title: F5H loss function fah-1, biological rep2

city: Denton

first: Lina

last: Gallego-Giraldo

state: Texas

address: 1155 Union Circle #311428

department: Biology

institute: University of north Texas, Biodiscovery Institute

description:
Gene expression data from inflorescence stem
ARABIDOPSIS fah-1-2

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Arabidopsis Genome Array (Affymetrix, http://www.affymetrix.com/) . 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:
Data normalization was conducted using robust multichip average (RMA) (Irizarry et al., 2003). The presence/absence call for each probe set was obtained from dCHIP (Li and Wong, 2001).
Genes with significantly different expression levels between the wild-type control and mutants were selected using associative analysis, as described by Dozmorov and Centola (Dozmorov and Centola, 2003). The type-I family-wise error rate was reduced by using a Bonferroni corrected P-value threshold of 0.05/N, where N represents the number of genes present on the chip. The false discovery rate was monitored and controlled by Q value (false discovery rate), calculated using Extraction of Differential Gene Expression (EDGE, http://www.biostat.washington.edu/software/

organism: Arabidopsis thaliana

source_name: F5H loss function fah-1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seeds were exposed to 4˚C for 2 days and then sown in a seedling mix substrate (Metro-Mix 360, SUN GRO)with controlled fertilizer (20-10-20; 20%N, 10%P2O5 and 20%K2O at the dose 200 ppm per gallon at 21˚C under a 16h-light/8h-dark photoperiod. Light intensity was 110 µmol m-2 s-1, supplied by both incandescent and fluorescent lights.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.RNA was cleaned using the RNA cleanup kit (Qiagen)

treatment_protocol: Stems were harvested, frozen at -80C and grinded

value: inflorescence stem

tag: ecotype

tag: genotype

value: F5H loss function fah-1

value: 1.5 months old plants


title: F5H-OVEREXPRESSION F5H-OE, biological rep3

status: Public on Nov 30 2017

type: RNA

country: USA

description:
Gene expression data from inflorescence stem
ARABIDOPSIS F5H-OE-3

label: biotin

molecule: total RNA

source_name: F5H-OVEREXPRESSION F5H-OE

tag: tissue

tag: age


title: F5H-OVEREXPRESSION F5H-OE, biological rep1

description:
Gene expression data from inflorescence stem
ARABIDOPSIS F5H-OE-1


title: F5H-OVEREXPRESSION F5H-OE, biological rep2

description:
Gene expression data from inflorescence stem
ARABIDOPSIS F5H-OE-2


title: F5H loss function fah-1, biological rep1

description:
Gene expression data from inflorescence stem
ARABIDOPSIS fah-1-1


title: WT STEM, biological rep3

description:
Gene expression data from inflorescence stem
ARABIDOPSIS WT-3

source_name: WT STEM

value: WT


title: WT STEM, biological rep2

description:
Gene expression data from inflorescence stem
ARABIDOPSIS WT-2


title: WT STEM, biological rep1

description:
Gene expression data from inflorescence stem
ARABIDOPSIS WT-1


title: SW_F6789_2

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

country: France

institute: INRA

description: Gene expression in sample from F6789 strain, biological rep 2, at 45 g/L released CO2 in sparking wine medium

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 038619 completed with the regions A, B and C + KHR1 + MPR1 from the new regions of EC1118  (Agilent Technologies, Santa Clara, CA, USA). 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plates were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software Pro7.

data_processing: Data normalization and statistical analysis were performed using the R 3.1.3 software and the limma package. Normalization was done by the quantile method considering all arrays.

organism: Saccharomyces cerevisiae

source_name: Strain F6789_45gCO2_SparkingWine

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific).

growth_protocol: Standard fermentation was conducted using the synthetic fermentation medium SM425 (glucose + fructose, 50 ⁄ 50), buffered to pH 3.3 at 24°C in laboratory-scale fermenters. The population inoculated in every flask was 1.5*106 cell/ml from fresh pre-adapted yeast cultures. Secondary fermentation experiments (sparkling wines) were conducted in a synthetic base wine according to Marti-Raga et al. (2015) with some modifications. It contained 24 g/l of sucrose, ethanol 8% v/v, tartaric acid 4 g/l, L-citric acid 0.5 g/l, malic acid 0.5 g/l, sodium acetate 0.134 g/l, YNB 1.7 g/l, glycerol 4.0 g/l, 0.1% v/v of lipid factors (LF), 0.46 g/l of ammonium chloride and 13.09 ml of aminoacid mix. The ﬁnal pH was adjusted to 3.3. Yeasts were inoculated into adaptation medium at 106 cells/ml and incubated for 4 to 5 days at 28 °C at 150 rpm.

extract_protocol: Total RNA extraction from synthetic medium fermentation were performed with Trizol reagent (Gibco BRL, Life Technologies). Total RNA extraction from sparking wine fermentation were performed using MOBIO RNA Power Soil kit (MO BIO Laboratories, Inc.) according to the manufacturer’s instructions. In both cases, total RNAs were purified by isopropanol precipitation then using RNeasy kit (Qiagen).

treatment_protocol: Cells were sampled during the alcoholic fermentation (45 g of CO2 released). 10^9 cells were pelleted (3000 rpm, 2 min), washed with DEPC-treated water and freezed in methanol at -80°C.

tag: strain

tag: medium

value: Sparking wine


title: P1368_79784_

type: genomic

city: Cologne

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

country: Germany

institute: University of Cologne (UoC), Germany

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Bioinformatics: To globally infer on sCNAs across the T-PLL genome, the T-PLL data sets were compared to the pooled controls (non-tumor hematopoietic cell DNA as ‘germline’ from T-PLL patients, n=13) obtained by the Affymetrix Power Tools, version 1.14.2 with duplicate SNP/CN markers (by identical position) removed. We segmented the called SNP / copy number (CN) markers by the Circular binary segmentation (CBS) algorithm (default options, p<0.01) within the DNAcopy R-package and converted the output files to .seg files to view them in the “Integrative Genome Viewer”. Since the CBS algorithm only reports significantly altered segments/regions and therefore disregards gene structure (perhaps splits them in two or more segments), we mapped regions on gene CDS (based on version 75 of the Ensembl annotation) within the GenomicRanges R package, version 1.16.4, and clustered CNs by gene names and 100kb regions with the gplots R package.
Globally, we identified gains (CN>2.5) in 19,590 genes and losses (CN<1.5) in 27,193 genes (Supplementary Data7). The number of sCNA-affected genes (median 3354) varied inter-individually (e.g. 13,862 in TP038 vs. 42 in TP033).

molecule: genomic DNA

organism: Homo sapiens

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Human T-PLL cells. Sample preparation: DNAs were isolated from PBMCs of T-PLL patients (n=83, >95% purity of T-cells) that included 13 CD4/CD8-enriched/depleted tumor/germline (t/g) pairs (see chapter “Magnetic-bead based cell enrichment” for details on cell purification) using the QIAamp DNA Kit (Qiagen). SNP-array analyses were conducted using Affymetrix SNP 6.0 chips according to manufacturer’s instructions.

tag: phenotype

value: T-PLL

value: POS

value: AWD

tag: pfs

tag: description

tag: cell type

value: T cells


title: P1332_

value: DOD

value: death; relapse or progression; primary treatment failure


title: P1337_

value: alive in ongoing CR or PR

value: late


title: P1339_

source_name: PATIENT_ID: P1339_


title: W5121_


title: P1349_

source_name: PATIENT_ID: P1349_


title: B706_

value: early


title: P1381_

source_name: PATIENT_ID: P1381_


title: W5155_

value: FU


title: P1348_

source_name: PATIENT_ID: P1348_

value: NEG


title: P1096_58342_


title: P1359_

source_name: PATIENT_ID: P1359_


title: P1350_75071_


title: P1345_73001_


title: B5221_


title: P540_

source_name: PATIENT_ID: P540_


title: P1356_76026_


title: P1376_

source_name: PATIENT_ID: P1376_


title: P1367_

source_name: PATIENT_ID: P1367_


title: P1379_

source_name: PATIENT_ID: P1379_


title: P1373_

source_name: PATIENT_ID: P1373_


title: P1377_

source_name: PATIENT_ID: P1377_


title: P1095_


title: P1378_


title: P1371_80278_


title: W5050_


title: P1352_


title: P1375_

source_name: PATIENT_ID: P1375_


title: P1384_093699_


title: P1354_

source_name: PATIENT_ID: P1354_


title: P1360_77051_


title: P1105_


title: P1358_

source_name: PATIENT_ID: P1358_


title: P1383_

source_name: PATIENT_ID: P1383_


title: P1387_


title: P271_

source_name: PATIENT_ID: P271_


title: P119_

source_name: PATIENT_ID: P119_


title: P967_


title: P216_

source_name: PATIENT_ID: P216_295_


title: P543_

source_name: PATIENT_ID: P543_


title: P210_

source_name: PATIENT_ID: P210_

value: DIM


title: P270_

value: HSTL


title: P447_

source_name: PATIENT_ID: P447_438_


title: P1335_


title: P656_

source_name: PATIENT_ID: P656_


title: P703_

source_name: PATIENT_ID: P703_


title: P1329_

source_name: PATIENT_ID: P1329_


title: P1_


title: P1331_

source_name: PATIENT_ID: P1331_


title: 492-001_


title: P626_

source_name: PATIENT_ID: P626_


title: P966_

source_name: PATIENT_ID: P966_957_


title: P1326_69118_


title: P598_ (2)

source_name: PATIENT_ID: P598_

value: replicate


title: P1336_

source_name: PATIENT_ID: P1336_


title: P1264_

source_name: PATIENT_ID: P1264_


title: P1330_

source_name: PATIENT_ID: P1330_


title: P1325_68859_


title: 508-001_


title: 465-002_


title: P1347_


title: 506-002_


title: 469-001_


title: 478-002_


title: 474-001_


title: 05PB2392_1-394_


title: 05PB1069_1-216_


title: 471-002_


title: 06PB1690_LG_02-195_


title: 03PB2939_KMM_01-017_


title: 04PB1398_1-005_


title: 04PB1117_1-009_


title: 05PB4449_1-168_


title: 03PB938_01-454_


title: 02PB2991_EK_01-008_


title: P1298_66897_


title: P1308_67689_


title: 04PB3269_RS_01-195_


title: 01KM3125_1-224_


title: P1265_

value: T-LGL


title: P1277_


title: P573_


title: P1231_

source_name: PATIENT_ID: P1231_


title: 01PB2820_KHD_01-128_


title: P1322_69153_


title: P598_


title: 02PB1148_WH_01-369_


title: P1323_72909_


title: P1210_62122_

value: T-ALL


title: P202_

source_name: PATIENT_ID: P202_


title: P704_

source_name: PATIENT_ID: P704_


title: 03PB2076_FD_01-393_


title: P1172_


title: P528_

source_name: PATIENT_ID: P528_

value: ALCL


title: P1023_

source_name: PATIENT_ID: P1023_

value: T-PLL


title: P1077_

source_name: PATIENT_ID: P1077_

value: POS


title: P1080_

source_name: PATIENT_ID: P1080_

value: AWD


title: N1330_

value: normal B-cells and monozytes; control

value: B cells


title: N1331_


title: P1158_

source_name: PATIENT_ID: P1158_

value: DOD

value: death; relapse or progression; primary treatment failure

value: T cells


title: N1326_69118_

value: alive in ongoing CR or PR


title: N1336_


title: N1325_68859_


title: P1223_

value: late


title: WB-547

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

description: Proband

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array at 50C for 17 hours according to the manufacturer's instructions.

scan_protocol: The array was washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
To achieve comprehensive CNV calling, we used three separate algorithms to detect CNVs: Affymetrix Chromosome Analysis Suite (ChAS), iPattern and GTC. We required CNVs called on the CytoHD platform to be found by at least 2 of the 3 different algorithms.
To achieve comprehensive CNV calling, we used three separate algorithms to detect CNVs: Birdsuite, iPattern and GTC. We required CNVs called on the Affymetrix 6.0 platform to be found by at least 2 of the 3 different algorithms.
affymetrix-array-type = CytoScanHD_Array
affymetrix-algorithm-param-ArraySet = CytoScanHD_Array
program-name = Affymetrix\ChAS\apt-copynumber-cyto-ssa.exe
program-version = 2.4.0

affymetrix-algorithm-name = birdseed-v2
affymetrix-algorithm-version = 2.4
affymetrix-array-type = GenomeWideSNP_6
program-name = apt-probeset-genotype.exe
program-version = 1.15.0

source_name: individual with schizophrenia_Low IQ

extract_protocol: genomic DNA was extracted

tag: gender

value: Male

tag: iq

value: Low IQ

value: Blood


title: N1265_


title: WB-537

description: Proband

source_name: individual with schizophrenia_Average IQ

value: Average IQ


title: WB-549

description: Proband

value: Female


title: N1277_

value: T-LGL

value: normal B-cells and monozytes; control; replicate


title: N1298_66897_

value: T-PLL

value: DIM


title: WB-552

description: Proband


title: P1346_

value: NEG

value: replicate


title: WB-539

description: Proband


title: N1335_

value: normal B-cells and monozytes; control

value: B cells


title: N1322_69153_

value: POS

value: DOD


title: WB-533

description: Proband


title: WB-535

description: Proband


title: WB-532

description: Proband


title: N1231_

value: death; relapse or progression; primary treatment failure


title: WB-548

description: Proband


title: WB-528

description: Proband


title: N1323_72909_


title: WB-531

description: Proband


title: WB-529

description: Proband


title: WB-546

description: Proband


title: WB-524

description: Proband


title: WB-530

description: Proband


title: WB-525

description: Proband


title: WB-523

description: Proband


title: WB-522

description: Proband


title: WB-526

description: Proband


title: N1308_67689_

value: AWD

value: alive in ongoing CR or PR


title: SAL-536

description: Proband

value: Male

value: Saliva


title: WB-534

description: Proband

value: Average IQ

value: Blood


title: WB-515

description: Proband


title: WB-517

description: Proband


title: WB-520

description: Proband


title: WB-516

description: Proband


title: WB-441

description: Proband


title: WB-445

description: Proband

value: Female


title: WB-514

description: Proband


title: WB-519

description: Proband

value: Low IQ


title: WB-521

description: Proband


title: WB-527

description: Proband


title: WB-444

description: Proband


title: SAL-436

description: Proband


title: WB-442

description: Proband


title: WB-513

description: Proband


title: WB-435

description: Proband


title: WB-437

description: Proband


title: SAL-440

description: Proband


title: WB-434

description: Proband


title: WB-438

description: Proband


title: WB-518

description: Proband


title: SAL-433

description: Proband


title: SAL-431

description: Proband


title: SAL-390

description: Proband


title: WB-388

description: Proband


title: SAL-432

description: Proband


title: SAL-387

description: Proband


title: WB-389

description: Proband


title: SAL-386

description: Proband


title: SAL-385

description: Proband


title: SAL-379

description: Proband


title: WB-382

description: Proband


title: WB-383

description: Proband


title: SAL-375

description: Proband


title: SAL-372

description: Proband


title: WB-380

description: Proband


title: SAL-373

description: Proband


title: WB-364

description: Proband


title: WB-376

description: Proband


title: WB-374

description: Proband


title: WB-368

description: Proband


title: WB-378

description: Proband


title: WB-371

description: Proband


title: SAL-381

description: Proband


title: WB-365

description: Proband


title: WB-366

description: Proband


title: WB-362

description: Proband


title: WB-370

description: Proband


title: WB-359

description: Proband


title: WB-360

description: Proband


title: WB-357

description: Proband


title: WB-358

description: Proband


title: WB-355

description: Proband


title: WB-354

description: Proband


title: WB-369

description: Proband


title: WB-353

description: Proband


title: WB-361

description: Proband


title: WB-352

description: Proband


title: WB-356

description: Proband


title: WB-351

description: Proband


title: WB-349

description: Proband


title: WB-363

description: Proband


title: LCL-346

description: Proband

value: LCL


title: WB-347

description: Proband


title: WB-339

description: Proband


title: WB-342

description: Proband


title: WB-348

description: Proband


title: WB-350

description: Proband


title: WB-344

description: Proband


title: SAL-338

description: Proband


title: WB-341

description: Proband


title: WB-336

description: Proband


title: WB-337

description: Proband


title: WB-340

description: Proband


title: WB-335

description: Proband


title: WB-343

description: Proband


title: WB-334

description: Proband


title: WB-330

description: Proband


title: WB-333

description: Proband


title: WB-329

description: Proband


title: WB-325

description: Proband


title: WB-345

description: Proband


title: WB-328

description: Proband


title: WB-332

description: Proband


title: WB-331

description: Proband


title: WB-327

description: Proband


title: WB-321

description: Proband


title: WB-326

description: Proband


title: WB-323

description: Proband


title: WB-320

description: Proband


title: WB-322

description: Proband


title: WB-318

description: Proband


title: WB-324

description: Proband


title: WB-308

description: Proband


title: WB-314

description: Proband


title: WB-307

description: Proband


title: WB-312

description: Proband


title: WB-310

description: Proband


title: WB-315

description: Proband


title: WB-306

description: Proband


title: WB-311

description: Proband


title: WB-319

description: Proband


title: WB-293

description: Proband


title: WB-316

description: Proband


title: WB-317

description: Proband


title: SAL-300

description: Proband


title: WB-305

description: Proband


title: WB-288

description: Proband


title: WB-290

description: Proband


title: WB-303

description: Proband


title: WB-295

description: Proband


title: WB-297

description: Proband


title: WB-301

description: Proband


title: WB-302

description: Proband


title: WB-283

description: Proband


title: SAL-284

description: Proband


title: WB-309

description: Proband


title: WB-313

description: Proband


title: WB-282

description: Proband


title: WB-298

description: Proband


title: WB-272

description: Proband


title: WB-289

description: Proband


title: WB-273

description: Proband


title: WB-275

description: Proband


title: WB-270

description: Proband


title: WB-271

description: Proband


title: WB-266

description: Proband


title: WB-274

description: Proband


title: WB-265

description: Proband


title: WB-277

description: Proband


title: SAL-263

description: Proband


title: SAL-262

description: Proband


title: WB-268

description: Proband


title: WB-259

description: Proband


title: WB-256

description: Proband


title: WB-285

description: Proband


title: WB-260

description: Proband


title: WB-269

description: Proband


title: WB-267

description: Proband


title: WB-255

description: Proband


title: WB-257

description: Proband


title: WB-254

description: Proband


title: WB-251

description: Proband


title: WB-253

description: Proband


title: WB-264

description: Proband


title: WB-245

description: Proband


title: WB-247

description: Proband


title: WB-248

description: Proband


title: WB-250

description: Proband


title: WB-238

description: Proband


title: WB-239

description: Proband


title: WB-243

description: Proband


title: WB-241

description: Proband


title: WB-244

description: Proband


title: WB-242

description: Proband


title: WB-240

description: Proband


title: WB-227

description: Proband


title: WB-249

description: Proband


title: WB-235

description: Proband


title: WB-228

description: Proband


title: WB-229

description: Proband


title: WB-230

description: Proband


title: WB-231

description: Proband


title: WB-232

description: Proband


title: WB-221

description: Proband


title: WB-246

description: Proband


title: WB-236

description: Proband


title: WB-226

description: Proband


title: WB-237

description: Proband


title: WB-225

description: Proband


title: WB-224

description: Proband


title: WB-223

description: Proband


title: WB-219

description: Proband


title: WB-222

description: Proband


title: AIMp1KO BMDC loaded with OVA+SIINFEKL and matured, biological rep 2

city: Houston

first: Dan

last: Liang

address: One baylor plaza, Room N920

department: Pathology and Immunology

institute: Baylor college of medicine

description:
AIMp1KO BMDC 2X loaded-2
Gene expression data

hyb_protocol: The fragmented and labeled sscDNA (5.5 µg) was then hybridized to Affymetrix Mouse Transcriptome 1.0 arrays (MTA 1.0) at 48ºC for 17h and subsequently washed and stained using Affymetrix proprietary reagents in the GeneChip Fluidics Station 450 (FS450).

scan_protocol: GeneChips were scanned in the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: CEL files generated after MTA 1.0 GeneChip scanning were uploaded onto the Expression Console software for analysis with SST-RMA algorithm (Affymetrix).

organism: Mus musculus

source_name: AIMp1KO BMDC, loaded with OVA and SIINFEKL

label_protocol: 100ng of total RNA was used to process the samples for Whole Transcriptome Expression Analysis with the WT Plus reagent kit (Affymetrix). Samples were reversed transcribed to generate amplified, fragmented and biotinylated sense-strand cDNA, according to manufacturer’s instructions.

growth_protocol: Mouse BMDCs were ex vivo differentiated with 20ng/mL GM-CSF and 10ng/mL IL-4 for 6 days prior to treatment.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The concentration of total RNA was assessed using the Nanodrop ND-1000 Spectrophotometer (ThermofisherScientific). Once the sample concentration was determined, the integrity of the total RNA was assessed using the Agilent 2100 Bioanalyzer Nanokit. Samples with a minimum concentration of 33 ng/ul were selected for target preparation using the WT Plus assay (Affymetrix).

treatment_protocol: Mouse BMDCs were unloaded or loaded with 10ug/mL endo-free OVA protein and 10ug/mL SIINFEKL peptide for 3 hours in 5% serum media. Cells were matured with cytokine cocktail (10ng/mL TNFa, 15ng/mL IL-6, 10ng/mL IL-1b, 1ug/mL PGE2) for 48hours prior to harvest.

tag: strain/background

tag: genotype/variation

value: Bone marrow-derived dendritic cells (BMDCs)

tag: antigen

value: OVA+SIINFEKL


title: AIMp1KO BMDC loaded with OVA+SIINFEKL and matured, biological rep 3

description:
AIMp1KO BMDC 2X loaded-3
Gene expression data


title: AIMp1KO BMDC loaded with OVA+SIINFEKL and matured, biological rep 1

description:
AIMp1KO BMDC 2X loaded-1
Gene expression data


title: SAL-217

description: Proband


title: SAL-218

description: Proband


title: AIMp1KO BMDC matured only, biological rep 2

description:
AIMp1KO BMDC Unloaded-2
Gene expression data

source_name: AIMp1KO BMDC, no antigen


title: SAL-220

description: Proband


title: AIMp1KO BMDC matured only, biological rep 3

description:
AIMp1KO BMDC Unloaded-3
Gene expression data


title: AIMp1KO BMDC matured only, biological rep 1

description:
AIMp1KO BMDC Unloaded-1
Gene expression data


title: WB-212

description: Proband


title: WB-211

description: Proband


title: WB-215

description: Proband


title: WB-208

description: Proband


title: WT BMDC loaded with OVA+SIINFEKL and matured, biological rep 2

description:
WT BMDC 2X loaded-2
Gene expression data

source_name: WT BMDC, loaded with OVA and SIINFEKL

value: WT


title: WT BMDC loaded with OVA+SIINFEKL and matured, biological rep 3

description:
WT BMDC 2X loaded-3
Gene expression data


title: WB-204

description: Proband


title: WT BMDC matured only, biological rep 2

description:
WT BMDC Unloaded-2
Gene expression data

source_name: WT BMDC, no antigen


title: WT BMDC loaded with OVA+SIINFEKL and matured, biological rep 1

description:
WT BMDC 2X loaded-1
Gene expression data


title: WT BMDC matured only, biological rep 3

description:
WT BMDC Unloaded-3
Gene expression data


title: WT BMDC matured only, biological rep 1

description:
WT BMDC Unloaded-1
Gene expression data


title: SAL-216

description: Proband


title: SAL-214

description: Proband


title: WB-203

description: Proband


title: SAL-202

description: Proband


title: SAL-201

description: Proband


title: WB-197

description: Proband


title: SAL-200

description: Proband


title: SAL-205

description: Proband


title: SAL-194

description: Proband


title: SAL-199

description: Proband


title: SAL-192

description: Proband


title: SAL-191

description: Proband


title: SAL-209

description: Proband


title: SAL-207

description: Proband


title: WB-210

description: Proband


title: WB-195

description: Proband


title: SAL-188

description: Proband


title: SAL-196

description: Proband


title: WB-193

description: Proband


title: WB-187

description: Proband


title: SAL-190

description: Proband


title: WB-182

description: Proband


title: SAL-198

description: Proband


title: WB-185

description: Proband


title: WB-180

description: Proband


title: SAL-189

description: Proband


title: SAL-183

description: Proband


title: SAL-181

description: Proband


title: WB-571

description: Proband


title: WB-573

description: Proband


title: WB-176

description: Proband


title: SAL-179

description: Proband


title: WB-186

description: Proband


title: WB-576

description: Proband


title: WB-567

description: Proband


title: WB-173

description: Proband


title: WB-570

description: Proband


title: WB-569

description: Proband


title: WB-572

description: Proband


title: WB-206

description: Proband


title: WB-574

description: Proband


title: WB-566

description: Proband


title: WB-174

description: Proband


title: WB-575

description: Proband


title: WB-175

description: Proband


title: WB-172

description: Proband


title: WB-170

description: Proband


title: WB-168

description: Proband


title: WB-568

description: Proband


title: WB-177

description: Proband


title: WB-565

description: Proband


title: WB-560

description: Proband


title: WB-562

description: Proband


title: WB-165

description: Proband


title: WB-167

description: Proband


title: WB-166

description: Proband


title: WB-559

description: Proband


title: WB-164

description: Proband


title: WB-561

description: Proband


title: WB-162

description: Proband


title: SAL-555

description: Proband


title: WB-554

description: Proband


title: WB-158

description: Proband


title: WB-171

description: Proband


title: WB-557

description: Proband


title: WB-161

description: Proband


title: WB-157

description: Proband


title: WB-558

description: Proband


title: WB-160

description: Proband


title: LCL-156

description: Proband


title: SAL-545

description: Proband


title: WB-564

description: Proband


title: WB-159

description: Proband


title: WB-553

description: Proband


title: WB-155

description: Proband


title: WB-544

description: Proband


title: WB-556

description: Proband


title: SAL-154

description: Proband


title: WB-550

description: Proband


title: WB-563

description: Proband


title: LCL-152

description: Proband


title: WB-543

description: Proband


title: LCL-153

description: Proband


title: SAL-148

description: Proband


title: WB-540

description: Proband


title: WB-146

description: Proband


title: LCL-150

description: Proband


title: WB-511

description: Proband


title: WB-542

description: Proband


title: WB-541

description: Proband


title: WB-538

description: Proband


title: WB-512

description: Proband


title: WB-147

description: Proband


title: WB-145

description: Proband


title: WB-507

description: Proband


title: WB-505

description: Proband


title: WB-510

description: Proband


title: WB-508

description: Proband


title: WB-149

description: Proband


title: WB-551

description: Proband


title: WB-151

description: Proband


title: WB-504

description: Proband


title: WB-509

description: Proband


title: WB-140

description: Proband


title: WB-142

description: Proband


title: WB-143

description: Proband


title: WB-144

description: Proband


title: WB-141

description: Proband


title: WB-503

description: Proband


title: WB-506

description: Proband


title: WB-139

description: Proband


title: WB-137

description: Proband


title: WB-501

description: Proband


title: WB-502

description: Proband


title: WB-136

description: Proband


title: WB-138

description: Proband


title: WB-499

description: Proband


title: WB-135

description: Proband


title: WB-132

description: Proband


title: WB-134

description: Proband


title: WB-498

description: Proband


title: WB-496

description: Proband


title: WB-497

description: Proband


title: WB-494

description: Proband


title: WB-133

description: Proband


title: WB-500

description: Proband


title: WB-126

description: Proband


title: WB-490

description: Proband


title: WB-131

description: Proband


title: WB-495

description: Proband


title: WB-128

description: Proband


title: WB-127

description: Proband


title: WB-122

description: Proband


title: SAL-492

description: Proband


title: SAL-123

description: Proband


title: WB-491

description: Proband


title: WB-493

description: Proband


title: WB-120

description: Proband


title: SAL-489

description: Proband


title: WB-487

description: Proband


title: WB-129

description: Proband


title: WB-117

description: Proband


title: WB-486

description: Proband


title: WB-114

description: Proband


title: SAL-482

description: Proband


title: SAL-488

description: Proband


title: WB-121

description: Proband


title: WB-119

description: Proband


title: WB-111

description: Proband


title: WB-118

description: Proband


title: SAL-484

description: Proband


title: WB-478

description: Proband


title: SAL-112

description: Proband


title: WB-109

description: Proband


title: WB-113

description: Proband


title: SAL-481

description: Proband


title: WB-115

description: Proband


title: WB-116

description: Proband


title: WB-107

description: Proband


title: SAL-475

description: Proband


title: WB-108

description: Proband


title: WB-476

description: Proband


title: SAL-477

description: Proband


title: WB-106

description: Proband


title: SAL-479

description: Proband


title: WB-480

description: Proband


title: SAL-474

description: Proband


title: WB-110

description: Proband


title: SAL-471

description: Proband


title: SAL-485

description: Proband


title: WB-105

description: Proband


title: SAL-103

description: Proband


title: WB-104

description: Proband


title: SAL-468

description: Proband


title: WB-483

description: Proband


title: SAL-470

description: Proband


title: WB-472

description: Proband


title: WB-469

description: Proband


title: WB-465

description: Proband


title: WB-473

description: Proband


title: WB-102

description: Proband


title: WB-99

description: Proband


title: WB-100

description: Proband


title: SAL-464

description: Proband


title: WB-98

description: Proband


title: WB-95

description: Proband


title: WB-91

description: Proband


title: SAL-467

description: Proband


title: SAL-462

description: Proband


title: SAL-463

description: Proband


title: WB-90

description: Proband


title: WB-94

description: Proband


title: SAL-89

description: Proband


title: WB-461

description: Proband


title: WB-96

description: Proband


title: WB-466

description: Proband


title: SAL-459

description: Proband


title: WB-88

description: Proband


title: WB-87

description: Proband


title: WB-456

description: Proband


title: WB-455

description: Proband


title: WB-457

description: Proband


title: SAL-84

description: Proband


title: SAL-82

description: Proband


title: SAL-454

description: Proband


title: WB-79

description: Proband


title: SAL-460

description: Proband


title: WB-78

description: Proband


title: WB-93

description: Proband


title: WB-451

description: Proband


title: WB-458

description: Proband


title: WB-453

description: Proband


title: WB-450

description: Proband


title: SAL-74

description: Proband


title: WB-448

description: Proband


title: WB-452

description: Proband


title: SAL-77

description: Proband


title: SAL-449

description: Proband


title: WB-85

description: Proband


title: WB-76

description: Proband


title: WB-71

description: Proband


title: WB-75

description: Proband


title: WB-67

description: Proband


title: WB-69

description: Proband


title: WB-447

description: Proband


title: SAL-439

description: Proband


title: WB-446

description: Proband


title: LCL-66

description: Proband


title: WB-428

description: Proband


title: SAL-430

description: Proband


title: WB-65

description: Proband


title: WB-64

description: Proband


title: SAL-68

description: Proband


title: WB-443

description: Proband


title: WB-429

description: Proband


title: WB-427

description: Proband


title: WB-63

description: Proband


title: WB-426

description: Proband


title: KO_s_dissociation3

city: Kurume

first: Hiroki

last: Aoki

state: Fukuoka

address: 67 Asahimachi

department: Cardiovascular Research Institute

country: Japan

institute: Kurume University

description: aorta, macrophage Socs3 knock-out, s_dissociation, replicate3

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Aortae were obtained from WT or KO mice with or without aortic stress for 7 days. Sham indicate mice treated with physiological saline instead of CaCl2. Intact indicates aorta without morphological changes after 7-day aortic stress. s_dissection indicates aorta with focal medial disruption between celiac trunk and superior mesenteric artery. l_dissection indicates aorta with visible aortic dissection beyond the celiac trunk or superior mesenteric artery.

value: aorta

value: macrophage Socs3 knock-out

tag: condition


title: WB-425

description: Proband


title: WB-61

description: Proband


title: KO_s_dissociation2

description: aorta, macrophage Socs3 knock-out, s_dissociation, replicate2


title: WB-57

description: Proband


title: WB-421

description: Proband


title: SAL-62

description: Proband


title: KO_s_dissociation4

description: aorta, macrophage Socs3 knock-out, s_dissociation, replicate4


title: WB-424

description: Proband


title: WB-422

description: Proband


title: KO_intact7

description: aorta, macrophage Socs3 knock-out, intact, replicate7

value: intact


title: KO_intact6

description: aorta, macrophage Socs3 knock-out, intact, replicate6


title: KO_s_dissociation1

description: aorta, macrophage Socs3 knock-out, s_dissociation, replicate1


title: WB-53

description: Proband


title: KO_intact5

description: aorta, macrophage Socs3 knock-out, intact, replicate5


title: SAL-58

description: Proband


title: WB-419

description: Proband


title: KO_intact4

description: aorta, macrophage Socs3 knock-out, intact, replicate4


title: WB-417

description: Proband


title: WB-51

description: Proband


title: WB-59

description: Proband


title: WB-418

description: Proband


title: KO_intact2

description: aorta, macrophage Socs3 knock-out, intact, replicate2


title: WB-55

description: Proband


title: KO_intact1

description: aorta, macrophage Socs3 knock-out, intact, replicate1


title: WB-415

description: Proband


title: WB-423

description: Proband


title: KO_sham4

description: aorta, macrophage Socs3 knock-out, sham, replicate4

source_name: aorta, macrophage Socs3 knock-out, sham

value: sham


title: WB-420

description: Proband


title: KO_sham2

description: aorta, macrophage Socs3 knock-out, sham, replicate2


title: WB-416

description: Proband


title: KO_intact3

description: aorta, macrophage Socs3 knock-out, intact, replicate3


title: WB-50

description: Proband


title: KO_sham3

description: aorta, macrophage Socs3 knock-out, sham, replicate3


title: WB-56

description: Proband


title: KO_preOPcontrol4

description: aorta, macrophage Socs3 knock-out, replicate4

source_name: aorta, macrophage Socs3 knock-out

value: control


title: WB-48

description: Proband


title: WB-47

description: Proband


title: WB-52

description: Proband


title: KO_preOPcontrol3

description: aorta, macrophage Socs3 knock-out, replicate3


title: KO_sham1

description: aorta, macrophage Socs3 knock-out, sham, replicate1


title: KO_preOPcontrol2

description: aorta, macrophage Socs3 knock-out, replicate2


title: WT_l_dissociation

description: aorta, wild type, I_dissociation

source_name: aorta, wild type, I_dissociation

value: wild type


title: WB-49

description: Proband


title: KO_preOPcontrol1

description: aorta, macrophage Socs3 knock-out, replicate1


title: WT_s_dissociation4

description: aorta, wild type, s_dissociation, replicate4

source_name: aorta, wild type, s_dissociation


title: WB-414

description: Proband


title: WB-46

description: Proband


title: WT_s_dissociation3

description: aorta, wild type, s_dissociation, replicate3


title: WB-411

description: Proband


title: WT_s_dissociation2

description: aorta, wild type, s_dissociation, replicate2


title: WT_s_dissociation1

description: aorta, wild type, s_dissociation, replicate1


title: WT_intact6

description: aorta, wild type, intact, replicate6

source_name: aorta, wild type, intact


title: WB-412

description: Proband


title: WT_intact5

description: aorta, wild type, intact, replicate5


title: WT_intact4

description: aorta, wild type, intact, replicate4


title: WB-45

description: Proband


title: WT_intact3

description: aorta, wild type, intact, replicate3


title: WB-413

description: Proband


title: WB-42

description: Proband


title: WT_intact1

description: aorta, wild type, intact, replicate1


title: WB-44

description: Proband


title: WT_sham4

description: aorta, wild type, sham, replicate4

source_name: aorta, wild type, sham


title: WT_sham2

description: aorta, wild type, sham, replicate2


title: WT_sham3

description: aorta, wild type, sham, replicate3


title: WT_intact2

description: aorta, wild type, intact, replicate2


title: WB-41

description: Proband


title: WB-409

description: Proband


title: WB-39

description: Proband


title: WT_preOPcontrol4

description: aorta, wild type, replicate4

source_name: aorta, wild type


title: WT_sham1

description: aorta, wild type, sham, replicate1


title: WT_preOPcontrol3

description: aorta, wild type, replicate3


title: WB-410

description: Proband


title: WB-40

description: Proband


title: WB-406

description: Proband


title: WB-36

description: Proband


title: WB-407

description: Proband


title: WT_preOPcontrol2

description: aorta, wild type, replicate2


title: WB-408

description: Proband


title: WB-405

description: Proband


title: WB-38

description: Proband


title: WB-34

description: Proband


title: WB-404

description: Proband


title: WB-403

description: Proband


title: WT_preOPcontrol1

description: aorta, wild type, replicate1


title: LCL-30

description: Proband


title: SAL-29

description: Proband


title: WB-402

description: Proband


title: WB-401

description: Proband


title: WB-32

description: Proband


title: WB-400

description: Proband


title: SAL-26

description: Proband


title: WB-398

description: Proband


title: WB-28

description: Proband


title: SAL-394

description: Proband


title: WB-397

description: Proband


title: SAL-395

description: Proband


title: WB-27

description: Proband


title: SAL-25

description: Proband


title: WB-23

description: Proband


title: SAL-392

description: Proband


title: WB-399

description: Proband


title: WB-18

description: Proband


title: SAL-393

description: Proband


title: WB-20

description: Proband


title: WB-396

description: Proband


title: WB-22

description: Proband


title: WB-391

description: Proband


title: WB-384

description: Proband


title: WB-19

description: Proband


title: WB-21

description: Proband


title: LCL-17

description: Proband


title: GPS23504

city: Castanet-Tolosan

first: Nathalie

last: Villa-Vialaneix

address: 24 chemin de Borde-Rouge

department: MIA

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313826

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Porcine GE microarray (8X60K, Design 037880)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min)./µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 INRA Sus scrofa  v1 GE microarray (8X60K, Design 037880) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 softwareMicroarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analThe scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a weight of 1 for 95 out of 118 microarrays or with a weight of 1 in all 24 microarrays from at least one experimental group. At this step, 27838 spots out of 62976 were selected.  The mean signal of the 31 first samples, 32 next, 32 next ones  and 23 last ones were substracted to individuals signals to correct the batch effect of the 4 serials observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 27837 rows each corresponding to a unique ProbeName (provided as data Matrix).yzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 32 out of 40 microarrays or with a minimal weight of 5 per group from at least one experimental group. At this step, 44640 spots out of 61626 were selected.  The mean signal of the 24 first samples and 16 last ones were substracted to individuals signals to correct the batch effect of the 2 serials observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 44639 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Sus scrofa

source_name: Whole blood, 01 h, individual: FR17MAG201313826

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts). Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: To explore individual variation in the biological response to LPS, whole blood from 30 juvenile Large White pigs (8 weeks of age) was collected at 4 time points ( t = 0, +1 h, +4 h, +24 h) for a total of 120 samples. All pigs were females and were raised in two batches. Arrays were designed such that all observations of a single individual were kept on the same array, with two individuals (one from each batch) on one array. This design secured the kinetics of the response for each individual and prevented confounding effects between batch and array. After quality control, all 120 samples were kept for normalization and analyses.

extract_protocol: A total RNA isolation and purification was done according to the manufacturer’s instructions using the Nucleospin RNA Blood kit (Macherey-Nagel, France) followed by DNase treatment. The quality of each RNA sample was checked through the Bioanalyser Agilent 2100 (Agilent Technologies,Massy, France) and low-quality RNA preparations were discarded (RIN < 8).

treatment_protocol: Each animal was injected in the neck muscles with LPS (E. coli serotype 055:B5, Sigma-Aldrich, Saint Quentin Fallavier, FR) at a dose of 15 µg/kg body weight.

tag: breed

value: Large White

value: whole blood

tag: agent

value: LPS injection

tag: individual

tag: time point (h)

value: female


title: GPS23506

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313826

source_name: Whole blood, 24 h, individual: FR17MAG201313826

tag: tissue


title: WB-304

description: Proband

value: Male

value: Blood


title: GPS23505

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313826

source_name: Whole blood, 04 h, individual: FR17MAG201313826


title: SAL-15

description: Proband

value: Female

value: Average IQ

value: Saliva


title: GPS23502

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313788

source_name: Whole blood, 24 h, individual: FR17MAG201313788


title: WB-377

description: Proband


title: KO3

city: Fontenay aux roses

first: Pierre

last: Fouchet

address: 10, route du panorama

institute: CEA

description: Gene expression data from Fancg-/-  E13.5 male Primordial Germ Cells

hyb_protocol: Following fragmentation, 3,6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip MouseGene2.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GC3000 Scanner.

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. CDF file V20 was used for annotation.

source_name: PGCs from KO E13.5 embryos

label_protocol: Biotinylated cDNA were prepared according to the standard Nugen Ovation PicoV2 protocol from 500 pg total RNA.

growth_protocol: og2.fvb.fancg -/- and og2.fvb.fancg +/+ mice were used to sort PGCs

extract_protocol: Cell suspension was analysed by flow cytometry and PGCs sorted according to GFP fluorescence. Sorted  PGC were retrieved in the lysis buffer from the the RNeasy micro kit from Qiagen and RNA repared  according to the manufacturer's instructions

treatment_protocol: Gonads were removed from E13.5 embryos and lysed  5 minutes at 37°C to obtain a single cells suspension, using a dissociation buffer containing PBS1X without Ca2+ and Mg2+, collagenase (final concentration 1 mg/ml), and DNase I (final concentration 0.02 mg/ml).

tag: strain/genotype

value: og2.fvb.fancg -/-

tag: developmental stage

value: male

value: Primordial Germ Cells


title: WB-367

description: Proband

source_name: individual with schizophrenia_Low IQ

value: Low IQ


title: KO2

description: Gene expression data from Fancg-/- E13.5 male Primordial Germ Cells


title: GPS23500

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313788

source_name: Whole blood, 01 h, individual: FR17MAG201313788


title: GPS23501

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313788

source_name: Whole blood, 04 h, individual: FR17MAG201313788


title: WB-299

description: Proband

source_name: individual with schizophrenia_Average IQ


title: WB-14

description: Proband


title: WB-13

description: Proband


title: WB-12

description: Proband


title: GPS23503

description: Gene expression in blood before LPS injection for individual: FR17MAG201313826

source_name: Whole blood, 00 h, individual: FR17MAG201313826


title: GPS23498

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313576

source_name: Whole blood, 24 h, individual: FR17MAG201313576


title: GPS23499

description: Gene expression in blood before LPS injection for individual: FR17MAG201313788

source_name: Whole blood, 00 h, individual: FR17MAG201313788


title: GPS23496

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313576

source_name: Whole blood, 01 h, individual: FR17MAG201313576


title: WT2

description: Gene expression data from WT E13.5 male Primordial Germ Cells

source_name: PGCs from WT E13.5 embryos

value: og2.fvb.fancg +/+


title: GPS23495

description: Gene expression in blood before LPS injection for individual: FR17MAG201313576

source_name: Whole blood, 00 h, individual: FR17MAG201313576


title: WB-11

description: Proband


title: WB-291

description: Proband


title: GPS23493

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313548

source_name: Whole blood, 04 h, individual: FR17MAG201313548


title: WB-9

description: Proband


title: WB-287

description: Proband


title: WB-294

description: Proband


title: GPS23494

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313548

source_name: Whole blood, 24 h, individual: FR17MAG201313548


title: GPS23492

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313548

source_name: Whole blood, 01 h, individual: FR17MAG201313548


title: WT3


title: KO1


title: WB-8

description: Proband


title: GPS23490

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313390

source_name: Whole blood, 24 h, individual: FR17MAG201313390


title: GPS23489

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313390

source_name: Whole blood, 04 h, individual: FR17MAG201313390


title: GPS23491

description: Gene expression in blood before LPS injection for individual: FR17MAG201313548

source_name: Whole blood, 00 h, individual: FR17MAG201313548


title: Sinorhizobium meliloti emmA::Tn5, biological rep3

city: Stanford

first: Melanie

middle: J

last: Barnett

state: CA

address: 371 Jane Stanford Way

institute: Stanford University

hyb_protocol: Four micrograms of biotinylated cDNA was hybridized to each chip at 48 degrees celsius for 16 hours as described by Barnett et al. 2004. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix scanner 3000 7G

data_processing: The data were analyzed using Affymetrix software GCOS v1.4 with Affymetrix default analysis setting and global scaling as the normalization method. The mean target intensity of each array was arbitrarily set to 500. Affymetrix Data Mining Tool v3.1 was used for data mining as previously described by Barnett et al. 2004.

organism: Sinorhizobium meliloti

source_name: wild type strain Rm1021 with a Tn5-110 insertion in emmA (mutant strain)

label_protocol: cDNA was fragmented and biotinylated as described by Barnett et al. 2004.

growth_protocol: Bacteria were cultured in LB medium supplemented with 500 ug/ml streptomycin. Cells were harvested at OD-600 = 0.61 - 0.69

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit with modifications as described by Barnett et al. 2004 Proc Natl Acad Sci USA volume 101 pages 16636 to 16641.

treatment_protocol: Stop solution (5% buffer equilibrated phenol in ethanol) was added to bacterial cultures, at one tenth the culture volume, before centrifugation at 4 degrees celsius. Bacterial cell pellets were frozen in liquid nitrogen and stored at -80 degrees celsius until RNA extraction.

tag: strain


title: GPS23488

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313390

source_name: Whole blood, 01 h, individual: FR17MAG201313390


title: WB-292

description: Proband


title: GPS23485

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313286

source_name: Whole blood, 04 h, individual: FR17MAG201313286


title: GPS23486

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313286

source_name: Whole blood, 24 h, individual: FR17MAG201313286


title: WB-16

description: Proband

source_name: individual with schizophrenia_Low IQ


title: WT1


title: Sinorhizobium meliloti SMb21477::Tn5, biological rep3

source_name: wild type strain Rm1021 with a Tn5-110 insertion in SMb21477 (control strain)


title: Sinorhizobium meliloti SMb21477::Tn5, biological rep1


title: Sinorhizobium meliloti emmA::Tn5, biological rep1


title: K14E6_PDZ.2.

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

description: Gene expression data from skin biopsy of transgenic mouse lacking the PDZ-binding domain

hyb_protocol: The labeled DNA was added to a hybridization cocktail and then the sample was injected into the array (GeneChip Mouse Gene 1.0 ST Array). Washing and staining steps were carried out using GeneChip Fluidics Station 450.

scan_protocol: The probe arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix, Santa Clara CA).

data_processing: Background correction (RMA) and quantile normalization were performed with the affy packages included in Bioconductor of R software. To define significant expression between the biological conditions a moderate T test were computed with limma package implemented in Bioconductor.

source_name: Mus musculus truncated version lacking the PDZ-binding domain

label_protocol: cDNA synthesis, amplification, and gene expression profiling were performed according to the manufacturer´s instructions. Specifically, 1 µg of total RNA was used to generate double-stranded cDNA by reverse transcription using an oligo(dT) primer containing a T7 RNA polymerase promoter followed by an in vitro transcription to obtain cRNA molecules. A second cDNA synthesis was performed incorporating dUTP nucleotides to the newly generated strand. Then, cDNA fragmentation was performed using a combination of uracil DNA glycosylase (UDG) and apurinic/apirymidinic endonuclease 1 (APE1). Following fragmentation, the resulting fragmented DNA was labeled using terminal deoxynucleotidyl transferase (TdT) in the presence of biotinylated nucleotides.

growth_protocol: The construction of transgenic mice expressing the full version of the HPV16-E6 oncogene (K14E6), or the truncated version lacking the PDZ-binding domain (K14E6!146-151) has been described previously (7, 8). The transgenic strains were housed and treated according to the American Association of Laboratory Animal Care (AALAC) regulations, and the research protocol were approved by our internal Research Unit for Laboratory 103! Animal Care Committee (UPEAL-CINVESTAV-IPN, Mexico; NOM-062-ZOO-1999).

extract_protocol: TRIzol method

treatment_protocol: Skin biopsies from the transgenic strains, and FvB/N nontransgenic mice (NTG) were resected and immediately frozen in liquid nitrogen

tag: age

value: 1.5 months-old

tag: sstrain/genotype

value: K14E6delta146-151 (which lacks the PDZ ligand-domain)

value: dorsal skin biopsies


title: K14E6_PDZ.1.


title: WB-286

description: Proband

source_name: individual with schizophrenia_Average IQ


title: Sinorhizobium meliloti SMb21477::Tn5, biological rep2


title: GPS23484

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313286

source_name: Whole blood, 01 h, individual: FR17MAG201313286

value: Large White


title: NTG.2.

description: Gene expression data from skin biopsy of FVB mouse

source_name: Mus musculus FVB

value: FvB/N nontransgenic mice


title: GPS23483

description: Gene expression in blood before LPS injection for individual: FR17MAG201313286

source_name: Whole blood, 00 h, individual: FR17MAG201313286

value: whole blood


title: KD 4 hours_biological rep 3

city: MADRID

first: Teresa

last: Fernandez-Acero

address: PLAZA DE RAMÓN Y CAJAL S/N

department: Departamento de Microbiología II

country: Spain

institute: Facultad de Farmacia UCM

description: All the procedure for microarrays experiments was carried out following the instructions of affymetrix for each of the steps

hyb_protocol: Following affymetrix hybridation instructions

scan_protocol: Following affymetrix scanning instructions

data_processing: CEL files from scaner were analyzed using GCRMA algorithm from Bioconductor software

source_name: yeast

label_protocol: Following affymetrix labelling instructions

growth_protocol: Saccharomyces cerevisiae strain YPH499 was grown overnight in SR and dilluted to 0.3 OD with fresh SR. Cultures were incubated for 4 hours at 30°C.

extract_protocol: Total RNA was isolated from exponentially growing cells by the “mechanical disruption protocol” using the RNeasy kit (Qiagen, Hilden, Germany), following the instructions of the manufacturer. RNA concentrations were determined by measuring absorbance at 260 nm. RNA purity and integrity were assessed using RNA Nano Labchips in an Agilent 2100B Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

treatment_protocol: Galactose was added to the cultures to a final concentration of 2% to induce PI3K-Akt/PI3K-Akt K179M-driven expression.

tag: genetic background

value: PI3K-AKT K179M


title: GPS22973

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313904

source_name: Whole blood, 24 h, individual: FR17MAG201313904

value: LPS injection

tag: gender

value: female


title: Akt 4 hours_biological rep 3


title: KD 4 hours_biological rep 2


title: Sinorhizobium meliloti emmA::Tn5, biological rep2


title: GPS23497

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313576

source_name: Whole blood, 04 h, individual: FR17MAG201313576


title: WB-5

description: Proband

value: Male

tag: iq

value: Blood


title: WB-6

description: Proband

value: Average IQ


title: WB-10

description: Proband


title: K14E6.2.

description: Gene expression data from skin biopsy of transgenic mouse expressing the full version of the HPV16-E6 oncogene.

source_name: Mus musculus expressing the full version of the HPV16-E6 oncogene

value: K14E6 transgenic mice


title: KD 4 hours_biological rep 1


title: GPS22972

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313904

source_name: Whole blood, 04 h, individual: FR17MAG201313904


title: WB-296

description: Proband


title: GPS23487

description: Gene expression in blood before LPS injection for individual: FR17MAG201313390

source_name: Whole blood, 00 h, individual: FR17MAG201313390


title: Akt 4 hours_biological rep 1


title: K14E6.1.


title: NTG.1.


title: Akt 4 hours_biological rep 2


title: HCC827_3D_matrigel.embedding rep2

city: Vienna

first: Thomas

last: Mohr

address: Borschkegasse 8a

department: Institute of Cancer Research

country: Austria

institute: Medical University of Vienna

description: HCC827, matrigel embedded, 3 dimensional

hyb_protocol: 15µg RNA using standard affymetrix protocols

scan_protocol: standard affymetrix protocols

data_processing:
Import into R, RMA normalization using the oligo package, summarization on gene level
RNA Signal estimate from rma normalization (oligo)

label_protocol: MassageAmpII-Biotin enhanced Kit (Ambion, Austin, TX, USA) according to the instructions of the manufacturer

growth_protocol: RPMI1640/McCoy‘s 5A-Glutamax, 10.15% FCS, 2mmol glutamine and antibiotics

extract_protocol: miRNAeasy Kit (Quiagen) according to the instructions of the manufacturer

treatment_protocol: 3D cultures where generated using the hanging drop method (GravyPlus microtissue culture system), Spheroids where embedded into Matrigel (Corning, USA)

tag: cell line

tag: coating

value: MC

tag: dimensionality


title: HCC827_3D_matrigel.embedding rep1


title: SAL-3

description: Proband

value: Female

value: Saliva


title: WB-7

description: Proband


title: HCC827_3D_matrigel.embedding rep3


title: GPS22971

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313904

source_name: Whole blood, 01 h, individual: FR17MAG201313904


title: GPS22967

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313633

source_name: Whole blood, 01 h, individual: FR17MAG201313633


title: GPS22964

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313547

source_name: Whole blood, 04 h, individual: FR17MAG201313547


title: GPS22965

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313547

source_name: Whole blood, 24 h, individual: FR17MAG201313547


title: GPS22966

description: Gene expression in blood before LPS injection for individual: FR17MAG201313633

source_name: Whole blood, 00 h, individual: FR17MAG201313633


title: B6 M TNF vs. B6 M ctrl

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: Whole mouse genome 44k microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSC wash protocol

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and XDR setting using a G2505C DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.9.5.3.1, Agilent). The extracted files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware) and with Gene Spring 12.6.1 software (Agilent Technologies).

source_name: B6 M TNF

label_protocol: RNA labeling was performed with the Quick Amp RNA Fluorescent Linear Amplification Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: Global gene expression analysis was performed in purified CD11b+/ Gr-1 (-) peripheral macrophages from WT and CIAP1 KO mice

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol.

treatment_protocol: CIAP1 WT and KO macrophages were purified and stimulated with TNF for 24h duration

value: macrophages

tag: genotype/variation

value: wild type

tag: treatment

value: TNF

source_name: B6 M ctrl

value: untreated ctrl


title: HCC827_2D_without.coating rep2

description: HCC827, without coating, 2 dimensional

value: control


title: GPS22969

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313633

source_name: Whole blood, 24 h, individual: FR17MAG201313633

tag: breed

value: Large White

tag: agent


title: AML patient sample (AML79)

city: Seattle

first: Pamela

middle: S.

last: Becker

state: WA

address: 1959 NE Pacific St

department: Medicine

institute: University of Washington

description: Gene expression data from human blood tissue with AML

hyb_protocol: Following fragmentation, 11ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Bioconductor/R version of Microarray Suite 5.0 (MAS5.0, the standard Affymetrix algorithm) used by the Affymetrix software suite.

source_name: AML patient from batch 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (GeneChip 3' IVT PLUS Reagent Kit , 2015, Affymetrix).

growth_protocol: Cells were cultured in long term bone marrow media, which has 15% fetal bovine serum, 15% horse serum, 1X Pen-Strep, 5x10-5M of b-Mercaptoethanol and 5x10-5M of Monothioglycerol, plus stem cell growth factor in IMDM.

extract_protocol: Methods for RNA isolation were followed by Qiagen RNeasy Mini kit

treatment_protocol: Cells were cultured on RetroNectin coated plates.

tag: disease state

value: AML

tag: relapse

value: no

tag: cytorisk

value: favorable


title: GPS22962

description: Gene expression in blood before LPS injection for individual: FR17MAG201313547

source_name: Whole blood, 00 h, individual: FR17MAG201313547

tag: tissue

value: whole blood

tag: individual

tag: time point (h)

value: female


title: GPS22963

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313547

source_name: Whole blood, 01 h, individual: FR17MAG201313547

value: LPS injection


title: WB-1

description: Proband

source_name: individual with schizophrenia_Average IQ

value: Male

value: Average IQ

value: Blood


title: B6 M CIAP ctrl vs. B6 M CIAP TNF

source_name: B6 M CIAP ctrl

tag: strain

value: CIAP1 KO

source_name: B6 M CIAP TNF


title: HCC827_2D_without.coating rep3

description: HCC827, without coating, 2 dimensional


title: HCC827_2D_without.coating rep1

description: HCC827, without coating, 2 dimensional


title: B6 M ctrl vs. B6 M TNF


title: AML patient sample (AML51)

tag: age

value: not done

value: adverse


title: WB-2

description: Proband

tag: gender


title: GPS22961

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313449

source_name: Whole blood, 24 h, individual: FR17MAG201313449


title: AML patient sample (AML98)


title: AML patient sample (AML99)


title: B6 M CIAP TNF vs. B6 M CIAP ctrl

value: macrophages


title: AML patient sample (AML13)


title: GPS22960

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313449

source_name: Whole blood, 04 h, individual: FR17MAG201313449


title: GPS22968

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313633

source_name: Whole blood, 04 h, individual: FR17MAG201313633


title: GPS22959

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313449

source_name: Whole blood, 01 h, individual: FR17MAG201313449


title: AML patient sample (AML10)


title: GPS22958

description: Gene expression in blood before LPS injection for individual: FR17MAG201313449

source_name: Whole blood, 00 h, individual: FR17MAG201313449


title: AML patient sample (AML83)

source_name: AML patient from batch 2


title: WB-4

description: Proband

tag: iq


title: AML patient sample (AML86)


title: GPS22956

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313389

source_name: Whole blood, 04 h, individual: FR17MAG201313389


title: GPS22953

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313350

source_name: Whole blood, 24 h, individual: FR17MAG201313350


title: GPS22957

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313389

source_name: Whole blood, 24 h, individual: FR17MAG201313389


title: AML patient sample (AML71)


title: GPS22955

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313389

source_name: Whole blood, 01 h, individual: FR17MAG201313389


title: AML patient sample (AML77)


title: GPS22954

description: Gene expression in blood before LPS injection for individual: FR17MAG201313389

source_name: Whole blood, 00 h, individual: FR17MAG201313389


title: AML patient sample (AML78)


title: GPS22952

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313350

source_name: Whole blood, 04 h, individual: FR17MAG201313350


title: AML patient sample (AML52)

value: yes


title: AML patient sample (AML39)


title: AML patient sample (AML63)


title: AML patient sample (AML62)


title: AML patient sample (AML74)


title: GPS22946

description: Gene expression in blood before LPS injection for individual: FR17MAG201313825

source_name: Whole blood, 00 h, individual: FR17MAG201313825


title: GPS22950

description: Gene expression in blood before LPS injection for individual: FR17MAG201313350

source_name: Whole blood, 00 h, individual: FR17MAG201313350


title: GPS22970

description: Gene expression in blood before LPS injection for individual: FR17MAG201313904

source_name: Whole blood, 00 h, individual: FR17MAG201313904


title: GPS22947

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313825

source_name: Whole blood, 01 h, individual: FR17MAG201313825


title: GPS22949

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313825

source_name: Whole blood, 24 h, individual: FR17MAG201313825


title: AML patient sample (AML69)

description: Gene expression data from human blood tissue with AML

source_name: AML patient from batch 1


title: AML patient sample (AML70)


title: GPS22951

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313350

source_name: Whole blood, 01 h, individual: FR17MAG201313350


title: AML patient sample (AML55)


title: AML patient sample (AML67)


title: AML patient sample (AML12)


title: GPS22948

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313825

source_name: Whole blood, 04 h, individual: FR17MAG201313825


title: AML patient sample (AML76)


title: GPS22944

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313787

source_name: Whole blood, 04 h, individual: FR17MAG201313787


title: AML patient sample (AML68)


title: GPS22940

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313664

source_name: Whole blood, 04 h, individual: FR17MAG201313664


title: age-matched C57BL/6 (wild-type) mice 3

hyb_protocol: As per manufacturer (Affymetrix)

data_processing:
Bioinformatics: Arrays were pre-processed and separately analyzed (‘chronic phase’ vs. ctrl., ‘exponential phase’ vs. ctrl.) with the ‘mouseDivGeno’ R-package.
primary data description: Murine TCL1A-driven T-PLL-like expansions generally revealed a lower sCNA abundance and recurrence (average 70.7 sCNAs in chronic phase (n=3) and 74.8 sCNAs in exponential phase (n=5; CN<1.8 or >2.2)).

extract_protocol: Murine T-cell leukemia. Sample preparation: We hybridized DNA samples (QIAamp DNA Kit, Qiagen) onto the Affymetrix MOUSEDIVm520650 chip. We compared 4 controls (DNA isolated from normal liver tissues of age- and background-matched wild-type mice) to 3 ‘chronic phase’ and 5 ‘exponential phase’ (defining features in 4.2) splenic isolates from T-cell leukemia / lymphoma bearing Lckpr-hTCL1A+/- mice. DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

value: liver

tag: Stage

value: normal

tag: genotype

value: C57BL/6 (wild-type)


title: age-matched C57BL/6 (wild-type) mice 2

source_name: DNA isolated from normal liver tissues of age- and background-matched wild-type mice


title: age-matched C57BL/6 (wild-type) mice 1


title: AML patient sample (AML60)

value: AML


title: GPS22941

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313664

source_name: Whole blood, 24 h, individual: FR17MAG201313664

value: Large White


title: age-matched C57BL/6 (wild-type) mice 4


title: AML patient sample (AML17)

value: no

value: favorable


title: AML patient sample (AML56)


title: GPS22943

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313787

source_name: Whole blood, 01 h, individual: FR17MAG201313787

value: whole blood

value: female


title: GPS22942

description: Gene expression in blood before LPS injection for individual: FR17MAG201313787

source_name: Whole blood, 00 h, individual: FR17MAG201313787


title: Lckpr-TCL1A+/- T-cells; ‘chronic phase’ 3

source_name: splenic isolates from T-cell leukemia / lymphoma bearing Lckpr-hTCL1A+/- mice

value: spleen

value: early


title: GPS22936

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313573

source_name: Whole blood, 04 h, individual: FR17MAG201313573

value: LPS injection


title: Lckpr-TCL1A+/- T-cells; ‘chronic phase’ 1


title: Lckpr-TCL1A+/- T-cells; ‘chronic phase’ 2


title: AML patient sample (AML44)

value: Blood


title: GPS22938

description: Gene expression in blood before LPS injection for individual: FR17MAG201313664

source_name: Whole blood, 00 h, individual: FR17MAG201313664


title: GPS22932

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313546

source_name: Whole blood, 04 h, individual: FR17MAG201313546


title: GPS22945

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313787

source_name: Whole blood, 24 h, individual: FR17MAG201313787


title: AML patient sample (AML61)


title: GPS22933

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313546

source_name: Whole blood, 24 h, individual: FR17MAG201313546


title: AML patient sample (AML59)


title: AML patient sample (AML30)


title: Lckpr-TCL1A+/- T-cells; ‘exponential phase’ 5

value: late


title: GPS22935

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313573

source_name: Whole blood, 01 h, individual: FR17MAG201313573


title: GPS22934

description: Gene expression in blood before LPS injection for individual: FR17MAG201313573

source_name: Whole blood, 00 h, individual: FR17MAG201313573


title: Lckpr-TCL1A+/- T-cells; ‘exponential phase’ 2


title: GPS22937

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313573

source_name: Whole blood, 24 h, individual: FR17MAG201313573


title: Lckpr-TCL1A+/- T-cells; ‘exponential phase’ 3


title: GPS22928

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313315

source_name: Whole blood, 04 h, individual: FR17MAG201313315


title: GPS22927

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313315

source_name: Whole blood, 01 h, individual: FR17MAG201313315


title: GPS22926

description: Gene expression in blood before LPS injection for individual: FR17MAG201313315

source_name: Whole blood, 00 h, individual: FR17MAG201313315


title: GPS22931

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313546

source_name: Whole blood, 01 h, individual: FR17MAG201313546


title: GPS22929

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313315

source_name: Whole blood, 24 h, individual: FR17MAG201313315


title: GPS22128

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313824

source_name: Whole blood, 24 h, individual: FR17MAG201313824


title: GPS22131

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313903

source_name: Whole blood, 04 h, individual: FR17MAG201313903


title: GPS22130

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313903

source_name: Whole blood, 01 h, individual: FR17MAG201313903


title: GPS22132

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313903

source_name: Whole blood, 24 h, individual: FR17MAG201313903


title: GPS22129

description: Gene expression in blood before LPS injection for individual: FR17MAG201313903

source_name: Whole blood, 00 h, individual: FR17MAG201313903


title: GPS22126

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313824

source_name: Whole blood, 01 h, individual: FR17MAG201313824


title: GPS22127

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313824

source_name: Whole blood, 04 h, individual: FR17MAG201313824


title: GPS22122

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313632

source_name: Whole blood, 01 h, individual: FR17MAG201313632


title: FACS Sorted Astrocytes FMR1-KO, Biological rep5

city: Cleveland

first: Ranjan

last: Dutta

state: OH

address: 9500 Euclid Avenue, NC-30

department: Neuroscience

institute: Lerner Research Institute

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: FACS sorting of cells were carried out using EGFP reporter expression on astrocytes. cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

tag: cell type

value: FACS Sorted Astrocytes

value: 8 wks

value: cortex


title: GPS22124

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313632

source_name: Whole blood, 24 h, individual: FR17MAG201313632


title: FACS Sorted Astrocytes FMR1-KO, Biological rep4


title: FACS Sorted Astrocytes FMR1-KO, Biological rep3


title: FACS Sorted Astrocytes FMR1-KO, Biological rep2


title: Lckpr-TCL1A+/- T-cells; ‘exponential phase’ 1

source_name: splenic isolates from T-cell leukemia / lymphoma bearing Lckpr-hTCL1A+/- mice


title: FACS Sorted Astrocytes FMR1-KO, Biological rep1


title: GPS22125

description: Gene expression in blood before LPS injection for individual: FR17MAG201313824

source_name: Whole blood, 00 h, individual: FR17MAG201313824


title: FACS Sorted Astrocytes Control, Biological rep5

source_name: wild-type

value: wild-type


title: GPS22123

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313632

source_name: Whole blood, 04 h, individual: FR17MAG201313632


title: FACS Sorted Astrocytes Control, Biological rep3


title: FACS Sorted Astrocytes Control, Biological rep4


title: GPS22120

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313545

source_name: Whole blood, 24 h, individual: FR17MAG201313545


title: GPS22119

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313545

source_name: Whole blood, 04 h, individual: FR17MAG201313545


title: GPS22121

description: Gene expression in blood before LPS injection for individual: FR17MAG201313632

source_name: Whole blood, 00 h, individual: FR17MAG201313632


title: GPS22930

description: Gene expression in blood before LPS injection for individual: FR17MAG201313546

source_name: Whole blood, 00 h, individual: FR17MAG201313546


title: GPS22116

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313447

source_name: Whole blood, 24 h, individual: FR17MAG201313447


title: FACS Sorted Astrocytes Control, Biological rep2


title: GPS22117

description: Gene expression in blood before LPS injection for individual: FR17MAG201313545

source_name: Whole blood, 00 h, individual: FR17MAG201313545


title: GPS22115

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313447

source_name: Whole blood, 04 h, individual: FR17MAG201313447


title: GPS22110

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313387

source_name: Whole blood, 01 h, individual: FR17MAG201313387


title: GPS22111

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313387

source_name: Whole blood, 04 h, individual: FR17MAG201313387


title: GPS22118

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313545

source_name: Whole blood, 01 h, individual: FR17MAG201313545


title: GPS22112

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313387

source_name: Whole blood, 24 h, individual: FR17MAG201313387


title: FACS Sorted Astrocytes Control, Biological rep1


title: GPS22113

description: Gene expression in blood before LPS injection for individual: FR17MAG201313447

source_name: Whole blood, 00 h, individual: FR17MAG201313447


title: GPS22114

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313447

source_name: Whole blood, 01 h, individual: FR17MAG201313447


title: GPS22098

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313631

source_name: Whole blood, 01 h, individual: FR17MAG201313631


title: E2, biological rep2

city: Ottawa

first: Barbara

last: Vanderhyden

address: 501 Smyth Road

department: Cellular and Molecular Medicine

institute: University of Ottawa

hyb_protocol: Samples were prepared for Affymetrix GeneChip miRNA 4.0 Array according to the GeneChipTM miRNA Array Procedure (P/N 703095).

scan_protocol: GeneChip miRNA 4.0 Arrays were scanned with the Affymetrix GeneChipTM Scanner 3000.

data_processing: Affymetrix Transcriptome Analysis Console Software 3.0 was used to analyze the resulting array data.

label: Biotin

source_name: MASE E2 24H

label_protocol: microRNA was labelled with the FlashTag Biotin HSR RNA labeling kit from Affymetrix.

growth_protocol: MASE cells were maintained at 37°C in OSE media that consists of α-MEM media with 5% fetal bovine serum, 2ng/mL epidermal growth factor, and 0.01mg/mL insulin-transferrin-sodium selenite supplement.

extract_protocol: microRNA was isolated from cells using a miRNeasy miRNA isolation kit from Qiagen.

treatment_protocol: Cells were seeded into tissue culture plates such that cells would be 80-90% confluent by the end of the experiment. Cells were allowed to attach overnight in OSE media. The next day, cells were washed with PBS and the media was changed to hormone-free media consisting of 5% charcoal stripped FBS in phenol red free DMEM-F12, 2ng/mL epidermal growth factor, and 0.01mg/mL insulin-transferrin-sodium selenite supplement. Cells were allowed to normalize to hormone-free media for 48 h before E2 treatment. Cells were treated with 100nM E2 for 24H. An equivalent volume of 100% EtOH (vehicle) was added to control plates for a final concentration of 0.0002% EtOH.

value: Female

value: Ovarian cancer ascites


title: E2, biological rep1


title: Control, biological rep3

source_name: MASE Control 24H


title: GPS22099

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313631

source_name: Whole blood, 04 h, individual: FR17MAG201313631


title: GPS22105

description: Gene expression in blood before LPS injection for individual: FR17MAG201313786

source_name: Whole blood, 00 h, individual: FR17MAG201313786


title: GPS22100

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313631

source_name: Whole blood, 24 h, individual: FR17MAG201313631


title: GPS22109

description: Gene expression in blood before LPS injection for individual: FR17MAG201313387

source_name: Whole blood, 00 h, individual: FR17MAG201313387


title: GPS22102

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313663

source_name: Whole blood, 01 h, individual: FR17MAG201313663


title: GPS22107

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313786

source_name: Whole blood, 04 h, individual: FR17MAG201313786


title: GPS22103

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313663

source_name: Whole blood, 04 h, individual: FR17MAG201313663


title: GPS22106

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313786

source_name: Whole blood, 01 h, individual: FR17MAG201313786


title: GPS22104

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313663

source_name: Whole blood, 24 h, individual: FR17MAG201313663


title: Control, biological rep2


title: GPS22097

description: Gene expression in blood before LPS injection for individual: FR17MAG201313631

source_name: Whole blood, 00 h, individual: FR17MAG201313631


title: GPS22108

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313786

source_name: Whole blood, 24 h, individual: FR17MAG201313786


title: E2, biological rep3


title: GPS22093

description: Gene expression in blood before LPS injection for individual: FR17MAG201313347

source_name: Whole blood, 00 h, individual: FR17MAG201313347


title: LARP1-IP rep1

type: SRA

city: L'Hospitalet de Llobregat

first: Francisco

middle: D.

last: Morón-Duran

address: Av. Gran Via de l'Hospitalet, 199

institute: IDIBELL

description: LARP1 RIP-seq from 40S monosome fraction, biological rep1

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8
rRNA reads filtered with Bowtie2
Remaining reads were aligned to the human transcriptome using TopHat 2.1.1
Multi-mapped and multi-overlapped reads were discarded
Unique-mapping alignments were counted against gene models with featureCounts from Subread aligner version 1.20.6
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files with raw gene counts

source_name: Colon epithelial cells

extract_protocol:
Immunocomplexes obtained by RNA-IP with anti-LARP1 antibody or Normal Rabbit Serum IgG control were RNA-purified with TRIzol reagent according to manufacturer's protocol
The libraries were prepared with the Illumina TruSeq Stranded mRNA Sample Prep Kit omitting the polyA selection

tag: cell line

tag: ip antibody

tag: polysomal fraction


title: LARP1-IP rep2

description: LARP1 RIP-seq from 40S monosome fraction, biological rep2


title: GPS22094

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313347

source_name: Whole blood, 01 h, individual: FR17MAG201313347

tag: breed

tag: agent


title: Control, biological rep1


title: GPS22095

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313347

source_name: Whole blood, 04 h, individual: FR17MAG201313347


title: GPS22091

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313313

source_name: Whole blood, 04 h, individual: FR17MAG201313313


title: GPS22092

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313313

source_name: Whole blood, 24 h, individual: FR17MAG201313313


title: GPS22101

description: Gene expression in blood before LPS injection for individual: FR17MAG201313663

source_name: Whole blood, 00 h, individual: FR17MAG201313663


title: GPS22096

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313347

source_name: Whole blood, 24 h, individual: FR17MAG201313347


title: GPS22090

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313313

source_name: Whole blood, 01 h, individual: FR17MAG201313313


title: INPUT rep1

description: Input RNA from 40S monosome fraction, biological rep1


title: NRS rep2

description: IgG RIP-seq from 40S monosome fraction, biological rep2

value: IgG


title: GPS22087

description: Gene expression in blood 4 h after LPS injection for individual: FR17MAG201313285

source_name: Whole blood, 04 h, individual: FR17MAG201313285

value: Large White


title: NRS rep1

description: IgG RIP-seq from 40S monosome fraction, biological rep1


title: GPS22089

description: Gene expression in blood before LPS injection for individual: FR17MAG201313313

source_name: Whole blood, 00 h, individual: FR17MAG201313313


title: Lckpr-TCL1A+/- T-cells; ‘exponential phase’ 4

source_name: splenic isolates from T-cell leukemia / lymphoma bearing Lckpr-hTCL1A+/- mice


title: INPUT rep2

description: Input RNA from 40S monosome fraction, biological rep2


title: GPS22088

description: Gene expression in blood 24 h after LPS injection for individual: FR17MAG201313285

source_name: Whole blood, 24 h, individual: FR17MAG201313285


title: AffyRefGen_FL_3.AxiomGT1 normal whole venous blood sample

city: Gainesville

first: Christopher

middle: Jordan

last: Clukay

state: Florida

department: Anthropology

institute: University of Florida

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the GeneTitan Multi-Channel Instrument.

data_processing:
Data was processed using the Affymetrix Genotyping Console (Version 4.2, Affymetrix Inc., Santa Clara, CA, USA).
normal whole venous blood sample. Genotype Call (SNP call): AA, AB, BB, NC, and NoCall

source_name: Array Reference

extract_protocol: Genomic DNA was isolated using Qiagen QIAamp DNA Midi Kits (Qiagen, Valencia, CA) according to the manufacturerÍs instructions

tag: Sex


title: C25m normal whole venous blood sample

description: normal whole venous blood sample

source_name: venous whole blood

value: whole venous blood


title: C24m normal whole venous blood sample

description: normal whole venous blood sample


title: C19m normal whole venous blood sample

description: normal whole venous blood sample


title: C18m normal whole venous blood sample

description: normal whole venous blood sample


title: C20m normal whole venous blood sample

description: normal whole venous blood sample


title: C23m normal whole venous blood sample

description: normal whole venous blood sample


title: C22m normal whole venous blood sample

description: normal whole venous blood sample


title: C17m normal whole venous blood sample

description: normal whole venous blood sample


title: C14m normal whole venous blood sample

description: normal whole venous blood sample


title: heart_ko_control_rep1

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

hyb_protocol: Prior to hybridization the slides were incubated in a prewarmed BSA blocking solution containing 5x SSC, 0.1% SDS, and 0.1 mg/ml BSA at 42°C for 45 to 60 minutes. Subsequently, slides were rinsed twice in 0.1x SSC for 5 minutes and for 30 seconds in double-distilled water, both at room temperature. The slides were then dried in a nitrogen flow. Cy3-labeled cRNA samples (2.5 µg) were dissolved in hybridization buffer (final concentration 50% formamide, 5x SSC, 0.1% SDS). Hybridization was carried out in a humid chamber at 42°C for 16 h. After the hybridization step, unbound cRNA and hybridization buffer were removed by several washing steps (2 times 10 minutes 2x SSC, 0.1% SDS, 5 times 1 minute 0.1x SSC, and 10 seconds 0.01x SSC).

scan_protocol: Fluorescence signals were visualized by a GenePix 4000B laser scanner (Axon). GenePix Pro software (v. 6.0) was used to calculate fluorescence intensities.

data_processing: Data analyses on microarray probe signal intensities were conducted with GeneSpring GX software (v. 11.0.2; Agilent Technologies). Probe signal intensities were quantile normalized across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples.

source_name: heart, ko, control

label_protocol: Labeled cRNA probes were synthesized from 500 ng of total RNA using the Quick Amp Labeling Kit (one-color; Agilent Technologies) according to the manufacturer’s protocol.

growth_protocol: 5-6 months old wildtype C57BL/6 mice and p27-deficient littermates received drinking water with 0.05% caffeine or water alone for 10 days.

extract_protocol: RNA was isolated from mouse hearts using Trizol according to the manufacturer`s instruction (Invitrogen) and subjected to a second purification step using RNeasy columns (Qiagen). RNA integrity was checked on an Agilent 2100 Bioanalyzer and concentrations were determined by photometric Nanodrop measurement. All samples in this study showed common high quality RNA Integrity Numbers (RIN 9.7-10).

treatment_protocol: Mice were sacrificed, the hearst excised and used for RNA preparation.

value: heart

tag: treatment

value: untreated control

value: 5-6 months old


title: heart_ko_caffeine_rep1

source_name: heart, ko, caffeine

tag: tissue

value: caffeine treated


title: heart_ko_caffeine_rep2


title: heart_wt_caffeine_rep1

source_name: heart, wt, caffeine

value: wild type


title: heart_wt_caffeine_rep2