title: RU_ni

status: Public on May 31 2014

type: RNA

city: Munich

first: Kilian

last: Eyerich

address: Biedersteiner Strasse 29

department: Department of Dermatology and Allergy

country: Germany

institute: Technische Universität München

description: Gene expression

hyb_protocol: Samples were hybridized to a SurePrint G3 Human GE 8X60K BeadChip (Agilent Technologies).

scan_protocol: Fluorescence signals were detected by reading the arrays in the microarray scanner system iScan (Agilent Technology).

data_processing: The Agilent Feature Extraction software was used to read and process microarray image files.

molecule: total RNA

organism: Homo sapiens

source_name: Non-involved skin of healthy individual

label_protocol: Samples were amplified and Cy3 labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions

extract_protocol: Total RNA was isolated with the PAXgene Tissue RNA Kit (Qiagen), according to the manufacturer’s protocol.

treatment_protocol: Clinically non-involved skin was directly investigated without in vitro modifications

tag: tissue

value: Non-involved skin of healthy individual

tag: gender

value: female

tag: age


title: IS_ni

description: Gene expression

source_name: Non-involved skin of lichen planus patient


title: LI_ni reanalysis

description: Gene expression

source_name: Non-involved skin of psoriasis patient

value: Non-involved skin of psoriasis patient


title: UH_ni

description: Gene expression


title: VI_ni reanalysis

description: Gene expression


title: SS2_ni reanalysis

description: Gene expression


title: BS_ni

description: Gene expression


title: FB_ni

description: Gene expression

value: Non-involved skin of lichen planus patient


title: RJ_ni

description: Gene expression


title: KT_ni

description: Gene expression

value: male


title: BA_ni reanalysis

description: Gene expression


title: YH_ni

description: Gene expression


title: KD_ni

description: Gene expression


title: EB_ni

description: Gene expression


title: HK_ni

description: Gene expression


title: Klose_ni reanalysis

description: Gene expression


title: SM_ni reanalysis

description: Gene expression


title: GS_ni

description: Gene expression


title: HEM-15

city: New York

first: Shaghayegh

last: Harbi

country: USA

institute: New York University

description: The cells were flow sorted directly into Miltenyi SuperAmp lysis buffer for SuperAmp preparation kit, and RNA amplification was performed on a global PCR protocol.

hyb_protocol: Cy3-labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent-028004 Whole Human Genome Oligo Microarrays (8x60K) using Agilent's recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

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

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

molecule: polyA RNA

source_name: Hem

label_protocol: 250 ng of each of the amplified cDNAs were used as template for Cy3 labeling, which was performed according to Miltenyi Biotec's undisclosed protocol.

extract_protocol: SuperAmplification was performed according to Miltenyi Biotec's undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

treatment_protocol: Cell samples were lysed using SuperAmp Lysis Buffer following manufacturer's instructions.

tag: cell type

value: primary IH


title: HEM-19


title: HEM-HETERO-4

source_name: Hem-hetero


title: HEM-13


title: BONE MARROW SC

source_name: bone marrow SC

value: primary SC control


title: HEM-17


title: HUVEC

source_name: HUVEC

value: primary vascular/endothelial control


title: HEM-HETERO-5


title: HEM-14


title: HEM-16


title: HEM-18


title: HEM-12


title: HEM-5


title: HEM-11


title: GLIOBLASTOMA CSC

source_name: glioblastoma CSC

value: primary CSC control


title: MESENCHYMAL SC

source_name: mesenchymal SC


title: HEM-10


title: HEM-8


title: DRUG HEM 21hr

source_name: drug Hem 21hr


title: DRUG HEM 2hr

source_name: drug Hem 2hr


title: CORD BLOOD SC

source_name: cord blood SC


title: HEM-6


title: HEM-9


title: HEM-7


title: HEM-HETERO-3


title: DRUG HEM HETERO 2hr

source_name: drug Hem-hetero 2hr


title: HEM-3


title: HEM-HETERO-2


title: HEM-HETERO-1


title: HEM-1


title: HEM-4


title: DRUG HEM HETERO 21hr

source_name: drug Hem-hetero 21hr


title: HEM-2


title: A549 cells transfected with miR-509-3p mimic rep2

city: Yongin

first: Young-Chul

last: Choi

state: Gyeonggi-do

address: 1 Seocheon-dong Giheung-gu

country: South Korea

institute: Kyung Hee University

description: 5093_2; test 2

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each human HT-12 expression v.4 bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).   Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the software provided by the manufacturer(Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected probe signal value was transformed by logarithm and normalized by quantile method. The comparative analysis between test group and control group was carried out using LPE test and fold-change. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

label: biotin

source_name: A549_miR-509-3p mimic

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions.

growth_protocol: A549 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol.

treatment_protocol: A549 cells were transfected with miR-509-3p and negative control mimics using Lipofectamine RNAiMAX and total RNA was prepared 24 hours post-transfection.

tag: cell line

value: lung cancer cells

tag: transfected with

value: miR-509-3p mimic


title: A549 cells transfected with miR-509-3p mimic rep1

description: 5093_1; test 1


title: JYH_cgs1_-N2_060m.gpr_1902

city: Singapore

first: Jianhua

last: Liu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: fission yeast log-phase growing kinase mutant cells in minimal medium with nitrogen supplement (0min).

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 or 4.0 analysis software.

data_processing: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.  After background correction and removal of flagged values, features with low intensity (F/B<2 at either 635 or 532 channel) were removed.  Meidans of log base 2 expression ratios were given in the data table.

organism: Schizosaccharomyces pombe

source_name: fission yeast culture of //kinase deletion strain// (OD600 was around 0.3) in Minimal Mediium without nitrogen supplement for 60min or // 60m //

label_protocol: For fluorescence labeling of cDNAs, ~30 micro gramme total RNA was used to synthesize cDNA coupled with amino allyl-dUTP (aa-dUTP) by reverse transcriptase (Superscript-II, Invitrogen, Carlsbad, CA) according to manufacturer¡¯s instruction. cDNA was subsequently washed with Milli-Q water using microcon-YM30 (Millipore, Billerica,MA). ~1.5 micro gramme cDNA was used to couple with Cy5-fluorescence dye for 1 h in dark and purified through a spin column (Qiagen, Hilden, Germany) followed by washing on a micorcon

growth_protocol: Yeast cells were cultivated at 30 degree centigrade.

extract_protocol: Total RNA of cell samples were extracted using a hot phenol protocol describled in materials and metholds.

tag: genotype

value: kinase deletion

source_name: Fission yeast cells

label_protocol: For fluorescence labeling of cDNAs, ~30 micro gramme total RNA was used to synthesize cDNA coupled with amino allyl-dUTP (aa-dUTP) by reverse transcriptase (Superscript-II, Invitrogen, Carlsbad, CA) according to manufacturer¡¯s instruction. cDNA was subsequently washed with Milli-Q water using microcon-YM30 (Millipore, Billerica,MA). ~1.5 micro gramme cDNA was used to couple with Cy3-fluorescence dye for 1 h in dark and purified through a spin column (Qiagen, Hilden, Germany) followed by washing on a micorcon

value: pool of wild type


title: JYH_cyr1_-N2_060m.gpr_1907


title: JYH_rst2_-N2_060m.gpr_1917


title: A549 cells transfected with negative control mimic rep2

description: NC_2; control 2

source_name: A549_negative control mimic

value: negative control mimics


title: JYH_atf1_-N2_060m.gpr_1032


title: JYH_wis4_-N2_060m.gpr_1178


title: JYH_skp1_-N2_060m.gpr_1162


title: JYH_sty1_-N2_060m.gpr_1547


title: JYH_spo4_-N2_060m.gpr_1169


title: JYH_spk1_-N2_060m.gpr_1165


title: JYH_wt_-N2_060m.gpr_1184


title: JYH_spm1_-N2_060m.gpr_1167


title: A549 cells transfected with negative control mimic rep1

description: NC_1; control 1


title: JYH_ssp1_-N2_060m.gpr_1174


title: JYH_win1_-N2_060m.gpr_1549


title: JYH_pap1_-N2_060m.gpr_1138


title: JYH_wis1_-N2_060m.gpr_1176


title: JYH_pck2_-N2_060m.gpr_1143


title: JYH_srk1_-N2_060m.gpr_1172


title: JYH_sck2_-N2_060m.gpr_1156


title: JYH_pka1_-N2_060m.gpr_1148


title: JYH_prk1_-N2_060m.gpr_1152


title: JYH_pit1_-N2_060m.gpr_1145


title: JYH_psk1_-N2_060m.gpr_1154


title: JYH_pck1_-N2_060m.gpr_1141


title: JYH_mph1_-N2_060m.gpr_1134


title: JYH_mde3_-N2_060m.gpr_1128


title: JYH_oca2_-N2_060m.gpr_1136


title: JYH_mik1_-N2_060m.gpr_1542


title: JYH_mak2_-N2_060m.gpr_1124


title: JYH_hri1_-N2_060m.gpr_1118


title: JYH_LKH1_-N2_060m.gpr_1122


title: JYH_dsk1_-N2_060m.gpr_1104


title: JYH_cdr2_-N2_060m.gpr_1084


title: JYH_cds1_-N2_060m.gpr_1086


title: JYH_cki2_-N2_060m.gpr_1094


title: JYH_fin1_-N2_060m.gpr_1106


title: JYH_mak3_-N2_060m.gpr_1126


title: JYH_CP1E11_02_-N2_060m.gpr_1102


title: JYH_CC1919_01_-N2_060m.gpr_1065


title: JYH_hhp1_-N2_060m.gpr_1113


title: JYH_gcn2_-N2_060m.gpr_1108


title: JYH_cki3_-N2_060m.gpr_1096


title: JYH_cek1_-N2_060m.gpr_1088


title: JYH_cmk2_-N2_060m.gpr_1100


title: JYH_cmk1_-N2_060m.gpr_1098


title: JYH_chk1_-N2_060m.gpr_1090


title: JYH_CC24B10_07_-N2_060m.gpr_1068


title: JYH_CC417_06C_-N2_060m.gpr_1071


title: JYH_CC63_08C_-N2_060m.gpr_1075


title: JYH_CC74_03C_-N2_060m.gpr_1079


title: JYH_BC32C12_03C_-N2_060m.gpr_1047


title: JYH_BP23A10_10_-N2_060m.gpr_1536


title: JYH_CC162_10_-N2_060m.gpr_1063


title: JYH_BC336_14C_-N2_060m.gpr_1050


title: JYH_BC337_04_-N2_060m.gpr_1534


title: JYH_byr1_-N2_060m.gpr_1058


title: JYH_BC119_07_-N2_060m.gpr_1034


title: JYH_AC890_03_-N2_060m.gpr_1030


title: JYH_BC18H10_15_-N2_060m.gpr_1043


title: JYH_AC167_01_-N2_060m.gpr_1008


title: JYH_AC29A4_16_-N2_060m.gpr_1018


title: JYH_AC823_03_-N2_060m.gpr_1028


title: JYH_AC3H1_13_-N2_060m.gpr_1024


title: JYH_AC16C9_07_-N2_060m.gpr_1010


title: JYH_AC23H4_02_-N2_060m.gpr_1016


title: JYH_AC2F3_15_-N2_060m.gpr_1022


title: JYH_BC1861_09_-N2_060m.gpr_1040


title: HEM CD105+

source_name: Hem CD105+

value: primary IH endoglin


title: JYH_APB18E9_02C_-N2_060m.gpr_1532


title: JYH_AC2C4_14C_-N2_060m.gpr_1020


title: JYH_AC22G7_08_-N2_060m.gpr_1014


title: JYH_AC15A10_13_-N2_060m.gpr_1006


title: JYH_AC4G8_05_-N2_060m.gpr_1026


title: JYH_pap1_MM.gpr_1137

source_name: fission yeast culture of //kinase deletion strain// (OD600 was around 0.3) in Minimal Mediium with nitrogen supplement  // 0m //


title: JYH_AC12B10_14C_-N2_060m.gpr_1004


title: JYH_rst2_MM.gpr_1914


title: JYH_cgs1_MM.gpr_1899


title: JYH_cyr1_MM.gpr_1904


title: JYH_atf1_MM.gpr_1031


title: JYH_wis1_MM.gpr_1175


title: JYH_AC110_01_-N2_060m.gpr_1002


title: JYH_wis4_MM.gpr_1177


title: JYH_wt_MM_nr2.gpr_1551

description: fission yeast log-phase growing wild type cells in minimal medium with nitrogen supplement (0min).

source_name: fission yeast culture of //wild type strain// (OD600 was around 0.3) in Minimal Mediium with nitrogen supplement  // 0m //

value: wt


title: JYH_win1_MM.gpr_1548


title: 232V

city: Palo Altp

first: Mollie

middle: Elizabeth

last: Jacobs

state: CA

address: 3801 Miranda AVE

department: Medicine

institute: Stanford University

hyb_protocol: Hybridization of labeled RNA to DNA chip, 3D-GeneTM for 16 hrs, 32℃, 250 rpm(Amersham Bioscience) and then hybridized for 17 h at 51C

scan_protocol: Toray 3D-GeneTM Scannerarrays were processed with L Process (Fuji Photo Film)  signal intensities quantified  TIFF images of all DNA chips are quantified using ExtractionTM

data_processing: Signal intensities quantified  TIFF images of all DNA chips are quantified using ExtractionTM

organism: Mus musculus

source_name: mIMCD-3 cells

label_protocol: 500 ng RNA was labeled with miRCURY LNA microRNA Hy5 Power labeling kit (208030-A, Exiqon)

growth_protocol: mIMCD-3 cells were grown in DMEM-F-12 (Genesee Scientific) supplemented with 10% fetal bovine serum (Invitrogen), and 50 µg/ml of gentamycin in T-75 flasks (Genesee Scientific) at 37 °C in 95% air and 5% CO2. 70,000 mIMCD-3 cells were plated in Corning® CoStar® transwell dishes to induce polarity. Cells were grown to confluence, and then the medium was replaced by hormone-free media for 24 hours

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen)

treatment_protocol: The cells were treated with either vehicle (ethanol) or 100nM aldosterone.

tag: agent

value: vehicle (ethanol)


title: JYH_skp1_MM.gpr_1161


title: JYH_sty1_MM.gpr_1546


title: JYH_spk1_MM.gpr_1163


title: 1117P20VEH


title: JYH_ssp1_MM.gpr_1173


title: 120P20VEH


title: 231V


title: JYH_psk1_MM.gpr_1153


title: JYH_srk1_MM.gpr_1170


title: JYH_spo4_MM.gpr_1168


title: JYH_spm1_MM.gpr_1166


title: 232A

value: 100 nM aldosterone


title: 107P19VEH


title: JYH_sck2_MM.gpr_1155


title: JYH_pka1_MM.gpr_1146


title: JYH_prk1_MM.gpr_1151


title: 231A


title: 107P19ALDO


title: JYH_pck1_MM.gpr_1139


title: JYH_pck2_MM.gpr_1142


title: JYH_oca2_MM.gpr_1135


title: 120P20ALDO


title: 1117P20ALDO


title: JYH_mik1_MM.gpr_1541


title: JYH_mph1_MM.gpr_1133


title: JYH_pit1_MM.gpr_1144


title: JYH_mak3_MM.gpr_1125


title: JYH_mde3_MM.gpr_1127


title: JYH_LKH1_MM.gpr_1121


title: JYH_mak2_MM.gpr_1123


title: JYH_hhp2_MM.gpr_1114


title: JYH_hri1_MM.gpr_1116


title: JYH_cmk1_MM.gpr_1097


title: JYH_hhp1_MM.gpr_1112


title: JYH_CP1E11_02_MM.gpr_1101


title: Colonic epithelia Muc2-/- mouse 3

city: Chicago

first: Wancai

last: Yang

state: IL

address: 840 South Wood Street

department: Pathology

institute: University of Illinois at Chicago

description: miRNA expression from Muc2-/- mouse colon

hyb_protocol: About 130 ul of Affymatrix hybridization cocktail buffer (FS450-002) were used for about 18 hours according to the FS450-002 protocl (Affymatrix).

scan_protocol: Affymatrix GeneChip Scanner 3000.

data_processing: Expression Console™ 1.2.0.20

label: FlashTag Biotin HSR

source_name: Mouse colonic epithelia (Muc2-/-)

label_protocol: Total of 200 ng of total RNA were labeled using  FlashTag Biotin HSR according prtotocol (Affymatrix: FlashTag™ Biotin HSR RNA Labeling Kit for Affymetrix® GeneChip® miRNA Arrays)

growth_protocol: Four mice from each genotype group were sacrificed at age of 3 months, and the colonic epithelial cells were isolated using 15 mM EDT buffer.

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

treatment_protocol: Isolated colonic epithelial cells were stored at -80 C degree for RNA extraction.

value: Colonic epithelia

tag: genotype/variation

value: 3 months


title: Colonic epithelia wild-type mouse 1

description: miRNA expression from wild-type mouse colon

source_name: Mouse colonic epithelia (wild-type)

value: wild type


title: JYH_gcn2_MM.gpr_1107


title: Colonic epithelia wild-type mouse 3


title: JYH_fin1_MM.gpr_1105


title: JYH_cmk2_MM.gpr_1099


title: Colonic epithelia wild-type mouse 4


title: JYH_dsk1_MM.gpr_1103


title: Colonic epithelia Muc2-/- mouse 1


title: JYH_cki3_MM.gpr_1095


title: Colonic epithelia Muc2-/- mouse 2


title: Colonic epithelia wild-type mouse 2


title: JYH_hhp2_-N2_060m.gpr_1115


title: Colonic epithelia Muc2-/- mouse 4


title: JYH_cki2_MM.gpr_1093


title: JYH_cek1_MM.gpr_1087


title: JYH_chk1_MM.gpr_1089


title: JYH_cds1_MM.gpr_1085


title: JYH_CC74_03C_MM.gpr_1076


title: JYH_CC24B10_07_MM.gpr_1066


title: JYH_CC417_06C_MM.gpr_1069


title: JYH_CC63_08C_MM.gpr_1072


title: JYH_CC1919_01_MM.gpr_1064


title: JYH_byr1_MM.gpr_1057


title: PBMC885

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

description: Participant

hyb_protocol: for each CpG site there were two allele-specific probes annealing to either the methylated or the unmethylated sequence. Annealed probes are then paired to locus-specific oligos, after which the ligated products are amplified using PCR.

scan_protocol: Plates werescanned using the BeadArray Reader with standard recommended Illumina scanner setting

data_processing: Before analysis, we removed all probes for SNPs and X-chromosome sites. Next, CpG sites where >23 subjects had beta values of zero, as well as sites where >3 subjects had signals below background detection were removed. Lastly, we removed probes with polymorphic CpGs that may interfere with the analysis (Byun et al. 2009).

label: Cy3 and Cy5

molecule: genomic DNA

source_name: peripheral blood mononuclear cell genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from buccal epithelial swabs and peripheral blood mononuclear cells using the Isohelix DNA isolation kit folowing manufacturer's instructions

value: M

tag: ethnicity

value: Caucasian

tag: body mass index

value: peripheral blood mononuclear cell


title: JYH_CC162_10_MM.gpr_1061


title: JYH_BP23A10_10_MM.gpr_1535


title: PBMC887

description: Participant

value: F


title: PBMC890

description: Participant


title: PBMC889

description: Participant

value: Non-caucasian


title: PBMC884

description: Participant


title: JYH_BC337_04_MM.gpr_1533


title: PBMC876

description: Participant


title: PBMC882

description: Participant


title: PBMC881

description: Participant


title: JYH_BC336_14C_MM.gpr_1049


title: JYH_AC3H1_13_MM.gpr_1023


title: JYH_AC4G8_05_MM.gpr_1025


title: JYH_BC1861_09_MM.gpr_1039


title: JYH_APB18E9_02C_MM.gpr_1531


title: JYH_BC119_07_MM.gpr_1033


title: PBMC877

description: Participant


title: JYH_AC2F3_15_MM.gpr_1021


title: JYH_AC823_03_MM.gpr_1027


title: JYH_cdr2_MM.gpr_1083


title: JYH_AC890_03_MM.gpr_1029


title: JYH_AC2C4_14C_MM.gpr_1019


title: JYH_BC32C12_03C_MM.gpr_1046


title: JYH_AC23H4_02_MM.gpr_1015


title: JYH_BC18H10_15_MM.gpr_1042


title: Chip-32, RB_Day16_BlueRep3 & RB_Day14_RedRep3

city: Fargo

first: Munevver

last: Dogramaci

state: ND

address: 1605 Albrecht Blvd N

institute: USDA-ARS

description: See Dogramaci et al. Plant Molecular Biology (2014) for more details.

hyb_protocol: Labeled cDNAs were hybridized to a custom-made 23K element microarray that contained 19,808 UniGenes from a leafy spurge EST database (Anderson et al. 2007) and an additional 4,129 UniGenes from a cassava EST database (Lokko et al. 2007). Comparison of gene expression between samples was accomplished using a rolling circle dye-swap hybridization scheme (Churchill 2002) to provide every biological replicate with technical replicates. In this experiment, each of the biological replicates included two technical replicates.

scan_protocol: Microarray hybridization was visualized using a GenePix 4000B scanner and probe intensities and background were quantified using GenePix 6.0 software (Molecular Devices, Sunnyvale, California, USA).

data_processing: A quality control value of “1” was assigned to all probes that had intensity values greater than 2 times the standard deviation over average of the negative control and empty probe intensities (after deleting 1% of the most intense negative/empty probe values). Intensity values of control spots (a total of 1455 spots including 3X SSC, blanks, and mouse) from MA chips were removed before bioinformatics. In this submission, the original “GPR” files include information for the control spots, while the Sample data tables include information only for the spots that were used for data analyses (a total of: 23937). Raw signal intensities of all DNA-containing spots were up-loaded into the GeneMaths XT 5.1 microarray data analysis program (Applied Maths Inc., Austin, TX, USA) for normalization following the Layer/Normalization/Arrays path with default settings (Offset: Average; Scaling: Standard deviation), and for statistical analysis and clustering of the dataset. Hybridization intensities were log2 transformed, and arrays were centered and normalized against each other; technical replicates within each biological replicate were averaged.

organism: Euphorbia esula

source_name: 16-day dehydration-stressed root buds

label_protocol: For microarray hybridizations, labeled cDNAs were prepared from 30 µg of total RNA using the Alexa Fluor cDNA labeling kit (Invitrogen, Carlsbad, CA, USA) according to manufacturer's protocols.

growth_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype 1984-ND001 and maintained in a greenhouse as described by Anderson and Davis (2004). Shoot cuttings were grown in No. 1 Ray Leach Cone-tainers (Stuewe and Sons Inc. Corvallis, OR, USA) in the greenhouse for three months prior to application of experimental treatments. The greenhouse was set at 25°C with a 16 h:8 h day:night photoperiod. Average daily light fluencies were approximately 350 μmol m-2 s-1 and 400 W high-pressure sodium lamps were used as to extend the day-length.

extract_protocol: At the end of each treatment, crown and root bud samples were collected, flash frozen in liquid N2, and stored at -80°C until RNA extraction. Crown and root bud samples were ground to a fine powder in liquid N2, and total RNA was extracted from approximately one gram of tissue according to the pine tree RNA extraction protocol (Chang et al. 1993). RNA quality and quantity was confirmed by spectrophotometry and agarose gel electrophoresis.

treatment_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype and maintained in a greenhouse. For dehydration studies, water was withheld from paradormant plants for 0, 3, 7, 14, and 21 days, and each treatment included three replicates for crown buds, and two/three replicates for root buds consisting of 40 plants per replicate. Relative water contents of aerial tissue and soil moisture levels were determined as previously described by Doğramacı et al. (2011). At the end of each dehydration treatment crown and root buds were collected from 34 plants, and samples were stored at -80OC. Additionally, at the end of each dehydration treatment,the aerial portions of remining six plants from each replicate were decapitated at the soil surface and vegetative growth from crown buds was monitored under growth-conducive conditions by re-hydrating the root system.

tag: biotype

value: root bud

tag: treatment

value: dehydration stress

tag: treatment time

value: 16 days

source_name: 14-day dehydration-stressed root buds

value: 14 days


title: JYH_AC29A4_16_MM.gpr_1017

value: kinase deletion

value: pool of wild type


title: PBMC874

description: Participant


title: PBMC875

description: Participant


title: Chip-31, RB_Day14_BlueRep3 & RB_Day7_RedRep3

source_name: 7-day dehydration-stressed root buds

value: 7 days


title: PBMC871

description: Participant


title: PBMC870

description: Participant


title: JYH_AC22G7_08_MM.gpr_1013


title: Chip-30, RB_Day7_BlueRep3 & RB_Day3_RedRep3

source_name: 3-day dehydration-stressed root buds

value: 3 days


title: PBMC872

description: Participant


title: Chip-29, RB_Day3_BlueRep3 & RB_Day0_RedRep3

source_name: 0-day dehydration-stressed root buds

value: 0 days


title: Chip-28, RB_Day0_BlueRep3 & RB_Day21_RedRep3

source_name: 21-day dehydration-stressed root buds

value: 21 days


title: JYH_AC16C9_07_MM.gpr_1009


title: JYH_AC167_01_MM.gpr_1007


title: PBMC869

description: Participant


title: PBMC868

description: Participant


title: JYH_AC12B10_14C_MM.gpr_1003


title: JYH_AC15A10_13_MM.gpr_1005


title: Chip-27, CB_Day21_BlueRep3 & CB_Day16_RedRep3

source_name: 21-day dehydration-stressed crown buds

value: crown bud

source_name: 16-day dehydration-stressed crown buds


title: PBMC867

description: Participant


title: Chip-26, CB_Day16_BlueRep3 & CB_Day14_RedRep3

source_name: 14-day dehydration-stressed crown buds


title: #17 skin

city: Silver Spring

first: BIJU

last: ISSAC

state: MD

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

institute: Walter Reed Army Institute of Research

description: SAMPLE 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was Quantile normalized and log2 transformed to median of samples using GeneSpring GX 12.6 software.

label: Biotin

source_name: Skin from DMBA treatment

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

growth_protocol: Mice were maintained by Institutional Animal Care Facility

extract_protocol: Total RNA was extracted with RNeasy Mini kit (Qiagen). RNA quality was analyzed by Bionalyzer RNA 6000 Nano (Agilent Technologies).

treatment_protocol: Dorsal skin 1-2 cm2 of 8-week old mice was shaved. For treatment with DMBA, 10 μg of DMBA in 100 µl of acetone was applied to shaved skin once per week for 18-20 weeks. 100 µl of acetone was applied to control groups.

tag: strain background

value: SKO; Sting -/-

value: 8-week old

value: Dorsal skin

tag: treated with

value: 10 μg of DMBA (in 100 µl of acetone) for 18-20 wks


title: #10 skin tumor

description: SAMPLE 3

source_name: Skin tumor from DMBA treatment

value: WT; Sting +/+


title: #11 skin

description: SAMPLE 4

source_name: Skin treated by acetone

value: 100 µl of acetone (control)


title: STKO_DMBA48

description: SAMPLE 12

data_processing: Data was Quantile normalized and log2 transformed to median of samples using GeneSpring GX 12.6 software

growth_protocol: Mouse embryonic fibroblasts (MEFs) were obtained from e13.5 embryos by a standard procedure and cultured in DMEM with 10% FBS.

extract_protocol: Total RNA was isolated from cells or tissues with RNeasy Mini kit (Qiagen). RNA quality was analyzed by Bionalyzer RNA 6000 Nano (Agilent Technologies).

treatment_protocol: Cells were treated with DMBA at 20 µg/ml for 24 and 48 hours.

value: STKO; Sting -/- Trex1 -/-

tag: developmental stage

value: E13.5 embryos

value: mouse embryonic fibroblast (MEFs)

value: 20 µg/ml DMBA for 48hrs


title: JYH_AC110_01_MM.gpr_1001

source_name: fission yeast culture of //kinase deletion strain// (OD600 was around 0.3) in Minimal Mediium with nitrogen supplement  // 0m //

value: kinase deletion

source_name: Fission yeast cells


title: Chip-23, CB_Day3_BlueRep3 & CB_Day0_RedRep3

source_name: 3-day dehydration-stressed crown buds

tag: tissue

value: dehydration stress

source_name: 0-day dehydration-stressed crown buds


title: Chip-24, CB_Day7_BlueRep3 & CB_Day3_RedRep3

source_name: 7-day dehydration-stressed crown buds

value: 7 days


title: Chip-22, CB_Day0_BlueRep3 & CB_Day21_RedRep3


title: #1 skin

description: SAMPLE 1


title: TKO_DMBA48

description: SAMPLE 10

value: TKO; Sting +/+ Trex1 -/-


title: SKO_DMBA48

description: SAMPLE 11

value: SKO; Sting -/- Trex1 +/+


title: PBMC866

description: Participant

source_name: peripheral blood mononuclear cell genomic DNA

tag: gender

value: F

value: Caucasian

value: peripheral blood mononuclear cell


title: #7 skin tumor

description: SAMPLE 2

tag: age

value: 8-week old


title: PBMC864

description: Participant

value: M

tag: cell type


title: #14 skin

description: SAMPLE 5

value: SKO; Sting -/-

value: Dorsal skin

value: 10 μg of DMBA (in 100 µl of acetone) for 18-20 wks


title: Chip-25, CB_Day14_BlueRep3 & CB_Day7_RedRep3

value: crown bud

value: 14 days


title: STKO_DMBA24

description: SAMPLE 8

value: STKO; Sting -/- Trex1 -/-

value: E13.5 embryos

value: mouse embryonic fibroblast (MEFs)

value: 20 µg/ml DMBA for 24hrs


title: Chip-21, RB_Day21_BlueRep2 & RB_Day16_RedRep2

value: root bud

value: dehydration stress

value: 21 days

source_name: 16-day dehydration-stressed root buds

value: 16 days


title: PBMC861

description: Participant

value: Caucasian


title: PBMC862

description: Participant

value: F

value: peripheral blood mononuclear cell


title: PBMC860

description: Participant

value: Non-caucasian


title: PBMC859

description: Participant

value: M


title: PBMC858

description: Participant


title: TKO_DMBA24

description: SAMPLE 6

value: TKO; Sting +/+ Trex1 -/-


title: Buccal890

description: Participant

source_name: buccal epithelial swab genomic DNA

value: buccal epithelial cell


title: Buccal889

description: Participant


title: Chip-20, RB_Day16_BlueRep2 & RB_Day14_RedRep2

source_name: 14-day dehydration-stressed root buds


title: WT_DMBA48

description: SAMPLE 9

value: WT; Sting +/+ Trex1 +/+

value: 20 µg/ml DMBA for 48hrs


title: Chip-19, RB_Day14_BlueRep2 & RB_Day7_RedRep2

value: 14 days

source_name: 7-day dehydration-stressed root buds

value: 7 days


title: SKO_DMBA24

description: SAMPLE 7

value: SKO; Sting -/- Trex1 +/+

value: E13.5 embryos

value: mouse embryonic fibroblast (MEFs)


title: STKO_DMSO

description: SAMPLE 4

value: STKO; Sting -/- Trex1 -/-

value: DMSO


title: SKO_DMSO

description: SAMPLE 3


title: Chip-12, CB_Day7_BlueRep2 & CB_Day3_RedRep2

value: crown bud

value: dehydration stress

value: 3 days


title: WT_DMBA24

description: SAMPLE 5

value: 20 µg/ml DMBA for 24hrs


title: Chip-16, RB_Day0_BlueRep2 & RB_Day21_RedRep2

source_name: 0-day dehydration-stressed root buds

value: root bud

value: 0 days

source_name: 21-day dehydration-stressed root buds

value: 21 days


title: TKO_DMSO

description: SAMPLE 2

value: TKO; Sting +/+ Trex1 -/-


title: Chip-13, CB_Day14_BlueRep2 & CB_Day7_RedRep2


title: Chip-14, CB_Day16_BlueRep2 & CB_Day14_RedRep2

source_name: 16-day dehydration-stressed crown buds

value: 16 days


title: PBMC857

description: Participant

value: M

value: Caucasian

value: peripheral blood mononuclear cell


title: Chip-18, RB_Day7_BlueRep2 & RB_Day3_RedRep2

value: 7 days

source_name: 3-day dehydration-stressed root buds


title: Buccal885

description: Participant

value: buccal epithelial cell


title: Chip-17, RB_Day3_BlueRep2 & RB_Day0_RedRep2


title: WT_DMSO

description: SAMPLE 1

value: WT; Sting +/+ Trex1 +/+

value: E13.5 embryos

value: mouse embryonic fibroblast (MEFs)


title: Buccal887

description: Participant

value: F


title: Chip-11, CB_Day3_BlueRep2 & CB_Day0_RedRep2

value: crown bud

value: dehydration stress


title: Buccal882

description: Participant


title: Chip-15, CB_Day21_BlueRep2 & CB_Day16_RedRep2

source_name: 21-day dehydration-stressed crown buds


title: Buccal884

description: Participant


title: gpd1 gpd2 expressing rAQP9, stressed with 1M xylitol at 5 min

city: Gothenburg

first: Abraham

last: Ericsson

address: Medicinaregatan 9C

department: Cell and Molecular Biology

country: Sweden

institute: Gothenburg University

description: biological replicate 1 of 3 scan 1

hyb_protocol: Hybridization was performed at 42°C over night. After hybridization, slides were washed sequential.

scan_protocol: Arrays were visualized using a VersArrayChipReader (BioRad). Gene assignment and signal quantification was carried out with ImaGene 6.0 (BioDiscovery, Inc.). A visual scan of each spot was performed to avoid spots expressing abnormal morphology.

data_processing: The microarray data was analyzed using LIMMA package (http://www.bioconductor.org) in the statistical language R (http://www.R-project.org). The data was normalized by subtracting a loess line from the M-value to remove intensity-dependent trends. The genes were ranked by the moderated t-statistic to avoid false positives. Each comparison consists of three independent experiments.

organism: Saccharomyces cerevisiae

label_protocol: Labeled probes were resuspended in DIG Easy Hyb (Roche), heated at 37°C for 30 min and applied to the slide (Yeast 6.4 KB, double-spotted array containing 6240 yeast ORFs, http://microarrays.ca)

growth_protocol: YNB-leu with 2% Glucose

extract_protocol: Total RNA was isolated. 20 µg of total RNA were primed with random primer (Invitrogen) and anchored oligo(dT) (ABgene) and labeled in a reverse transcription reaction with Cy3-dUTP or Cy5-dUTP (Amersham Biosciences), according to standard protocols (http://cmgm.stanford.edu/pbrown).

tag: strain

value: 1M xylitol

tag: time

value: 5 min

tag: expression

source_name: gpd1 gpd2 expressing rAQP9, prior to polyol exposure

value: untreated


title: Buccal877

description: Participant


title: gpd1 gpd2 expressing rAQP9, stressed with 1M sorbitol at 90 min

description: biological replicate 1 of 3 scan 1

value: 1M sorbitol

value: 90 min


title: gpd1 gpd2 expressing rAQP9, stressed with 1M xylitol at 30 min

description: biological replicate 1 of 3 scan 1

value: 30 min


title: Buccal876

description: Participant


title: Buccal875

description: Participant

value: Non-caucasian


title: gpd1 gpd2 expressing rAQP9, stressed with 1M sorbitol at 60 min

description: biological replicate 1 of 3 scan 1

value: 60 min


title: Chip-8, RB_Day16_BlueRep1 & RB_Day14_RedRep1

value: root bud

value: 16 days

value: 14 days


title: gpd1 gpd2 expressing rAQP9, stressed with 1M sorbitol at 30 min

description: biological replicate 1 of 3 scan 1


title: Chip-7, RB_Day14_BlueRep1 & RB_Day21_RedRep1

value: 21 days


title: Chip-10, CB_Day0_BlueRep2 & CB_Day21_RedRep2

value: 0 days


title: Buccal881

description: Participant

value: Caucasian

value: buccal epithelial cell


title: gpd1 gpd2 expressing rAQP9, stressed with 1M xylitol at 20 min

description: biological replicate 1 of 3 scan 1

value: 20 min


title: Buccal871

description: Participant

value: F


title: Chip-9, RB_Day21_BlueRep1 & RB_Day16_RedRep1

value: dehydration stress


title: Buccal874

description: Participant


title: gpd1 gpd2 expressing rAQP9, stressed with 1M xylitol at 10 min

description: biological replicate 1 of 3 scan 1

value: 1M xylitol

value: 10 min


title: Buccal872

description: Participant

value: M


title: Chip-5, CB_Day16_BlueRep1 & CB_Day14_RedRep1

value: crown bud

source_name: 14-day dehydration-stressed crown buds


title: Chip-3, CB_Day7_BlueRep1 & CB_Day3_RedRep1

value: 7 days

value: 3 days


title: gpd1 gpd2 expressing rAQP9, stressed with 1M sorbitol at 20 min

description: biological replicate 1 of 3 scan 1

value: 1M sorbitol

value: untreated


title: Chip-6, CB_Day21_BlueRep1 & CB_Day16_RedRep1

value: 16 days


title: Chip-4, CB_Day14_BlueRep1 & CB_Day7_RedRep1

value: 14 days


title: gpd1 gpd2 expressing rAQP9, stressed with 1M sorbitol at 10 min

description: biological replicate 1 of 3 scan 1


title: gpd1 gpd2 expressing rAQP9, stressed with 1M sorbitol at 5 min

description: biological replicate 1 of 3 scan 1

value: 5 min


title: gpd1 gpd2 expressing rAQP9, stressed with 1M glycerol at 20 min

description: biological replicate 1 of 3 scan 1

value: 1M glycerol


title: Buccal869

description: Participant

value: Caucasian


title: Buccal870

description: Participant

value: Non-caucasian

value: buccal epithelial cell


title: Buccal868

description: Participant


title: gpd1 gpd2 expressing rAQP9, stressed with 1M glycerol at 10 min

description: biological replicate 1 of 3 scan 1


title: gpd1 gpd2 expressing rAQP9, stressed with 1M erythritol at 20 min

description: biological replicate 1 of 3 scan 1

value: 1M erythritol

value: 20 min


title: Chip-2, CB_Day3_BlueRep1 & CB_Day0_RedRep1

value: dehydration stress

value: 0 days


title: gpd1 gpd2 expressing rAQP9, stressed with 1M erythritol at 10 min

description: biological replicate 1 of 3 scan 1

value: 10 min


title: Chip-1, CB_Day0_BlueRep1 & CB_Day21_RedRep1

value: crown bud

value: 21 days


title: Buccal867

description: Participant

value: F


title: Buccal862

description: Participant


title: Buccal866

description: Participant


title: Buccal864

description: Participant

value: M


title: Buccal860

description: Participant


title: gpd1 gpd2 expressing rAQP9, stressed with 1M glycerol at 5 min

description: biological replicate 1 of 3 scan 1

value: untreated


title: Buccal861

description: Participant


title: Sample 3 Twin_01 at relapse

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000

data_processing: The data were normalized using RMA, R bioconductor (v.2.14.1).

source_name: JMML_Twin01 at relapse

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 500ng of total RNA (3'IVT Express Protocol, Affymetrix, Santa Clara, CA, USA).

growth_protocol: No growth protocols were used

extract_protocol: Total RNA with Trizol protocol

treatment_protocol: Fresh Bone Marrow  and Peripheral Blood cells

tag: disease

value: Juvenile Myelomonocytic Leukemia (JMML)

value: Peripheral Blood cells


title: Buccal858

description: Participant


title: Buccal857

description: Participant


title: Sample 2 Twin_02 at dignosis

source_name: JMML_Twin02 at diagnosis

value: Bone Marrow cells


title: Buccal859

description: Participant


title: gpd1 gpd2 expressing rAQP9, stressed with 1M erythritol at 5 min

description: biological replicate 1 of 3 scan 1

value: 5 min


title: Sample 1 Twin_01 at diagnosis

source_name: JMML_Twin01 at diagnosis


title: Low photosynthetic rate gene pool,L_F,biological rep3

city: Beijing

first: Bowen

last: Wang

address: Beijing Forest University

country: China

institute: Beijing Forest University

description:
Expression data from two years old leaves of F1 interspecific population
Leaves from 5 low photosynthetic rate individuals.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: (Populus alba x Populus glandulosa) x Populus tomentosa

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: A total of 1200 progeny, which were randomly selected from the F1 interspecific population of 5000 pedigree, were used in this study. They established by controlled crossing between two elite poplar parents, the female hybrid clone “YX01” (P. alba × P. glandulossa) and the male clone “LM50” (P. tomentosa). The progeny was grown in Xiao Tangshan horticulture fields of Beijing Forestry University, Beijing, China (40°2′N, 115°50′E), using a randomized complete block design with three replications in 2008.

extract_protocol: Total RNA was extracted using the Plant Qiagen RNAeasy kit (Qiagen China, Shanghai) according to the manufacturer’s instructions. Each replicate mixed RNA extractions of 5 individuals to equal quantities (2 mg) for later microarray analysis. All the RNA samples including every individual and the mixed integrities were examined by Agilent 2100 Bioanalyzer (Agilent Technologies, USA) according to the manufacturer’s instructions, and no evidence of degradation was noted. They subsequently were reverse transcribed into cDNA utilizing the SuperScript First-Strand Synthesis system and the supplied polythymine primers (Invitrogen).

treatment_protocol: Photosynthetic characteristics was collected from fully expanded leaves using the LI-6400 portable photosynthesis system (Li-Cor Inc., Lincoln, NE, USA) at 9:00–11:30 on sunny days. Three functional leaves, the fourth to sixth counting from the individual stem head of all of the population were measured. According to the average of the data, fifty individuals which the value was in the peak were measured again to ensure the phenotype was stable. Among them leaves from thirty samples including fifteen individuals of high and fifteen individuals of low photosynthetic rate were selected to construct gene pool and immediately placed into liquid nitrogen in the field and stored at -80°C until used for isolating RNA.

value: leaves

tag: phenotype

value: low photosynthetic rate

tag: genotype

value: F1 interspecific population (the female hybrid clone “YX01” (P. alba × P. glandulossa) and the male clone “LM50” (P. tomentosa))


title: CCLP1 cells_scrambled control

city: New Orleans

first: Tong

last: Wu

state: Louisiana

address: 1430 TULANE AVE SL-79

department: Pathology and Laboratory Medicine

institute: TULANE UNIVERSITY

description: scrambled control CCLP-1

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner.

data_processing:
Data was extracted using Agilent Feature Extraction software. Normalization was performed using Agilent GeneSpring GX 11.5.1 software. Further data analysis was performed using Agilent GeneSpring GX 11.5.1 software.
To identify differentially expressed genes, we performed a Fold Change filtering between two samples. The default threshold is Fold Change>=2.0.

source_name: CCLP-1 cells

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies)

growth_protocol: DMEM medium contaning 10% heat-inactivated fetal bovine serum,the cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Cellular total RNA was prepared using Trizol reagent (Invitrogen)  following the manufacturer's recommendations.The integrity of RNA can be assessed by electrophoresis on a denaturing agarose gel. Intact total RNA run on a denaturing gel will have sharp 28S and 18S rRNA bands (eukaryotic samples). The 28S rRNA band should be approximately twice as intense as the 18S rRNA band. This 2:1 intensity ratio indicates that the RNA is intact. The NanoDrop ND-1000 was used for accurately measuring RNA concentrations (OD260), protein contamination (ratio of OD260/OD280) and organic compound contamination (ratio of OD260/OD230).  Total RNA with OD260/OD280 ratio higher than 1.8.

tag: cell line


title: Low photosynthetic rate gene pool,L_D,biological rep1

source_name: Leaves from 5 low photosynthetic rate individuals.


title: Low photosynthetic rate gene pool,L_E,biological rep2


title: High photosynthetic rate gene pool,H_B,biological rep2

description:
Expression data from two years old leaves of F1 interspecific population
Leaves from 5 high photosynthetic rate individuals.

value: high photosynthetic rate


title: CCLP-1 cells_miR-17-92 cluster

description: miR-17-92 cluster overexpression CCLP-1


title: High photosynthetic rate gene pool,H_C,biological rep3

source_name: Leaves from 5 high photosynthetic rate individuals.


title: CW vs OW (in autumn), Rep2 (Dye swap)

status: Public on May 30 2014

city: Canberra

first: Xinguo

last: Li

state: ACT

address: Building 602, Black Mountain Laboratories

department: Plant Industry

country: Australia

institute: CSIRO

hyb_protocol: Labelled cDNA was hybridised using the radiata pine 18K cDNA microarrays developed in CSIRO Plant Industry. Slides were placed in water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS) at 42 °C, 0.1x SSC (+0.1 % SDS), 0.1x SSC and 0.01x SSC at room temperature, each for 5 min prior to drying and scanning.

scan_protocol: Hybridized microarray slides were scanned using GenePix Personal 4100A microarray scanner (Axon Instruments, CA). Image pre-processing was performed using GenePix® Pro 6.0 and Acuity software (Axon Instruments, CA).

data_processing: Data analysis was carried out using GEPAS v3.1. The mean values from each channel were log2 transformed and normalized using print-tip lowess and slide scale normalization.

label: Alexa Fluor 647

organism: Pinus radiata

label_protocol: Equal amounts of total RNA (20 µg) extracted from the underside and upperside branches were reversely transcribed using Superscript reverse transcriptase, and then were used to generate fluorescently labelled cDNA using Alexa Fluor® 555-aha-dUTP and Alexa Fluor® 647-aha-dUTP, following the protocol of the SuperScriptTM Plus Direst cDNA Labelling System (Invitrogen, CA).

growth_protocol: Radiata pine trees used for microarray experiment were selected from a commercial plantation located at Bondo, NSW, Australia (35º 16' 44.04 S, 148º 26' 54.66 E). These trees were 13 years old. The plantation was in normal growth conditions without disease infection.

extract_protocol: Developing xylem tissues were ground and total RNA was extracted using the method of Chang et al (1993) with a slight modification

treatment_protocol: Six trees with well-developed branches were selected from a radiata pine commercial plantation (aged 13 years) located at Bondo, NSW, Australia (35º 16' 44.04 S, 148º 26' 54.66 E). The largest branch from each tree was further selected for sampling, including three branches sampled in April 2007 (autumn in Bondo) and three sampled in October 2007 (spring). Bark was removed from the base part (about 10 cm in length) of each branch. Developing xylem tissues were scraped from the exposed upperside and underside surface respectively with a sharp chisel. Samples were immediately placed into 50 ml BD FalconTM tubes filled with liquid nitrogen. Gene expression in the underside and upperside of branches was compared using radiata pine cDNA microarrays.

value: Opposite Wood (OW)

label: Alexa Fluor 555

value: Compression Wood (CW)


title: CW vs OW (in autumn), Rep3


title: High photosynthetic rate gene pool,H_A,biological rep1


title: CW vs OW (in autumn), Rep3 (Dye swap)


title: CW vs OW (in autumn), Rep2


title: CW vs OW (in spring), Rep3 (Dye swap)


title: CW vs OW (in autumn), Rep1


title: CW vs OW (in spring), Rep1


title: Sample 102

city: Seoul

first: Seon Young

last: Kim

address: 101 Daehak-ro, Jongno-gu,

institute: Seoul National University College of Medicine

hyb_protocol: Automatic Verigene instrument.  Gold nanoparticles are functionalized with target DNA-specific oligonucleotide probes and mixed with genomic DNA from samples.  Gold nanoparticle-targetDNA duplexes hybridize with target-specific capture oligonucleotides, each in a separate spot on the microarray.  Gold nanoparticles are coated with silver to amplify signal.

scan_protocol: Verigene Reader used to scan microarray.  Signal strength on the spots is proportional to the concentration of target DNA in the sample.

data_processing: Scatter signal intensity after illumination at 150 ms exposure without normalization, without transformation. The non-normalized signals form the basis of conclusions in the accompanying manuscript.

label: Silver-enhanced gold nanoparticle

organism: Streptococcus constellatus

source_name: Blood culture

label_protocol: Silver-enhancement of gold nanoparticle probe signals (light scatter).

growth_protocol: Blood culture bottle

extract_protocol: Automatic extractor in Verigene system of genomic DNA

treatment_protocol: Direct testing of culture broth (Standard) or after centrifugation of culture broth (Supernatant)

tag: gram status

value: Gram-positive

tag: culture system

value: BacTALERT

value: Standard

tag: source

value: Peripheral blood


title: Sample 103

organism: Streptococcus mitis

tag: treatment


title: Sample 96

organism: Staphylococcus aureus


title: Sample 104

organism: Enterococcus faecalis

value: BACTEC


title: CW vs OW (in spring), Rep2


title: CW vs OW (in spring), Rep1 (Dye swap)


title: CW vs OW (in spring), Rep2 (Dye swap)


title: Sample 101


title: Sample 97

organism: Staphylococcus epidermidis


title: Sample 99

organism: Streptococcus parasanguinis


title: Sample 98


title: Sample 100


title: Sample 105

organism: Enterococcus faecium


title: CW vs OW (in spring), Rep3


title: Sample 95

organism: Streptococcus thermophilus


title: Sample 94


title: Sample 93

organism: Listeria monocytogenes


title: CW vs OW (in autumn), Rep1 (Dye swap)


title: Sample 91


title: Sample 90


title: Sample 87


title: Sample 89


title: Sample 88


title: Sample 92


title: Sample 84


title: Sample 85


title: Sample 86


title: Sample 83


title: Sample 81


title: Sample 80

organism: Klebsiella pneumoniae

value: Gram-negative

value: Supernatant


title: Sample 82


title: Sample 76

organism: Corynebacterium striatum

value: Colony diluent


title: Sample 75


title: Sample 74

organism: Corynebacterium afermentans


title: Sample 73

organism: Bacillus licheniformis


title: Sample 72

organism: Enterococcus gallinarum


title: Sample 68


title: Sample 69


title: Sample 70

organism: Leuconostoc lactis


title: Sample 71


title: Sample 67


title: A01/A03

city: Pullman

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: MxC sample 1 verses control sample 1 is compared to MxC sample 3 verses control sample 3

hyb_protocol: Roche Nimblegen’s Rat DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array which contains three identical sub-arrays, with 720,000 probes per sub-array, scanning a total of 15,287 promoters (3,880 bp upstream and 970 bp downstream from transcription start site).  Probe sizes range from 50-75 bp in length with the median probe spacing of 100 bp. Three different comparative (MeDIP vs. MeDIP) hybridization experiments were performed (3 sub-arrays) for methoxychlor lineage versus control, with each subarray encompassing DNA samples from 6 animals (3 each from methoxychlor and control).

scan_protocol: Scanning and image acquisition was performed in-house by Nimblegen Inc.

data_processing:
The statistical analysis was performed in pairs of comparative IP hybridizations between methoxychlor (M) and controls (C) (e.g. M1-C1 and M2-C2; M1-C1 and M3-C3; M2-C2 and M3-C3). In order to assure the reproducibility of the candidates obtained, the intersection epimutations candidates showing significant changes in all of the single paired comparisons were examined as a having a significant change in DNA methylation between methoxychlor lineage and control lineage. This is a very stringent approach to select for changes, since it only considers repeated changes in all paired analysis. Alternately, the average epimutations obtained through an average of the three experiments (i.e. comparisons) were also examined. Clustered regions of interest were then determined by combining consecutive probes within 600 bases of each other, and based on whether their mean M values were positive or negative, with significance P-values less than 10-5. The statistically significant differential DNA methylated regions were identified and P-value associated with each region presented. Each region of interest was then annotated for gene and CpG content. This list was further reduced to those regions with an average intensity value exceeding 9.5 (log scale) and a CpG density ≥ 1 CpG/100 bp. Processed data files are attached for the intersection epimutation candidates that meet the criteria listed previously.
R-code data processing of raw data as described was used as the basis for conlusions in this study. Value definitions for processed data files: processed data files: #ClusterID = ID and chrolosomal location for cluster of probes showing a significant difference (p<1.0E-5) between red and green channel hybridization (treated vs. control), #Chromosome = Chromosome number, #cSTART = Cluster start site, #cSTOP = Cluster stop site, #meanM = mean log2 intensity ratio (treated vs. control) across all microarray chips for this treatment/control group, #meanA = mean log2 hybridization intensity (both red and green channel) across all microarray chips for this treatment/control group, #minP = p-value for difference between treated and control intensity as calculated by indicated R-code from raw data files.  P-value must be p<1.0E-5 or less for inclusion, #nProbes = number of consecutive probes with p<1.0E-5 included in cluster, #CG = CG content of cluster, #CpG = CpG content of cluster, and #CpGdensity = number of CpGs per hundred base pairs.

organism: Rattus norvegicus

source_name: MeDIP ChIP DNA from F3 methoxychlor

label_protocol: Samples from experimental groups were labeled with Cy3 and MeDIP DNA samples from the control groups were labeled with Cy5

growth_protocol: The F0 generation pregnant females were exposed to a methoxychlor treatment, during days 8 to 14 of gestation. Non-littermate females and males aged 70-90 days from F1 generation of control or methoxychlor lineages were bred to obtain F2 generation offspring. The F2 generation rats were bred to obtain F3 generation offspring.

extract_protocol: DNA was extracted from purified sperm heads from a total of nine F3 generation rats per lineage (control or methoxychlor) that were 120 days of age. Equal concentrations of DNA from three individual sperm samples were used to produce three DNA pools per lineage and employed for chromatin immunoprecipitation of methylated DNA fragments (MeDIP). MeDIP was performed as follows: 6 µg of genomic DNA was subjected to series of three 20 pulse sonications at 20% amplitude and the appropriate fragment size (200–1000 ng) was verified through 2% agarose gels; the sonicated genomic DNA was resuspended in 350 ul TE and denaturated for 10 min at 95°C and then immediately placed on ice for 5 min; 100 ul of 5× IP buffer (50 mM Na-phosphate pH 7, 700 mM NaCl, 0.25% Triton X-100) was added to the sonicated and denatured DNA. An overnight incubation of the DNA was performed with 5 ug of antibody anti-5-methylCytidine monoclonal from Diagenode S.A (Denville, NJ) at 4°C on a rotating platform. Protein A/G beads from Santa Cruz (Santa Cruz, CA) were prewashed on PBS-BSA 0.1% and resuspended in 40 ul 1× IP buffer. Beads were then added to the DNA-antibody complex and incubated 2 h at 4°C on a rotating platform. Beads bound to DNA-antibody complex were washed 3 times with 1 ml 1× IP buffer; washes included incubation for 5 min at 4°C on a rotating platform and then centrifugation at 6000 rpm for 2 min. Beads-DNA-antibody complex were then resuspended in 250 ul digestion buffer (50 mM Tris HCl pH 8, 10 mM EDTA, 0.5% SDS) and 3.5 ul of proteinase K (20 mg/ml) was added to each sample and then incubated overnight at 55°C on a rotating platform. DNA purification was performed first with phenol and then with chloroform:isoamyl alcohol. Two washes were then performed with 70% ethanol, 1 M NaCl and glycogen. MeDIP selected DNA was then resuspended in 30 ul TE buffer.

treatment_protocol: methoxychlor

tag: generation

value: sperm

value: methoxychlor

source_name: MeDIP ChIP DNA from F3 control

treatment_protocol: Control

value: control


title: A02/A03

description: MxC sample 2 verses control sample 2 is compared to MxC sample 3 verses control sample 3


title: A01/A02

description: MxC sample 1 verses control sample 1 is compared to MxC sample 2 verses control sample 2


title: Sample 79

organism: Escherichia coli


title: Sample 66


title: Sample 65

organism: Micrococcus luteus


title: Sample 63


title: Sample 78


title: Sample 64


title: Sample 62


title: Sample 61


title: Sample 59


title: Sample 58


title: Sample 60


title: Sample 55


title: Sample 57


title: Sample 56


title: Sample 54


title: Sample 52

organism: Streptococcus gallolyticus


title: Sample 53


title: Rb;E2f8, DKO  biological rep3

city: Newark

first: Lizhao

address: 205 S Orange Ave

department: Microbiology and Mol. Genetics

institute: Rutgers

description: Gene expression data from sorted Ter19+CD71high spleen cells from Rb;E2f8 KO mouse

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

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

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

organism: Mus musculus

source_name: Rb;E2f8 Mouse spleen Ter19+CD71high sorted cells

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

growth_protocol: Spleen cells were harvested from 3-month old mice.

extract_protocol: RNA was isolated from the sorted Ter119+CD71high population with RNeasy Plus (Qiagen).

treatment_protocol: Ter119+CD71high spleen cells were sorted by FACS.

value: spleen Ter19+CD71high sorted cells

value: Rb;E2f8 KO


title: Sample 51

organism: Streptococcus gordonii


title: Rb KO, biological rep3

description: Gene expression data from sorted Ter19+CD71high spleen cells from Rb KO mouse

source_name: Rb Mouse spleen Ter19+CD71high sorted cells

value: Rb KO


title: Rb;E2f8, DKO  biological rep1


title: Rb KO, biological rep2


title: Rb KO, biological rep1


title: E2f8 KO, biological rep3

description: Gene expression data from sorted Ter19+CD71high spleen cells from E2f8 KO mouse

source_name: E2f8 KO Mouse spleen Ter19+CD71high sorted cells

value: E2f8 KO


title: E2f8 KO, biological rep1


title: E2f8 KO, biological rep2


title: WT, biological rep3

description: Gene expression data from sorted Ter19+CD71high spleen cells from WT mouse

source_name: WT Mouse spleen Ter19+CD71high sorted cells

value: WT


title: Sample 49

organism: Streptococcus dysgalactiae


title: Sample 50

organism: Streptococcus salivarius


title: Rb;E2f8, DKO  biological rep2


title: Sample 48


title: Sample 47


title: Sample 46


title: Sample 45


title: WT, biological rep1


title: WT, biological rep2


title: Control-treatment

city: Buffalo

first: AC

last: CHANG

address: Elm and Carlton

institute: RPCI

description: Control

data_processing: Normalization and data analysis were performed according to the manufacturer’using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php

label: SYBR Green

organism: Homo sapiens

source_name: HMEC cells

label_protocol: SYBR-ROX PCR assays were performed using specific primers for mature miRNAs (SA Biosciences) following the manufacturer’s instructions.

growth_protocol: Primary human mammary epithelial cells (HMECs), purchased from Lonza Inc. were cultured in MEGM Mammary Epithelial Cell Growth Medium.

extract_protocol: Total RNA was extracted by Rneasy mini plus kit followed by Dnase I treatment.

treatment_protocol: HMEC cells were treated with 40mM of Jagged1 active peptide or control peptide (Anaspec) for 24hrs.

value: human mammary epithelial cells


title: JAG1-treatment

description: Test


title: Sample 44

organism: Streptococcus australis

value: Gram-positive


title: blood_postraining_m2

city: Sao Paulo

first: Rodrigo

middle: Gonçalves

last: Dias

state: Sao Paulo

address: Av. Dr. Eneas Carvalho de Aguiar, 44

country: Brazil

institute: Heart Institute (InCor)

hyb_protocol: Affymetrix standard procedure.

scan_protocol: Affymetrix standard procedure.

data_processing: Raw data were preprocessed in R with affy and multtest packages from Bioconductor. Robust Multi-array Average (RMA) algorithm was used for background correction, quantile normalization and median polish summarization. Negative and positive controls were excluded. Differentially expressed transcripts were identified using ANOVA with P<0.05 (ANOVA) and as those with fold change (FC) above 1.3.

source_name: PBMCs at resting state, post-training

label_protocol: Affymetrix standard procedure.

extract_protocol: Total RNA was extracted from peripheral blood mononuclear cells (PBMCs) isolated with Ficoll-Paque and using TRIzol.

treatment_protocol: Fasting blood samples for gene expression measurements at baseline and after the exercise training protocol, 48 hours after the last exercise session.

tag: individual

value: m

value: peripheral blood mononuclear cells

value: male

tag: disease state

value: healthy

value: endurance training protocol

tag: time point

value: post-training

tag: body mass (kg)

tag: peak velocity (mph)

tag: peak inclination (%)

tag: peak duration (%)

tag: peak power (w)

tag: peak hr (bpm)

tag: peak vo2 (l/min)

tag: peak vo2 (ml/kg/min)

tag: peak rr (breaths/min)

tag: peak ve (l/min)

tag: peak rr


title: blood_postraining_h2

value: h

tag: cell type

tag: gender


title: blood_postraining_l2

value: l

tag: treatment


title: blood_postraining_j2

tag: individual

value: j


title: Sample 43

tag: gram status

tag: culture system

value: BACTEC

value: Supernatant

tag: source

value: Colony diluent


title: blood_postraining_k2

value: k

tag: disease state

tag: time point

tag: body mass (kg)

tag: peak velocity (mph)


title: Sample 42

organism: Streptococcus mitis


title: blood_postraining_i2

value: i

tag: peak inclination (%)

tag: peak duration (%)

tag: peak power (w)

tag: peak hr (bpm)


title: blood_postraining_g2

value: g

tag: peak vo2 (l/min)

tag: peak vo2 (ml/kg/min)

tag: peak rr (breaths/min)

tag: peak ve (l/min)


title: Sample 41

organism: Streptococcus constellatus

tag: treatment


title: Sample 40

organism: Streptococcus anginosus

value: BacTALERT


title: blood_postraining_f2

tag: individual

value: f

tag: cell type

tag: gender

tag: peak rr


title: blood_postraining_e2

value: e

tag: disease state


title: blood_postraining_d2

value: d

value: peripheral blood mononuclear cells

tag: time point


title: blood_postraining_a2

value: a

value: male

value: healthy

tag: body mass (kg)


title: blood_postraining_b2

value: b

value: endurance training protocol

value: post-training

tag: peak velocity (mph)


title: Naïve CD4+ T 2

city: Yokohama

first: Takaharu

last: Okada

address: 1-7-22 Suehiro-cho, Tsurumi

department: IMS

country: Japan

institute: RIKEN

hyb_protocol: The labeled cDNA was hybridized with Mouse Genome 430 2.0 Arrays (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Expression values for each probe set were calculated with the GC-RMA method in the GeneSpring GX 7.3 software package.

source_name: Splenocytes from 2 S1pr2V/+ mice immunized with CGG/CFA 10 days before sorting

label_protocol: Biotinylated cRNA were prepared from 20 ng total RNA by using Ovation RNA Amplification System V2 (Nugen) according to the manufacturer's instructions.

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

treatment_protocol: Mice were subcutaneously immunized with CGG in CFA 10 days prior to experiment.

tag: sorting gate

value: CD4+ CD44-low CD62L-high Dump-


title: F480 CD11b P55

city: Madrid

first: Mirna

last: Perez-Moreno

state: Madrid

address: Calle Melchor Fdez Almagro

department: Cancer Cell Biology

country: Spain

institute: CNIO

description: Gene expression at different age

hyb_protocol: Microarray: Mouse Gene Expression G3 8x60K (Agilent microarray design ID 028005, P/N G4852A)  Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: ~250 ng. Volume: 40 uL. Temperature (ºC): 65. Duration: 40 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 10.7).

data_processing: Raw data files: FeatureExtraction generated Txt files (quantification, background subtraction, annotation and flagging). FE Software performs intra-array Lowess global normalization.

label_protocol: Amount of nucleic acid labeled: 250ng. Commercial Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis. ULS Labeling for Blood, Cells, Tissues or FFPE (with a High Throughput option) version 3.2 kit was used. Recommendations from Sigma-Aldrich for the integration of TransPlex WTA with the Agilent microarray workflow were followed, such as the omission of Cot-1 DNA. Briefly, cDNA is non-enzymatically labeled with ULS technology (Kreatech), in which a platinum dye complexed with either Cy3 or Cy5 fluorophores couples preferentially with guanine molecules of the sample. Labeled samples are purified with gel filtration columns.

extract_protocol: Total RNA fraction. RNA Integrity Numbers were in the range 8,6 to 9,6 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer. Available RNA amounts in the range of 0.05-1 ng were subjected to a preliminary amplification step with a TransPlex Whole Transcriptome Amplification WTA2 kit (Sigma-Aldrich). Optimal cycle number was set at 20, by proceeding 2–3 cycles beyond the amplification “plateau” as observed with real-time qPCR.

value: skin resident macrophages

tag: age

value: postnatal day 55

tag: tissue

value: skin

tag: genetic background


title: F480 CD11b P69

description: Gene expression at different age

value: postnatal day 69


title: PD1-intermediate Th 2

source_name: LN cells from 4 S1pr2V/+ mice immunized with CGG/CFA 10 days before sorting

value: CD4+ CXCR5+ PD1-intermediate CD44-high Dump-


title: Sample 39

tag: gram status

value: Gram-positive

tag: culture system

value: BACTEC

value: Supernatant

tag: source

value: Colony diluent


title: blood_pretraining_m1

source_name: PBMCs at resting state, baseline

value: m

value: peripheral blood mononuclear cells

value: pre-training

tag: peak inclination (%)

tag: peak duration (%)

tag: peak power (w)

tag: peak hr (bpm)

tag: peak vo2 (l/min)

tag: peak vo2 (ml/kg/min)

tag: peak rr (breaths/min)

tag: peak ve (l/min)


title: Sample 38

value: BacTALERT

tag: treatment


title: Naïve CD4+ T 1


title: PD1-low Th 1

source_name: LN cells from 6 S1pr2V/+ mice immunized with CGG/CFA 10 days before sorting

value: CD4+ CXCR5-low PD1-low CD44-high Dump-


title: F480 CD11b P42

description: Gene expression at different age

tag: cell type

value: postnatal day 42


title: PD1-intermediate Th 1

tag: sorting gate


title: blood_postraining_c2

tag: individual

value: c

tag: gender

value: male

tag: disease state

value: healthy

value: endurance training protocol

tag: time point

value: post-training

tag: body mass (kg)

tag: peak velocity (mph)

tag: peak rr


title: Sample 37

organism: Streptococcus agalactiae

tag: gram status

tag: culture system

tag: source


title: Venus-low Tfh 3

value: CD4+ Venus-low CXCR5+ PD1-high CD44-high Dump-


title: Venus-low Tfh 2


title: Sample 36


title: PD1-low Th 2


title: Venus-low Tfh 1


title: blood_pretraining_k1

value: k

tag: peak inclination (%)

tag: peak duration (%)

tag: peak power (w)

tag: peak hr (bpm)

tag: peak vo2 (l/min)


title: Sample 35

value: Gram-positive

tag: treatment

value: Peripheral blood


title: blood_pretraining_j1

value: j

tag: cell type

tag: peak vo2 (ml/kg/min)

tag: peak rr (breaths/min)

tag: peak ve (l/min)


title: blood_pretraining_l1

tag: individual

value: l

tag: gender

tag: disease state

tag: time point


title: Venus-high Tfh 3

tag: sorting gate

value: CD4+ Venus-high CXCR5+ PD1-high CD44-high Dump-


title: Venus-high Tfh 2


title: Venus-high Tfh 1


title: blood_pretraining_i1

value: i

value: peripheral blood mononuclear cells

tag: body mass (kg)

tag: peak velocity (mph)

tag: peak rr


title: Sample 34

organism: Streptococcus pyogenes

tag: gram status

tag: culture system

value: BacTALERT

value: Supernatant

tag: source

value: Colony diluent


title: ComboTreatment_10_TNFR_Ig_and_P2D10_7

city: Cambridge

first: Suzanne

last: Szak

state: MA

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

hyb_protocol: The Mouse 430_2 GeneChip probe arrays were pre-hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol. 15 ug of labeled cRNA was fragmented in 30 uL 1X fragmentation buffer 100 mM KOAc, 30 mM MgOAc at 95°C for 35 minutes. The fragmented labeled cRNA was resuspended in 300 uL 1X hybridization buffer containing 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20, 0.5 mg/mL Aceylated BSA, 0.1 mg/mL herring sperm DNA, control oligo B2, and control transcripts bioB 1.5 pM, bioC 5 pM, bioD 25 pM, and cre 100 pM, and hybridized to Genechip probe arrays according to manufacturer’s protocol (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip probe arrays were scanned using GeneArray Scanner (Hewlett Packard, Corvallis, OR).

data_processing: CEL files were subjected to GC-content-based Robust Multi-array Average (GCRMA) normalization (version 2.20.0).  Expression levels were log (base 2) transformed.  All calculations and analyses were carried out using R (version 2.11.1) and Bioconductor computational tools.  Analyses were applied to discover genes that were differentially expressed between specific sets of tissue.  First, to identify differentially expressed genes between groups of samples, we applied the linear modeling approach (MANOVA) to fit gene expression levels (log2 transformed) according to the defined groups of samples and Bayesian posterior error analysis (limma version 3.4.5).  Genes that exhibited a log-odds score greater than zero and fold change greater then 1.5 were considered significantly different.

label_protocol: Five ug of purified total RNA was used in a 20 uL first strand reaction with 200U SuperScript II (Invitrogen, Carlsbad,CA) and 0.5ug (dT) T7primer [5’GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG(T)24] in 1X first strand buffer (Invitrogen Life Technologies, Carlsbad, CA) with a 42°C incubation for 1 hour. Second strand synthesis was carried out by the addition of 40 U E. coli DNA Polymerase, 2 U E. coli RNase H, 10 U E. coli DNA Ligase in 1X second strand buffer (Invitrogen Life Technologies, Carlsbad, CA) followed by incubation at 16°C for 2 hrs.  The second strand synthesis reaction was purified using the Genechip Sample Cleanup Module according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA). The purified cDNA was amplified using BioArray high yield RNA transcription labeling kit (Enzo Life Sciences, Inc., Parmingdale, NY) according to manufacturer’s protocol to produce 70-120 ?g of biotin labeled cRNA (compliment RNA).

extract_protocol: Mice were sacrificed after colitis induction.  Colons were harvested for total RNA.

tag: strain

value: Balb/c

tag: genotype/variation

value: wild type

tag: injected with

value: trinitrobenzene sulfonic acid (TNBS)

tag: treated with

value: combination of TNFR-Fc (0.3 mg/kg) and anti-TWEAK mP2D10 (10 mg/kg)

tag: tissue

value: colon


title: Sample 33

value: BACTEC

tag: treatment


title: ComboTreatment_10_TNFR_Ig_and_P2D10_6


title: ComboTreatment_10_TNFR_Ig_and_P2D10_8


title: Sample 32

organism: Streptococcus pneumoniae


title: blood_pretraining_h1

tag: individual

value: h

tag: cell type

value: male

value: healthy

value: pre-training

tag: peak inclination (%)

tag: peak duration (%)

tag: peak power (w)

tag: peak hr (bpm)

tag: peak vo2 (l/min)

tag: peak vo2 (ml/kg/min)

tag: peak rr (breaths/min)

tag: peak ve (l/min)


title: ComboTreatment_10_TNFR_Ig_and_P2D10_3


title: ComboTreatment_10_TNFR_Ig_and_P2D10_5


title: ComboTreatment_10_TNFR_Ig_and_P2D10_2


title: P2D10_Comb10_8

value: 10 mg/kg anti-TWEAK mP2D10


title: blood_pretraining_g1

value: g

tag: gender

tag: disease state

tag: time point

tag: body mass (kg)

tag: peak velocity (mph)

tag: peak rr


title: blood_pretraining_f1

value: f

tag: treatment


title: ComboTreatment_10_TNFR_Ig_and_P2D10_1

tag: strain

tag: genotype/variation

tag: injected with

tag: treated with

tag: tissue


title: Sample 29

organism: Staphylococcus haemolyticus

tag: gram status

value: Gram-positive

tag: culture system

tag: source


title: Sample 31

value: BacTALERT

value: Peripheral blood


title: Sample 30

value: Supernatant


title: blood_pretraining_e1

tag: individual

value: e

tag: cell type

value: peripheral blood mononuclear cells

tag: peak inclination (%)

tag: peak duration (%)

tag: peak power (w)

tag: peak hr (bpm)

tag: peak vo2 (l/min)

tag: peak vo2 (ml/kg/min)

tag: peak rr (breaths/min)


title: Sample 28

organism: Staphylococcus saprophyticus

tag: treatment

value: Colony diluent


title: blood_pretraining_b1

value: b

tag: gender

tag: disease state

tag: time point

tag: body mass (kg)

tag: peak velocity (mph)

tag: peak ve (l/min)

tag: peak rr


title: P2D10_Comb10_2

tag: strain

value: Balb/c

tag: genotype/variation

value: wild type

tag: injected with

value: trinitrobenzene sulfonic acid (TNBS)

tag: treated with

tag: tissue

value: colon


title: P2D10_Comb10_3


title: blood_pretraining_d1

tag: individual

value: d

tag: cell type

value: male

value: healthy

tag: peak inclination (%)

tag: peak duration (%)

tag: peak power (w)

tag: peak hr (bpm)


title: P2D10_Comb10_7

value: 10 mg/kg anti-TWEAK mP2D10


title: blood_pretraining_c1

value: c

tag: gender

tag: disease state

tag: treatment

value: pre-training

tag: peak vo2 (l/min)

tag: peak vo2 (ml/kg/min)

tag: peak rr (breaths/min)


title: P2D10_Comb10_6

tag: strain


title: TNFR_Ig_Comb10_8

tag: genotype/variation

value: 0.3 mg/kg TNFR-Ig


title: blood_pretraining_a1

value: a

tag: time point

tag: body mass (kg)

tag: peak velocity (mph)

tag: peak ve (l/min)

tag: peak rr


title: TNFR_Ig_Comb10_7

tag: injected with

tag: treated with

tag: tissue


title: P2D10_Comb10_1


title: TNFR_Ig_Comb10_5


title: TNFR_Ig_Comb10_4


title: ahuCD20_Comb10_IsotypeControlTreatment_8

value: 10 mg/kg control IgG2a mAb (anti-human CD20)


title: TNFR_Ig_Comb10_6


title: Sample 27

tag: gram status

value: Gram-positive

tag: culture system

value: BACTEC

value: Supernatant

tag: source


title: Sample 25

organism: Staphylococcus hominis

value: BacTALERT

tag: treatment

value: Peripheral blood


title: Sample 26

organism: Staphylococcus caprae


title: Sample 23


title: Sample 24

organism: Staphylococcus capitis


title: ahuCD20_Comb10_IsotypeControlTreatment_6

organism: Mus musculus

value: Balb/c

value: wild type


title: Sample 21


title: Disease_No_treat_Comb10_3

value: trinitrobenzene sulfonic acid (TNBS)

value: none (untreated control)

value: colon


title: ahuCD20_Comb10_IsotypeControlTreatment_2


title: ahuCD20_Comb10_IsotypeControlTreatment_7


title: Sample 20


title: KJD+E2F7b+doxorubicin_rep2

city: Brisbane

first: Mehlika

last: Hazar-Rethinam

state: QLD

address: Translational Research Institute, 37 Kent Street, Woolloongabba

institute: The University of Queensland Diamantina Institute

data_processing: The data were log2 transformed and normalised using robust spline normalisation with lumi R package

source_name: cell line

label_protocol: Biotynlated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (illumina) for Illumina Arrays

growth_protocol: KJD and SCC25 cells were maintained in SCC Media, consisting of equal parts DMEM (Invitrogen) and Ham’s F12 Nutrient Mix pH 7.1 (Sigma Aldrich), supplemented with 10 μg/mL gentamycin (Pfizer), 1% v/v penicillin/streptomycin/glutamine (Invitrogen), 5% FBS (Bovogen Biologicals) and 0.43 μg/mL hydrocortisone (Sigma Aldrich). Doxorubicin treated cells were treated with 1µM doxorubicin for 48 hours prior to RNA extraction. 3 µg of E2F7b or pcDNA plasmids were transfected into KJD cells prior to RNA extraction. 40nM of E2F7siRNA or GFP control siRNA were transfected into SCC25 cells prior to RNA extraction.

extract_protocol: RNA was isolated with TRIzol reagent (Life Technologies) and further purified using the RNAeasy mini kit from Qiagen following the manufacturer's protocol. Quality control was performed with Agilent Bioanalyser.

tag: cell line

value: KJD

tag: transformation

value: SV40 virus transformed

tag: cell type

value: epidermal keratinocyte

value: E2F7b + doxorubicin


title: SCC25+E2F7siRNA+doxorubicin_rep2

value: tongue

value: E2F7 siRNA + doxorubicin


title: ahuCD20_Comb10_IsotypeControlTreatment_5

tag: strain

value: 10 mg/kg control IgG2a mAb (anti-human CD20)


title: Sample 22

value: Gram-positive

value: Colony diluent


title: Disease_No_treat_Comb10_2

tag: genotype/variation


title: SCC25+E2F7siRNA+doxorubicin_rep1


title: Naïve_Comb10_NoDisease_NoTreatment_8

value: none (naïve control)


title: ahuCD20_Comb10_IsotypeControlTreatment_1


title: ahuCD20_Comb10_IsotypeControlTreatment_4


title: KJD+E2F7b_rep2


title: KJD+pcDNA3+doxorubicin_rep1

value: pcDNA3 + doxorubicin


title: KJD+E2F7b_rep1


title: Sample 19

organism: Staphylococcus simulans

value: BACTEC

value: Supernatant


title: Naïve_Comb10_NoDisease_NoTreatment_7

value: Balb/c

value: wild type


title: Disease_No_treat_Comb10_1

value: trinitrobenzene sulfonic acid (TNBS)

value: none (untreated control)


title: Disease_No_treat_Comb10_5

value: colon


title: KJD+E2F7b+doxorubicin_rep1

value: KJD

value: SV40 virus transformed


title: Sample 18

organism: Staphylococcus lugdunensis


title: KJD+pcDNA3+doxorubicin_rep2

value: epidermal keratinocyte


title: Naïve_Comb10_NoDisease_NoTreatment_3


title: KJD+pcDNA3_rep2


title: Naïve_Comb10_NoDisease_NoTreatment_5


title: Sample 16

organism: Staphylococcus epidermidis


title: Sample 17


title: Naïve_Comb10_NoDisease_NoTreatment_2


title: Naïve_Comb10_NoDisease_NoTreatment_6


title: ComboTreatment_7_TNFR_Ig_and_P2D10_7

value: combination of TNFR-Fc (0.3 mg/kg) and anti-TWEAK mP2D10 (10 mg/kg)


title: Sample 15

value: BacTALERT

value: Peripheral blood


title: Sample 14

value: Gram-positive


title: KJD+doxorubicin_rep2

organism: Homo sapiens

value: doxorubicin


title: ComboTreatment_7_TNFR_Ig_and_P2D10_8


title: ComboTreatment_7_TNFR_Ig_and_P2D10_5


title: Naïve_Comb10_NoDisease_NoTreatment_1

value: none (naïve control)


title: ComboTreatment_7_TNFR_Ig_and_P2D10_3


title: KJD+pcDNA3_rep1


title: ComboTreatment_7_TNFR_Ig_and_P2D10_4


title: KJD+doxorubicin_rep1


title: Sample 13


title: Sample 12


title: P2D10_Comb7_8

value: 10 mg/kg anti-TWEAK mP2D10


title: SCC25+E2F7siRNA_rep1

value: tongue

value: E2F7 siRNA


title: SCC25+E2F7siRNA_rep2


title: ComboTreatment_7_TNFR_Ig_and_P2D10_2

value: Balb/c


title: P2D10_Comb7_7

value: wild type


title: Sample 11

value: BACTEC

value: Supernatant

value: Colony diluent


title: P2D10_Comb7_6

value: trinitrobenzene sulfonic acid (TNBS)

value: colon


title: SCC25+GFPsiRNA+doxorubicin_rep1

value: epidermal keratinocyte

value: GFP siRNA + doxorubicin


title: P2D10_Comb7_5


title: P2D10_Comb7_3


title: ComboTreatment_7_TNFR_Ig_and_P2D10_1

value: combination of TNFR-Fc (0.3 mg/kg) and anti-TWEAK mP2D10 (10 mg/kg)


title: Sample 9

organism: Staphylococcus aureus

value: BacTALERT

value: Peripheral blood


title: P2D10_Comb7_4


title: TNFR_Ig_Comb7_7

value: 0.3 mg/kg TNFR-Ig


title: P2D10_Comb7_1


title: Sample 10

value: Gram-positive


title: ComboTreatment_7_TNFR_Ig_and_P2D10_6


title: SCC25+GFPsiRNA_rep1

value: GFP siRNA


title: P2D10_Comb7_2

value: 10 mg/kg anti-TWEAK mP2D10


title: TNFR_Ig_Comb7_3


title: SCC25+GFPsiRNA+doxorubicin_rep2

value: tongue


title: TNFR_Ig_Comb10_1

value: Balb/c


title: TNFR_Ig_Comb7_4

value: wild type


title: TNFR_Ig_Comb7_2


title: SCC25+GFPsiRNA_rep2


title: 15hPRRSV+Mhp3

city: Nanjing

first: li

last: bin

state: Jiangsu

address: Zhong-ling street 50

institute: Jiangsu Academy of Agricultural Sciences

description: PRRSV+Mhp

hyb_protocol: These labeled cDNA fragments were hybridized to NimbleGen Porcine Genome Expression Arrays for 16 h at 42uC using the Roche NimbleGen Hybridization System 12.

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.

organism: Sus scrofa

label_protocol: 5 mg cRNA was reverse transcribed to cDNA, fragmented, and then labeled with Cy3-dCTP (GE Healthcare) using Klenow.

growth_protocol: Porcine alveolar macrophages were obtained with consent from one healthy pig (serologically negative for PRRSV, M. hyopneumoniae and porcine circovirus type 2)

treatment_protocol: Cells and tracheal explants from each of the donor pigs were subjected to all treatments. M. hyopneumoniae was inoculated onto the tracheal rings of the appropriate groups 6 h prior to their addition to the PAMs. PAMs from the PRRSV-infected groups were inoculated with PRRSV 1 h prior to the addition of the tracheal rings. The tracheal ring inserts and their supernatants were transferred to the cultured PAMs, and the mixture was incubated at 37°C in 5%CO2 for 6 or 15 hpi prior to harvesting of the PAMs with a cell scraper. The supernatant from the tracheal cultures was dripped through the insert over the PAMs so no cell-to-cell contact between the tracheal rings and PAMs occurred

value: porcine alveolar macrophage

tag: infection

value: PRRSV+Mhp

tag: time point

value: 15 hours


title: Sample 6

value: BACTEC

value: Supernatant

value: Colony diluent


title: Sample 5


title: Sample 7


title: SCC25+doxorubicin_rep2

value: epidermal keratinocyte

value: doxorubicin


title: Sample 8

value: BacTALERT


title: TNFR_Ig_Comb7_5

value: trinitrobenzene sulfonic acid (TNBS)

value: colon


title: TNFR_Ig_Comb7_1

value: 0.3 mg/kg TNFR-Ig


title: ahuCD20_Comb7_IsotypeControlTreatment_8

value: 10 mg/kg control IgG2a mAb (anti-human CD20)


title: Sample 3

value: Gram-positive

value: Peripheral blood


title: Sample 4


title: 15hPRRSV+Mhp2

description: PRRSV+Mhp


title: SCC25_rep2

value: tongue


title: Sample 2


title: 15hPRRSV+Mhp1

description: PRRSV+Mhp


title: Sample 1


title: SCC25+doxorubicin_rep1


title: 15hPRRSV3

description: PRRSV

value: PRRSV


title: SCC25_rep1


title: KJD_rep1

value: KJD

value: SV40 virus transformed


title: ahuCD20_Comb7_IsotypeControlTreatment_5

value: Balb/c

value: wild type


title: ahuCD20_Comb7_IsotypeControlTreatment_3


title: ahuCD20_Comb7_IsotypeControlTreatment_6


title: KJD_rep2


title: ahuCD20_Comb7_IsotypeControlTreatment_7


title: ahuCD20_Comb7_IsotypeControlTreatment_4


title: 15hPRRSV1

description: PRRSV

value: porcine alveolar macrophage

value: 15 hours


title: 15hMhp2

description: Mhp

value: Mhp


title: ahuCD20_Comb7_IsotypeControlTreatment_2


title: ahuCD20_Comb7_IsotypeControlTreatment_1


title: 15hPRRSV2

description: PRRSV


title: 15hMhp1

description: Mhp


title: 15hMhp3

description: Mhp


title: 15hControl3

description: uninfection


title: Naïve_Comb10_NoDisease_NoTreatment_4

value: none (naïve control)

value: none (untreated control)


title: 15hControl2

description: uninfection


title: Disease_No_treat_Comb7_3

value: trinitrobenzene sulfonic acid (TNBS)


title: Disease_No_treat_Comb7_2

value: colon


title: 6hPRRSV+Mhp1

description: PRRSV+Mhp

value: PRRSV+Mhp

value: 6 hours


title: Disease_No_treat_Comb7_1


title: 15hControl1

description: uninfection


title: 6hPRRSV+Mhp3

description: PRRSV+Mhp


title: 6hPRRSV+Mhp2

description: PRRSV+Mhp


title: Disease_No_treat_Comb7_5


title: Y79 cells_normal culture_rep2

first: Jeong Hun

address: 101, Daehak-ro, Jongno-gu

institute: Seoul National University

description: miRNA

hyb_protocol: After purification, labeled samples were resuspended with Gene Expression blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s miRNA Microarray and hybridized for 20 hours at 55°C with 20 RPM rotating in Agilent Hybridization oven (Agilent Technology, USA).

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

data_processing: All data normalization and further analysis were performed using Genowiz 4.0TM (Ocimum Biosolutions, India)

source_name: Y79 cells, normal culture, 24 hours

label_protocol: For control and test RNAs, the synthesis of target miRNA probes and hybridization were performed using Agilent’s miRNA Labeling Reagent and Hybridization kit (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 100 ng of total RNA were dephosphorylated with ~15 Units of calf intestine alkaline phosphatase (CIP), followed by RNA denaturation with ~40% DMSO and 10 min incubation at 100 °C. Dephosphorylated RNA were ligated with pCp-Cy3 mononucleotide and purified with MicroBioSpin 6 columns (Bio-rad, USA).

growth_protocol: Y79 cells were maintained in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% (v/v) penicillin-streptomycin.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA).

treatment_protocol: No additional treatment was performed other than normal culture conditions. Cells were prepared when they reached the concentration of 5 x 10^5 cells/mL.

value: Y79 cell line


title: Y79 cells_normal culture_rep3

description: miRNA


title: PC3 siCARLo-1 v2&4 -2

city: Columbus

first: Taewan

state: OH

institute: The Ohio State University

description:
raw data file: PC3 siCARLo-1 v2&4.txt
nCounter Virtual Cell Cycle Gene Set

hyb_protocol: Hybridization reactions were performed according to manufacturer’s instructions with 5µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 64°C for a minimum of 18 h.

scan_protocol: A high density scan (600 fields of view) was performed

data_processing: The analysis of raw data was performed with nSlover Analysis Software provided by Nanostring Technologies.

source_name: Prostate cancer-derived PC3 cell line

growth_protocol: Cells were grown in 37 degree humidified incubator with 5% CO2.

extract_protocol: Total RNA samples were prepared usin TRIZOL (Invitrogen) in accordance with manufacturer's instruction

treatment_protocol: Cells were transfected with siRNA (Final concentration: 50nM for HCT116 and 100nM for PC3) by using Lipofectamine RNAiMAX from Invitrogen as the instruction of manufacturer

value: Prostate cancer-derived PC3 cell line

value: siRNA targeting CARLo-1 v2&4


title: PC3 siCARLo-1 v2&4 -3


title: 6hMhp3

description: Mhp


title: PC3 siCARLo-1 v2&4 -1


title: 6hPRRSV1

description: PRRSV

value: PRRSV


title: 6hPRRSV3

description: PRRSV


title: PC3 siCTRL-2

description:
raw data file: PC3 siCTRL.txt
nCounter Virtual Cell Cycle Gene Set

hyb_protocol: Hybridization reactions were performed according to manufacturer's instructions with 5µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 64°C for a minimum of 18 h.

scan_protocol: A high-density scan (600 fields of view) was performed.

extract_protocol: Total RNA samples were prepared using TRIZOL (Invitrogen) in accordance with manufacturer's instruction

treatment_protocol: Cells were transfected with siRNA (Final concentration: 50nM for HCT116 and 100nM for PC3) by using Lipofectamine RNAiMAX from Invitrogen as the instruction of manufacturer.

value: control siRNA


title: PC3 siCTRL-3


title: 6hMhp2

description: Mhp


title: HCT116 siCARLo-7 v2 -3

description:
raw data file: HCT116 siCARLo-7 v2.txt
nCounter Virtual Cell Cycle Gene Set

source_name: Colorectal cancer-derived HCT116 cell line

value: siRNA targeting CARLo-7 v2


title: HCT116 siCARLo-7 v2 -2

value: Colorectal cancer-derived HCT116 cell line


title: Y79 cells_normal culture_rep1

description: miRNA


title: HCT116 siCARLo-7 v2 -1


title: 6hPRRSV2

description: PRRSV


title: HCT116 siCARLo-4 -3

description:
raw data file: HCT116 siCARLo-4.txt
nCounter Virtual Cell Cycle Gene Set

value: siRNA targeting CARLo-4


title: HCT116 siCARLo-4 -2


title: 6hMhp1

description: Mhp

value: porcine alveolar macrophage


title: HCT116 siCARLo-4 -1


title: 6hControl2

description: uninfection


title: HCT116 siCARLo-3 -2

description:
raw data file: HCT116 siCARLo-3.txt
nCounter Virtual Cell Cycle Gene Set

value: siRNA targeting CARLo-3


title: HCT116 siCARLo-3 -3


title: HCT116 siCARLo-1 v3 -3

description:
raw data file: HCT116 siCARLo-1 v3.txt
nCounter Virtual Cell Cycle Gene Set

value: siRNA targeting CARLo-1 v3


title: HCT116 siCARLo-1 v3 -2


title: 6hControl1

description: uninfection


title: PC3 siCTRL-1


title: HCT116 siCARLo-3 -1


title: 6hControl3

description: uninfection


title: HCT116 siCARLo-1 v3 -1


title: MS301 periplaque region

city: Lyon

first: Serge

last: Nataf

address: 8 Rue Guillaume Paradin

department: Inserm U1028 - CNRS UMR5292

country: France

institute: Neuroscience Research Center of Lyon

hyb_protocol: Following an Affymetrix protocol, 10 ug of labeled cRNA were fragmented and hybridized on GeneChip Human Genome U133 plus 2.0 array (Affymetrix) during 16 hours at 45°C. Arrays were washed and stained with streptavidin-phycoerythrin (GeneChip Hybridization Wash and Stain kit) in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were read with the GeneChip scanner 3000 7G (Affymetrix).

data_processing: The CEL Files were generated using the Affymetrix GeneChip Command Console (AGCC) software 3.0. Data were normalized using Affymtrix Expression Console software using MAS5 statistical algorithm.

source_name: periplaque region from MS spinal cord 301

label_protocol: Total RNA was triple amplified using an ExpressArt mRNA amplification Pico kit (Amptec GmbH) and biotin-labelled by a round of in vitro transcription using a BioArray HighYield RNA transcript Labeling kit (Enzo Life Sciences) following he manufacturer's protocol.

growth_protocol: Snap frozen spinal cord samples were used.

extract_protocol: RNA extraction were performed using the Rneasy Micro kit (Qiagen).

treatment_protocol: Spinal cord sections were dehydrated and microdissected using the PixCell LCM System (Arcturus)

value: periplaque region from MS spinal cord

tag: organ

value: spinal cord

tag: disease course

value: secondary progressive multiple sclerosis

tag: Sex

value: F

tag: age at death

tag: disease duration


title: MS402 normal appearing white matter

source_name: normal appearing white matter from MS spinal cord 402

tag: tissue

value: M


title: MS301 normal appearing white matter

source_name: normal appearing white matter from MS spinal cord 301


title: MS413 normal appearing white matter

source_name: normal appearing white matter from MS spinal cord 413


title: MS341 periplaque region

source_name: periplaque region from MS spinal cord 341


title: P24

city: Rio de Janeiro

first: Renata

last: Binato

state: Rio de Janeiro

address: Praça Cruz Vermelha 23/ 6 andar ala C

institute: INCA

description: RMA expression value derived from Expression Console software; core-gene analysis

hyb_protocol: The biotinylated cRNA was subsequently hybridized to a GeneChip Human Exon 1.0 ST Array (Affymetrix, CA, USA).

scan_protocol: The GeneChip arrays were washed and stained according to the manufacturer’s protocols and scanned using a GeneChip® Scanner 3000 (Affymetrix)

data_processing: Affymetrix Expression Console Software version 1.0 was used to create summarized expression values (CHP-files). The Robust Multichip Analysis (RMA) algorithm was applied. The data were analyzed with Partek® software (http://www.partek.com). Hierarchical clustering of chip array data was based on the PAM 50 classifier genes

source_name: woman with breast cancer

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: The breast cancer tissues were obtained from patients diagnosed with unilateral primary ductal infiltrative carcinoma of the breast at Instituto do Câncer de Londrina (Londrina, Paraná, Brazil) and Instituto Nacional de Câncer (Rio de Janeiro, Brazil).

extract_protocol: Total RNA from all breast cancer tissues used in this study was obtained using the RNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer's instructions.

value: breast cancer


title: MS403 periplaque region

source_name: periplaque region from MS spinal cord 403


title: MS166 periplaque region

source_name: periplaque region from MS spinal cord 166


title: MS403 normal appearing white matter

source_name: normal appearing white matter from MS spinal cord 403