_name: HI4320 wild type

value: wild type

source_name: HI4320 ΔmrpJ

value: ΔmrpJ


title: ED-1

address: 湖北省武汉市江汉区唐家墩156号

description:
miRNAs expression before treatment
012001-2&001

tag: gender

value: male

tag: age

value: small cell lung cancer (SCLC) patient


title: HI4320 vs. ΔmrpJ, replicate 2

description: wt vs. mrpJ#2


title: HI4320 vs. ΔmrpJ, replicate 1

description: wt vs. mrpJ#1


title: HI4320 vs. ΔmrpJ, replicate 4

description: wt vs. mrpJ#4


title: pLX3607 vector vs. pLX3805 mrpJ, replicate 1

description: vector vs. pmrpJ#1


title: Wounded/GFP-, replicate II

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description:
Strain PucE69-Gal4 I; UAS-GFP (yw; UAS-GFP; pucE69-Gal4 I/TM6B): Pastor-Pareja et al. (2004) Developmental Cell 7: 387-399.
Third instar larvae wing imaginal disc cells.

hyb_protocol: The resulting cRNAs were hybridized to GeneChip Drosophila Genome 2.0 Arrays (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned.

data_processing:
Microarrays raw intensities were converted to gene expression estimates using the Robust Multichip Average procedure (RMA) on the FIESTA web server: Oliveros, J.C. (2007). FIESTA@BioinfoGP. An interactive server for analyzing DNA microarray experiments with replicates.
http://bioinfogp.cnb.csic.es/tools/FIESTA

organism: Drosophila melanogaster

source_name: Wing discs, wounded, GFP-

label_protocol: Due to the small size of the sample, the RNA was indirectly labeled with two rounds of linear amplification.

growth_protocol: Third instar larvae wing imaginal discs were dissected and incubated in a MM3 medium (Shields and Sang's) supplied with fly extract.The fly extract was prepared following the protocol suggested by the DGRC, Indiana University (Lin G, Zhang X, Ren J, Pang Z, Wang C, et al. (2013) Integrin signaling is required for maintenance and proliferation of intestinal stem cells in Drosophila. Dev Biol 377: 177-187). This modified media allows the culture of the wing imaginal discs for more than 24 hours.

extract_protocol: RNA was extracted using the Qiagen RNeasy® Micro Kit. In order to obtain approximately 10 ng of RNA, we employed around 30,000 to 40,000 cells. The quality and quantity of the extracted RNA were analyzed using the RNA Pico Lab Chip with an Agilent Bioanalyzer (Agilent Technologies).

treatment_protocol: Third instar larvae imaginal disc dissections were performed in cultured medium and incisions of precise sizes were carefully executed with a pair of tungsten needles.This was followed by static culture in supplemented MM3 media for 16-18 hours. Before sorting cells by FACS, imaginal discs were dissociated by trypsinization. Trypsinization was done in 35 mm dishes (Nunclon) with 1 ml of Trypsin-EDTA (Sigma –T4174) 9 X and 5 ml of Hoechst 33342 (final dilution 0.1 μg/ml). Around 100 imaginal discs were shaked 2-3 hours (170 rpm) at room temperature. During the last 30 minutes, 5 ml of propidium iodide (1 mg/ml, Invitrogen) were added to detect dead cells. The degree of dissociation was monitored under the scope. The selection and sorting of GFP-positive and -negative cells were done by Flow Cytometry using a MoFlo equipment based on drop formation (DakoCytomation).

value: wing imaginal disc cells

tag: developmental stage

value: third instar larvae

tag: treatment

value: wounded

tag: gfp

value: negative (Gal4-UAS system, puc enhancer)


title: Non-wounded/GFP-, replicate 3

source_name: Wing discs, non-wounded, GFP-

value: PucE69-Gal4 I; UAS-GFP (yw; UAS-GFP; pucE69-Gal4 I/TM6B)

value: non-wounded


title: Non-wounded/GFP+, replicate 3

source_name: Wing discs, non-wounded, GFP+

value: positive (Gal4-UAS system, puc enhancer)


title: Wounded/GFP-, replicate 1A


title: Wounded/GFP+, replicate B

source_name: Wing discs, wounded, GFP+


title: Wounded/GFP+, replicate A


title: Wounded/GFP+, replicate I


title: Non-wounded/GFP+, replicate 2


title: Wounded/GFP-, replicate I


title: Non-wounded/GFP+, replicate 1


title: Wounded/GFP+, replicate II


title: Non-wounded/GFP-, replicate 2


title: 4.NB4-ATRA

status: Public on Apr 12 2015

city: Boston

first: Kun Ping

last: Lu

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

description: NB4 cells treated with ATRA

hyb_protocol: Amplified, fragmented, and biotin labeled single-stranded cDNA (ss-cDNA) material was hybridized in Affymetrix GeneChip Mouse Transcription Assay 1.0

scan_protocol: Hybridized arrays were proceeding with Affymetrix GeneChip Hybridization Wash and Stain kit and then scanned.

data_processing: The data were analyzed with Affymetrix ExpressionConsole and TranscriptomeAnalysisConsole using Affymetrix default analysis settings

source_name: NB4 cell line

label_protocol: Target preparation performed using Affymetrix (Technical Manual) WT Plus reagent kit, including labeling

growth_protocol: NB4 cells were cultured in RPMI1640 mudium with 10% fetal bovine serum (FBS) and all of the cells were cultured at 37°C in a humidified incubator containing 5% CO2

treatment_protocol: NB4 cells were treated with 10 uM ATRA (Sigma Aldrich) or doxycycline-induced Pin1 knockdown for 3 days. When harvesting, cells were washed with  Hank's Balanced Salt Solution(HBSS) (Invitrogen) and placed on ice in the Trizol solution (GibcoBRL).

tag: disease state

value: acute promyelocytic leukemia (APL)

value: treated with ATRA


title: Non-wounded/GFP-, replicate 1


title: 3.NB4-DMSO

description: NB4 cells treated with DMSO

value: treated with DMSO


title: Wounded/GFP-, replicate 1B


title: 2.NB4-TETON.377

description: NB4 cells transfected with Pin1 KD (TET-ON)

value: transfected with Pin1 KD (TET-ON)


title: KO muscle, biological rep3

first: Raul

last: Mostoslavsky

address: 185 Cambridge Street, CPZN 4100

institute: Massachusetts General Hospital

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing:
The clustering figures were generated using dChip2006 Hierarchical clustering feature, and genes in each of these pathways were filtered using the dChip Software Tool Analysis.
For normalization, the normalization method included in dchip2006 (described at: http://www.hsph.harvard.edu/cli/complab/dchip/normalizing%20arrays.htm) was used.

source_name: muscle from SIRT6KO mouse

label_protocol: Affymetrix standard protocol

extract_protocol: TriPure (Roche) extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain background

value: muscle


title: KO muscle, biological rep2


title: WT muscle, biological rep1

source_name: muscle from WT mouse


title: WT muscle, biological rep2


title: P6c1_MGR3

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description: MD230-D9 vs YMD1124

hyb_protocol: reference URL : http://dunham.gs.washington.edu/UWAgilentDNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2013-05-17 Scan Time : 10:44:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : Hoffman-Winston prep http://dunham.gs.washington.edu/UWyeastDNAprep.pdf

tag: strain name


title: P6c1_SPO12

description: MD229-A12 vs DBY9500

scan_protocol: Pixel Size : 5 Scan Date : 2013-06-07 Scan Time : 08:57:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

label_protocol: reference URL : http://dunham.gs.washington.edu/UWAgilentDNA.pdf


title: KO muscle, biological rep1


title: S8c2_chr5.10

description: 110106_10265_1C_2N_1to4_array, YMD1685; 110106_10265_1C_2N_1to4_array

scan_protocol: Pixel Size : 5 Scan Date : 2011-01-06 Scan Time : 12:28:53 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: P6c1_PHO84

description: P6c1-F5 vs DBY9500; MD144-F5

scan_protocol: Pixel Size : 5 Scan Date : 2013-02-12 Scan Time : 09:24:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1