title: scWAT_sedentary_11days_rep6

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

hyb_protocol: 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Intensity values were quantified by MAS 5.0 software (Affymetrix). All chips were subjected to global scaling to a target intensity of 1500.

source_name: scWAT, sedentary, 11 days

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

extract_protocol: Total RNA was isolated and purified from frozen scWAT from trained or sedentary mice using an RNeasy Mini Kit (Valencia, CA)  from trained or sedentary mice using an RNeasy Mini Kit (Valencia, CA), and was subjected to  cDNA and cRNA preparations

tag: group

value: sedentary

value: subcutaneous white adipose tissue (scWAT)


title: scWAT_exercised_11days_rep5

status: Public on Apr 22 2015

type: RNA

state: MA

country: USA

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: scWAT, exercised, 11 days

value: exercised

tag: strain

tag: gender

value: male

tag: age

value: 12 weeks

tag: tissue


title: scWAT_exercised_11days_rep4


title: scWAT_exercised_11days_rep1


title: scWAT_exercised_11days_rep3


title: PBCS-1023

type: protein

city: Tempe

first: Jie

last: Wang

state: Arizona

address: 1001 S. McAllister Ave.

department: Center for Personalized Diagnostics

institute: Arizona State University

description: The serum was applied on the protein array, secondary anti-human IgG antibody used for detection.

hyb_protocol: Plasma hybridization was performed on TECAN HS 4800 Pro. 1. Protein Arrays were blocked with 5% milk PBST (0.2% Tween) for 1 hour at RT; 2. 150uL 1:50 diluted serum was applied to each slide with medium agitation 16 hrs at 4oC; 3. Slides were incubated with 150uL 1:500 dilution of Dylight649-linked anti-human secondary antibodies (Jackson Immunoresearch) in Milk PBST.

scan_protocol: Slides were scanned by TECAN PowerScanner at 50% gain, 50% laser and 10 μm resolution.

data_processing: 1. The background signal estimated by the 25th percentile of the negative control; 2. Normaliza the array data by median.

label: Serum sample are not labeled

molecule: protein

organism: Homo sapiens

source_name: Peripheral blood

label_protocol: No label was performed on the serum sample.

extract_protocol: Peripheral blood samples were drawn from the antecubital vein and serum was prepared according to a standardized protocol before freezing serum aliquots at -80oC

value: Plasma

tag: type

value: BLBC

tag: array batch

value: Female


title: scWAT_sedentary_11days_rep7


title: scWAT_exercised_11days_rep2


title: scWAT_exercised_11days_rep6


title: scWAT_exercised_11days_rep7


title: scWAT_sedentary_11days_rep5


title: LCM current smoker #5

city: bethesda

first: Stefan

last: Ambs

state: md

address: 37 convent cir

institute: NIH

description: Gene expression data from current smoker of prostate cancer

hyb_protocol: the cRNA was fragmented and hybridized overngiht to Affymetrix GeneCip HG-U133 A2.0 arrays

scan_protocol: Hybridization signals were visualized using phycoerythrin-conjugated streptavidin and scanned using a GeneChip scanner 3000 7G

data_processing: R/bioconductor and Partek

source_name: current smoking

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

extract_protocol: total RNA from tissues and cultured cells was isolated by TRIzol(Invitrogen) according to the manufacturer instructions

value: prostate

tag: smoking

value: current smoking


title: PBCS-906


title: PBCS-603


title: scWAT_sedentary_11days_rep4


title: PBCS-506


title: PBCS-4419

value: control


title: PBCS-4544


title: PBCS-684


title: PBCS-4082


title: PBCS-4128


title: scWAT_sedentary_11days_rep1


title: PBCS-67


title: scWAT_sedentary_11days_rep2


title: PBCS-447


title: PBCS-4032


title: PBCS-3771


title: PBCS-178


title: scWAT_sedentary_11days_rep3


title: PBCS-640


title: PBCS-1161


title: PBCS-2858


title: PBCS-2930


title: PBCS-1529


title: PBCS-1002


title: PBCS-4512


title: PBCS-1325


title: PBCS-110


title: TRAMP mouse 250 microgram nicotine-treated #2

description: Gene expression data from mouse treated with 250 microgram nicotine

hyb_protocol: hybridized for 17 hr at 45C on Affymetrix GeneChip mouse gene 1.0 st array

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

data_processing: R/bioconductor

label_protocol: Amplify 250 ng of RNA using the Ambion WT Expression Kit (per directions) Fragment and label 5.5 ug of ssDNA using Affymetrix GeneChip WT Terminal Labeling and controls kit

growth_protocol: Male TRAMP mice were bred at the Assisted Reproduction Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.

extract_protocol: Trizol extraction as per manufacturer instructions. Check quality with Agilent Bioanalyzer

treatment_protocol: Beginning at 8 to 9 weeks of age, TRAMP mice received either tap water or a solution of 250 µg/ml of nicotine [nicotine tartrate salt (Sigma-Aldrich, St. Louis, MO)] in tap water

value: 250 microgram nicotine-treated


title: PBCS-3452


title: PBCS-2991


title: Trem2-Ctl

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:
Sample name: 23167
TREM2 control
gene expression from purifed microglia

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

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

data_processing: Data were analyzed using GenePattern (Broad Institute)

label: Biotin

source_name: microglia

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

growth_protocol: 8-12 weeks C57BL/6  or TREM2-/- male mice

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

treatment_protocol: C57BL/6 or TREM2-/- mice were fed on a 0.2% curpizone diet for 4 or 12 weeks to induce demyelination. Separate groups of mice were fed with a normal diet after cuprizone feeding for 2 weeks to allow recovery.

value: 8-12 weeks

tag: genotype/variation

tag: agent

tag: time

tag: cell type

value: microglia


title: PBCS-3254


title: PBCS-231


title: PBCS-2247


title: PBCS-1807


title: PBCS-2988


title: PBCS-2970


title: PBCS-3392


title: PBCS-3253


title: PBCS-3234


title: PBCS-3098


title: PBCS-3492


title: PBCS-1002


title: PBCS-106


title: PBCS-994


title: PBCS-924


title: PBCS-647


title: PBCS-914


title: PBCS-559


title: PBCS-1247


title: PBCS-1414


title: PBCS-2415


title: PBCS-648


title: PBCS-923


title: PBCS-568


title: PBCS-1910


title: PBCS-67


title: PBCS-863


title: PBCS-189


title: PBCS-658


title: PBCS-654


title: PBCS-4544


title: PBCS-250


title: PBCS-3890


title: PBCS-4457


title: PBCS-4356


title: PBCS-4464


title: PBCS-4454


title: PBCS-3754


title: PBCS-3961


title: PBCS-2213


title: PBCS-2197


title: PBCS-2020


title: PBCS-1243


title: PBCS-1572


title: PBCS-1573


title: PBCS-1498


title: Tet2-/-_AML1_ETO_p10_Rep3

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

country: United Kingdom

institute: School of Life Sciences, University of Dundee

description: Gene expression data from Tet2-/-;AML1_ETO cells grown for 10 passages following Tet2 disruption

hyb_protocol: Affymetrix EukGE-WS2v4_450 hybridization protocol according to manufacturers instructions

scan_protocol: Cell intensity files (CEL files) were generated in the GeneChip Command Console Software (AGCC) (Affymetrix, Santa Clara, CA, USA)

data_processing: Raw vaules RMA-normalized and summarized using Affymetrix Power Tools (APT). Unix command: apt-probeset-summarize -a rma -a rma-bg,quant-norm.sketch=-1.bioc=true.lowprecision=false.usepm=true,pm-only,med-polish.expon=true -a pm-only,dabg.chisq=true -p ${affy_dir}/MoGene-2_0-st.pgf -c ${affy_dir}/MoGene-2_0-st.clf -b ${affy_dir}/MoGene-2_0-st.bgp --qc-probesets ${affy_dir}/MoGene-2_0-st.qcc -m ${affy_dir}/MoGene-2_0-st.mps ${cel_dir}/*.CEL -o ${out_dir}/gene_level

source_name: Kit-enriched hematopoietic bone marrow cells retrovirally transduced with AML1-ETO

label_protocol: 100ng of total RNA of each sample was labeled using Ambion® WT Expression Kit (Ambion) according to manufacturers instructions

growth_protocol: Primary Kit-enriched bone marrow cells from Tet2fl/fl;CreER mice were freshly transduced with MigR1-AE-IRES-GFP, sorted for GFP and plated in methylcellulose medium (M3534, StemCell Technologies). After three rounds of replating, the cells were shifted to grow in suspension in non-tissue culture treated plasticware in media containing 1× StemPro®-34 SFM (Invitrogen), 1x L-Glutamine, with SCF (CHO producer cell line), 10ng/ml IL-3 (Peprotech), 10ng/ml IL-6 (Peprotech) and 0.1mM 2-mercapto-ethanol. Primary hematopoietic cell lines expressing MLL-AF9 in the Tet2fl/fl;CreER background was generated and maintained in suspension media as previously described (Somervaille, T.C.P., and Cleary, M.L. (2006), Cancer Cell 10, 257–268)

extract_protocol: Immature myeloid cells (GFP+, CD11b-, Gr1-, CD16/32+) were sorted from AML1-ETO cultures. Total RNA was isolated using the AllPrep DNA/RNA micro kit (Qiagen).

treatment_protocol: To induce the CreER-mediated excision of Tet2, the cells were treated with 200 nM 4-OHT (Experimental) or EtOH (Control) for 2 passages (4 days). The cells were subsequently washed to remove residual 4-OHT and passaged every 2 days for a total of 10 to 20 passages.

tag: genotype

tag: passage number


title: PBCS-886


title: Tet2-/-_AML1_ETO_p10_Rep2


title: Tet2fl/fl_AML1_ETO_p10_Rep2

description: Gene expression data from Tet2fl/fl;AML1_ETO cells grown for 10 passages following Tet2 disruption


title: Tet2fl/fl_AML1_ETO_p10_Rep1


title: Tet2-/-_AML1_ETO_p2_Rep1

description: Gene expression data from Tet2-/-;AML1_ETO cells grown for 2 passages following Tet2 disruption


title: PBCS-1754


title: Tet2-/-_AML1_ETO_p10_Rep1


title: Tet2-/-_AML1_ETO_p2_Rep2


title: Tet2fl/fl_AML1_ETO_p10_Rep3


title: Tet2-/-_AML1_ETO_p2_Rep3


title: PBCS-3771


title: Tet2fl/fl_AML1_ETO_p2_Rep3

description: Gene expression data from Tet2fl/fl;AML1_ETO cells grown for 2 passages following Tet2 disruption


title: PBCS-2020


title: PBCS-2213


title: PBCS-4470


title: PBCS-1807


title: PBCS-1573


title: PBCS-4492


title: PBCS-2247


title: PBCS-4102


title: PBCS-1572


title: Tet2fl/fl_AML1_ETO_p2_Rep2


title: PBCS-3560


title: Tet2fl/fl_AML1_ETO_p2_Rep1


title: PBCS-1498


title: PBCS-4067


title: PBCS-3486


title: PBCS-886


title: PBCS-3425


title: PBCS-3227


title: PBCS-2192


title: PBCS-3226


title: PBCS-3191


title: PBCS-4470


title: PBCS-1243


title: PBCS-2006


title: PBCS-1860


title: PBCS-1864


title: PBCS-4492


title: PBCS-1293


title: PBCS-1736


title: PBCS-1233


title: PBCS-1211


title: PBCS-1074


title: PBCS-1089


title: PBCS-1023


title: PBCS-1910


title: Feeding against starvation_sample3_dye swap

city: Tsukuba

first: Yuki

last: Nakamura

state: Ibaraki

address: 1-2 Owashi

country: Japan

institute: National Institute of Agrobiological Sciences

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed with AgilentExpression Wash Buffer Kit.

scan_protocol: Scanned on an Agilent G2565BA scanner with 5 μm scan resolution.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5)

organism: Nilaparvata lugens

label_protocol: Total RNA (400 ng each for Cy3 and Cy5) was processed to cRNA using Agilent Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: Total RNA extracted using RNeasy Mini Kit (Qiagen) following manufacturer's instructions

treatment_protocol: Feeding or only water supplied for 24 h

tag: treatment

value: feeding

value: starvation


title: DNA_Sample 39

type: genomic

city: Atlanta

first: M. Katharine

last: Rudd

address: 1518 Clifton Rd, CNR 5043

department: Human Genetics

institute: Emory University School of Medicine

hyb_protocol: Labeled DNA and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on Agilent high-resolution C scanner.

data_processing: Signal intensities were evalutated using Feature Extraction software and Genomic Workbench was used to analyze array data and make breakpoint predictions

molecule: genomic DNA

source_name: patient genomic DNA

label_protocol: Genomic DNA, 0.5-1ug, from patient samples and controls were Cy3/Cy5 labeled with Agilent Genomic DNA Enzymatic Labeling Kit following manufacture's protocol

extract_protocol: Genomic DNA was extracted from peripheral blood or cell lines using Gentra Puregene DNA Extraction kit following manufacturers protocol

tag: Sex

value: m

tag: array number

tag: affected chromosomes

tag: type of rearrangement

value: complex translocation

source_name: Normal control DNA

value: f

tag: cell line


title: PBCS-906

tag: gender


title: PBCS-684

tag: tissue


title: Feeding against starvation_sample3

tag: strain


title: DNA_Sample 38

value: unbalanced translocation


title: DNA_Sample 37


title: PBCS-2006

tag: type

tag: array batch


title: Feeding against starvation_sample2


title: Feeding against starvation_sample2_dye swap


title: PBCS-506


title: Feeding against starvation_sample1


title: PBCS-447


title: PBCS-231


title: PBCS-1074


title: PBCS-1864


title: PBCS-1860


title: Feeding against starvation_sample1_dye swap


title: DNA_Sample 36

value: chromothripsis


title: PBCS-110


title: PBCS-684


title: PBCS-178


title: PBCS-603


title: PBCS-1023


title: DNA_Sample 35

value: Xq; 5p


title: DNA_Sample 34


title: DNA_Sample 57


title: DNA_Sample 28


title: DNA_Sample 30


title: DNA_Sample 51


title: DNA_Sample 54


title: DNA_Sample 53


title: DNA_Sample 31


title: DNA_Sample 55


title: DNA_Sample 32


title: DNA_Sample 49


title: DNA_Sample 56


title: DNA_Sample 27


title: DNA_Sample 48


title: DNA_Sample 52


title: DNA_Sample 33


title: DNA_Sample 26


title: DNA_Sample 29


title: DNA_Sample 22

value: Xp; 7q


title: MeWo_PAEPsiRNA_3

city: Heidelberg

first: Marc

middle: Andre

last: Schneider

address: Amalienstraße 5

department: Translational Research Unit

country: Germany

institute: Thoraxklinik am Universitätsklinikum Heidelberg

hyb_protocol: Fragmented cRNAs (10 µg each) were hybridized to Affymetrix U133 Plus 2.0 arrays at 45 ºC for 16 hours (GeneChip®  Hybridization Oven 640, Affymetrix). Washing and staining involving conjugate R-Phycoerythrin Streptavidin SAPE (Invitrogen, Carlsbad, CA, USA) and Biotinylated anti-streptavidin antibody (Vector Laboratories, Burlingame, CA, USA) was performed using an Affymetrix GeneChip® Fluidics Station 450

scan_protocol: Arrays were scanned with an Affymetrix GeneChip® Scanner 3000 using Affymetrix ROC protocol.

data_processing: Bioconductor and R were used for pre-processing of the hybridizations. The microarray data were normalized by the gcRMA method.

label: total RNA

source_name: cell line MeWo

label_protocol: cRNA was generated, biotin-labeled and fragmented using GeneChip Expression 3´-Amplification Reagents for IVT Labeling Kit and GeneChip Sample Cleanup Module, Affymetrix. RNA integrity was controlled with an Agilent 2100 Bioanalyzer and an Agilent RNA 6000 Nano Kit

growth_protocol: 170000 cells (2106T and H1975) and 250000 cells (MeWo) were seeded out in a 12 well plate.

extract_protocol: Cells were washed, detached and frozen prior to RNA extraction with AllPreP DNA/RNA Mini Kit (Qiagen)

treatment_protocol: The next day, cells were treated with contro siRNA or PAEP siRNA pool of 4 siRNAs for 72h.

value: PAEP siRNA

value: MeWo

value: squamous cell carcinoma cell line

value: skin


title: DNA_Sample 25


title: DNA_Sample 50


title: DNA_Sample 24


title: DNA_Sample 23


title: DNA_Sample 19


title: DNA_Sample 21


title: DNA_Sample 20


title: DNA_Sample 47


title: MeWo_PAEPsiRNA_2


title: DNA_Sample 46


title: DNA_Sample 45

value: Xq; 7q


title: MeWo_PAEPsiRNA_1


title: MeWo_controlsiRNA_3

value: control siRNA


title: DNA_Sample 40


title: DNA_Sample 44


title: R4A + 7B

city: Łódź

first: Ida

last: Franiak-Pietryga

address: Pomorska 251

department: Clinical Genetics

country: Poland

institute: Medical Univ. of Lódź

description: Sample 16

hyb_protocol: Hybridization was prepared with the use of lyophylised 10x Blocking Agent supplied with the Agilent Gene Expression Hybrydization Kit with nuclease free water and 25x Fragmentation Buffer.   Arrays were placed onto the gaskets and than to the slide chamber in rotisserie in a hybridization oven set.  Hybrydization was carried out at 65-Celsius degrees for 17 hours.   Hybridization was prepared with the use of lyophylised 10x Blocking Agent supplied with the Agilent Gene Expression Hybrydization Kit with nuclease free water and 25x Fragmentation Buffer. Arrays were placed onto the gaskets and than to the slide chamber in rotisserie in a hybridization oven set.  Hybrydization was carried out at 65-Celsius degrees for 17 hours.

scan_protocol: Arrays were scanning using Agilent Microarray Scanner. Scan resolution was set up for 3μM. Scanning had been done on 17 April 2014

data_processing:
r/gProcessedSignal was calculated as spacially detrended, background substraced signal, with Linear&LOWESS method of dye bias correction.
Agilent Feature Extraction Software ver. 10.10, protocol GE2_1010_Sep10 (Samples 1-8) and FE ver. 11.5, protocol GE2_1105_Oct12 (Samples 9-16) was used.

label_protocol: Labelling had been proceeded according to the protocol available with the Two-Color RNA Spike-In Kit and can be downloaded from the Agilent Web site at www.agilent.com/chem/dnamanuals-protocols. Spike A Mix with cyanine 3 (Cy3) and spike B mix with cyanine 5 (Cy5) were labeled. 100 ng of total RNA was used for each sample. Agilent’s Low Input Quick Amp Labeling Kit was used to generate fluorescent cRNA (complimentary RNA) with a sample input 100ng of total RNA for two-color processing. The method uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP. Amplification is typically at least a 100-fold from total RNA to cRNA with the use of this kit. cRNA quantification had been done using NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1. Qiagen’s RNeasy Mini Spin Column were used for purification of the amplified cRNA samples.

growth_protocol:
Cells’ morphology: round to polymorphic cells growing in suspension, singly or partly in small aggregates, a few cells are slightly adherent.
Medium: 90% Iscove’s MDM + 10% h.i. FBS;
Subculture: split saturated culture 1:2 to 1:3 every 2-3 days; seed out at ca. 0.5 x 1mln cells/ml; after thawing, during the first week cells should be kept with 20% FBS initially; culture; culture in 24-well-plate is of advantage; maintain at about 0.5-2.0 mln cells/ml.
Incubation: at 37-Celsius degree with 5% CO2.
Doubling time: ca. 40 hours;
Harvest: cell harvest of about 2.0 mln cells/ml;
Storage: frozen with 70% medium, 20% FBS, 10% DMSO;
Immunology: CD3 -, CD10 -, CD13 -, CD19 +, CD20 +, CD34 -, CD37 +, CD38 +, cyCD79a +, CD80 +, CD138 +, HLA-DR +;
Cytogenetics: del(17)(p11) – small acf/mar present in most cells

extract_protocol: Total RNA was prepared from cell lysates using the RNeasy total RNA Mini kit (Qiagen, France), according to the manufacturer’s protocol. The amount and purity of total RNA was determined (NanoDrop, Thermo Fisher Scientific, USA) and the integrity of RNA was assessed by means of a 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: For in vitro culture, homogenous cell line MEC-1 (DSMZ) cells were suspended in RPMI 1640 (PAA, Germany), supplemented with 20% (v/v) foetal bovine serum (FBS, Invitrogen, Scotland), and antibiotics (100 U/mL penicillin, 100 mg/ml streptomycin) (Invitrogen, Scotland) and cultured for up to 48h in an atmosphere of 5% CO2, at a temperature of 37°C, and in full humidity (98%). MEC1 were incubated in 24-well plates (1 × 10^6 cells/ml) with PPI-G4-OS-Mal-III or PPI-G4-DS-Mal III dendrimers at the concentration of 8 mg/ml or FA (fudarabine) in the concentration of 1.6 μM. The cultures without dendrimers were considered as reference.

value: chronic lymphocytic leukemia cell line

tag: treated with

value: none (untreated control)

value: 1.6 μM fudarabine (FA)


title: DNA_Sample 42


title: MeWo_controlsiRNA_2


title: RA + 8B

description: Sample 15


title: RB + 8A

description: Sample 11


title: PBCS-1211

value: Plasma

value: BLBC

value: Female


title: DNA_Sample 41

value: f

value: m


title: H1975_PAEPsiRNA_1

source_name: cell line H1975

value: adenocarcinoma cell line

value: lung


title: R4A + 5B

description: Sample 13

source_name: MEC1_PPI-G4-DS-Mal III_4hrs_cy5

value: 8 mg/ml PPI-G4-DS-Mal III


title: MeWo_controlsiRNA_1


title: H1975_controlsiRNA_3


title: R4A + 6B

description: Sample 14

source_name: MEC1_PPI-G4-OS-Mal III_4hrs_cy5

value: 8 mg/ml PPI-G4-OS-Mal III


title: H1975_PAEPsiRNA_2

value: PAEP siRNA


title: R4B + 7A

description: Sample 12


title: H1975_controlsiRNA_1


title: RA + 4B

description: Sample 7

source_name: MEC1_PPI-G4-OS-Mal III_48hrs_cy5


title: H1975_PAEPsiRNA_3


title: R4B + 6A

description: Sample 10

source_name: MEC1_PPI-G4-OS-Mal III_4hrs_cy3


title: H1975_controlsiRNA_2


title: DNA_Sample 43

value: chromothripsis


title: R4B + 5A

description: Sample 9

source_name: MEC1_PPI-G4-DS-Mal III_4hrs_cy3


title: RB + 4A

description: Sample 8

source_name: MEC1_PPI-G4-OS-Mal III_48hrs_cy3


title: DNA_Sample 18

value: unbalanced translocation


title: 2106T_PAEPsiRNA_3

source_name: cell line 2106T

value: squamous cell carcinoma cell line


title: RA + 3B

description: Sample 5


title: DNA_Sample 17


title: DNA_Sample 16


title: DNA_Sample 15


title: RB  + 2A

description: Sample 4

source_name: MEC1_PPI-G4-DS-Mal III_48hrs_cy3


title: DNA_Sample 13


title: 2106T_PAEPsiRNA_1


title: DNA_Sample 14


title: 2106T_PAEPsiRNA_2


title: RA + 2B

description: Sample 3

source_name: MEC1_PPI-G4-DS-Mal III_48hrs_cy5


title: DNA_Sample 5


title: DNA_Sample 2


title: DNA_Sample 11


title: 2106T_controlsiRNA_3

value: control siRNA


title: RB + 1A

description: Sample 2

value: chronic lymphocytic leukemia cell line


title: 2106T_controlsiRNA_1


title: DNA_Sample 7


title: DNA_Sample 6


title: DNA_Sample 3


title: DNA_Sample 4


title: RB + 3A

description: Sample 6

value: none (untreated control)


title: DNA_Sample 1


title: 2106T_controlsiRNA_2


title: DNA_Sample 12


title: DNA_Sample 8


title: RA + 1B

description: Sample 1


title: LNCaP_Scr_36h_B2

status: Public on Apr 21 2015

city: HELSINKI

first: Anna

last: Aakula

address: Tukholmankatu 8

country: Finland

institute: Institute for Molecular Medicine Finland, FIMM

description: LNCaP cells transfected with Ambion pre-miR negative control #1 (scrambled pre-miR, Scr) at 20 nM, and incubated for 36h

hyb_protocol: 750 ng of each cRNA sample were hybridized into Illumina’s Sentrix HumanHT-12 v4 Expression Bead Chips at 58 °C overnight according to Illuminaâ Whole-Genome Gene Expression Direct Hybridization Assay Guide (part # 11322355, rev.A)

scan_protocol: Chips were scanned with Illumina Bead Array Reader (Factor=1.5, PMT=552, Filter=100%).

data_processing: The numerical results were extracted with GenomeStudio v. 2010.2; Gene Expression Module v. 1.7.0 without any normalization or background subtraction. The data was preprocessed by Bioconductor lumi package (version 1.8.3). It was vst transformed and quantile normalized.

label_protocol: Illumina Total Prep RNA Amplification kit (Ambion). In vitro transcription reaction overnight (14h) and during it cRNA was biotinylated. The cRNA concentrations where checked with Nanodrop ND-1000 and cRNA quality was controlled by BioRad™s Experion electrophoresis station.

growth_protocol: Normal growth conditions, according to instructions by provider

extract_protocol: The total cellular RNAs were isolated with MiRVana total RNA isolation kit (Ambion).

treatment_protocol: LNCaP cells were transfected with Ambion pre-miR™ construct for miR-135b or with pre-miR negative control #1 (scrambled pre-miR) at 20 nM, and incubated for 12h, 24h or 36h

value: LNCaP

tag: dsmz  cat. #

value: ACC 256

value: Prostate carcinoma

tag: cell line origin

value: Left supraclavicular lymph node metastasis from a 50-year-old man with prostate carcinoma in 1977

tag: cell morphology

value: Adherent fibroblastoid cells growing in aggregates and as single cells

tag: transfected with

tag: incubation time


title: LNCaP_Scr_36h_B1

tag: cell type

value: Ambion pre-miR negative control #1 (scrambled pre-miR, Scr) at 20 nM


title: DNA_Sample 9

tag: Sex

value: f

value: m


title: DNA_Sample 10

tag: array number


title: LNCaP_Scr_24h_B2

description: LNCaP cells transfected with Ambion pre-miR negative control #1 (scrambled pre-miR, Scr) at 20 nM, and incubated for 24h


title: LNCaP_Scr_12h_B2

description: LNCaP cells transfected with Ambion pre-miR negative control #1 (scrambled pre-miR, Scr) at 20 nM, and incubated for 12h


title: LNCaP_Scr_12h_B1


title: LNCaP_Scr_24h_B1


title: LNCaP_miR-135b_36h_B2

description: LNCaP cells transfected with Ambion pre-miR™ construct for miR-135b at 20 nM, and incubated for 36h


title: LNCaP_miR-135b_36h_B1

value: Ambion pre-miR™ construct for miR-135b at 20 nM


title: LNCaP_miR-135b_24h_B1

description: LNCaP cells transfected with Ambion pre-miR™ construct for miR-135b at 20 nM, and incubated for 24h


title: LNCaP_miR-135b_24h_B2


title: LNCaP_miR-135b_12h_B2

description: LNCaP cells transfected with Ambion pre-miR™ construct for miR-135b at 20 nM, and incubated for 12h


title: △codY_1

city: shanghai

first: liping

last: feng

address: No. 3577 Jinke Rd., Shanghai

country: China

institute: Shanghai Laboratory Animal Research Center

description: gene expression of codY mutation in Streptococcus suis serotype 2 SC19 strain

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.

organism: Streptococcus suis

source_name: codY mutation in streptococcus suis serotype 2 SC19 strain

growth_protocol: The Streptococcus suis serotype 2 was cultured in the TSB medium with 10% (vol/vol) new-born bovine serum at 37℃.

treatment_protocol: Based upon the whole genome sequence of SC19 , specific 60-mer oligonucleotide probes were designed using eArray (https://earray.chem.agilent.com/earray/), to cover most annotated genes. Probes were printed seven times on microarray slides. Two biological replicates of total RNA from wild type strain and codY mutant strain were amplified and labeled with Cy3-CTP using Low Input Quick Amp Labeling Kit, one-color(Agilent technologies, US), following the manufacturer’s instructions. Labeled cRNA was purified using the RNeasy mini kit (Qiagen). After fragmentation, microarray slides were hybridized with 600 ng Cy3-labeled cRNA. Hybridization was performed at 65 °C for 17 h with rotation at 10 rpm.

tag: serotype

value: serotype 2

value: SC19 strain

tag: genotype

value: CodY null

tag: Stage

value: exponential phase


title: WT_1

description: gene expression of Streptococcus suis serotype 2 SC19 strain

hyb_protocol: Labeled cRNA was purified using the RNeasy mini kit (Qiagen). After fragmentation, microarray slides were hybridized with 600 ng Cy3-labeled cRNA. Hybridization was performed at 65 °C for 17 h with rotation at 10 rpm

source_name: wild type of streptococcus suis serotype 2 SC19 strain

extract_protocol: Two biological replicates of total RNA from wild type strain and codY mutant strain were amplified and labeled with Cy3-CTP using Low Input Quick Amp Labeling Kit, one-color(Agilent technologies, US), following the manufacturer’s instructions

value: wild type


title: WT NaCl x WT no stress- rep3

city: Greifswald

first: Christian

last: Kohler

address: Martin Luther Strasse 6

department: Medical Microbiology University Medicine

institute: Friedrich Loeffler Institute for Medical Microbiology

hyb_protocol: Agilent protocol  Agilent protocol  Agilent protocol  Agilent protocol

scan_protocol: Agilent protocol  Agilent protocol

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 9.0. Agilent output files were then opened using Excell and the log10 values extracted with no additional processing or filtering

organism: Caulobacter vibrioides NA1000

source_name: WT- NaCl

label_protocol: Standard Cy3-dCTP and Cy5-dCTP incorporations  standard Cy3-dCTP incorporation  standard Cy3-dCTP incorporation  standard Cy3-dCTP incorporation

growth_protocol: Overnight C. crescentus cultures were diluted to an optical density at 600 nm (OD600) of 0.1 in minimal salt medium supplemented with glucose and grown until midlog phase (OD600 ~ 0.5)

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

treatment_protocol: Cultures were kept under no stress condition or treated with either 110 mM sucrose or 60 mM NaCl

value: NA1000 cells

tag: growth condition

value: under NaCl stress

source_name: WT- no stress

value: under no stress condition


title: 6485_after

city: Stockholm

first: Birgitta

last: Sander

country: Sweden

institute: Karolinska Institutet

description: MN12_6485A (after treatment)

hyb_protocol: Targets were hybridized in Affymetrix GeneChip Hybridization oven 640 and washed and stained in Affymetrix Fluidics station 450

scan_protocol: Arrays were scanned in Affymetrix GeneChip scanner 3000 7g

data_processing: The data were analyzed with Affymetrix Expression Console  (vesion 1.4.1.46) using the default RMA analysis method

source_name: PBMC cells

label_protocol: GeneChip WT cDNA Synthesis and Amplification kit and GeneChip WT Terminal labeling kit

growth_protocol: Ficoll separated peripheral blood mononuclear cells

extract_protocol: Total RNA was extracted using Qiagen Mini Plus kit

treatment_protocol: Human obese patients before and during treatment with rimonabant

tag: time

value: after treatment

tag: treatment

value: rimonabant

value: PBMC


title: 6187_after

description: MN14_6187A (after treatment)


title: WT NaCl x WT no stress- rep2

tag: strain


title: BM_Ter119+_WT_rep2

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Five micrograms of cDNA was hybridized for 16h at 45C on a Mouse Gene 2.0 ST GeneChip array.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).

growth_protocol: Ter119 positive cells from bone marrow were separated via autoMACS® Pro Sepaerator (Miltenyi Biotec) through depletion of CD45 with CD45 MicroBeads (130-052-301, Miltenyi Biotec) and then Ter119 positive selection by Ter119 microbeads (130-049-901, Miltenyi Biotec).

extract_protocol: Total RNA was isolated from cells using RNeasy Mini Kit (Cat. No. 74104, QIAGEN).

tag: strain background

value: offspring from mating Atg7 flox/flox Epo-cre wt/wt PolG wt/mt (female) X Atg7 flox/flox Epo-cre ki/wt PolG wt/mt (male)

tag: genotype/variation

value: Polgtm1Lrsn wt/wt

tag: tissue

value: bone marrow

value: Ter119+ cells


title: BM_Ter119+_Polg_mutant_rep2

value: Polgtm1Lrsn mt/mt


title: 5093_before

description: MN09_5093B (before treatment)

value: before treatment

value: baseline


title: BM_Ter119+_Polg_mutant_rep1


title: 6485_before

description: MN11_6485B (before treatment)


title: WT NaCl x WT no stress- rep1


title: WT sucrose x WT no stress- rep1

source_name: WT- sucrose

value: under sucrose stress


title: WT NaCl x WT sucrose- rep1

source_name: WT- sucrose stress


title: 5214_after

description: MN13_5214A (after treatment)


title: WT NaCl x WT sucrose- rep2


title: LNCaP_miR-135b_12h_B1

tag: cell line

value: LNCaP

tag: dsmz  cat. #

value: ACC 256

value: Prostate carcinoma

tag: cell line origin

value: Left supraclavicular lymph node metastasis from a 50-year-old man with prostate carcinoma in 1977

value: Adherent fibroblastoid cells growing in aggregates and as single cells

value: Ambion pre-miR™ construct for miR-135b at 20 nM


title: BM_Ter119+_Polg_mutant_rep3


title: WT NaCl x WT sucrose- rep3

value: NA1000 cells

value: under NaCl stress


title: WT sucrose x WT no stress- rep3

value: under no stress condition


title: 6845_after

description: MN08_6845A (after treatment)

value: after treatment

value: rimonabant

value: PBMC


title: 6845_before

description: MN07_6845B (before treatment)


title: 5823_after

description: MN06_5823A (after treatment)


title: 4007_after

description: MN02_4007A (after treatment)


title: 5823_before

description: MN05_5823B (before treatment)


title: 4007_before

description: MN01_4007B (before treatment)


title: 5307_before

description: MN03_5307B (before treatment)


title: 5307_after

description: MN04_5307A (after treatment)


title: M16 Macrophage replicate 2

city: Mexico City

first: Carmen

last: Sánchez-Torres

department: Molecular Biomedicine

country: Mexico

institute: CINVESTAV-IPN

description: Gene expression of M16 (Donor #2) after 7 days of culture

hyb_protocol: 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies).

scan_protocol: Arrays were scanned at 5 um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays. Images provided by the scanner were analyzed using Feature Extraction software (Agilent Technologies).

data_processing: Data files from Feature Extraction were imported into GeneSpring® GX software version 9.0. (Agilent Technologies). Quantile normalization was performed and expression values (log2 transformed) were obtained for each probe

source_name: M16 Macrophage

label_protocol: For each sample, we generated cyanine 3-labeled cRNA from one microgram of total RNA, using the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color. Briefly, total RNA was reverse-transcribed using T7-oligo (dT) primer; after first and second strand cDNA synthesis, cRNA was synthesized from the double-stranded cDNA using T7 RNA polymerase, which simultaneously incorporates cyanine 3.

growth_protocol: Freshly isolated CD14+CD16- and CD16+ monocytes were cultured for 7 days in RPMI 1640 supplemented with 10% FCS, 2 mM L-glutamine and 1% penicillin/streptomycin, containing either GM-CSF or M-CSF

extract_protocol: Total RNA from each condition was extracted and purified using the RNeasy kit (Qiagen). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.

treatment_protocol: Cells were were treated with GM-CSF (1000 U/ml) or M-CSF (10 ng/ml) every 48 hours

value: CD16+ monocyte-derived macrophages

value: M-CSF (10 ng/ml)

value: whole blood


title: BM_Ter119+_WT_rep1

value: offspring from mating Atg7 flox/flox Epo-cre wt/wt PolG wt/mt (female) X Atg7 flox/flox Epo-cre ki/wt PolG wt/mt (male)

value: Polgtm1Lrsn wt/wt

value: bone marrow

value: Ter119+ cells


title: GM14 Macrophage replicate 3

description: Gene expression of GM14(Donor #3) after 7 days of culture

source_name: GM14 Macrophage

value: CD14+CD16- monocyte-derived macrophages

value: GM-CSF (1000 U/ml)


title: GM16 Macrophage replicate 2

description: Gene expression of GM16 (Donor #2) after 7 days of culture

source_name: GM16 Macrophage


title: H9 hESCs, replicate 1

city: Berlin

first: Alessandro

last: Prigione

state: Berlin

address: Robert-Roessle-Str. 10

institute: Max Delbrueck Center for Molecular Medicine

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina BeadStudio software version 3

source_name: embryo

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively detected for downstream analysis.

extract_protocol: The RNA was isolated using RNeasy Mini Kit (Quiagen), and DNase digestion (RNase-free DNase Set, Quiagen) has been applied on the columns during isolation.

tag: age

value: Passage 55

value: hESCs


title: WT sucrose x WT no stress- rep2

value: NA1000 cells

value: under sucrose stress


title: OiPS6, replicate 2

description: replicate 2

source_name: reprogramming

value: Passage 15

value: iPSCs from NFH2 fibroblasts


title: AD-iPS5, replicate 1

description: replicate 1

value: iPSCs from NFH46 ibroblasts


title: M14 Macrophage replicate 3

description: Gene expression of M14 (Donor #3) after 7 days of culture

source_name: M14 Macrophage

tag: cell type


title: GM14 Macrophage replicate 2

description: Gene expression of GM14(Donor #2) after 7 days of culture


title: GM14 Macrophage replicate 1

description: Gene expression of GM14(Donor #1) after 7 days of culture


title: Postnatal P12, biological rep3

city: Paris

first: Sonia

last: Alonso-Martin

address: 105 bd de l'Hôpital

department: Development and stem cells

country: France

institute: Myology Research Center U974-INSERM - UPMC-Paris VI - Institut de Myologie

description: Sample name: P-12.C.2006

hyb_protocol: High-density oligonucleotide arrays containing 45,000 sets of oligonucleotide probes (25 mers) that cover all 30,000 genes encoded by the murine genome (Affymetrix Mouse Genome 430 2.0 Arrays, Ref 900495) were used for gene expression detection. Hybridization during 16 hours at 45°C in a rotary oven (Affymetrix), washing and staining (GeneChip® Fluidics Station 450) and scanning (GeneChip Scanner 3000) were carried out according to NuGEN and Affymetrix protocols.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing:
Expression Console software (Affymetrix) was used for image analysis and to determine probe signal levels. The quality and statistical analysis of the data were made using the GeneSpring GX11 analysis software (Agilent Technologies).
Data needed to be pre-treated before final analysis to normalize two different sets of arrays (2006 or 2012, as indicated in the sample names).
Expression profiles were normalized in batch using the RMA algorithm (affy R package) yielding a (probe sets, samples) matrix. As the 11 samples were obtained by merging two series, the Combat algorithm (Johnson WE, et al. Biostatistics, 2007) was used to normalize the corresponding batch effect. Expression profiles were aggregated by Gene Symbol (mean across probe sets) using Affymetrix csv annotation file (na32 version).

source_name: mouse trunk muscles including skeletal muscle proliferant satellite cells, P12

label_protocol: Biotinylated cRNA were prepared according to the Encore Biotin Module (NuGEN) protocol from 100ng total RNA (http://www.nugen.com/nugen/index.cfm/support/product-resources/tech/encore-biotin-module-performance/). Single-stranded cDNA is fragmented and characterized by chemical and enzymatic methods leading to molecules of about 50 to 100 bases. Next, a biotin-labeled nucleotide is attached to the 3' end of each fragment.

growth_protocol: Pax3GFP/+ mice were bred with C57BL/6J and the day where plugs were detected was considered as E0.5 (E, embryonic days).

extract_protocol: RNeasy® Micro Kit (QIAGEN) RNA extraction protocol was used according to the manufacturer's instructions.

treatment_protocol: Pax3GFP/+ mice of the appropriate age were detected by PCR and splotch white tag in the belly, and GFP confirmed under fluorescent stereoscope. Muscle samples were isolated from the trunk and digested in DMEM high glucose but no phenol red, 0.1% Trypsin, 0.1% Collagenase D and 0.01mg/mL DNaseI, and purified by filtration using 100µm and 40µm cell strainers. GFP cells were stained using propidium iodide to exclude dead cells and purified via FACS Aria II based on gating of GFP signal.

tag: strain/background

value: postnatal day 12


title: M16 Macrophage replicate 1

description: Gene expression of M16 (Donor #1) after 7 days of culture

value: CD16+ monocyte-derived macrophages


title: AD-iPS26B, replicate 1

description: replicate 1


title: M16 Macrophage replicate 3

description: Gene expression of M16 (Donor #3) after 7 days of culture

value: M-CSF (10 ng/ml)


title: M14 Macrophage replicate 1

description: Gene expression of M14 (Donor #1) after 7 days of culture

value: whole blood


title: GM16 Macrophage replicate 3

description: Gene expression of GM16 (Donor #3) after 7 days of culture


title: Postnatal P28, biological rep3

description: Sample name: P-1.C.2012

source_name: mouse abdominal, pectoral and intercostal muscle including skeletal muscle satellite cells, P28

value: postnatal day 28


title: Postnatal P12, biological rep4

description: Sample name: P-12.D.2006

value: trunk muscles including skeletal muscle proliferant satellite cells


title: H9 hESCs, replicate 2

description: replicate 2

value: Passage 56


title: H1 hESCs, replicate 2

description: replicate 2


title: GM16 Macrophage replicate 1

description: Gene expression of GM16 (Donor #1) after 7 days of culture


title: Postnatal P28, biological rep1

description: Sample name: P-1.A.2012

value: abdominal, pectoral and intercostal muscle including skeletal muscle satellite cells


title: H1 hESCs, replicate 1

description: replicate 1


title: M14 Macrophage replicate 2

description: Gene expression of M14 (Donor #2) after 7 days of culture

value: CD14+CD16- monocyte-derived macrophages


title: Postnatal P12, biological rep2

description: Sample name: P-12.B.2006


title: Postnatal P28, biological rep2

description: Sample name: P-1.B.2012


title: OiPS3, replicate 2

description: replicate 2


title: MDA-MB-231_NBAT1_rep3

city: Guangzhou

first: Pengnan

last: Hu

state: Guangdong

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

description: Gene expression after transfected with NBAT1 in breast cancer cell line MDA-MB-231

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

label_protocol: Total RNA was amplified and labeled by 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 by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: MDA-MB-231 breast cancer cell line was obtained from American Type Culture Collection and cultured according to the recommended protocols.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: MDA-MB-231 cells were transfected with pcDNA3 vector expressing NBAT1 (or not) construct using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instruction. Three days after transfection total RNA was extracted using TRIZOL Reagent.

tag: tissue type

value: breast cancer


title: Postnatal P12, biological rep1

description: Sample name: P-12.A.2006


title: MDA-MB-231_vector_rep3

description: Gene expression after transfected with empty vector in breast cancer cell line MDA-MB-231


title: OiPS6, replicate 1

description: replicate 1


title: MDA-MB-231_NBAT1_rep1


title: MDA-MB-231_vector_rep2


title: MDA-MB-231_NBAT1_rep2


title: Postnatal P1, biological rep3

description: Sample name: P-1.C.2006

source_name: mouse trunk muscles including skeletal muscle proliferant satellite cells, P1

value: postnatal day 1


title: NFH-2, replicate 2

description: replicate 2

source_name: derma

value: 84 year old woman, passage 4

value: dermal fibroblasts


title: Trf2F/F type II pneumocytes - biological rep1

status: Public on Apr 20 2015

city: Baltimore

first: Mary

last: Armanios

state: MD

address: 401 North Broadway

department: School of Medicine

institute: The Johns Hopkins University

description: sorted GFP+, 7 days after tamoxifen

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.na32.mm9.probeset_extended.mps

source_name: GFP+, Trf2F/FmTmG-Sftpc-CreER

label_protocol: The NuGEN Pico WTA v2 kit was used as described in the manufacturer's manual.

extract_protocol: Total RNA was isolated from sorted cells using RNA easy kit (Qiagen)

treatment_protocol: Mice were treated with tamoxifen 7-days prior to harvesting lungs and sorting GFP+ cells.

value: B6;129X1 mouse, type II pneumocyte


title: Trf2F/F type II pneumocytes - biological rep2

description: sorted GFP+, 7 days after tamoxifen


title: Trf2F/F type II pneumocytes - biological rep3

description: sorted GFP+, 7 days after tamoxifen


title: Postnatal P1, biological rep2

description: Sample name: P-1.B.2006


title: Trf2F/+ type II pneumocytes - biological rep2

description: sorted GFP+, 7 days after tamoxifen

source_name: GFP+, Trf2F/+mTmG-Sftpc-CreER


title: Trf2F/+ type II pneumocytes - biological rep1

description: sorted GFP+, 7 days after tamoxifen


title: MDA-MB-231_vector_rep1


title: NFH-46, replicate 1

description: replicate 1

value: 81 year old woman, passage 4


title: Postnatal P1, biological rep1

description: Sample name: P-1.A.2006


title: Postnatal P1, biological rep4

description: Sample name: P-1.D.2006


title: NFH-2, replicate 1

description: replicate 1


title: SS_VS_5d_24h_rep5

city: Fort Detrick

first: seid

last: muhie

address: 568 Doughten Dr

department: Systems Biology Enterprise

institute: USACEHR

description:
SS_VS_5d_24h_rep5
US09493743_251486832371_1_1 - T5-105 5day 24hr.txt

hyb_protocol: The slides were hybridized at 60ºC for 16 h

scan_protocol: Hybridized slides were scanned and recorded using a Agilent's Feature Extraction Software v 10.9  (Agilent Technology Inc.)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent's Feature Extraction Software V10.9 was used.

source_name: pooled whole mouse tissue cell line

label_protocol: RNA was reverse transcribed and labeled using Agilent's Mouse Chip Labeling and Detection Kit (Agilent Technologies, Inc.) following the manufacturer’s protocol.

extract_protocol: Total RNA extracted using Trizol from brain regions and organs and using PAXgene from blood following the manufacturers' instructions

treatment_protocol: C57B6 mice were exposed to SJL aggressor mice for periods of 5 days and 10days (6 hours each day) to induce anxiety/stress which parallels to PTSD in human. Organs, blood and brain regions were collected after 24 hours and 1.5 week of post 5 days social defeat period; and 24 hour and 6 weeks post 10 days social stress period.

tag: sample type

value: Strategen universal reference RNA (Cat. No. 740100)

value: social stress (SS)

tag: time point

value: after 24 hrs post 5 days social defeat period

value: ventral striatum (VS)


title: SS_VS_5d_1.5w_rep2

description:
SS_VS_5d_1.5w_rep2
US09493743_251486832346_1_1 - T10-114 5day 1.5wk.txt

value: after 1.5 wk post 5 days social defeat period


title: SS_VS_5d_24h_rep3

description:
SS_VS_5d_24h_rep3
US09493743_251486832370_1_1  - T5-135 5day 24hr.txt


title: SS_VS_5d_24h_rep4

description:
SS_VS_5d_24h_rep4
US09493743_251486832370_1_2 - T5-136 5day 24hr.txt


title: SS_VS_5d_24h_rep2

description:
SS_VS_5d_24h_rep2
US09493743_251486832366_1_3 - T5-138 5day 24hr.txt


title: Trf2F/+ type II pneumocytes - biological rep3

description: sorted GFP+, 7 days after tamoxifen

tag: genotype


title: SS_VS_5d_1.5w_rep4

description:
SS_VS_5d_1.5w_rep4
US09493743_251486832367_1_1 - T10-112 5day 1.5wk.txt


title: SS_VS_5d_24h_rep1

description:
SS_VS_5d_24h_rep1
US09493743_251486832366_1_1 - T5-137 5day 24hr.txt


title: SS_VS_5d_1.5w_rep1

description:
SS_VS_5d_1.5w_rep1
US09493743_251486832345_1_1 - T10-116 5day 1.5wk.txt


title: SS_VS_5d_1.5w_rep3

description:
SS_VS_5d_1.5w_rep3
US09493743_251486832346_1_3 - T10-115 5day 1.5wk.txt


title: SS_VS_10d_6w_rep2

description:
SS_VS_10d_6w_rep2
US09493743_251486832363_1_3  - T10-63 10day 6wk.txt

value: after 6wks post 10 days social stress period


title: SS_VS_10d_6w_rep3

description:
SS_VS_10d_6w_rep3
US09493743_251486832369_1_1  - T10-59 10day 6wk.txt


title: SS_VS_10d_24h_rep4

description:
SS_VS_10d_24h_rep4
US09493743_251486832365_1_3 - T10-111  10day 24hr.txt

value: after 24 hrs post 10 days social stress period


title: SS_VS_10d_24h_rep3

description:
SS_VS_10d_24h_rep3
US09493743_251486832365_1_1 - T10-110  10day 24hr.txt


title: SS_VS_10d_6w_rep4

description:
SS_VS_10d_6w_rep4
US09493743_251486832369_1_2  - T10-60 10day 6wk.txt


title: SS_VS_10d_6w_rep1

description:
SS_VS_10d_6w_rep1
US09493743_251486832363_1_1  - T10-57 10day 6wk.txt


title: SS_VS_10d_24h_rep2

description:
SS_VS_10d_24h_rep2
US09493743_251486832364_1_3 - T10-109  10day 24hr.txt


title: SS_VS_10d_24h_rep1

description:
SS_VS_10d_24h_rep1
US09493743_251486832364_1_1 - T10-107  10day 24hr.txt


title: SS_ST_5d_24h_rep5

description:
SS_ST_5d_24h_rep5
US09493743_251486832424_1_1  - T10-105 5day 24hr.txt

value: striatum (ST)


title: SS_ST_5d_24h_rep4

description:
SS_ST_5d_24h_rep4
US09493743_251486832340_1_4  - T5-138 5day 24hr.txt


title: SS_ST_5d_24h_rep3

description:
SS_ST_5d_24h_rep3
US09493743_251486832340_1_1  - T5-137 5day 24hr.txt


title: SS_ST_5d_24h_rep2

description:
SS_ST_5d_24h_rep2
US09493743_251486832339_1_3  - T5-136 5day 24hr.txt


title: SS_ST_5d_1.5w_rep5

description:
SS_ST_5d_1.5w_rep5
US09493743_251486832344_1_4  - T10-116 5day 1.5wk.txt


title: SS_ST_5d_1.5w_rep2

description:
SS_ST_5d_1.5w_rep2
US09493743_251486832342_1_2  - T10-115 5day 1.5wk.txt


title: SS_ST_5d_1.5w_rep4

description:
SS_ST_5d_1.5w_rep4
US09493743_251486832344_1_3  - T10-114 5day 1.5wk.txt


title: SS_ST_5d_1.5w_rep1

description:
SS_ST_5d_1.5w_rep1
US09493743_251486832342_1_1 - T10-112 5day 1.5wk.txt


title: SS_ST_10d_6w_rep3

description:
SS_ST_10d_6w_rep3
US09493743_251486832360_1_3   - T10-64 10day 6wk.txt


title: SS_ST_10d_24h_rep3

description:
SS_ST_10d_24h_rep3
US09493743_251486832341_1_3  - T10-111 10day 24hr.txt


title: SS_ST_5d_24h_rep1

description:
SS_ST_5d_24h_rep1
US09493743_251486832339_1_1 - T5-135 5day 24hr.txt


title: SS_ST_10d_24h_rep4

description:
SS_ST_10d_24h_rep4
US09493743_251486832343_1_3  - T10-110 10day 24hr.txt


title: SS_ST_5d_1.5w_rep3

description:
SS_ST_5d_1.5w_rep3
US09493743_251486832344_1_2  - T10-113 5day 1.5wk.txt


title: SS_ST_10d_6w_rep4

description:
SS_ST_10d_6w_rep4
US09493743_251486832424_1_4  - T10-59 10day 6wk.txt


title: SS_ST_10d_6w_rep2

description:
SS_ST_10d_6w_rep2
US09493743_251486832360_1_1   - T10-57 10day 6wk.txt


title: SS_ST_10d_24h_rep1

description:
SS_ST_10d_24h_rep1
US09493743_251486832341_1_1 - T10-108 10day 24hr.txt


title: SS_ST_10d_6w_rep1

description:
SS_ST_10d_6w_rep1
US09493743_251486832359_1_3   - T10-60 10day 6wk.txt


title: SS_ST_10d_24h_rep2

description:
SS_ST_10d_24h_rep2
US09493743_251486832341_1_2  - T10-109 10day 24hr.txt


title: SS_SE_5d_1.5w_rep3

description:
SS_SE_5d_1.5w_rep3
US09493743_251486832415_1_3 - T10-115 5day 1.5wk.txt

value: septal nucleus (SE)


title: SS_SE_5d_1.5w_rep2

description:
SS_SE_5d_1.5w_rep2
US09493743_251486832415_1_1 - T10-116 5day 1.5wk.txt


title: SS_SE_5d_24h_rep2

description:
SS_SE_5d_24h_rep2
US09493743_251486832416_1_4 - T5-138 5day 24hr.txt


title: SS_SE_5d_1.5w_rep1

description:
SS_SE_5d_1.5w_rep1
US09493743_251486832414_1_3 - T10-113 5day 1.5wk.txt


title: SS_SE_5d_24h_rep1

description:
SS_SE_5d_24h_rep1
US09493743_251486832414_1_1 - T5-136 5day 24hr.txt


title: SS_SE_10d_6w_rep3

description:
SS_SE_10d_6w_rep3
US09493743_251486832428_1_1 - T10-64 10day 6wk.txt


title: SS_SE_10d_6w_rep2

description:
SS_SE_10d_6w_rep2
US09493743_251486832416_1_3 - T10-57 10day 6wk.txt


title: SS_SE_10d_24h_rep3

description:
SS_SE_10d_24h_rep3
US09493743_251486832427_1_1 - T10-108 10day 24hr.txt


title: SS_MPFC_5d_24h_rep5

description:
SS_MPFC_5d_24h_rep5
US09493743_251486832428_1_3 - T10-105 5day 24hr.txt

value: medial prefrontal cortex (MPFC)


title: SS_MPFC_5d_24h_rep2

description:
SS_MPFC_5d_24h_rep2
US09493743_251486831989_1_3 - T5-138 5day 24hr.txt


title: SS_MPFC_5d_1.5w_rep4

description:
SS_MPFC_5d_1.5w_rep4
US09493743_251486831990_1_1 - T10-112 5day 1.5wk.txt


title: SS_SE_10d_6w_rep1

description:
SS_SE_10d_6w_rep1
US09493743_251486832413_1_2 - T10-59 10day 6wk.txt


title: SS_SE_10d_24h_rep2

description:
SS_SE_10d_24h_rep2
US09493743_251486832416_1_1 - T10-111 10day 24hr.txt


title: OiPS3, replicate 1

description: replicate 1

value: Passage 15

value: iPSCs from NFH2 fibroblasts


title: SS_MPFC_5d_24h_rep4

description:
SS_MPFC_5d_24h_rep4
US09493743_251486831991_1_3 - T5-137 5day 24hr.txt


title: SS_MPFC_5d_24h_rep3

description:
SS_MPFC_5d_24h_rep3
US09493743_251486831991_1_1 - T5-135 5day 24hr.txt


title: SS_MPFC_5d_1.5w_rep1

description:
SS_MPFC_5d_1.5w_rep1
US09493743_251486831988_1_1 - T10-113 5day 1.5wk.txt


title: SS_MPFC_5d_24h_rep1

description:
SS_MPFC_5d_24h_rep1
US09493743_251486831989_1_1 - T5-136 5day 24hr.txt


title: SS_SE_10d_24h_rep1

description:
SS_SE_10d_24h_rep1
US09493743_251486832413_1_3 - T10-107 10day 24hr.txt


title: SS_MPFC_10d_6w_rep3

description:
SS_MPFC_10d_6w_rep3
US09493743_251486831998_1_1 - T10-63 10day 6wk.txt


title: SS_MPFC_10d_6w_rep1

description:
SS_MPFC_10d_6w_rep1
US09493743_251486831906_1_1 - T10-57 10day 6wk.txt


title: SS_MPFC_5d_1.5w_rep3

description:
SS_MPFC_5d_1.5w_rep3
US09493743_251486831989_1_4 - T10-116 5day 1.5wk.txt


title: SS_MPFC_5d_1.5w_rep5

description:
SS_MPFC_5d_1.5w_rep5
US09493743_251486832429_1_4 -T10-114 5day 1wk.txt

value: after 1wk post 5 days social defeat period


title: SS_MPFC_10d_6w_rep2

description:
SS_MPFC_10d_6w_rep2
US09493743_251486831906_1_3 - T10-59 10day 6wk.txt


title: SS_MPFC_10d_24h_rep3

description:
SS_MPFC_10d_24h_rep3
US09493743_251486831990_1_3 - T10-108 10day 24hr.txt


title: SS_MPFC_10d_24h_rep4

description:
SS_MPFC_10d_24h_rep4
US09493743_251486832429_1_3 - T10-109 10day 24hr.txt


title: SS_MPFC_10d_6w_rep4

description:
SS_MPFC_10d_6w_rep4
US09493743_251486832429_1_1 - T10-64 10day 6wk.txt


title: SS_MPFC_5d_1.5w_rep2

description:
SS_MPFC_5d_1.5w_rep2
US09493743_251486831988_1_3 - T10-115 5day 1.5wk.txt


title: SS_VS_5d_1.5w_rep5

description:
SS_VS_5d_1.5w_rep5
US09493743_251486832367_1_3 - T10-113 5day 1.5wk.txt


title: SS_MPFC_10d_24h_rep1

description:
SS_MPFC_10d_24h_rep1
US09493743_251486831987_1_1 - T10-107 10day 24hr.txt


title: SS_heart_5d_1.5w_rep5

description:
SS_heart_5d_1.5w_rep5
US09493743_251486832361_1_4 -  T10-116 5day 1.5wk.txt

value: heart


title: SS_heart_5d_24h_rep3

description:
SS_heart_5d_24h_rep3
US09493743_251486832357_1_2  T5-136 5day 24hr.txt


title: SS_heart_5d_24h_rep4

description:
SS_heart_5d_24h_rep4
US09493743_251486832357_1_3  T5-137 5day 24hr.txt


title: SS_heart_5d_24h_rep5

description:
SS_heart_5d_24h_rep5
US09493743_251486832357_1_4  T5-138 5day 24hr.txt


title: SS_heart_5d_24h_rep1

description:
SS_heart_5d_24h_rep1
US09493743_251486832348_1_1 - T10 -105 5day 24hrs.txt


title: SS_heart_5d_1.5w_rep3

description:
SS_heart_5d_1.5w_rep3
US09493743_251486832361_1_2 -  T10-114 5day 1.5wk.txt


title: SS_heart_5d_1.5w_rep4

description:
SS_heart_5d_1.5w_rep4
US09493743_251486832361_1_3 -  T10-115 5day 1.5wk.txt


title: SS_heart_5d_1.5w_rep2

description:
SS_heart_5d_1.5w_rep2
US09493743_251486832361_1_1 -  T10-113 5day 1.5wk.txt


title: SS_heart_10d_6w_rep4

description:
SS_heart_10d_6w_rep4
US09493743_251486832352_1_4 -  T10-63 10day 6wk.txt


title: SS_heart_10d_6w_rep5

description:
SS_heart_10d_6w_rep5
US09493743_251486832353_1_1 -  T10-64 10day 6wk.txt


title: SS_heart_10d_6w_rep2

description:
SS_heart_10d_6w_rep2
US09493743_251486832352_1_2 - T10-59 10day 6wk.txt


title: SS_MPFC_10d_24h_rep2

description:
SS_MPFC_10d_24h_rep2
US09493743_251486831987_1_3 - T10-111 10day 24hr.txt


title: SS_heart_10d_6w_rep1

description:
SS_heart_10d_6w_rep1
US09493743_251486832352_1_1 -  T10-57 10day 6wk.txt


title: SS_heart_10d_24h_rep3

description:
SS_heart_10d_24h_rep3
US09493743_251486832355_1_1 - T10-109 10day 24hrs.txt


title: SS_heart_10d_24h_rep4

description:
SS_heart_10d_24h_rep4
US09493743_251486832355_1_2 - T10-110 10day 24hrs.txt


title: SS_HC_5d_24h_rep5

description:
SS_HC_5d_24h_rep5
US09493743_251486832501_1_4 T5-136 5day 24hrs rerun.txt

value: hippocampus (HC)


title: SS_heart_10d_24h_rep1

description:
SS_heart_10d_24h_rep1
US09493743_251486832354_1_3 - T10-107 10day 24hrs.txt


title: SS_heart_10d_24h_rep2

description:
SS_heart_10d_24h_rep2
US09493743_251486832354_1_4 - T10-108 10day 24hrs.txt


title: SS_HC_5d_24h_rep3

description:
SS_HC_5d_24h_rep3
US09493743_251486832305_1_4  - T5 - 138 5day 24hr.txt


title: SS_HC_5d_24h_rep2

description:
SS_HC_5d_24h_rep2
US09493743_251486832305_1_3 - T5 - 137 5day 24hr.txt


title: SS_heart_10d_24h_rep5

description:
SS_heart_10d_24h_rep5
US09493743_251486832355_1_3 - T10-111 10day 24hrs.txt


title: SS_HC_5d_1.5w_rep4

description:
SS_HC_5d_1.5w_rep4
US09493743_251486832501_1_1  - T10 - 113 5day 1.5wk rerun.txt


title: SS_HC_5d_1.5w_rep5

description:
SS_HC_5d_1.5w_rep5
US09493743_251486832501_1_2  T10-115 5day 1.5wk rerun.txt


title: SS_HC_10d_6w_rep3

description:
SS_HC_10d_6w_rep3
US09493743_251486832437_1_1  T10-63 10day 6wk.txt


title: SS_HC_5d_24h_rep4

description:
SS_HC_5d_24h_rep4
US09493743_251486832501_1_3 T5-135 5day 24hrs rerun.txt


title: SS_heart_5d_1.5w_rep1

description:
SS_heart_5d_1.5w_rep1
US09493743_251486832349_1_4 - T10-112 5day 1.5wk.txt


title: SS_HC_5d_24h_rep1

description:
SS_HC_5d_24h_rep1
US09493743_251486832302_1_4 - T10 - 105 5day 24hr.txt


title: SS_heart_5d_24h_rep2

description:
SS_heart_5d_24h_rep2
US09493743_251486832357_1_1  T5-135 5day 24hr.txt


title: SS_HC_5d_1.5w_rep2

description:
SS_HC_5d_1.5w_rep2
US09493743_251486832303_1_4 T10-114 5day 1.5wk.txt


title: SS_HC_10d_6w_rep4

description:
SS_HC_10d_6w_rep4
US09493743_251486832437_1_2 T10-64 10day 6wk.txt


title: SS_HC_10d_24h_rep1

description:
SS_HC_10d_24h_rep1
US09493743_251486832358_1_1 T10-110 10day 24hrs rerun.txt


title: SS_HC_10d_24h_rep4

description:
SS_HC_10d_24h_rep4
US09493743_251486832435_1_4 - T10 - 109 10day 24hr.txt


title: SS_heart_10d_6w_rep3

description:
SS_heart_10d_6w_rep3
US09493743_251486832352_1_3 - T10-60 10day 6wk.txt


title: SS_HC_10d_6w_rep1

description:
SS_HC_10d_6w_rep1
US09493743_251486832358_1_3  T10-60 10day 6wk rerun.txt


title: SS_HC_10d_6w_rep5

description:
SS_HC_10d_6w_rep5
US09493743_251486832502_1_1  - T10 - 57 10day 6wk rerun.txt


title: SS_HC_10d_24h_rep2

description:
SS_HC_10d_24h_rep2
US09493743_251486832358_1_2 T10-111 10day 24hrs rerun.txt


title: SS_HC_5d_1.5w_rep3

description:
SS_HC_5d_1.5w_rep3
US09493743_251486832304_1_2  - T10 - 116 5day 1.5wk.txt


title: SS_HC_10d_24h_rep3

description:
SS_HC_10d_24h_rep3
US09493743_251486832435_1_2 - T10 - 107 10day 24hr.txt


title: SS_HC_10d_6w_rep2

description:
SS_HC_10d_6w_rep2
US09493743_251486832436_1_3  - T10 - 59 10day 6wk.txt


title: SS_HC_5d_1.5w_rep1

description:
SS_HC_5d_1.5w_rep1
US09493743_251486832303_1_2  - T10 - 112 5day 1.5wk.txt


title: SS_AY_5d_1.5w_rep2

description:
SS_AY_5d_1.5w_rep2
US09493743_251486832433_1_2  - T10-113 5days 1.5wk.txt

value: amygdala (AY)


title: SS_AY_5d_24h_rep2

description:
SS_AY_5d_24h_rep2
US09493743_251486832434_1_1  - T5 -135 5day 24hrs.txt


title: SS_AY_5d_1.5w_rep3

description:
SS_AY_5d_1.5w_rep3
US09493743_251486832433_1_3  - T10 - 114 5days 1.5wk.txt


title: SS_AY_5d_1.5w_rep4

description:
SS_AY_5d_1.5w_rep4
US09493743_251486832433_1_4  - T10 - 116 5days 1.5wk.txt


title: SS_AY_10d_24h_rep4

description:
SS_AY_10d_24h_rep4
US09493743_251486832504_1_1 -  T10-110 10day 24hr.txt


title: SS_AY_10d_24h_rep2

description:
SS_AY_10d_24h_rep2
US09493743_251486829574_1_2 - T10 - 111 10days 24hrs.txt


title: SS_AY_10d_6w_rep1

description:
SS_AY_10d_6w_rep1
US09493743_251486829574_1_4  - T10 - 60 10days 6wk.txt

value: after 6 wks post 10 days social stress period


title: SS_AY_5d_24h_rep1

description:
SS_AY_5d_24h_rep1
US09493743_251486832432_1_3  - T10 - 105 5days 24hrs.txt

value: Strategen universal reference RNA (Cat. No. 740100)


title: SS_AY_10d_6w_rep4

description:
SS_AY_10d_6w_rep4
US09493743_251486832503_1_1  T10-59 10day 6wk.txt

value: social stress (SS)


title: SS_AY_10d_6w_rep2

description:
SS_AY_10d_6w_rep2
US09493743_251486832430_1_1  - T10 - 63 10days 6wk.txt


title: C_VS_5d_24h_rep3

description:
C_VS_5d_24h_rep3
US09493743_251486832370_1_3  - C5-128 5day 24hr control.txt

value: control (C)


title: SS_AY_10d_6w_rep3

description:
SS_AY_10d_6w_rep3
US09493743_251486832430_1_2 - T10 - 64 10days 6wk.txt


title: SS_AY_10d_24h_rep3

description:
SS_AY_10d_24h_rep3
US09493743_251486832503_1_4 - T10-109 10day 24hrs.txt


title: C_VS_5d_24h_rep4

description:
C_VS_5d_24h_rep4
US09493743_251486832370_1_4 - C5-129 5day 24hr control.txt

value: ventral striatum (VS)


title: C_VS_5d_24h_rep1

description:
C_VS_5d_24h_rep1
US09493743_251486832366_1_2  - C5-127 5day 24hr control.txt


title: SS_AY_10d_24h_rep1

description:
SS_AY_10d_24h_rep1
US09493743_251486829573_1_3 - T10 - 108 10days 24hrs.txt


title: C_VS_5d_24h_rep5

description:
C_VS_5d_24h_rep5
US09493743_251486832371_1_3 - C5-131 5day 24hr control.txt


title: C_VS_5d_1.5w_rep5

description:
C_VS_5d_1.5w_rep5
US09493743_251486832367_1_4 - C5-133 5day 1.5wk Control.txt


title: C_VS_5d_24h_rep2

description:
C_VS_5d_24h_rep2
US09493743_251486832366_1_4  - C5-130 5day 24hr control.txt


title: C_VS_10d_6w_rep3

description:
C_VS_10d_6w_rep3
US09493743_251486832363_1_4 - C10-48 10day 6wk control.txt


title: C_VS_10d_6w_rep4

description:
C_VS_10d_6w_rep4
US09493743_251486832369_1_3  - C10-47 10day 6wk control.txt


title: C_VS_5d_1.5w_rep2

description:
C_VS_5d_1.5w_rep2
US09493743_251486832346_1_2  - C5-134 5day 1.5wk Control.txt


title: C_VS_5d_1.5w_rep4

description:
C_VS_5d_1.5w_rep4
US09493743_251486832367_1_2  - C5-132 5day 1.5wk Control.txt


title: C_VS_5d_1.5w_rep3

description:
C_VS_5d_1.5w_rep3
US09493743_251486832346_1_4  - HC-125 5day 1.5wk Control.txt


title: C_VS_10d_6w_rep1

description:
C_VS_10d_6w_rep1
US09493743_251486832345_1_3  - C10-50 10day 6wk control.txt


title: C_VS_10d_24h_rep3

description:
C_VS_10d_24h_rep3
US09493743_251486832365_1_4 - C10-97  10day 24hr Control.txt


title: C_VS_10d_6w_rep5

description:
C_VS_10d_6w_rep5
US09493743_251486832369_1_4  - C10-49 10day 6wk control.txt


title: SS_AY_5d_1.5w_rep1

description:
SS_AY_5d_1.5w_rep1
US09493743_251486832433_1_1  - T10 - 112 5days 1.5wk.txt

value: after 1.5 wk post 5 days social defeat period


title: C_VS_10d_24h_rep2

description:
C_VS_10d_24h_rep2
US09493743_251486832365_1_2 - C10-96  10day 24hr Control.txt


title: C_VS_10d_6w_rep2

description:
C_VS_10d_6w_rep2
US09493743_251486832363_1_2 - C10-46 10day 6wk control.txt


title: C_ST_5d_24h_rep4

description:
C_ST_5d_24h_rep4
US09493743_251486832340_1_3  - C5-130 5day 24hr control.txt


title: C_ST_5d_24h_rep5

description:
C_ST_5d_24h_rep5
US09493743_251486832424_1_3  - C5-131 5day 24hr control.txt


title: C_VS_10d_24h_rep1

description:
C_VS_10d_24h_rep1
US09493743_251486832364_1_2 - C10-93  10day 24hr Control.txt


title: C_VS_5d_1.5w_rep1

description:
C_VS_5d_1.5w_rep1
US09493743_251486832345_1_2  - HC-126 5day 1.5wk Control.txt


title: C_ST_10d_24h_rep3

description:
C_ST_10d_24h_rep3
US09493743_251486832343_1_4  - C10-97 10day 24hr control.txt


title: C_ST_5d_24h_rep3

description:
C_ST_5d_24h_rep3
US09493743_251486832340_1_2  - C5-129 5day 24hr control.txt


title: C_ST_10d_24h_rep2

description:
C_ST_10d_24h_rep2
US09493743_251486832343_1_2  - C10-96 10day 24hr control.txt


title: C_ST_5d_1.5w_rep5

description:
C_ST_5d_1.5w_rep5
US09493743_251486832371_1_4   - HC-126 5day 1.5wk control.txt


title: C_ST_5d_24h_rep2

description:
C_ST_5d_24h_rep2
US09493743_251486832339_1_4  - C5-128 5day 24hr control.txt


title: C_ST_5d_1.5w_rep2

description:
C_ST_5d_1.5w_rep2
US09493743_251486832342_1_4  - C5-134 5day 1.5wk control.txt


title: C_ST_5d_1.5w_rep4

description:
C_ST_5d_1.5w_rep4
US09493743_251486832344_1_1  - C5-132 5day 1.5wk control.txt


title: C_ST_5d_1.5w_rep1

description:
C_ST_5d_1.5w_rep1
US09493743_251486832342_1_3  -  C5-133 5day 1.5wk control.txt


title: C_ST_10d_6w_rep3

description:
C_ST_10d_6w_rep3
US09493743_251486832360_1_2   - C10-46 10day 6wk control.txt


title: C_ST_10d_24h_rep4

description:
C_ST_10d_24h_rep4
US09493743_251486832345_1_4 - C10-93 10day 24hr control.txt


title: C_ST_5d_24h_rep1

description:
C_ST_5d_24h_rep1
US09493743_251486832339_1_2  - C5-127 5day 24hr control.txt


title: C_ST_5d_1.5w_rep3

description:
C_ST_5d_1.5w_rep3
US09493743_251486832343_1_1  - HC-125 5day 1.5wk control.txt


title: C_SE_5d_24h_rep2

description:
C_SE_5d_24h_rep2
US09493743_251486832414_1_4 - C5-127 5day 24hr control.txt


title: C_ST_10d_6w_rep2

description:
C_ST_10d_6w_rep2
US09493743_251486832359_1_2   - C10-49 10day 6wk control.txt


title: C_MPFC_5d_24h_rep4

description:
C_MPFC_5d_24h_rep4
US09493743_251486831998_1_3 - C5-128 5day 24hr control.txt


title: C_SE_10d_24h_rep2

description:
C_SE_10d_24h_rep2
US09493743_251486832414_1_2 - C10-97 10day 24hr control.txt


title: C_ST_10d_6w_rep4

description:
C_ST_10d_6w_rep4
US09493743_251486832360_1_4   - C10-50 10day 6wk control.txt


title: C_SE_5d_1.5w_rep2

description:
C_SE_5d_1.5w_rep2
US09493743_251486832415_1_4 - C5-132 5day 1.5wk control.txt


title: C_SE_5d_24h_rep3

description:
C_SE_5d_24h_rep3
US09493743_251486832427_1_3 - C5-128 5day 24hr Control.txt


title: C_SE_10d_24h_rep3

description:
C_SE_10d_24h_rep3
US09493743_251486832428_1_2 - C10-96 10day 24hr Control.txt


title: C_ST_10d_6w_rep1

description:
C_ST_10d_6w_rep1
US09493743_251486832359_1_1   - C10-48 10day 6wk control.txt


title: C_MPFC_5d_24h_rep3

description:
C_MPFC_5d_24h_rep3
US09493743_251486831991_1_4 - C5-131 5day 24hr control.txt


title: C_SE_10d_6w_rep3

description:
C_SE_10d_6w_rep3
US09493743_251486832427_1_4 - C10-46 10day 6wk control.txt


title: C_MPFC_5d_24h_rep2

description:
C_MPFC_5d_24h_rep2
US09493743_251486831991_1_2 - C5-130 5day 24hr control.txt


title: C_SE_5d_24h_rep1

description:
C_SE_5d_24h_rep1
US09493743_251486832413_1_1 - C5-129 5day 24hr Control.txt


title: C_ST_10d_24h_rep1

description:
C_ST_10d_24h_rep1
US09493743_251486832341_1_4 - C10-94 10day 24hr control.txt


title: C_SE_10d_24h_rep1

description:
C_SE_10d_24h_rep1
US09493743_251486832413_1_4  - C10-93 10day 24hr Control.txt


title: C_SE_5d_1.5w_rep1

description:
C_SE_5d_1.5w_rep1
US09493743_251486832415_1_2 - HC-126 5day 1.5wk control.txt


title: C_SE_10d_6w_rep2

description:
C_SE_10d_6w_rep2
US09493743_251486832427_1_2 - C10-49 10day 6wk Control.txt


title: C_SE_10d_6w_rep1

description:
C_SE_10d_6w_rep1
US09493743_251486832416_1_2 - C10-50 10day 6wk control.txt


title: C_MPFC_5d_24h_rep1

description:
C_MPFC_5d_24h_rep1
US09493743_251486831989_1_2 - C5-129 5day 24hr control.txt


title: C_MPFC_10d_6w_rep4

description:
C_MPFC_10d_6w_rep4
US09493743_251486831998_1_4 - C10-49 10day 6wk control.txt


title: C_MPFC_5d_1.5w_rep4

description:
C_MPFC_5d_1.5w_rep4
US09493743_251486831990_1_4 - HC-125 5day 1.5wk control.txt


title: C_heart_10d_6w_rep5

description:
C_heart_10d_6w_rep5
US09493743_251486832354_1_2 - C10-50 10day 6wk control.txt


title: C_heart_5d_24h_rep5

description:
C_heart_5d_24h_rep5
US09493743_251486832349_1_3 - C5 -131 control 5 day 24hr.txt


title: C_MPFC_5d_1.5w_rep5

description:
C_MPFC_5d_1.5w_rep5
US09493743_251486832429_1_2 - C5-134 5day 1.5wk control.txt


title: C_heart_5d_24h_rep3

description:
C_heart_5d_24h_rep3
US09493743_251486832349_1_1 - C5 -129 control 5 day 24h.txt


title: C_MPFC_10d_6w_rep2

description:
C_MPFC_10d_6w_rep2
US09493743_251486831906_1_4 - C10-50 10day 6wk control.txt


title: C_heart_5d_1.5w_rep4

description:
C_heart_5d_1.5w_rep4
US09493743_251486832362_1_4 - HC -125 5day-1.5wk control.txt


title: C_MPFC_5d_1.5w_rep1

description:
C_MPFC_5d_1.5w_rep1
US09493743_251486831988_1_2 - C5-132 5day 1.5wk control.txt


title: C_heart_5d_1.5w_rep1

description:
C_heart_5d_1.5w_rep1
US09493743_251486832362_1_1 - C5-132 5day 1.5wk control.txt


title: C_heart_5d_1.5w_rep3

description:
C_heart_5d_1.5w_rep3
US09493743_251486832362_1_3 - C5 -134 5day-1.5wk control.txt


title: C_MPFC_5d_1.5w_rep2

description:
C_MPFC_5d_1.5w_rep2
US09493743_251486831988_1_4 - HC-126 5day 1.5wk control.txt


title: C_heart_10d_6w_rep4

description:
C_heart_10d_6w_rep4
US09493743_251486832354_1_1 - C10-49 10day 6wk control.txt


title: C_heart_5d_24h_rep2

description:
C_heart_5d_24h_rep2
US09493743_251486832348_1_4 -  C5-128 5day 24hrs control.txt


title: C_heart_10d_24h_rep4

description:
C_heart_10d_24h_rep4
US09493743_251486832356_1_3 - C10-96 10day 24hrs control.txt


title: C_MPFC_10d_24h_rep1

description:
C_MPFC_10d_24h_rep1
US09493743_251486831987_1_2 - C10-96 10day 24hr control.txt


title: C_heart_5d_24h_rep4

description:
C_heart_5d_24h_rep4
US09493743_251486832349_1_2 - C5 -130 control 5 day 24h.txt


title: C_heart_10d_24h_rep3

description:
C_heart_10d_24h_rep3
US09493743_251486832356_1_2 - C10-95 10day 24hrs control.txt


title: C_MPFC_10d_6w_rep1

description:
C_MPFC_10d_6w_rep1
US09493743_251486831906_1_2 - C10-46 10day 6wk control.txt


title: C_MPFC_5d_1.5w_rep3

description:
C_MPFC_5d_1.5w_rep3
US09493743_251486831990_1_2 - C5-133 5day 1.5wk control.txt


title: C_heart_10d_6w_rep1

description:
C_heart_10d_6w_rep1
US09493743_251486832353_1_2 -  C10-46 10day 6wk control.txt


title: C_heart_5d_1.5w_rep2

description:
C_heart_5d_1.5w_rep2
US09493743_251486832362_1_2 - C5-133 5day 1.5wk control.txt


title: C_MPFC_10d_6w_rep3

description:
C_MPFC_10d_6w_rep3
US09493743_251486831998_1_2 - C10-48 10day 6wk control.txt


title: C_MPFC_10d_24h_rep2

description:
C_MPFC_10d_24h_rep2
US09493743_251486831987_1_4- C10-97 10day 24hr control.txt


title: C_heart_5d_24h_rep1

description:
C_heart_5d_24h_rep1
US09493743_251486832348_1_3 -  C5-127 5day 24hrs control.txt


title: C_MPFC_10d_24h_rep3

description:
C_MPFC_10d_24h_rep3
US09493743_251486832428_1_4- C10-93 10day 24hr control.txt


title: C_heart_10d_6w_rep3

description:
C_heart_10d_6w_rep3
US09493743_251486832353_1_4  C10-48 10day 6wk control.txt


title: C_heart_10d_6w_rep2

description:
C_heart_10d_6w_rep2
US09493743_251486832353_1_3 -  C10-47 10day 6wk control.txt


title: C_heart_10d_24h_rep5

description:
C_heart_10d_24h_rep5
US09493743_251486832356_1_4 - C10-97 10day 24hrs control.txt


title: C_heart_10d_24h_rep2

description:
C_heart_10d_24h_rep2
US09493743_251486832356_1_1 - C10-94 10day 24hrs control.txt


title: C_HC_5d_24h_rep1

description:
C_HC_5d_24h_rep1
US09493743_251486832358_1_4  C5-127 5day 24hrs control.txt


title: C_HC_5d_24h_rep2

description:
C_HC_5d_24h_rep2
US09493743_251486832437_1_4  C5-128 5day 24hrs control.txt


title: C_HC_5d_1.5w_rep3

description:
C_HC_5d_1.5w_rep3
US09493743_251486832500_1_4  HC-125 5day 1.5wk control rerun.txt


title: C_HC_10d_6w_rep1

description:
C_HC_10d_6w_rep1
US09493743_251486832347_1_1  C10-46 10day 6wk control rerun.txt


title: C_HC_5d_24h_rep3

description:
C_HC_5d_24h_rep3
US09493743_251486832500_1_1  C5-129 5day 24hrs control.txt


title: C_HC_5d_1.5w_rep1

description:
C_HC_5d_1.5w_rep1
US09493743_251486832500_1_2 C5-133 5day 1.5wk control rerun.txt


title: C_HC_10d_6w_rep3

description:
C_HC_10d_6w_rep3
US09493743_251486832347_1_3  C10-49 10day 6wk control rerun.txt


title: C_HC_5d_1.5w_rep4

description:
C_HC_5d_1.5w_rep4
US09493743_251486832502_1_4  - HC - 126 5day 1.5wk control rerun.txt


title: C_HC_10d_24h_rep5

description:
C_HC_10d_24h_rep5
US09493743_251486832502_1_3  C10-96 10day 24hrs control.txt


title: C_HC_5d_1.5w_rep2

description:
C_HC_5d_1.5w_rep2
US09493743_251486832500_1_3 C5-134 5day 1.5wk control rerun.txt


title: C_AY_5d_1.5w_rep1

description:
C_AY_5d_1.5w_rep1
US09493743_251486832431_1_2  - C5 - 132 5days 1.5wk control.txt


title: C_heart_10d_24h_rep1

description:
C_heart_10d_24h_rep1
US09493743_251486832355_1_4 - C10-93 10day 24hrs control.txt


title: C_HC_10d_24h_rep3

description:
C_HC_10d_24h_rep3
US09493743_251486832423_1_4 C10 - 95 10days 24hrs control.txt


title: C_AY_5d_1.5w_rep2

description:
C_AY_5d_1.5w_rep2
US09493743_251486832503_1_3 C5-134 5day 1.5wk control.txt


title: C_AY_5d_24h_rep1

description:
C_AY_5d_24h_rep1
US09493743_251486832430_1_3  - C5 - 128 5days 24hrs control.txt


title: C_AY_5d_1.5w_rep4

description:
C_AY_5d_1.5w_rep4
US09493743_251486832432_1_1  - HC - 125 5days 1.5wk control.txt


title: C_HC_10d_6w_rep2

description:
C_HC_10d_6w_rep2
US09493743_251486832347_1_2 C10-48 10day 6wk control rerun.txt


title: C_AY_10d_6w_rep2

description:
C_AY_10d_6w_rep2
US09493743_251486829572_1_2 - C10 - 48 10days 6wk control.txt


title: C_AY_10d_24h-rep3

description:
C_AY_10d_24h-rep3
US09493743_251486829573_1_2 - C10 - 96 10days 24hrs control.txt


title: C_HC_10d_6w_rep4

description:
C_HC_10d_6w_rep4
US09493743_251486832434_1_3 - C10 - 47 10day 6wk control.txt


title: C_HC_10d_24h_rep4

description:
C_HC_10d_24h_rep4
US09493743_251486832435_1_1  - C10 - 97 10day 24hr control.txt


title: C_AY_5d_24h_rep3

description:
C_AY_5d_24h_rep3
US09493743_251486832503_1_2 - C5-131 5day 24hrs control.txt


title: C_AY_5d_1.5w_rep5

description:
C_AY_5d_1.5w_rep5
US09493743_251486832432_1_2  - HC - 126 5days 1.5wk control.txt


title: C_HC_10d_24h_rep2

description:
C_HC_10d_24h_rep2
US09493743_251486832423_1_2 C10 - 93 10days 24hrs control.txt


title: C_HC_10d_24h_rep1

description:
C_HC_10d_24h_rep1
US09493743_251486832347_1_4  C10-94 10day 24hrs control rerun.txt


title: C_AY_10d_24h-rep2

description:
C_AY_10d_24h-rep2
US09493743_251486829573_1_1 - C10 - 95 10days 24hr control.txt


title: C_AY_5d_24h_rep2

description:
C_AY_5d_24h_rep2
US09493743_251486832430_1_4  - C5 - 130 5days 24hrs control.txt


title: C_AY_10d_6w_rep3

description:
C_AY_10d_6w_rep3
US09493743_251486829572_1_3 - C10 - 50 10days 6wk control.txt


title: C_AY_5d_1.5w_rep3

description:
C_AY_5d_1.5w_rep3
US09493743_251486832431_1_3  - C5 - 133 5days 1.5wk control.txt


title: C_AY_10d_6w_rep1

description:
C_AY_10d_6w_rep1
US09493743_251486829572_1_1  C10 - 46 10days 6wk control.txt


title: C_AY_10d_24h-rep1

description:
C_AY_10d_24h-rep1
US09493743_251486829572_1_4 - C10 - 93 10days 24hrs control.txt


title: Microglia_WT 6h biol. repl. 2

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

description: Gene expression data from primary microglia stimulated for 6 h with IFN-b

hyb_protocol: Biotinylated cRNA was hybridized on MOE430A 2.0 GeneChips, that were stained, washed and scanned following standard procedures.

data_processing: Background correction and normalization was performed on Affymetrix CEL files using the Bioconductor/R package affy.

source_name: primary microglia, WT mice, 6h IFN-b stimulation

label_protocol: Total RNA was processed using the GeneChip Expression 3’ Amplification One-Cycle Target Labeling Kit according to the manufacturer’s instruction.

growth_protocol: Cell were were grown in DMEM GlutaMAX supplemented with 10% fetal calf serum and 1% penicillin/streptomycin at 37 °C and 5% CO2

extract_protocol: RNA was isolated using the RNeasy Mini Kit

treatment_protocol: Cells were either left untreated or incubated with 500U/ml IFN-b for 6h or 24h.

value: primary microglia

value: WT


title: hasmc_rofecoxib_tp2hr_biological rep1

city: Philadelphia

first: Emanuela

last: Ricciotti

state: PA

address: 3400 Civic Center Blvd.

department: Department of Pharmacology/Institute for Translational Medicine and Therapeutics

institute: University of Pennsylvania

description: Pretreatment with rofecoxib, sampled after 2 h IL-1beta exposure

hyb_protocol: Hybridization was carried out at the Penn Microarray Facility. Affymetrix Human Genome U133A v2 was used.

scan_protocol: Data were collected at the Penn Microarray Facility.

data_processing: Expression values were generated using RMA as implemented in the Affymetrix Expression Console software.

source_name: human aortic smc, 2hr rofecoxib exposure, 2 hr IL-1beta exposure

label_protocol: Labeling was carried out at the Penn Microarray Facility.

growth_protocol: Primary human aortic smooth muscle cells (3F1243) from Lonza were cultured using standard cell culture. Cells were harvested from culture after 0, 2, 8, or 24 hours incubation with interleukin 1beta (10 ng/mL).

extract_protocol: Qiagen kit was used to isolate total RNA.

treatment_protocol: Cells were incubated with rofecoxib (500 nM), celecoxib (500 nM) or DMSO for 2 hours. Subsequently, cells were stimulated with interleukin 1beta (10 ng/mL). The start of incubation with interleukin 1beta is taken to be time zero.

tag: gender

value: male

tag: race

value: white

value: aortic smooth muscle cell

tag: material type

value: primary cell

tag: nsaid treatment

value: rofecoxib


title: Microglia_C61A 0h biol. repl. 1

description: Gene expression data from untreated primary microglia

scan_protocol: Biotinylated cRNA was hybridized on MOE430A 2.0 GeneChips, that were stained, washed and scanned following standard procedures.

source_name: primary microglia, Usp18_C61A mice, untreated


title: hasmc_rofecoxib_tp24hr_biological rep2

description: Pretreatment with rofecoxib, sampled after 24 h IL-1beta exposure

source_name: human aortic smc, 2hr rofecoxib exposure, 24 hr IL-1beta exposure


title: hasmc_rofecoxib_tp8hr_biological rep2

description: Pretreatment with rofecoxib, sampled after 8 h IL-1beta exposure

source_name: human aortic smc, 2hr rofecoxib exposure, 8 hr IL-1beta exposure


title: hasmc_rofecoxib_tp24hr_biological rep3


title: hasmc_rofecoxib_tp24hr_biological rep4


title: Microglia_C61A 6h biol. repl. 1

source_name: primary microglia, Usp18_C61A mice, 6h IFN-b stimulation


title: hasmc_rofecoxib_tp8hr_biological rep3


title: Microglia_WT 6h biol. repl. 1


title: hasmc_rofecoxib_tp2hr_biological rep4


title: Microglia_WT 24h biol. repl. 1

description: Gene expression data from primary microglia stimulated for 24 h with IFN-b

source_name: primary microglia, WT mice, 24h IFN-b stimulation


title: Microglia_WT 0h biol. repl. 2

source_name: primary microglia, WT mice, untreated


title: hasmc_rofecoxib_tp8hr_biological rep4


title: hasmc_rofecoxib_tp2hr_biological rep2


title: Microglia_C61A 24h biol. repl. 2

source_name: primary microglia, Usp18_C61A mice, 24h IFN-b stimulation


title: Microglia_WT 24h biol. repl. 2


title: hasmc_rofecoxib_tp8hr_biological rep1


title: hasmc_rofecoxib_tp24hr_biological rep1


title: Microglia_C61A 6h biol. repl. 2


title: Microglia_WT 0h biol. repl. 1


title: Microglia_C61A 0h biol. repl. 2


title: hasmc_rofecoxib_tp2hr_biological rep3


title: hasmc_rofecoxib_tp0hr_biological rep2

description: Pretreatment with rofecoxib, sampled after 0 h IL-1beta exposure

source_name: human aortic smc, 2hr rofecoxib exposure, 0 hr IL-1beta exposure


title: BV-2 cells siRNA co 6h biol. repl. 2

description: Gene expression data from BV-2 cells stimulated for 6 h with IFN-b

source_name: BV-2 cells siRNA control, 6h IFN-b stimulation

value: si RNA control


title: BV-2 cells siRNA co 24h biol. repl. 2

description: Gene expression data from BV-2 cells stimulated for 24 h with IFN-b

source_name: BV-2 cells siRNA control, 24h IFN-b stimulation


title: Microglia_C61A 24h biol. repl. 1


title: hasmc_rofecoxib_tp0hr_biological rep3


title: hasmc_rofecoxib_tp0hr_biological rep4


title: BV-2 cells siRNA co 0h biol. repl. 2

description: Gene expression data from untreated BV-2 cells

source_name: BV-2 cells siRNA control, untreated


title: hasmc_rofecoxib_tp0hr_biological rep1


title: BV-2 cells siRNA Usp18 24h biol. repl. 2

source_name: BV-2 cells siRNA Usp18, 24h IFN-b stimulation

value: si RNA Usp18


title: hasmc_none_tp24hr_biological rep4

description: Control : Pretreatment with dimethyl sulfoxide, sampled after 24 h IL-1beta exposure

source_name: human aortic smc, control 24hr IL-1beta exposure


title: BV-2 cells siRNA Usp18 24h biol. repl. 1


title: hasmc_none_tp24hr_biological rep3


title: BV-2 cells siRNA co 0h biol. repl. 1


title: BV-2 cells siRNA Usp18 0h biol. repl. 2

source_name: BV-2 cells siRNA Usp18, untreated


title: hasmc_none_tp8hr_biological rep2

description: Control : Pretreatment with dimethyl sulfoxide, sampled after 8 h IL-1beta exposure

source_name: human aortic smc, control 8hr IL-1beta exposure


title: hasmc_none_tp8hr_biological rep1


title: hasmc_none_tp8hr_biological rep3


title: hasmc_none_tp2hr_biological rep4

description: Control : Pretreatment with dimethyl sulfoxide, sampled after 2 h IL-1beta exposure

source_name: human aortic smc, control 2hr IL-1beta exposure


title: BV-2 cells siRNA Usp18 6h biol. repl. 1

source_name: BV-2 cells siRNA Usp18, 6h IFN-b stimulation


title: Vector pReceiver-M02 control, biological replicate 2_LNCaP

city: Toronto

first: Yu-Jia

last: Shiah

state: Ontario

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

country: Canada

institute: Ontario Institute for Cancer Research

description:
Gene expression data from LNCaP prostate cancer cells containing empty vector pReceiver-M02
5B

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45C on GeneChip Human Transcriptome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: All preprocessing was performed using R (v 3.0.3). Background correction and normalization algorithms were implemented in the affy (v 1.40.0) packages from the BioConductor (v2.14) open-source project . The robust multichip average (RMA) algorithm was applied to the raw intensity data. The algorithm process data based on background subtraction, quantile normalization and summarization (via median-polish).

source_name: LNCaP cells transfected with vector pReceiver-M02, control cells

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip WT Plus Reagent Kit User Manual (P/N 703174, Rev. 2)

growth_protocol: Cells were grown in RPMI1640 media (Life Technologies) containing 250 µg/ml geneticin (Life Technologies) at 37°C with 5% CO2.

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen)

tag: transfection status

value: cell line transfected with empty vector - stable, pool

value: LNCaP

value: Prostate cancer cell line


title: Microglia_WT 24h biol. repl. 2

tag: genotype/variation


title: MYCL1 NM_005376.4 overexpression, biological replicate 2_LNCaP

description:
Gene expression data from LNCaP prostate cancer cells overexpressing MYCL1  NM_005376.4
4B

source_name: LNCaP cells transfected with ORF expression clone for MYCL (NM_005376.4)

value: cell line transfected with MYCL1 overexpression construct - stable, pool


title: hasmc_none_tp2hr_biological rep1


title: hasmc_none_tp24hr_biological rep2


title: BV-2 cells siRNA co 6h biol. repl. 1


title: BV-2 cells siRNA Usp18 6h biol. repl. 2


title: hasmc_none_tp24hr_biological rep1


title: Vector pReceiver-M02 control, biological replicate 1_LNCaP

description:
Gene expression data from LNCaP prostate cancer cells containing empty vector pReceiver-M02
5A


title: hasmc_none_tp8hr_biological rep4


title: Untransfected cells, biological replicate 1_LNCaP

description:
Gene expression data from LNCaP prostate cancer cells
0A

source_name: LNCaP cells - untreated

value: untreated cell line


title: BV-2 cells siRNA co 24h biol. repl. 1


title: hasmc_none_tp2hr_biological rep2


title: hasmc_none_tp2hr_biological rep3


title: Microglia_WT 6h biol. repl. 2

description: Gene expression data from primary microglia stimulated for 6 h with IFN-b

source_name: primary microglia, WT mice, 6h IFN-b stimulation


title: BV-2 cells siRNA Usp18 0h biol. repl. 1


title: Untransfected cells, biological replicate 2_LNCaP

description:
Gene expression data from LNCaP prostate cancer cells
0B


title: Microglia_WT 6h biol. repl. 1


title: Microglia_WT 0h biol. repl. 2

description: Gene expression data from untreated primary microglia


title: MYCL1 NM_005376.4 overexpression, biological replicate 1_LNCaP

description:
Gene expression data from LNCaP prostate cancer cells overexpressing MYCL1  NM_005376.4
4A


title: hasmc_none_tp0hr_biological rep4

description: Control : Pretreatment with dimethyl sulfoxide, sampled after 0 h IL-1beta exposure

source_name: human aortic smc, control 0hr timepoint, no NSAID, no IL-1beta


title: MYC1L NM_001033081.2 overexpression, biological replicate 2_LNCaP

description:
Gene expression data from LNCaP prostate cancer cells overexpressing MYCL1 NM_001033081.2
2B

source_name: LNCaP cells transfected with ORF expression clone for MYCL (NM_001033081.2)


title: MYCL1 NM_001033082.2 overexpression, biological replicate 1_LNCaP

description:
Gene expression data from LNCaP prostate cancer cells overexpressing MYCL1 NM_001033082.2
3A

source_name: LNCaP cells transfected with ORF expression clone for MYCL (NM_001033082.2)


title: MYCL1 NM_001033082.2 overexpression, biological replicate 2_LNCaP

description:
Gene expression data from LNCaP prostate cancer cells overexpressing MYCL1 NM_001033082.2
3B


title: hasmc_none_tp0hr_biological rep3


title: MYCL1 NM_001033081.2 overexpression, biological replicate 1_LNCaP

description:
Gene expression data from LNCaP prostate cancer cells overexpressing MYCL1 NM_001033081.2
2A


title: MYCL1 BC011864.2 overexpression, biological replicate 1_LNCaP

description:
Gene expression data from LNCaP prostate cancer cells overexpressing MYCL1 BC011864.2
1A

source_name: LNCaP cells transfected with ORF expression clone for MYCL (BC011864.2)


title: Microglia_WT 24h biol. repl. 1

description: Gene expression data from primary microglia stimulated for 24 h with IFN-b

source_name: primary microglia, WT mice, 24h IFN-b stimulation


title: MYCL1 BC011864.2 overexpression, biological replicate 2_LNCaP

description:
Gene expression data from LNCaP prostate cancer cells overexpressing MYCL1 BC011864.2
1B


title: hasmc_none_tp0hr_biological rep2


title: Untransfected cells, biological replicate 2_22RV1

description:
Gene expression data from 22RV1 prostate cancer cells
22RVI-MYCL1-0B

source_name: 22RV1 cells - untreated


title: Vector pReceiver-M02 control, biological replicate 1_22RV1

description:
Gene expression data from 22RV1 prostate cancer cells containing empty vector pReceiver-M02
22RVI-MYCL1-5A

source_name: 22RV1 cells transfected with vector pReceiver-M02, control cells


title: Microglia_WT 0h biol. repl. 1

source_name: primary microglia, WT mice, untreated


title: MYCL1 NM_005376.4 overexpression, biological replicate 1_22RV1

description:
Gene expression data from 22RV1 prostate cancer cells overexpressing MYCL1  NM_005376.4
22RVI-MYCL1-4A

source_name: 22RV1 cells transfected with ORF expression clone for MYCL (NM_005376.4)


title: Microglia_KO 0h biol. repl. 2

source_name: primary microglia, Usp18ko mice, untreated

value: Usp18 ko


title: hasmc_none_tp0hr_biological rep1


title: untransfected cells, biological replicate 1_22RV1

description:
Gene expression data from 22RV1 prostate cancer cells
22RVI-MYCL1-0A


title: MYCL1 NM_001033082.2 overexpression, biological replicate 2_22RV1

description:
Gene expression data from 22RV1 prostate cancer cells overexpressing MYCL1 NM_001033082.2
22RVI-MYCL1-3B

source_name: 22RV1 cells transfected with ORF expression clone for MYCL (NM_001033082.2)


title: Microglia_KO 24h biol. repl. 2

source_name: primary microglia, Usp18ko mice, 24h IFN-b stimulation


title: Vector pReceiver-M02 control, biological replicate 2_22RV1

description:
Gene expression data from 22RV1 prostate cancer cells containing empty vector pReceiver-M02
22RVI-MYCL1-5B


title: hasmc_none_tp-2hr_biological rep1

description: Control: no pre-treatment or IL-1beta exposure, sampled at t = -2 h

source_name: human aortic smc, control -2hr timepoint, no NSAID, no IL-1beta


title: hasmc_none_tp-2hr_biological rep4


title: Microglia_KO 6h biol. repl. 2

description: Gene expression data from primary microglia stimulated for 6 h with IFN-b

source_name: primary microglia, Usp18ko mice, 6h IFN-b stimulation


title: Microglia_KO 24h biol. repl. 1


title: MYCL1 NM_001033082.2 overexpression, biological replicate 1_22RV1

description:
Gene expression data from 22RV1 prostate cancer cells overexpressing MYCL1 NM_001033082.2
22RVI-MYCL1-3A


title: MYC1L NM_001033081.2 overexpression, biological replicate 2_22RV1

description:
Gene expression data from 22RV1 prostate cancer cells overexpressing MYCL1 NM_001033081.2
22RVI-MYCL1-2B

source_name: 22RV1 cells transfected with ORF expression clone for MYCL (NM_001033081.2)


title: Microglia_KO 6h biol. repl. 1


title: MYCL1 NM_005376.4 overexpression, biological replicate 2_22RV1

description:
Gene expression data from 22RV1 prostate cancer cells overexpressing MYCL1  NM_005376.4
22RVI-MYCL1-4B


title: Microglia_KO 0h biol. repl. 1

description: Gene expression data from untreated primary microglia


title: hasmc_none_tp-2hr_biological rep3


title: hasmc_none_tp-2hr_biological rep2


title: hasmc_celecoxib_tp24hr_biological rep4

description: Pretreatment with celecoxib, sampled after 24 h IL-1beta exposure

source_name: human aortic smc, 2hr celecoxib exposure, 24 hr IL-1beta exposure

value: celecoxib


title: MYCL1 NM_001033081.2 overexpression, biological replicate 1_22RV1

description:
Gene expression data from 22RV1 prostate cancer cells overexpressing MYCL1 NM_001033081.2
22RVI-MYCL1-2A


title: MYCL1 BC011864.2 overexpression, biological replicate 1_22RV1

description:
Gene expression data from 22RV1 prostate cancer cells overexpressing MYCL1 BC011864.2
22RVI-MYCL1-1A

source_name: 22RV1 cells transfected with ORF expression clone for MYCL (BC011864.2)


title: MYCL1 BC011864.2 overexpression, biological replicate 2_22RV1

description:
Gene expression data from 22RV1 prostate cancer cells overexpressing MYCL1 BC011864.2
22RVI-MYCL1-1B


title: IFNARko repl. 2

description: Gene expression data from IFNAR1ko mice

source_name: total brain lysate from IFNAR1ko mice

growth_protocol: Mice were kept under SPF conditions

treatment_protocol: Mice were untreated

tag: tissue

value: total brain lysate

value: IFNARko


title: hasmc_celecoxib_tp24hr_biological rep3


title: USP18ko:IFNARko repl.2

description: Gene expression data from USP18ko:IFNAR1ko mice

source_name: total brain lysate from USP18ko:IFNAR1ko mice


title: USP18ko:IFNARko repl.3


title: hasmc_celecoxib_tp8hr_biological rep3

description: Pretreatment with celecoxib, sampled after 8 h IL-1beta exposure

source_name: human aortic smc, 2hr celecoxib exposure, 8 hr IL-1beta exposure


title: USP18 ko repl.3

description: Gene expression data from USP18ko mice

source_name: total brain lysate from USP18ko mice


title: hasmc_celecoxib_tp24hr_biological rep1


title: IFNARko repl. 1

description: Gene expression data from IFNAR1ko mice


title: IFNARko repl. 3

description: Gene expression data from IFNAR1ko mice


title: hasmc_celecoxib_tp8hr_biological rep2


title: hasmc_celecoxib_tp2hr_biological rep4

description: Pretreatment with celecoxib, sampled after 2 h IL-1beta exposure

source_name: human aortic smc, 2hr celecoxib exposure, 2 hr IL-1beta exposure


title: hasmc_celecoxib_tp24hr_biological rep2


title: hasmc_celecoxib_tp8hr_biological rep4


title: USP18 ko repl.2

description: Gene expression data from USP18ko mice


title: hasmc_celecoxib_tp2hr_biological rep3


title: USP18ko:IFNARko repl.1


title: hasmc_celecoxib_tp8hr_biological rep1


title: forelimb T28 replicate 8

city: Lexington

first: Stephen

middle: Randal

last: Voss

state: KY

address: 675 Rose Street

department: Biology

institute: University of Kentucky

description:
Gene expression data from 1.0mm distal tip of heterogeneous tissue from axolotl limb amputated at mid zeugopod 28 days post amputation.
CF22

hyb_protocol: Affymetrix Gene Chip 3'IVT Reagent Kit was used according to manufacturer's instructions.

scan_protocol: Affymetrix Command Console was used according to manufacturer's instructions

data_processing: RMA was performed in Affymetrix Expression Console.

organism: Ambystoma mexicanum

source_name: 1.0mm distal tip of regenerating axolotl limb amputated at mid zeugopod at T28

label_protocol: Biotinylation was carried out according to the instructions in Affymetrix's 3'IVT Reagent Kit user's manual

growth_protocol: Animals were maintained at 17-18C and fed California blackworms once a week.  Rearing water (40% modified Holtfretter's solution) was changed three times per week.

extract_protocol: RNA was extracted using Trizol Reagent

treatment_protocol: Axolotols were anesthetized in 0.01% benzocaine and sterile razor blades were used to perform amputations.

tag: time (dpa)

tag: amputation site

value: mid zeugopod


title: forelimb T28 replicate 9

description:
Gene expression data from 1.0mm distal tip of heterogeneous tissue from axolotl limb amputated at mid zeugopod 28 days post amputation.
CF25


title: forelimb T28 replicate 6

description:
Gene expression data from 1.0mm distal tip of heterogeneous tissue from axolotl limb amputated at mid zeugopod 28 days post amputation.
CF07


title: WT repl. 3

description: Gene expression data from wildtype mice

source_name: total brain lysate from wildtype mice

value: WT


title: forelimb T28 replicate 4

description:
Gene expression data from 1.0mm distal tip of heterogeneous tissue from axolotl limb amputated at mid zeugopod 28 days post amputation.
BLP43


title: forelimb T28 replicate 3

description:
Gene expression data from 1.0mm distal tip of heterogeneous tissue from axolotl limb amputated at mid zeugopod 28 days post amputation.
BLP38


title: forelimb T28 replicate 5

description:
Gene expression data from 1.0mm distal tip of heterogeneous tissue from axolotl limb amputated at mid zeugopod 28 days post amputation.
BLP48


title: USP18 ko repl.1

description: Gene expression data from USP18ko mice


title: forelimb T28 replicate 7

description:
Gene expression data from 1.0mm distal tip of heterogeneous tissue from axolotl limb amputated at mid zeugopod 28 days post amputation.
CF16


title: hasmc_celecoxib_tp2hr_biological rep2

value: male

value: white


title: WT repl. 2

description: Gene expression data from wildtype mice


title: hasmc_celecoxib_tp2hr_biological rep1

value: aortic smooth muscle cell

value: primary cell


title: forelimb T28 replicate 1

description:
Gene expression data from 1.0mm distal tip of heterogeneous tissue from axolotl limb amputated at mid zeugopod 28 days post amputation.
BLP8


title: forelimb T28 replicate 2

description:
Gene expression data from 1.0mm distal tip of heterogeneous tissue from axolotl limb amputated at mid zeugopod 28 days post amputation.
BLP11