title: 6hpa regenerating heart tissue, replicate 3

city: Orono

first: Benjamin

middle: L

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

description: Adult Ekkwill (EK) fish

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

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

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

organism: Danio rerio

source_name: Heart Tissue

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3/Cy5 dye staining.

growth_protocol: Adult Ekkwill (EK) zebrafish were housed and maintained in tanks at 26oC and exposed to a 12:12 hour light:dark cycle.

extract_protocol: Total RNA was isolated using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) following manufacturer’s protocol.

treatment_protocol: Heart resection surgeries were performed with iridectomy scissors following anesthesia (0.6mM MS222) as previously described (Poss et al, Science (2002) 298,2188-2190).

tag: hours post amputation

value: heart


title: H19 deleted ahESC line-1 vs OG-3

status: Public on Nov 05 2015

type: genomic

city: Beijing

first: Meili

last: Zhang

address: Dong Dan San Tiao 5

department: State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics

country: China

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

description: CGH analysis of  H19Δ1vs OG-3

hyb_protocol: Hybridization was processed for 40 hr at 65℃ in Agilent hybridization system.  Genechips were washed in 2×SSC (0.2% SDS) at  42 ℃ and in 0.2×SSC at room temperature.

scan_protocol: Arrays were scanned on the Agilent G2565CA Microarray Scanner.

data_processing: The images were processed using Agilent Feature Extraction software (v10.10), which transformed the image signal to digital signal. The data was analyzed using Agilent Genomic Workbench  Software.

molecule: genomic DNA

organism: Mus musculus

source_name: androgenetic haploid ES cells, control

label_protocol: The gDNA samples were labelled using a Agilent SureTag Complete DNA Labeling Kit (5190-4240). Genomic DNA from control sample was lablled with Cy3-dCTP, and DNA from experimental samples were lablled with Cy5-dCTP.

growth_protocol: The cells were cultured in ESC medium supplemented with 15% fetal bovine serum, 1,000 U/ml leukemia inhibitory factor (LIF), 3 M CHIR99021, and 1 M PD0325901.

extract_protocol: Genomic DNA  was extracted using the Wizard Genomic DNA Purification Kit (Promega, A1120) according to the manufacturer’s instructions.

treatment_protocol: ES cells were cultured under normal culture conditions and dissociated with 0.05% Trypsin-EDTA. The harvested cells were then allowed to sit in tissue culture plates for 30-40 min to deplete the feeder cells.

tag: cell line

tag: karyotype

value: haploid

tag: cell type

value: haploid embryonic stem cells from androgenetic blastocysts (ahESCs)

source_name: H19 deleted (H19Δ) ahESCs


title: 6hpa regenerating heart tissue, replicate 2

type: RNA

country: USA

description: Adult Ekkwill (EK) fish

molecule: total RNA

tag: tissue


title: Uninjured heart tissue, replicate 3

description: Adult Ekkwill (EK) fish


title: 6hpa regenerating heart tissue, replicate 1

description: Adult Ekkwill (EK) fish


title: Uninjured heart tissue, replicate 2

description: Adult Ekkwill (EK) fish


title: Fasting_50h_rep1

city: Ft. Detrick

first: Christine

last: Baer

state: MD

address: 568 Doughten Drive

department: Environmental Health Program

institute: Excet, Inc. / USACEHR

hyb_protocol: 1.65 ug 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 55 uL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 uL of 2x Agilent GEx hybridization buffer HI-RPM was added to the fragmentation mixture to stop the reaction. For each reaction 100 uL was hybridized to an Agilent Zebrafish custom Genome Oligo Microarrays (G2517A001, design 017662) for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 seconds with acetonitrile, and 30 seconds with Stabilization and Drying solution (Agilent) then scanned immediately.

scan_protocol: Dichlorvos exposure slides were scanned twice immediately after washing using a GenePix 4200 AL with a scan resolution of 5 um, standard green filter, PMT gain set at 400 and scan power set to 30% (first) then 100% (second). NOTE: GenePix scans are combined such that any probes which are offscale in the 100% scan are replaced by probes from the 30% scan. Fasting slides were scanned immediately after washing using an Agilent C2505C scanner following protocol GE1-107-Sep09 with default settings.

data_processing: Dichlorvos exposure study array scanned images were analyzed with GenePix Pro 6.1.0.4 using GalFile Zv2_019161_D_20080131.gal. Instrument default setting settings were used with the following exceptions: Background Subtraction: width of background = 2 feature diameters; Resize Features: minimum diameter = 80%, maximum diameter = 110%; Feature Movement: maximum translation = 20 um; CPI threshold = 0 with local background subtraction. Fasting study array scanned images were analyzed with Agilent Feature Extraction Software using grid template 019161_D_2008131 with default settings.

source_name: liver

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug pooled RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were verified with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All exposures were conducted in 5-gallon glass aquaria adapted for flow-through use (60 mL/min; 5.4 turnovers/day) and maintained at 25°C with a 12h:12h (light:dark) photoperiod.

extract_protocol: Fish livers were homogenized in Trizol then total RNA was isolated from the homogenate following the Trizol manufacturer protocol (Invitrogen, Carlsbad, CA) followed by column purification with RNeasy Mini kits (Qiagen, GmbH, Germany) to remove salt and organic solvents. Total RNA quality and quantity were evaluated using an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA) and verified using the NanoDrop ND-1000 Spectrophotometer (NanoDrop, Wilmington, DE).

treatment_protocol: Dichlorvos exposures were conducted for 24 h using control (no toxicant) plus the high, mid, and low concentrations of dichlorvos in the flow-through aquaria with concentrations maintained for the duration of the exposure. Fasting exposures were conducted using a control set with normal feeding (two times per day), a 24 h fasted group and a 50 h fasted group in the same flow-through aquaria as used previously. No toxicants were introduced during the fasting portion of this study.

value: liver

tag: age

value: adult (6 - 9 months)

tag: chemical group

value: Fasting

tag: dose

value: 50h no food

tag: concentration


title: Fasting_control_rep4

value: control


title: Fasting_50h_rep3


title: Fasting_50h_rep4


title: Uninjured heart tissue, replicate 1

description: Adult Ekkwill (EK) fish


title: Fasting_50h_rep2


title: Fasting_control_rep1


title: Fasting_control_rep2


title: Fasting_24h_rep3

value: 24h no food


title: Fasting_control_rep3


title: Fasting_24h_rep2


title: Day 3 MIXL1+ FACS sorted cells

city: Los Angeles

first: Rhys

middle: John Powling

last: Skelton

state: CA

address: 675 Charles E Young Dr S, Room 3645

department: Eli and Edythe Broad Stem Cell Research Center

institute: UCLA

description: Gene expression data from H3 MIXL1eGFP+ human embryonic stem cells at day 3 of cardiac differentiation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® System 3000

data_processing: Publically available meta-analysis tools were used to interpret the microarray data generated in these experiments including the DAVID Bioinformatics resource (NIH) data-mining tool and GenePattern (MIT).  An Exploring gene expression data set and Gene Expression Commons were also used for data analysis.

label: Biotin

organism: Homo sapiens

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

growth_protocol: Cells were adapted to feeder free growth conditions using first MEF conditioned media (CM) and then into a fully defined mTESR1 (Stem Cell Technologies) on a soluble matrix solution Geltrex (Invitrogen, 1:200 in DMEM/F12). Colonies were passed every 2-3 days using Accutase. Single cell suspension of hESC cell lines were prepared by harvesting a plate of hESC that had reached approximately 75-80% percent confluency to ensure cells are in optimal growth phase on plating. Optimal cell seeding density were determined for all tested lines and were chosen based on the density that would allow the cells to grow over the course of 48 hours into the geometry of the stencil before induction with morphogens. On day -2, 5 x 103 cells were incubated on the stencil at 37 degrees for a minimum of 1 hour to allow for the cells to settle onto the Geltrex matrix. After this time 500uL of mTESR1+10uM Rock Inhibitor (Y-27632, Sigma Aldrich) was added per well of the 24-well plate and then the stencil was carefully removed using tweezers leaving only a small colony plated in the center of the well. The media was changed the following day and the cells filled into the geometry of the stencil over the next 2 days. The confluency of the cells was carefully tracked to ensure that the cells had not reached 100% confluency before the start of differentiation.

extract_protocol: Total RNA from FACS isolated cells was harvested using Trizol (Invitrogen).

treatment_protocol: Mesoderm Basal differentiation media consisted of RPMI basal media with B27 supplement (Invitrogen). On Day 0, 10ng/mL BMP-4 (R&D), 5ng/mL Activin A (R&D), and 5ng/mL bFGF (R&D) were added to the basal differentiation media. Cells were sorted and RNA was extracted at day 3.

value: hESC derived mesoderm progenitor


title: Day 3 MIXL1- FACS sorted cells

description: Gene expression data from H3 MIXL1eGFP- human embryonic stem cells at day 3 of cardiac differentiation

value: hESC derived endoderm progenitor


title: Fasting_24h_rep1


title: PGP1_hIPSC_mGata6_Day5-CD34enriched_rep2

city: Cambridge

first: Ron

last: Weiss

state: MA

address: 500 Technology sq. NE47-257

institute: MIT

description: Gene expression after 5 days of Gata6 induction, enriched for CXCR4+ cells

hyb_protocol: 700ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented used Agilent Gene expression Hybridization kit ( part # 5188-5242 ) at 60°C for 30 minutes in a reaction volume of 25ul  following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent GEx hybridization buffer HI-RPM (part # 5188-5242) was added to the fragmentation mixture and hybridized to Agilent Suprint G3 Human GE 8X60K array (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds at room temperature with Stabilization and Drying Solution ( Agilent, part # 5185-5979) , then  Airdry for 5 minutes.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner with Surescan High-Resolution Technology used one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The raw data files were analyzed using Genespring GX 12.6 (Agilent Technologies) using the default protocol for Agilent single color microarrays.

source_name: iPS cells, PGP1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng  RNA using the One-Color Microarray-Based Gene Expression Analysis, Low  Input Quick  Amplification Labeling kit (Agilent, Part # 5190-2305) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA, Part # 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: PGP1 hiPS cells were grown in Matrigel-coated in 6-well plates. The growth medium was changed daily (mTeSR1 and Doxycycline at 500 ng/ml the first 5 days, subsequently APEL medium without Doxycycline). mTeSR1 and APEL medium: Stem Cell Technologies

extract_protocol: The RNA extraction was performed using the mirVana Isolation Kit (AM1560, Ambion) following their protocol, omitting the last step for miRNA enrichment (resulting in total RNA extraction)

treatment_protocol: Cells were isolated (if not total) using antibody-coated magnetic beads (Miltenyi). Cell pellets were lysed in Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) (Invitrogen) and two wells were pooled per replicate for RNA extraction

value: Fibroblast derived iPS cells with Dox-inducible expression of murine Gata6


title: PGP1_hIPSC_mGata6_Day5_rep2

description: Gene expression after 5 days of Gata6 induction


title: Fasting_24h_rep4


title: Dichlorvos_high_rep4

value: Dichlorvos

value: High

value: 32 mg/L


title: Dichlorvos_mid_rep4

value: Mid

value: 19 mg/L


title: PGP1_hIPSC_mGata6_Day5_rep3


title: Day 0 MIXL1 hESC

description: Gene expression data from H3 MIXL1eGFP human embryonic stem cells

source_name: H3 MIXL1eGFP human embryonic stem cells

value: Pluripotent human embryonic stem cells


title: PGP1_hIPSC_mGata6_Day5-CD34depleted_rep3

description: Gene expression after 5 days of Gata6 induction, depleted for CXCR4+ cells


title: Dichlorvos_high_rep1


title: Dichlorvos_high_rep2


title: Dichlorvos_mid_rep1


title: PGP1_hIPSC_mGata6_Day5-CD34enriched_rep3


title: Dichlorvos_mid_rep3


title: Dichlorvos_mid_rep2


title: Dichlorvos_high_rep3


title: PGP1_hIPSC_mGata6_Day5-CD34depleted_rep2


title: PGP1_hIPSC_mGata6_Day5-CD34enriched_rep1


title: Dichlorvos_control2_rep4

value: 0 mg/L


title: 01_WT mTEC

city: Bunkyo

first: Hiroyuki

last: Takaba

state: Tokyo

department: Immunology

country: Japan

institute: University of Tokyo

description: 01_WT mTEC

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

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

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

label: biotin

source_name: CD45-,EpCAM+,CD80hi mTECs sorted from WT thymus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001,Affymetrix).

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions. (QIAGEN RNeasy)

tag: strain background

value: 3 weeks

tag: genotype/variation

value: wild type

value: thymus

value: CD45-,EpCAM+,CD80hi Medullary thymic epithelial cells (mTECs)


title: PGP1_hIPSC_mGata6_Day15_rep3

description: Gene expression after 5 days of Gata6 induction, 15 days total culture


title: colon epithelial cell_WT_DSS_rep1

city: guangzhou

first: zhipeng

last: zou

state: guangdong

address: tonghe road

department: Cell Biology

institute: southern medical university

description: mRNAs expression in colon epithelial cells from wild-type mice treated with DSS for 7 days

hyb_protocol: For hybridization, each slide was hybridized with 1.65 μg Cy3-labeled cRNA using a Gene Expression Hybridization Kit (Cat#5188-5242, Agilent) in a Hybridization Oven (Cat#G2545A, Agilent), according to the manufacturer’s instructions.

scan_protocol: After 17 h of hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with a Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent), following the manufacturer’s instructions. Slides were scanned by an Agilent Microarray Scanner (Cat#G2565CA, Agilent) with the following default settings: dye channel, green; scan resolution, 5 μm; PMT 100%, 10%, 16 bit.

data_processing: For data acquisition, data were extracted with Feature Extraction software 10.7 (Agilent). Raw data were normalized by the Quantile algorithm, Gene Spring Software 11.0 (Agilent).

source_name: colon epithelial cell, wild-type, DSS treatment for 7 days, rep1

label_protocol: For RNA amplification and labeling, total RNA was amplified and labeled using a Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified with an RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Female floxed TSC1 mice (TSC1FL/FL) containing LoxP sites flanking exons 17 and 18 of the TSC1 gene were crossed with male carbonic anhydrase 1 (CA1)-Cre mice, whose expression of Cre recombinase is under control of the CA1 promoter and limited to the epithelial cells of the cecum and colon. The resulting CA1-Cre; TSC1FL/FL (CEC-TSC1 KO) mice are hemizygous for the CA1-Cre transgene and homozygous for the floxed TSC1 allele. All animals were backcrossed for 8 generations onto the C57BL/6 background.

extract_protocol: total RNA of colon epithelial cells from 3 mice were extracted with TRIZOL Reagent and pooled together.

treatment_protocol: Wile type or CEC-specific TSC1 KO mice (about 8-weeks) were treated by 3% dextran sulfate sodium (DSS) FOR 7 days. The mice with resultant colitis were then sacrificed and harvested for colon epithelial cells.

tag: background strain

value: epithelial cell

value: colon

tag: genotype

value: wildtype


title: PGP1_hIPSC_mGata6_Day10-Dlk1enriched_rep2

description: Gene expression after 5 days of Gata6 induction, 10 days total culture, enriched for Dlk1+ cells


title: PGP1_hIPSC_mGata6_Day5_rep1


title: PGP1_hIPSC_mGata6_Day10_rep1

description: Gene expression after 5 days of Gata6 induction, 10 days total culture


title: PGP1_hIPSC_mGata6_Day10_rep3


title: PGP1_hIPSC_mGata6_Day15_rep1


title: PGP1_hIPSC_mGata6_Day5-CD34depleted_rep1


title: PGP1_hIPSC_mGata6_Day10-Dlk1enriched_rep1


title: PGP1_hIPSC_mGata6_Day10_rep2


title: PGP1_hIPSC_mGata6_Day15_rep2


title: PGP1_hIPSC_mGata6_Day10-CD34enriched_rep3

description: Gene expression after 5 days of Gata6 induction, 10 days total culture, enriched for CD34+ cells


title: Dichlorvos_control2_rep2

value: liver

value: adult (6 - 9 months)


title: Dichlorvos_low_rep2

value: Low

value: 6 mg/L


title: Dichlorvos_low_rep3

value: Dichlorvos


title: Dichlorvos_control2_rep1


title: Dichlorvos_low_rep4


title: Dichlorvos_control2_rep3


title: PGP1_hIPSC_mGata6_Day0_rep3

description: Gene expression of uninduced cells

value: Fibroblast derived iPS cells with Dox-inducible expression of murine Gata6


title: ABX naïve_Macs_rep3

city: New York

first: Michael

middle: C

last: Abt

state: NY

institute: Memorial Sloan Kettering Cancer Center

description: ABX Naïve-2

hyb_protocol: cDNA was amplied with NuGen WT Ovation Pico kit and hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST microarrays at the University of Pennsylvania’s Microarray facility.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Power Tools were used to process and quantile normalize fluorescent hybridization signals using Robust Multichip Averaging. Transcript values were log2 normalized.

source_name: naïve ABX mice

label_protocol: Microarrays were washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

growth_protocol: not applicable

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

treatment_protocol: not applicable

tag: strain

tag: gender

value: female

value: wild-type

tag: treatment

value: ABX

value: naïve peritoneum


title: PGP1_hIPSC_mGata6_Day10-CD34enriched_rep2


title: PGP1_hIPSC_mGata6_Day10-CD34enriched_rep1


title: Dichlorvos_control1_rep3

value: 0 mg/L


title: Dichlorvos_control1_rep2


title: ABX naïve_Macs_rep2

description: ABX Naïve-1


title: Dichlorvos_low_rep1


title: Dichlorvos_control1_rep1


title: ABX naïve_Macs_rep1

description: ABX Naïve


title: CNV naïve_Macs_rep1

description: CNV Naïve

source_name: naïve CNV mice

value: CNV


title: CNV naïve_Macs_rep2

description: CNV Naïve-1


title: CNV naïve_Macs_rep3

description: CNV Naïve-2


title: C. elegans with OP50 (control)

city: Jeonju

first: Younghoon

last: Kim

address: 567 Baekje-Daero, Deokjin-Gu

department: Department of Animal Science

country: South Korea

institute: Chonbuk National University

description: Biological replication 1 of 1

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

organism: Caenorhabditis elegans

source_name: C. elegans exposed to E. coli OP50 for 24 h

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: C. elegans were normally grown in NGM agar with E. coli OP50 normal feed upto L4/Young adult.

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

treatment_protocol: For replacing bacterial source, L4/young adult C. elegas were exposed to the lawn of B. licheniformis 141 strain in NGM agar for 24 h.


title: PGP1_hIPSC_mGata6_Day0_rep2

description: Gene expression of uninduced cells


title: PGP1_hIPSC_mGata6_Day0_rep1

description: Gene expression of uninduced cells


title: astrocytes_WT_1

status: Public on Nov 04 2015

city: Utrecht

first: Elly

middle: M

last: Hol

address: Universiteitsweg 100

department: Department of Translational Neuroscience

country: Netherlands

institute: University Medical Center Utrecht

description:
raw data in Cy5 channel of file:
US12302316_252665511016_S02_GE2-v5_95_Feb07_1_4.txt

hyb_protocol: Prior to hybridization, equal amounts (825 ng) of Cy3- and Cy5-labelled RNA were hydrolyzed for 30 min at 60C in 1x fragmentation buffer (Agilent Technologies). The fragmented targets were hybridized to a microarray by incubating for 17 h at 60C in 1 x target solution (Agilent Technologies) in a rotating hybridization chamber. Specifically, each hybridization consisted of two individual samples, one labelled with Cy3 and one with Cy5. After hybridization, the arrays were washed at room temperature for 5 min in 6x salinesodium phosphate–EDTA (SSPE)/0.005% N-Lauroylsarcosine (Sigma-Aldrich, St Louis, MO, USA), 1 min in 0.06x SSPE/0.005% N-Lauroylsarcosine and 30 s in acetonitrile (Sigma-Aldrich), then dried in a nitrogen flow.

scan_protocol: The arrays were scanned at a resolution of 5 um at 5% and 100% photomultiplier tube (PMT) with an Agilent Technologies Scanner G2505A. Scan data were extracted using Agilent Feature Extraction software (version 8.5.1, Agilent).

data_processing: Raw data from the extraction software was imported to R statistical processing environment using a LIMMA/Bioconductor package. Nonuniformity outliers and background outliers were removed. Data were normalized using between-array normalization with the “quantile” algorithm (Bolstad et al., 2003). The Cy3 and Cy5 normalized log2 intensities were used as separate channels for further analysis, as previously shown in Bossers et al. (2010).  Inter-sample gene variation because of technical reasons, such as contamination of myelin, were defined using the Weighted Gene Co-expression Network Analysis (WGCNA) (Langfelder and Horvath, 2008) as shown previously (see Orre et al., 2014) and excluded before normalization in this current analysis.

source_name: cortical astrocytes (glt1), WT mouse

label_protocol: RNA was linearly amplified and fluorescently labelled with either Cy3-CTP or Cy5-CTP using the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies).

extract_protocol: Sorted cells were incubated in TRIsure (Bioline) for 5 minutes on ice with thorough mixing and/or vortexing. For all samples, RNA was isolated by overnight precipitation in isopropanol to which 20 microgram of glycogen had been added.

treatment_protocol: The mice were anesthetized by pentobarbital and transcardially perfused with HBSS (-Ca/-Mg) (Invitrogen). Thereafter, cortical tissue was macro-dissected and, subsequently, used for mechanical dissociation using a Tissue Chopper, the tissue was subjected to enzymatic dissociation using Papain (Worthington) at a final concentration of 8 U/mL in combination with DNase I at 80 Kunitz units/mL final concentration (Sigma; D4263) in a PIPES based buffer with addition of L-cystein- HCl and EDTA in 37C incubator for 50 minutes on a rocker, followed by the addition of another 25 Kunits/mL DNase I and a further incubation at 37C for 15 minutes. A Percoll gradient and myelin removal were performed on single cells before labeling (Myelin Removal Beads II [MiltenyiBiotec; 130-096e733]) according to the manufacturer’s protocol. Pelleted cells were resuspended in PBS (0.5% BSA) and stained with unconjugated rabbit polyclonal GLT-1 (1:100, custom made, Biomatik, 0.6 mg/mL), mouse anti O4 (1:400, Millipore, MAB345), CD11b-APC (1:200, eBioscience, 17-0112-82), CD45-(1:200, eBioscience, 12-0451-82), Fc-receptor block CD16/32 (1:200, BD Pharmingen, 553142), and polyclonal rabbit IgG isotype control (1:150; Thermo Scientific, NC-100-P1) (at 4 _C for 30 minutes). After washing, secondary anti-rabbit biotin antibody (1:100, Jackson Immunoresearch, 111-065e144) and PE conjugated goat anti-mouse (1:125, eBioscience, 12-4010-82) (for visualization of O4 staining) was added and incubated for 30 minutes at 4C. After washing, streptavidin-APC-Cy7 (1:125, Biolegend, 405208) was allowed to incubate for 15 minutes at 4C in the dark. The cells were washed and resuspended in GKN/PBS and cell viability staining 7AAD (BD bioscience). Using BD FACS Aria I (BD bioscience), GLT1 positive cells were sorted on GLT1+/CD11b- expression and microglia cells were sorted on CD11b+/CD45+ expression after gating away the dead cell population on 7AAD signal. The sorted cells were directly subjected to RNA isolation.

value: brain

value: WT

value: 15-18 months

tag: cell population selection

value: myelin- / O4- / cd11b- / glt+


title: astrocytes_WT_3

description:
raw data in Cy3 channel of file:
US12302316_252665511016_S02_GE2-v5_95_Feb07_1_2.txt


title: astrocytes_AD_4

description:
raw data in Cy5 channel of file:
US12302316_252665511016_S02_GE2-v5_95_Feb07_1_3.txt

source_name: cortical astrocytes (glt1), APPswe/PS1dE9 mouse


title: astrocytes_WT_2

description:
raw data in Cy5 channel of file:
US12302316_252665511016_S02_GE2-v5_95_Feb07_1_1.txt


title: C. elegans with B. licheniformis 141 (treatment)

description: Biological replication 1 of 1

source_name: C. elegans exposed to B. licheniformis 141 for 24 h


title: astrocytes_AD_1

description:
raw data in Cy3 channel of file:
US12302316_252665511016_S02_GE2-v5_95_Feb07_1_4.txt


title: astroyctes_WT_4

description:
raw data in Cy3 channel of file:
US12302316_252665511016_S02_GE2-v5_95_Feb07_1_3.txt


title: astrocytes_WT_GFAP-_Vim-_1

description:
raw data in Cy5 channel of file:
US12302316_252665516042_S01_GE2-v5_95_Feb07_1_1.txt

hyb_protocol: Hybridization was carried out with 825 ng labeled RNA per sample. Specifically, each hybridization consisted of two individual samples, one labelled with Cy3 and one with Cy5. RNA was hydrolyzed for 30 min at 60C in 1x fragmentation buffer (Agilent Technologies). The fragmented targets were hybridized to a microarray by incubating for 17 h at 60C in 1 x target solution (Agilent Technologies) in a rotating hybridization chamber. After hybridization, the arrays were washed at room temperature for 5 min in 6x salinesodium phosphate–EDTA (SSPE)/0.005% N-Lauroylsarcosine (Sigma-Aldrich, St Louis, MO, USA), 1 min in 0.06x SSPE/0.005% N-Lauroylsarcosine and 30 s in acetonitrile (Sigma-Aldrich), then dried in a nitrogen flow.

scan_protocol: The arrays were scanned at a resolution of 5 um at 10% and 100% PMT using an Agilent Technologies Scanner G2505A. Scan data was extracted using Agilent Feature Extraction software (version 8.5.1, Agilent).

data_processing: Raw data from the extraction software was imported to R statistical processing environment using a LIMMA/Bioconductor package. Non-uniformity outliers and background outliers were removed. The data was normalized using between-array normalization with the “quantile” algorithm. The Cy3 and Cy5 normalized log2 intensities were used as separate channels for further analysis

source_name: cortical astrocytes (glt1), APPwt, PS1wt, GFAP-/-, Vim-/- mouse

label_protocol: 50-75 ng RNA was amplified and labeled (two-color Low Input Quick Amp Labeling Kit- Agilent Technologies) using the manufacturer’s instructions.

extract_protocol: Sorted cells were incubated in TRIsure (Bioline) for 5 minutes on ice with thorough mixing/vortexing. Isolated whole cortex tissue, from a single hemisphere, was homogenized in 1 ml TRIsure. For all samples, RNA was isolated by overnight precipitation in isopropanol to which 20 ug glycogen had been added.

treatment_protocol: Mice of 15-18 month old were anesthetized and transcardially perfused with cold HBSS (-Ca/-Mg) (Invitrogen). After mechanical dissociation using a Tissue Chopper, the tissue was subjected to enzymatic dissociation using Papain and DNase I. A Percoll gradient and myelin removal were performed on single cells prior to labeling (Myelin Removal Beads II (MiltenyiBiotec; 130-096-733) according to manufacturer’s protocol. Pelleted cells were resuspended in PBS (0.5% BSA) and stained with unconjugated rabbit polyclonal GLT-1 (1:100) (custom made, Biomatik, 0.6mg/ml), CD11b-APC (17-0112-82; eBioscience, 1:200), Fc-receptor block CD16/32 (1:200) (BD Pharmingen, 553142) and polyclonal rabbit IgG isotype control (1:150; Thermo Scientific, NC-100-P1) (at 4°C for 30 min). After washing, secondary anti-rabbit biotin antibody (1:100; Jackson Immunoresearch, 111-065-144) was added and incubated for 30 min at 4 °C. After washing, streptavidin APC-Cy7 (1:125; Biolegend, 405208) was allowed to incubate for 15 min at 4 °C in the dark. The cells were washed and resuspended in GKN/PBS and cell viability staining 7AAD (BD bioscience). Using BD FACS Aria I (BD bioscience), GLT1 positive cells were sorted on GLT1+/CD11bneg expression and microglia cells were sorted on CD11b+ expression after gating away the dead cell population on 7AAD signal. The sorted cells were directly subjected to RNA isolation.

value: APPwt, PS1wt, GFAP-/-, Vim-/-

value: predominantly C57BL/6, but with a variable contribution of 129Sv and 129Ola

value: Myelin- / cd11b- / glt1+


title: astrocytes_AD_3

description:
raw data in Cy5 channel of file:
US12302316_252665511016_S02_GE2-v5_95_Feb07_1_2.txt


title: astrocytes_AD_GFAP-_Vim-_4

description:
raw data in Cy5 channel of file:
US12302316_252665516042_S01_GE2-v5_95_Feb07_1_4.txt

source_name: cortical astrocytes (glt1), APPswe, PS1dE9, GFAP-/-,Vim-/- mouse

value: APPswe, PS1dE9, GFAP-/-,Vim-/-


title: astrocytes_AD_GFAP-_Vim+_4

description:
raw data in Cy5 channel of file:
US12302316_252665516041_S01_GE2-v5_95_Feb07_1_4.txt

source_name: cortical astrocytes (glt1), APPswe, PS1dE9, GFAP-/-, Vim+/+ mouse

value: APPswe, PS1dE9, GFAP-/-, Vim+/+


title: astrocytes_AD_2

description:
raw data in Cy3 channel of file:
US12302316_252665511016_S02_GE2-v5_95_Feb07_1_1.txt


title: astrocytes_AD_GFAP+_Vim+_4

description:
raw data in Cy5 channel of file:
US12302316_252665516040_S01_GE2-v5_95_Feb07_1_4.txt

source_name: cortical astrocytes (glt1), APPswe, PS1dE9, GFAP+/+, Vim+/+ mouse

value: APPswe, PS1dE9, GFAP+/+, Vim+/+


title: astrocytes_WT_GFAP-_Vim+_1

description:
raw data in Cy5 channel of file:
US12302316_252665516041_S01_GE2-v5_95_Feb07_1_1.txt

source_name: cortical astrocytes (glt1), APPwt, PS1wt, GFAP-/-, Vim+/+ mouse

value: APPwt, PS1wt, GFAP-/-, Vim+/+


title: astrocytes_AD_GFAP-_Vim-_3

description:
raw data in Cy5 channel of file:
US12302316_252665516042_S01_GE2-v5_95_Feb07_1_3.txt


title: astrocytes_WT_GFAP+_Vim+_1

description:
raw data in Cy5 channel of file:
US12302316_252665516040_S01_GE2-v5_95_Feb07_1_1.txt

source_name: cortical astrocytes (glt1), APPwt, PS1wt, GFAP+/+, Vim+/+ mouse

value: APPwt, PS1wt, GFAP+/+, Vim+/+


title: astrocytes_AD_GFAP-_Vim+_3

description:
raw data in Cy5 channel of file:
US12302316_252665516041_S01_GE2-v5_95_Feb07_1_3.txt


title: astrocytes_WT_GFAP-_Vim-_2

description:
raw data in Cy5 channel of file:
US12302316_252665516042_S01_GE2-v5_95_Feb07_1_2.txt


title: astrocytes_WT_GFAP-_Vim+_2

description:
raw data in Cy5 channel of file:
US12302316_252665516041_S01_GE2-v5_95_Feb07_1_2.txt


title: microglia_AD_GFAP-_Vim-_4

description:
raw data in Cy5 channel of file:
US12302316_SLOT03_S01_GE2-v5_95_Feb07_1_4.txt

source_name: cortical microglia (cd11b), APPswe, PS1dE9, GFAP-/-,Vim-/- mouse

value: Myelin- / cd11b+


title: astrocytes_WT_GFAP+_Vim+_2

description:
raw data in Cy5 channel of file:
US12302316_252665516040_S01_GE2-v5_95_Feb07_1_2.txt


title: microglia_WT_GFAP-_Vim-_2

description:
raw data in Cy5 channel of file:
US12302316_SLOT03_S01_GE2-v5_95_Feb07_1_2.txt

source_name: cortical microglia (cd11b), APPwt, PS1wt, GFAP-/-, Vim-/- mouse


title: astrocytes_AD_GFAP+_Vim+_3

description:
raw data in Cy5 channel of file:
US12302316_252665516040_S01_GE2-v5_95_Feb07_1_3.txt


title: microglia_AD_GFAP-_Vim-_3

description:
raw data in Cy5 channel of file:
US12302316_SLOT03_S01_GE2-v5_95_Feb07_1_3.txt


title: microglia_AD_GFAP-_Vim+_4

description:
raw data in Cy5 channel of file:
US12302316_SLOT02_S01_GE2-v5_95_Feb07_1_4.txt

source_name: cortical microglia (cd11b), APPswe, PS1dE9, GFAP-/-, Vim+/+ mouse


title: microglia_WT_GFAP-_Vim-_1

description:
raw data in Cy5 channel of file:
US12302316_SLOT03_S01_GE2-v5_95_Feb07_1_1.txt


title: microglia_WT_GFAP-_Vim+_2

description:
raw data in Cy5 channel of file:
US12302316_SLOT02_S01_GE2-v5_95_Feb07_1_2.txt

source_name: cortical microglia (cd11b), APPwt, PS1wt, GFAP-/-, Vim+/+ mouse


title: microglia_AD_GFAP-_Vim+_3

description:
raw data in Cy5 channel of file:
US12302316_SLOT02_S01_GE2-v5_95_Feb07_1_3.txt


title: microglia_AD_GFAP+_Vim+_3

description:
raw data in Cy5 channel of file:
US1230214_SLOT01_S01_GE2-v5_95_Feb07_1_3.txt

source_name: cortical microglia (cd11b), APPswe, PS1dE9, GFAP+/+, Vim+/+ mouse


title: astrocytes_AD_GFAP-_Vim+_2

description:
raw data in Cy3 channel of file:
US12302316_252665516041_S01_GE2-v5_95_Feb07_1_2.txt


title: astrocytes_WT_GFAP-_Vim+_3

description:
raw data in Cy3 channel of file:
US12302316_252665516041_S01_GE2-v5_95_Feb07_1_3.txt


title: astrocytes_WT_GFAP+_Vim+_3

description:
raw data in Cy3 channel of file:
US12302316_252665516040_S01_GE2-v5_95_Feb07_1_3.txt


title: astrocytes_AD_GFAP+_Vim+_2

description:
raw data in Cy3 channel of file:
US12302316_252665516040_S01_GE2-v5_95_Feb07_1_2.txt


title: microglia_AD_GFAP+_Vim+_4

description:
raw data in Cy5 channel of file:
US1230214_SLOT01_S01_GE2-v5_95_Feb07_1_4.txt


title: microglia_WT_GFAP-_Vim+_1

description:
raw data in Cy5 channel of file:
US12302316_SLOT02_S01_GE2-v5_95_Feb07_1_1.txt


title: astrocytes_WT_GFAP-_Vim-_3

description:
raw data in Cy3 channel of file:
US12302316_252665516042_S01_GE2-v5_95_Feb07_1_3.txt


title: astrocytes_WT_GFAP-_Vim+_4

description:
raw data in Cy3 channel of file:
US12302316_252665516041_S01_GE2-v5_95_Feb07_1_4.txt


title: microglia_WT_GFAP+_Vim+_2

description:
raw data in Cy5 channel of file:
US1230214_SLOT01_S01_GE2-v5_95_Feb07_1_2.txt

source_name: cortical microglia (cd11b), APPwt, PS1wt, GFAP+/+, Vim+/+ mouse


title: astrocytes_WT_GFAP-_Vim-_4

description:
raw data in Cy3 channel of file:
US12302316_252665516042_S01_GE2-v5_95_Feb07_1_4.txt


title: astrocytes_WT_GFAP+_Vim+_4

description:
raw data in Cy3 channel of file:
US12302316_252665516040_S01_GE2-v5_95_Feb07_1_4.txt


title: microglia_WT_GFAP-_Vim+_4

description:
raw data in Cy3 channel of file:
US12302316_SLOT02_S01_GE2-v5_95_Feb07_1_4.txt


title: microglia_WT_GFAP-_Vim-_4

description:
raw data in Cy3 channel of file:
US12302316_SLOT03_S01_GE2-v5_95_Feb07_1_4.txt


title: microglia_AD_GFAP-_Vim-_2

description:
raw data in Cy3 channel of file:
US12302316_SLOT03_S01_GE2-v5_95_Feb07_1_2.txt


title: microglia_AD_GFAP-_Vim+_2

description:
raw data in Cy3 channel of file:
US12302316_SLOT02_S01_GE2-v5_95_Feb07_1_2.txt


title: microglia_WT_GFAP+_Vim+_1

description:
raw data in Cy5 channel of file:
US1230214_SLOT01_S01_GE2-v5_95_Feb07_1_1.txt


title: astrocytes_AD_GFAP-_Vim-_1

description:
raw data in Cy3 channel of file:
US12302316_252665516042_S01_GE2-v5_95_Feb07_1_1.txt


title: astrocytes_AD_GFAP-_Vim+_1

description:
raw data in Cy3 channel of file:
US12302316_252665516041_S01_GE2-v5_95_Feb07_1_1.txt


title: microglia_WT_GFAP-_Vim+_3

description:
raw data in Cy3 channel of file:
US12302316_SLOT02_S01_GE2-v5_95_Feb07_1_3.txt


title: microglia_WT_GFAP-_Vim-_3

description:
raw data in Cy3 channel of file:
US12302316_SLOT03_S01_GE2-v5_95_Feb07_1_3.txt


title: microglia_WT_GFAP+_Vim+_3

description:
raw data in Cy3 channel of file:
US1230214_SLOT01_S01_GE2-v5_95_Feb07_1_3.txt


title: microglia_WT_GFAP+_Vim+_4

description:
raw data in Cy3 channel of file:
US1230214_SLOT01_S01_GE2-v5_95_Feb07_1_4.txt


title: microglia_AD_GFAP-_Vim-_1

description:
raw data in Cy3 channel of file:
US12302316_SLOT03_S01_GE2-v5_95_Feb07_1_1.txt


title: astrocytes_AD_GFAP+_Vim+_1

description:
raw data in Cy3 channel of file:
US12302316_252665516040_S01_GE2-v5_95_Feb07_1_1.txt


title: microglia_AD_GFAP-_Vim+_1

description:
raw data in Cy3 channel of file:
US12302316_SLOT02_S01_GE2-v5_95_Feb07_1_1.txt


title: microglia_AD_GFAP+_Vim+_2

description:
raw data in Cy3 channel of file:
US1230214_SLOT01_S01_GE2-v5_95_Feb07_1_2.txt


title: microglia_AD_GFAP+_Vim+_1

description:
raw data in Cy3 channel of file:
US1230214_SLOT01_S01_GE2-v5_95_Feb07_1_1.txt


title: Multiple_Sclerosis_plus_Bexarotene_Donor_3

city: Bethesda

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

hyb_protocol: Labeled cRNA were hybridized to Affymetrix Human Gene 1.0 ST Arrays (Affymetrix, Inc) in blinded interleaved fashion.

scan_protocol: The Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate one .CEL file per hybridized cRNA.

data_processing: The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 33,297 RMA normalized gene fragment expression values for each hybridized cRNA.

label_protocol: Total RNA was labeled on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Gene 1.0 ST Array (Affymetrix, Inc).

growth_protocol: PBMCs were isolated from whole blood using lymphocyte separation medium (Lonza). CD14+ monocytes were isolated by positive selection (MACS Miltenyi) and counted by a Neubauer hemacytometer (Hausser Scientific). Monocytes were plated in 6-well plates at 1x106/well.

extract_protocol: RNA was isolated using miRNeasy kit (Qiagen) according to manufacturer’s instructions.  RNA concentration was measured using a Nanodrop ND-1000 and RNA integrity was assessed using the Bioanalyzer 2100 (Agilent).

treatment_protocol: Plated monocytes representing (-) phagocystosis (-) bexarotene were not treated.  Plated monocytes representing (+) phagocystosis (-) bexarotene were treated with myelin (10µg/ml) isolated from a post-mortem brain of a primary progressive MS patient.  Plated monocytes representing (+) phagocystosis (+) bexarotene were treated with both the same myelin isolate (10ug/ml) and 1uM Bexarotene (Sigma).  Monocyte exposure time to treatment was 2h. Afterwards, cells from all plated monocytes, treated and untreated, were collected in Trizol (Invitrogen) and stored at −80 °C until RNA isolation.

tag: diagnosis

value: Multiple Sclerosis

value: CD14+ Monocytes

value: PPMS Myelin-isolate (10ug/ml) and Bexarotene (1uM)


title: NSC

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku,

department: Institute for Genetic Medicine

institute: Hokkaido University

description: Gene expression

hyb_protocol: 1.5 ug 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) 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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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: mouse NSC

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.

growth_protocol: The cells were cultured in serum-free NSC medium.

extract_protocol: Total RNA was prepared using a RNeasy Mini Kit (QIAGEN).

treatment_protocol: After transfection of the expression vectors, the transformants were selected in the presence of hygromycin for 1 week.

value: E14.5 embryo


title: astrocytes_AD_GFAP-_Vim-_2

description:
raw data in Cy3 channel of file:
US12302316_252665516042_S01_GE2-v5_95_Feb07_1_2.txt

value: brain


title: NSCL61-Ceacam1sh

description: Gene expression

tag: cell line


title: NSCL61

description: Gene expression


title: Dichlorvos_control1_rep4

source_name: liver

value: liver

value: adult (6 - 9 months)

value: Dichlorvos

value: 0 mg/L


title: Multiple_Sclerosis_Control_Donor_3


title: Multiple_Sclerosis_plus_Bexarotene_Donor_2


title: Multiple_Sclerosis_no_Bexarotene_Donor_1

value: PPMS Myelin-isolate (10ug/ml)


title: Multiple_Sclerosis_plus_Bexarotene_Donor_1


title: Multiple_Sclerosis_no_Bexarotene_Donor_4


title: Multiple_Sclerosis_plus_Bexarotene_Donor_4


title: Multiple_Sclerosis_Control_Donor_4


title: Multiple_Sclerosis_no_Bexarotene_Donor_2


title: Multiple_Sclerosis_Control_Donor_1


title: Healthy_Volunteer_Phagocytosis_plus_Bexarotene_Donor_3

value: Healthy


title: Healthy_Volunteer_Phagocytosis_plus_Bexarotene_Donor_1


title: Healthy_Volunteer_Phagocytosis_plus_Bexarotene_Donor_2


title: Healthy_Volunteer_Phagocytosis_plus_Bexarotene_Donor_4


title: Healthy_Volunteer_Control_Donor_1


title: Healthy_Volunteer_Phagocytosis_no_Bexarotene_Donor_2


title: Healthy_Volunteer_Control_Donor_2


title: Healthy_Volunteer_Phagocytosis_no_Bexarotene_Donor_1


title: Multiple_Sclerosis_no_Bexarotene_Donor_3


title: Healthy_Volunteer_Phagocytosis_no_Bexarotene_Donor_3


title: Healthy_Volunteer_Control_Donor_3


title: Multiple_Sclerosis_Control_Donor_2


title: E18.5 FoxD1;Dicer L2

city: New York City

first: Dr. Yu Leng

last: Phua

state: New York

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

description: Litter 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were vst transformed and rns normalized using lumi in R

source_name: Whole kidney

label_protocol: Biotinylated cRNA were prepared from total RNA with the use of Illumina TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: The Qiagen RNeasy mini kit with an on-column DNase digestion was used for the total RNA isolation. The quality of the RNA was assessed by an Agilent Bioanalyzer test prior to the microarray procedures.

value: Whole kidney

tag: developmental stage


title: E15.5 Control L1

description: Litter 1


title: E18.5 FoxD1;Dicer L3

description: Litter 3


title: E15.5 FoxD1;Dicer L2

description: Litter 2


title: E15.5 FoxD1;Dicer L3

description: Litter 3


title: Il34LacZ/LacZ

city: Saint Louis

first: Marco

last: Colonna

state: MO

address: 660 S Euclid Ave.

department: Pathology and Immunology

institute: Washinton University School of Medicine

description: gene expression from purifed Langerhans cells

hyb_protocol: Samples are prepared using a Nugen Ovation Pico SL kit.

data_processing: Data were analyzed using GenePattern (Broad Institute)

source_name: Langerhans cells

label_protocol: Biotinylated cRNA were prepared using a Nugen Encore Biotin kit from 2 ng total RNA.

growth_protocol: 8-12 weeks old Il34+/LacZ and Il34LacZ/LacZ mice were used

extract_protocol: Cells were sorted directly into RLT buffer (Qiagen). A Rneasy micro kit (Qiagen) was used for subsquent RNA extraction.

treatment_protocol: Mice were treated with UV for 30 min. Langerin+Epcam+Langherhans cells were purified 21 days after the treatment.

tag: stress

value: UV for 30 min

tag: time

value: 21 Days after UV

tag: cell type

value: Langerhans cells


title: Healthy_Volunteer_Control_Donor_4


title: E15.5 FoxD1;Dicer L1

description: Litter 1

tag: tissue


title: E18.5 FoxD1;Dicer L1

description: Litter 1


title: E18.5 Control L3

description: Litter 3


title: E18.5 Control L2

description: Litter 2


title: E15.5 Control L2

description: Litter 2


title: E15.5 Control L3

description: Litter 3


title: siSOX2 2nd replicate

city: Toulouse

first: Nicolas

last: Chassaing

address: Place du Dr Baylac

department: Service de Génétique Médicale

country: France

institute: CHU Toulouse

description: 64-10_Si SOX2-2.CEL

hyb_protocol: Following fragmentation and labeling, ss-cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Raw data from all hybridizations were background corrected, normalized and summarized using robust multi-array average (RMA) for all conditions together as implemented in R with the oligo package.
Consequently, all data were log2 transformed. Significant genes were identified using the limma package. An FDR (False Discovery Rate) corrected p-value ≤0.05 and log2 fold change > 0.5 or < -0.5 were used as the criterion for significance.

source_name: CCE-Rx cells_siSOX2

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (WT PLUS Reagent kit User Manual, Affymetrix).

growth_protocol: 1.2x106 undifferentiated adherent CCE-RX cells were plated in 6cm tissue-culture-treated Petri dishes in LIF-free DMEM supplemented with 10% of BSA, 100 µM 2-mercaptoethanol, 2mM glutamin and 100 µM non-essential amino acids. In addition, when resuspended, cells were transfected (Effecten protocol: 8µl Effectene, 2.4 µl Enhancer) with either 400nM of siRNA against SOX2 (Invitrogen, Stealth™ siRNA MSS277200), or scramble siRNA (Invitrogen Negative Control Medium GC ). 48 hours after transfection in quadruplicate of either the siSOX2 or the siScramble, total RNA was isolated using the GenElute Mammalian Total RNA Miniprep kit (Sigma-Aldrich).

treatment_protocol: Transfection with siSOX2 or siScramble were performed when cells were plated. RNA were extracted 48H after transfection.

value: Stem cells overexpressing the RAX gene (PMID:15121868)

tag: transfected with

value: siRNA against SOX2

tag: time point

value: 48H after transfection


title: siSOX2 4th replicate

description: 64-10_Si SOX2-4.CEL

extract_protocol: GenElute Mammalian Total RNA Miniprep kit (Sigma-Aldrich)


title: siSOX2 3th replicate

description: 64-10_Si SOX2-3.CEL


title: siScramble 4th replicate

source_name: CCE-Rx cells_siScramble

value: siRNA against scramble siRNA


title: E18.5 Control L1

description: Litter 1


title: siSOX2 1st replicate

description: 64-10_Si SOX2-1.CEL


title: siScramble 3th replicate


title: siScramble 2nd replicate


title: siScramble 1st replicate


title: CEM_BTZ100

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

hyb_protocol: hybridization to the Agilent human miRNA microarray using the miRNA Complete Labeling and Hyb Kit (Agilent p/n 5190-0456)

scan_protocol: Agilent DNA microarray scanner.

data_processing: The raw miRNA expression data were extracted from the scanned image using Agilent Feature Extraction Software V10

source_name: CCRF-CEM resistant to 100 nM bortezomib,cultured in presence of 100nM bortezomib

label_protocol: not provided

growth_protocol: RPMI +10%fcs, in presence of indicated concentration of BTZ for several weeks

extract_protocol: Total RNA, including small RNAs was extracted using MiRNeasy Kit (Qiagen, Valencia, CA)

treatment_protocol: Cultured in presence of indicated concentration of BTZ for several weeks

value: CCRF-CEM

value: T Lymphoblast


title: CEM_WT Replicate 1

source_name: CCRF-CEM-WT


title: CEM_WT Replicate 2


title: Colonic epithelium, Sel1L knockout, replicate 3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the GeneChip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.30.0).

source_name: Colon epithelium isolated from an enterocyte-specific Sel1L knockout mice aged 8 wks

label_protocol: The Ambion WT Expression kit (Life Technologies, Carlsbad, CA; P/N 4411974) in conjunction with the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA; P/N 900671) was used for the preparation of labeled cDNA from 100ng of total RNA without rRNA reduction.

growth_protocol: The Sel1ltm1e(KOMP)Wtsi (Sel1Lflox/+) ES cells on the C57BL/6J background were purchased from the KOMP Repository Project (ID CSD44577, UC Davis, http://www.knockoutmouse.org/martsearch/project/44577). Exon 6 of Sel1L gene is flanked by two loxP sites (floxed). The lacZ-neo cassette was deleted by crossing the animals onto the βActin-FLPe deleter mice on the C57BL/6J background (JAX 003800). The resulting Sel1Lflox/+ animals were intercrossed to generate Sel1Lflox/flox mice. The Sel1Lflox/flox mice were then crossed with villin-1 promoter-driven Cre mice (B6.SJL-Tg(Vil-cre)997Gum/J, JAX 004586), which have been backcrossed to the C57BL/6J background for more than five generations.

extract_protocol: Total RNA was extracted using Trizol and RNA miniprep kit (Sigma RTN350) with DNaseI digestion (Roche). RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Colon epithelium was isolated from 8-week-old male wild type and enterocyte-specific Sel1L knockout (Sel1LΔIEC) mice and snap frozen in liquid nitrogen.

tag: strain/background

tag: age

value: 8 wk

value: male

value: colon epithelium


title: CEM_BTZ200

source_name: CCRF-CEM resistant to 200 nM bortezomib,cultured in presence of 200nM bortezomib


title: Colonic epithelium, wild type, replicate 2

source_name: Colon epithelium isolated from a wild type (C57BL/6J) mice aged 8 wks

tag: genotype/variation

value: wild type


title: Il34+/LacZ


title: Colonic epithelium, Sel1L knockout, replicate 1


title: Colonic epithelium, Sel1L knockout, replicate 2


title: Colonic epithelium, wild type, replicate 1


title: Colonic epithelium, wild type, replicate 3


title: Olfactory epithelium of 4 mice, CT20

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

country: Germany

institute: BIH at Charité

description:
MS_03_CT20
Gene expression data from olfactory epithelium pooled from 4 mice at CT20.

hyb_protocol: The biotinylated DNA was added to a hybridization cocktail for hybridization to the Affymetrix Mouse Gene 1.0 ST Array, also containing 50pM control oligonucleotide B2, eukaryotic hybridization controls (bioB, bioC, bioD, 1,5, 5; 25 pM respectively), according to the manufacturer’s protocol (Hybridization Wash and Stain Kit, Affymetrix). The hybridization in the Affymetrix hybridization oven 640 at 45°C and 60 rpm for 16hrs, the staining and washing, processed in the Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 G7 system as recommended by Affymetrix.

data_processing: Data were preprocessed and normalized using the affy package in R.

source_name: 4 male C57BL/6 mice, olfactory epithelium, CT20

label_protocol: For the first cycle cDNA synthesis, 300ng of total RNA was used. During the following in vitro transcription reaction, cRNA was obtained and used as starting material for the second cycle cDNA synthesis. The second cycle random-primed single strand DNA synthesis resulted in a product containing incorporated deoxyuridine at predefined ratios relative to thymidine (Ambion® WT Expression Kit (Ambion, Austin, Texas, USA)). Subsequently, 5.5 μg of this generated single-strand DNA was fragmented with a combination of uracil DNA glucosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) and then labeled using the WT terminal labeling kit (Affymetrix, Inc., Santa Clara, CA, USA).

growth_protocol: 48 male C57BL/6 mice were exposed to a 12 h : 12 h light/dark (LD) cycle for at least 14 days to ensure proper entrainment of the circadian system to the ambient LD cycle.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA integrity was checked by analyzing on the 2100 Bioanalyzer (Agilent Technologies, PA, USA).

treatment_protocol: Subsequently, animals were transferred into constant darkness (DD) and killed by cervical dislocation at 4 h intervals starting 24 hours after lights off (= circadian time (CT) 12). The bilateral OEs were then explanted and shock-frozen in liquid nitrogen.

value: olfactory epithelium


title: Olfactory epithelium of 4 mice, CT36

description:
MS_07_CT36
Gene expression data from olfactory epithelium pooled from 4 mice at CT36.

source_name: 4 male C57BL/6 mice, olfactory epithelium, CT36


title: Olfactory epithelium of 4 mice, CT48

description:
MS_10_CT48
Gene expression data from olfactory epithelium pooled from 4 mice at CT48.

source_name: 4 male C57BL/6 mice, olfactory epithelium, CT48


title: Olfactory epithelium of 4 mice, CT40

description:
MS_08_CT40
Gene expression data from olfactory epithelium pooled from 4 mice at CT40.

source_name: 4 male C57BL/6 mice, olfactory epithelium, CT40


title: Olfactory epithelium of 4 mice, CT56

description:
MS_12_CT56
Gene expression data from olfactory epithelium pooled from 4 mice at CT56.

source_name: 4 male C57BL/6 mice, olfactory epithelium, CT56


title: Olfactory epithelium of 4 mice, CT52

description:
MS_11_CT52
Gene expression data from olfactory epithelium pooled from 4 mice at CT52.

source_name: 4 male C57BL/6 mice, olfactory epithelium, CT52


title: Olfactory epithelium of 4 mice, CT44

description:
MS_09_CT44
Gene expression data from olfactory epithelium pooled from 4 mice at CT44.

source_name: 4 male C57BL/6 mice, olfactory epithelium, CT44


title: Olfactory epithelium of 4 mice, CT24

description:
MS_04_CT24
Gene expression data from olfactory epithelium pooled from 4 mice at CT24.

source_name: 4 male C57BL/6 mice, olfactory epithelium, CT24


title: NSC-Ceacam1L

description: Gene expression

source_name: mouse NSC

tag: genotype

value: brain

value: E14.5 embryo


title: Olfactory epithelium of 4 mice, CT28

description:
MS_05_CT28
Gene expression data from olfactory epithelium pooled from 4 mice at CT28.

source_name: 4 male C57BL/6 mice, olfactory epithelium, CT28


title: Olfactory epithelium of 4 mice, CT16

description:
MS_02_CT16
Gene expression data from olfactory epithelium pooled from 4 mice at CT16.

source_name: 4 male C57BL/6 mice, olfactory epithelium, CT16


title: LNCaP treated with OBP-801-3

city: Nagoya

first: Shinya

last: Sato

address: kawasumi1, mizuho-ku

institute: Nagoya City University

description: Gene expression in OBP-801 treated prostate cancer cell line

hyb_protocol: 480ng 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 25 x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's 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 Human GE Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slide (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies) using default parameters (protocol GE１_1010_Sep10 and Grid: 028004_D_F_20110325).   Genes-screening was performed using the GeneSpring GX v12.0.0 software package (Agilent Technologies).

source_name: LNCaP treated with OBP-801

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ｎg RNA using the Low Input Quick Amp labeling kit, one-color (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNAs were isolated from the prostate cancer cell lines  using an RNeasy Mini kit (Qiagen, Valencia, CA, USA) and  treated with RQ1 RNase-free DNase (Promega, Madison, WI,  USA) according to the manufacturer’s instructions. Reverse  transcription of RNA was carried out in a final volume of 20 mL  containing buffer, 0.1 M DTT, Oligo (DT)20, 10 mM dNTPs,  0.4 U/mL of RNase inhibitor, 1.25 U/mL of reverse transcriptase  (Invitrogen Corp) and 1 mg of total RNA.

value: LNCaP (CRL-1740)

value: prostate cancer cells metastasized to a lymph nodes


title: Olfactory epithelium of 4 mice, CT12

description:
MS_01_CT12
Gene expression data from olfactory epithelium pooled from 4 mice at CT12.

source_name: 4 male C57BL/6 mice, olfactory epithelium, CT12


title: LNCaP treated with OBP-801-2


title: DT40 H2A.Z-1 and H2A.Z-2 double knockout cells_tetracycline_3 days

city: Sendai

first: Yukako

last: Oma

address: Tsutsumidori-Amamiyamachi 1-1, Aoba-ku

department: Graduate School of Agricultural Science

institute: Tohoku University

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0).

organism: Gallus gallus

source_name: Gallus gallus DT40 B cell H2A.Z-1 and H2A.Z-2 double knockout clone

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ug total RNA (GeneChip 3' IVT Express Kit, Affymetrix).

growth_protocol: DT40 cells were cultured at 38˚C in Dulbecco's modified medium supplemented with 10% fetal calf serum, 1% chicken serum, 2-mercaptoethanol, penicillin, and streptomycin.

extract_protocol: Total RNA was extracted with the RNeasy Mini kit (QIAGEN) according to the manufacturer’s protocol.

treatment_protocol: To suppress expression of the tetracycline (tet)-responsive H2A.Z-1 transgene, tetracycline was added to the culture medium to a final concentration of 2 mg/ml.

value: bursa of Fabricius

value: DT40 B

value: H2A.Z-1 and H2A.Z-2 double knockout


title: gArp6 KO 6days

description: To suppress expression of gArp6, conditional konckout cells for gArp6 were cultured with tetracycline to a final concentration of 2 ug/ml for 6 days.

hyb_protocol: For hybridization, 15 ug of biotinylated cRNA was fragmented and added into a hybridization cocktail containing four biotinylated hybridization controls (bioB, bioC, bioD, and cre) as recommended by the manufacturer. GeneChip Chicken genome Arrays (Affymetrix) were hybridized with the cocktail at 45˚C for 16 hours.

scan_protocol: After washing with Non-Stringent wash buffer (6xSSPE, 0.01% Tween20) and staining with SAPE in the Affymetrix GeneChip Fluidics Station 400, the GeneChips were read using the Affymetrix GeneChip scanner 3000 7G.

data_processing: These systems and data analyses were operated with the GeneChip Operating Software 1.3.

molecule: polyA RNA

source_name: gArp6 KO 6days

label_protocol: Biotinylated cRNA was synthesized according to Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix)Shortly, 2 ug of poly-A mRNA was reverse transcribed to cDNA using 100 pmol of a T7-oligo (dT) primer (Invitrogen), and biotinylated cRNA was prepared by using the cDNA as template.

growth_protocol: The chicken DT40 cells and conditional knockout cells for Arp6 with DT40 cell were cultured at 38˚C in Dulbecco’s modified medium supplemented with 10% fetal calf serum, 1% chicken serum, penicillin and streptomycin. To suppress expression of the tetracycline - responsive Arp6 transgene, tetracycline (Sigma) was added to the culture medium to a final concentration of 2 ug/ml.

extract_protocol: The total RNA was extracted with RNeasy Maxi (QIAGEN) according to the manufacturer protocol. The poly-A mRNA was isolated from total RNA using Oligotex-dT30 Super (JSR corporation).

treatment_protocol: Targeted disruption constructs for the ARP6 gene were generated so that genetic fragments encoding exons 6-11 were replaced with a histidinol- (hisD) or puromycin- (puro) resistance cassette under the control of the beta-actin promoter. DT40 cells were cultured at 38˚C in Dulbecco’s modified medium supplemented with 10% fetal calf serum, 1% chicken serum, penicillin and streptomycin. The target constructs were transfected with a Gene Pulser II electroporator (Bio-Rad, Tokyo, Japan). Histidinol (Sigma) at a final concentration of 1 mg/ml, zeocin (Invitrogen) at a final concentration of 1 mg/ ml, and puromycin (Clontech) at a final concentration of 0.5 ug/ml were used to select stable transfectants.

tag: gArp6 KO 6days


title: DT40 WT cell

source_name: Gallus gallus DT40 B cell wild-type clone


title: LNCaP treated with NCC-149-3

description: Gene expression in NCC-149 treated prostate cancer cell line

source_name: LNCaP treated with NCC-149


title: LNCaP treated with NCC-149-2


title: Olfactory epithelium of 4 mice, CT32

description:
MS_06_CT32
Gene expression data from olfactory epithelium pooled from 4 mice at CT32.

source_name: 4 male C57BL/6 mice, olfactory epithelium, CT32

tag: gender


title: LNCaP treated with DMSO2

description: Gene expression in DMSO treated prostate cancer cell line

source_name: LNCaP treated with DMSO


title: LNCaP treated with DMSO3


title: gArp6 KO 2days

description: To suppress expression of gArp6, conditional konckout cells for gArp6 were cultured with tetracycline to a final concentration of 2 ug/ml for 2 days.

source_name: gArp6 KO 2days

tag: conditinoal knockout chicken DT40 cell for gArp6


title: LNCaP treated with OBP-801-1


title: CEM_BTZ-200

hyb_protocol: Equal amounts of Cy3-CTP and Cy5-CTP labeled samples were hybridized to Agilent 4 × 44K Whole Human Genome arrays (Agilent Technologies) according to the manufacturer's instructions. Hybridization was carried out for 17 h with rotation at 65 °C in a hybridization oven.

scan_protocol: Microarrays were scanned using the Agilent DNA Microarray Scanner (Agilent Technologies)

data_processing: Raw expression data generated by the Feature Extraction software were imported into the R statistical environment using the LIMMA package in bioconductor (http://www.bioconductor.org). After background correction, the intensity distributions within and between arrays were normalized using the Loess [92] and quantile [93] algorithm, respectively.

source_name: CCRF-CEM resistant to 200 nM bortezomib, cultured in absence of bortezomib for several months

label_protocol: labeling performed with Agilent Low RNA Input Fluorescent Linear Amplification Kit, Agilent Technologies

extract_protocol: RNA was isolated using RNAbee (AMSBiotechnology), according to the protocol provided by AMSBiotechnology.

treatment_protocol: Cultured in presence of indicated concentration of BTZ for several weeks. 24 hour before RNA extraction, medium was refreshed and the corrensponding concentration bortezomib was added. RNA of was extracet from untreated cells and WT cells treated with 7nM of bortezomib for 24hours.


title: LNCaP treated with TSA3

description: Gene expression in TSA treated prostate cancer cell line

source_name: LNCaP treated with TSA


title: CEM_BTZ100

source_name: CCRF-CEM resistant to 100 nM bortezomib,cultured in presence of 100nM bortezomib


title: LNCaP treated with TSA1


title: CEM_BTZ7 Replicate 2

source_name: CCRF-CEM resistant to 7 nM bortezomib, cultured in presence of 7nM bortezomib


title: CEM_BTZ7 Replicate 1


title: CEM_BTZ200

source_name: CCRF-CEM resistant to 200 nM bortezomib,cultured in presence of 200nM bortezomib


title: CEM_BTZ7 Replicate 3


title: LNCaP treated with DMSO1


title: CEM_WT_BTZ Replicate 3

source_name: CCRF-CEM-WT, treated with 7nM bortezomib for 24hours


title: gArp6 KO 4days

description: To suppress expression of gArp6, conditional konckout cells for gArp6 were cultured with tetracycline to a final concentration of 2 ug/ml for 4 days.

source_name: gArp6 KO 4days

tag: gArp6 KO 4days


title: gArp6 KO 0day (control)

description: Conditional konckout cells for gArp6 were cultured without induction of knockout.

source_name: gArp6 KO 0day

tag: no induction


title: CEM_WT_BTZ Replicate 1

tag: cell line


title: Tumor_biological rep1

city: Salt Lake City

first: Kevin

middle: B

last: Jones

state: Utah

address: 2000 Circle of Hope Drive, Room 4263

department: Department of Orthopaedics

institute: University of Utah

description: Gene expression data from mouse synovial sarcomas with genetically stabilized beta-catenin.

hyb_protocol: Biotin-labeled cRNA samples (15 µg) were fragmented and combined with Affymetrix hybridization reagents (50 pM Control Oligonucleotide B2, Eukaryotic hybridization controls, 0.1 mg/ml Herring Sperm DNA, 0.5 mg/ml BSA, 1X Hybridization Buffer, 10% DMSO). The hybridization mixture was injected into a GeneChip cartridge and hybridizations were performed in an Affymetrix GeneChip Hybridization Oven 450, set to 45ºC. GeneChip cartridges were rotated within the hybridization oven at 60 rpm for approximately 16 hours. Following hybridization, the mixture was removed from the GeneChip cartridge and replaced with Non-Stringent Wash Buffer (6X SSPE, 0.01% Tween-20). Wash and Stain steps on the hybridized microarray were accomplished by loading the GeneChip into an Affymetrix Fluidics Station 450 and running the EukGE-WS2v5_450 fluidics script.

scan_protocol: Affymetrix GeneChips were scanned in an Affymetrix 3000 7G Microarray Scanner. The scanner detects fluorescent signal from R-phycoerythrin bound to the hybridized microarray. Data captured from the scanned microarray image were saved as a DAT file.

data_processing: DAT files generated from the scanned microarray image were loaded into Affymetrix GeneChip Operating Software Version 1.4. The software automatically positions a grid and finds the positions of each feature on the microarray. This information is used to perform calculations that include feature intensities, background measurements and statistical analyses. Data generated by the software is recorded as a CEL file. CEL files were analyzed with dChip processing using Invariant set normalization.

source_name: tumor generated from Ad-Cre injection into a Rosa26 hSS2/wt; Ctnnb1 ex3fl/wt mouse

label_protocol: GeneChip Hybridization Control Kit by Affymetrix using a GeneChip Fluidics Station 450.

growth_protocol: Mice were bred from parents each homozygous for one of the alleles.

extract_protocol: Immediate post-mortem tumor specimens were collected and snap frozen. Total RNA was extracted with the Qiagen RNeasy mini kit.

treatment_protocol: 10^7 units of AdCre were injected at age 4 weeks into bilateral anterior leg compartments.

tag: strain

value: Rosa26-hSS2/wt; Ctnnb1-ex3fl/wt

value: 4 months

value: synovial sarcoma


title: Healthy_Volunteer_Phagocytosis_no_Bexarotene_Donor_4

tag: diagnosis

value: Healthy

value: CD14+ Monocytes

tag: treatment

value: PPMS Myelin-isolate (10ug/ml)


title: Tumor_biological rep2


title: CEM_WT Replicate 2

source_name: CCRF-CEM-WT

value: CCRF-CEM

tag: cell type

value: T Lymphoblast


title: Tumor_biological rep6

tag: tissue


title: LNCaP treated with TSA2


title: Tumor_biological rep5


title: HCT116 un-transfected

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

country: Spain

institute: Cancer Research Center (CiC-IBMCC)

description: Gene expression data from human clinical samples

hyb_protocol: Hybridized to the Affymetrix GeneChip Human Gene 1.0 ST microarray, after quality checking on GeneChips Test Arrays

scan_protocol: The justRMA() function provided by the package Affy from R/Bioconductor was applied to the raw expression data. The probes were mapped to GENE LOCi by the CDF built by GATExplorer, which can be found at http://bioinfow.dep.usal.es/xgate/mapping/mapping.php

data_processing: Labeling and hybridization were performed according to protocols from Affymetrix. Briefly, 100 ng of total RNA was amplified and labeled using the GeneChip two-cycle cDNA synthesis kit and GeneChip IVT labeling kit (Affymetrix Inc.).

source_name: HCT116 un-transfected

growth_protocol: HCT116 cells stably expressing cystatin D (HCT116-CST5 clone 9 and clone 20), mock-transfected (HCT116-Mock) and un-transfected (HCT116-Untransfected) were generated as described (Álvarez-Díaz et al., 2009)

extract_protocol: RNA isolation, labelling and microarray hybridization was done following the manufacturer’s protocols for the GeneChip platform by Affymetrix were used

value: colon adenocarcinoma

tag: transfection

value: un-transfected


title: CEM_WT Replicate 1


title: Tumor_biological rep4


title: HCT116 mock-transfected

source_name: HCT116 mock-transfected

label_protocol: Labeling and hybridization were performed according to protocols from Affymetrix. Briefly, 100 ng of total RNA was amplified and labeled using the GeneChip two-cycle cDNA synthesis kit and GeneChip IVT labeling kit (Affymetrix Inc.).

treatment_protocol: HCT116 cells stably expressing cystatin D (HCT116-CST5 clone 9 and clone 20), mock-transfected (HCT116-Mock) and un-transfected (HCT116-Untransfected) were generated as described (Álvarez-Díaz et al., 2009)

value: mock-transfected


title: Healthy control 12

city: Jaen

first: Octavio

last: Caba

state: Jaen

address: Paraje de las Lagunillas

department: Health Sciences

institute: University of Jaen

description:
Transcriptome profile of peripheral blood before treatment from healthy control 12
SAMPLE 48

hyb_protocol: Standard Illumina Human-HT12 Version 4

scan_protocol: Standard Illumina Genome Studio

data_processing: The data were background corrected and normalized using the neqc function from the Limma package

source_name: Peripheral blood from healthy control 12

label_protocol: Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA was extracted using the PAXgene Blood RNA Kit (PreAnalytiX) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Before any type of chemotherapy was received peripheral blood samples were collected in PAXgene Blood RNA Tubes (PreAnalytix)

value: healthy

value: male

tag: pathological staging

tag: diabetes

value: no

tag: chronic pancreatitis


title: HCT116 CST5 clone 20

source_name: HCT116 CST5 clone 20

value: CST5 clone 20


title: Tumor_biological rep3

tag: age


title: Healthy control 10

description:
Transcriptome profile of peripheral blood before treatment from healthy control 10
SAMPLE 46

source_name: Peripheral blood from healthy control 10


title: Healthy control 9

description:
Transcriptome profile of peripheral blood before treatment from healthy control 9
SAMPLE 45

source_name: Peripheral blood from healthy control 9


title: Healthy control 14

description:
Transcriptome profile of peripheral blood before treatment from healthy control 14
SAMPLE 50

source_name: Peripheral blood from healthy control 14


title: HCT116 CST5 clone 9

source_name: HCT116 CST5 clone 9

value: CST5 clone 9


title: Healthy control 13

description:
Transcriptome profile of peripheral blood before treatment from healthy control 13
SAMPLE 49

source_name: Peripheral blood from healthy control 13

value: female


title: Healthy control 1

description:
Transcriptome profile of peripheral blood before treatment from healthy control 1
SAMPLE 37

source_name: Peripheral blood from healthy control 1


title: Healthy control 11

description:
Transcriptome profile of peripheral blood before treatment from healthy control 11
SAMPLE 47

source_name: Peripheral blood from healthy control 11


title: Healthy control 3

description:
Transcriptome profile of peripheral blood before treatment from healthy control 3
SAMPLE 39

source_name: Peripheral blood from healthy control 3


title: Healthy control 2

description:
Transcriptome profile of peripheral blood before treatment from healthy control 2
SAMPLE 38

source_name: Peripheral blood from healthy control 2


title: LNCaP treated with NCC-149-1

description: Gene expression in NCC-149 treated prostate cancer cell line

source_name: LNCaP treated with NCC-149

value: LNCaP (CRL-1740)

value: prostate cancer cells metastasized to a lymph nodes


title: PDAC patient 34

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 34
SAMPLE 34

source_name: Peripheral blood before treatment from PDAC patient 34

value: pancreatic ductal adenocarcinoma

value: UK

value: yes


title: PDAC patient 32

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 32
SAMPLE 32

source_name: Peripheral blood before treatment from PDAC patient 32


title: Healthy control 4

description:
Transcriptome profile of peripheral blood before treatment from healthy control 4
SAMPLE 40

source_name: Peripheral blood from healthy control 4


title: PDAC patient 28

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 28
SAMPLE 28

source_name: Peripheral blood before treatment from PDAC patient 28


title: PDAC patient 35

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 35
SAMPLE 35

source_name: Peripheral blood before treatment from PDAC patient 35


title: PDAC patient 31

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 31
SAMPLE 31

source_name: Peripheral blood before treatment from PDAC patient 31


title: Healthy control 5

description:
Transcriptome profile of peripheral blood before treatment from healthy control 5
SAMPLE 41

source_name: Peripheral blood from healthy control 5


title: Healthy control 6

description:
Transcriptome profile of peripheral blood before treatment from healthy control 6
SAMPLE 42

source_name: Peripheral blood from healthy control 6


title: PDAC patient 29

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 29
SAMPLE 29

source_name: Peripheral blood before treatment from PDAC patient 29


title: Healthy control 7

description:
Transcriptome profile of peripheral blood before treatment from healthy control 7
SAMPLE 43

source_name: Peripheral blood from healthy control 7


title: PDAC patient 23

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 23
SAMPLE 23

source_name: Peripheral blood before treatment from PDAC patient 23


title: PDAC patient 20

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 20
SAMPLE 20

source_name: Peripheral blood before treatment from PDAC patient 20


title: PDAC patient 30

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 30
SAMPLE 30

source_name: Peripheral blood before treatment from PDAC patient 30


title: PDAC patient 36

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 36
SAMPLE 36

source_name: Peripheral blood before treatment from PDAC patient 36


title: PDAC patient 22

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 22
SAMPLE 22

source_name: Peripheral blood before treatment from PDAC patient 22


title: PDAC patient 25

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 25
SAMPLE 25

source_name: Peripheral blood before treatment from PDAC patient 25


title: PDAC patient 24

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 24
SAMPLE 24

source_name: Peripheral blood before treatment from PDAC patient 24


title: semen-BTLM5

city: Beltsville

first: Derek

middle: Martens

last: Bickhart

address: Building 005, Rm 318, BARC-West 10300 Baltimore Ave

department: BARC

institute: USDA ARS

description: Processed data files are bed file coordinates for probe locations. Columns 4 and 5 indicate the normalized aCGH copy number value and the rCV value, respectively

hyb_protocol: Hybridization was performed by the third party provider, Nimblegen. Dye swap experiments with the Dominette reference sample were performed to test probe quality

scan_protocol: Scanning was performed by the third party provider, Nimblegen

data_processing:
Data processing was performed similar to Sudmant et al. 2010 's single channel aCGH methodology. In short, single channel array intensities were transformed into integer copy number estimates by using normalized reference signal intensity derived from all tested array samples.
Median reference signal intensity normalized log2 ratios, and rCV estimates of probe sequence copy number fluctuation.

organism: Bos taurus

source_name: frozen semen stock

label_protocol: Labeling was performed by the third party provider, Nimblegen

extract_protocol: DNA was extracted from semen using a Qiagen DNEasy tissue and blood kit

tag: breed

value: Limousin

source_name: L1 Dominette whole blood DNA extract

value: Hereford


title: PDAC patient 26

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 26
SAMPLE 26

source_name: Peripheral blood before treatment from PDAC patient 26


title: PDAC patient 33

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 33
SAMPLE 33

source_name: Peripheral blood before treatment from PDAC patient 33


title: semen-BTLM6


title: semen-BTLM4


title: semen-BTLM2


title: CEM_WT_BTZ Replicate 2

source_name: CCRF-CEM-WT, treated with 7nM bortezomib for 24hours

value: CCRF-CEM

value: T Lymphoblast


title: semen-BTLM1


title: semen-BTLM3


title: PDAC patient 18

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 18
SAMPLE 18

source_name: Peripheral blood before treatment from PDAC patient 18


title: semen-BTJE6

value: Jersey


title: semen-BTJE5


title: semen-BTJE4


title: PDAC patient 27

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 27
SAMPLE 27

source_name: Peripheral blood before treatment from PDAC patient 27


title: PDAC patient 19

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 19
SAMPLE 19

source_name: Peripheral blood before treatment from PDAC patient 19


title: semen-BTJE3


title: semen-BTJE2


title: PDAC patient 14

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 14
SAMPLE 14

source_name: Peripheral blood before treatment from PDAC patient 14


title: PDAC patient 16

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 16
SAMPLE 16

source_name: Peripheral blood before treatment from PDAC patient 16


title: PDAC patient 21

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 21
SAMPLE 21

source_name: Peripheral blood before treatment from PDAC patient 21


title: semen-BTJE1


title: PDAC patient 15

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 15
SAMPLE 15

source_name: Peripheral blood before treatment from PDAC patient 15


title: PDAC patient 17

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 17
SAMPLE 17

source_name: Peripheral blood before treatment from PDAC patient 17


title: semen-BTAN7

value: Angus


title: PDAC patient 13

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 13
SAMPLE 13

source_name: Peripheral blood before treatment from PDAC patient 13


title: semen-BTAN6


title: semen-BTAN5


title: semen-BTAN4


title: PDAC patient 11

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 11
SAMPLE 11

source_name: Peripheral blood before treatment from PDAC patient 11


title: semen-BTAN3


title: semen-BTAN2


title: PDAC patient 9

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 9
SAMPLE 9

source_name: Peripheral blood before treatment from PDAC patient 9


title: PDAC patient 6

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 6
SAMPLE 6

source_name: Peripheral blood before treatment from PDAC patient 6


title: PDAC patient 7

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 7
SAMPLE 7

source_name: Peripheral blood before treatment from PDAC patient 7


title: PDAC patient 4

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 4
SAMPLE 4

source_name: Peripheral blood before treatment from PDAC patient 4


title: PDAC patient 10

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 10
SAMPLE 10

source_name: Peripheral blood before treatment from PDAC patient 10


title: PDAC patient 2

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 2
SAMPLE 2

source_name: Peripheral blood before treatment from PDAC patient 2


title: semen-BTAN1

description: Processed data files are bed file coordinates for probe locations. Columns 4 and 5 indicate the normalized aCGH copy number value and the rCV value, respectively

source_name: frozen semen stock

source_name: L1 Dominette whole blood DNA extract


title: PDAC patient 8

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 8
SAMPLE 8

source_name: Peripheral blood before treatment from PDAC patient 8


title: PDAC patient 1

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 1
SAMPLE 1

source_name: Peripheral blood before treatment from PDAC patient 1


title: PDAC patient 12

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 12
SAMPLE 12

source_name: Peripheral blood before treatment from PDAC patient 12


title: OVCAR5 control rep2

city: Baltimore

first: Ie-Ming

last: Shih

state: Maryland

address: 1550 Orleans St. CRB-II, Room 305

institute: Johns Hopkins University School of Medicine

data_processing: The data were background subtracted, quantile normalized, and log2 transformed using neqc function in limma package in R.

source_name: OVCAR5 cell culture control

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

growth_protocol: RPMI-1640 supplemented with 10% fetal calf serum

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit and cleaned-up with DNAse I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: 10 uM Lovastatin or DMSO for 48 hours

value: DMSO


title: PDAC patient 3

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 3
SAMPLE 3

source_name: Peripheral blood before treatment from PDAC patient 3


title: OVCAR5 statin rep1

source_name: OVCAR5 cell culture treated with statin

value: lovastatin


title: PDAC patient 5

description:
Transcriptome profile of peripheral blood before treatment from PDAC patient 5
SAMPLE 5

source_name: Peripheral blood before treatment from PDAC patient 5

value: male

value: no


title: D-U87-87aa

city: Guangzhou

first: Maolei

last: Zhang

state: Guangdong

address: Zhongshan two Road 58，Guangzhou City，Guangdong Province

department: Neurosurgery

institute: The 1st Affiliated Hospital of Sun Yat-sen University

description: Gene expression in glioma cell line U87 of Stable expression 87aa small peptides

hyb_protocol: According to the manufacturer's instructions,Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):

scan_protocol: Agilent Microarray Scanner (Agilent p/n G2565BA)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 2 out of 4 samples have flags in Detected (   All Targets Value   ) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: glioblastoma cell line U87 of Stable expression 87aa small peptides

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 μg RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442)  according to the manufacturer's instructions.

extract_protocol: RNA was isolated using TRIzol according to standard protocols.Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present

treatment_protocol: For stable GFP or 87aa overexpression, the GFPor 87aa ORF was cloned into the psin-EF2 vector with the EcoRI and BamHI for lentiviral production. The glioma U251 or U87 cell lines were then infected and followed by selection with 2 μg/ml of puromycin for 72 h.


title: A-U251-GFP

description: Gene expression in glioma cell line U251 of Stable expression GFP protein

source_name: glioblastoma cell line U251 of Stable expression GFP protein


title: SKOV3 statin rep1

source_name: SKOV3 cell culture treated with statin


title: OVCAR5 control rep1


title: C-U87-GFP

description: Gene expression in glioma cell line U87 of Stable expression GFP protein

source_name: glioblastoma cell line U87 of Stable expression GFP protein


title: Hu_REF_Cy5_3

hyb_protocol: Hybridization on an Agilent SurePrint G3 Human CGH Microarray 4 x 180K array the design of which can be found in the Gene Expression Omnibus (GEO)[87] platform GPL8687 (http://www.ncbi. nlm.nih.gov/geo) was performed for 24h at 65 °C

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505C (Agilent Technologies), and scans were quantified using the Agilent Feature Extraction software (version 10.5.1.1; Agilent Technologies, protocol CGH_105_Dec08) using default settings

data_processing: Genome data analysis was performed using R Version 2.6.2. The aCGH profiles were dewaved , and median was normalized. Segmentation was performed using the Bioconductor R-package DNAcopy version 1.22.1  and subsequently DNA copy number calls for loss, normal, gain or amplification were made using the using R-package CGHcall version 2.8.0

source_name: Human Reference DNA (female)

label_protocol: labeling (Enzo Genomic DNA Labeling kit, Enzo Life Sciences, Raamsdonksveer, Netherlands) and purification were undertaken (QIAGEN MinElute PCR Purification Kit, Westburg, Leusden, Netherlands) with an elution volume of 2 × 10.5 μl, according to the manufacturer’s instructions. Cy3- and Cy5-labelled DNA samples were combined with Cot-1 DNA (Invitrogen, Breda, Netherlands)

extract_protocol: DNA isolation was perfomed using column-based method (QIAamp DNA Mini Kit, Westburg, Leusden, Netherlands)

value: homogeneous genomic human DNA pool from 100 female individuals


title: B-U251-87aa

description: Gene expression in glioma cell line U251 of Stable expression 87aa small peptides

source_name: glioblastoma cell line U251 of Stable expression 87aa small peptides


title: OVCAR5 statin rep2


title: SKOV3 control rep2

source_name: SKOV3 cell culture control


title: SKOV3 statin rep2


title: Healthy control 8

description:
Transcriptome profile of peripheral blood before treatment from healthy control 8
SAMPLE 44

source_name: Peripheral blood from healthy control 8

value: healthy

value: female


title: SKOV3 control rep1


title: Hu_REF_Cy5_2