title: bsgs_802

value: 17 yrs


title: bsgs_798

status: Public on Dec 11 2013

type: RNA

city: Brisbane

first: Joseph

middle: E

last: Powell

state: Qld

address: St lucia

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

hyb_protocol: 750ng of cRNA was hybridised to Illumina HT12-v4.0 beadarray according to the whole-genome gene expression direct hybridization assay guide

scan_protocol: samples were scanned using an Illumina bead array reader

data_processing: preprocessing was done using genomestudio and included correction for chip background effects, removal of outlier beads and computation of average bead signal and detection p-values.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood, healthy

label_protocol: not provided

extract_protocol: Total RNA extracted using the WB gene RNA purification kit.

treatment_protocol: Whole blood collected into PAXgene tubes. Quality assessed using agilent bioanalyzer.

tag: gender

value: F

tag: twin

tag: age

value: 43 yrs


title: bsgs_794

value: M

value: DZ

value: 14 yrs


title: bsgs_796

value: 12 yrs


title: bsgs_793

value: MZ


title: bsgs_788

value: 16 yrs


title: bsgs_790


title: bsgs_792

value: 13 yrs


title: bsgs_791


title: bsgs_784


title: bsgs_787


title: bsgs_781


title: bsgs_780


title: bsgs_789


title: bsgs_799


title: prefrontal_cortex_79_autism

status: Public on Dec 12 2013

type: genomic

city: Baltimore

first: Christine

last: Ladd-Acosta

state: MD

address: 615 N. Wolfe Street, E6518

department: Epidemiology

country: USA

institute: Johns Hopkins University

description:
prefrontal_cortex_79_autism
6264496103_R01C01

hyb_protocol: We utilized the standard Illumina protocol for the 450K BeadChip

scan_protocol: BeadChip arrays were imaged using the Illumina iScan using settings recommended by Illumina

data_processing: We used the minfi bioconductor package to process the raw data

label: Cy5 and Cy3

molecule: genomic DNA

extract_protocol: For the cerebellum samples genomic DNA was extracted using the MasterPure DNA purification kit (EpiCentre Biotechnologies) according to the manufacturers specifications. We utilized Trizol (Invitrogen) to isolate genomic DNA from the prefrontal and temporal cortex tissue samples according to the manufacturers recommendations. 500ng of genomic DNA was bisulfite treated using the EZ DNA methylation kit (Zymo Research), as specificed for downstrem Illumina BeadChip processing.

tag: Sex

value: male

tag: tissue

value: brain

tag: brain region

value: prefrontal cortex

tag: disease state

value: autism

tag: sampletype

value: postmortem brain tissue


title: bsgs_782


title: bsgs_785

value: 18 yrs


title: bsgs_777


title: bsgs_776


title: bsgs_778


title: bsgs_786

value: 21 yrs


title: bsgs_775


title: bsgs_783

value: 17 yrs


title: bsgs_770

value: F


title: bsgs_767

value: 20 yrs


title: bsgs_774

value: M

value: 15 yrs


title: bsgs_771


title: bsgs_766

value: DZ

value: 14 yrs


title: bsgs_768

value: 11 yrs


title: bsgs_773


title: bsgs_761


title: bsgs_772

value: 12 yrs


title: bsgs_763


title: bsgs_762


title: bsgs_765

value: 16 yrs


title: bsgs_759


title: bsgs_764


title: bsgs_760

value: MZ


title: bsgs_752

value: 39 yrs


title: bsgs_750


title: bsgs_758


title: bsgs_755


title: bsgs_753

value: 10 yrs


title: bsgs_749


title: bsgs_757


title: bsgs_751


title: bsgs_747


title: bsgs_745


title: bsgs_754


title: bsgs_746


title: bsgs_748


title: bsgs_756


title: bsgs_744


title: bsgs_741


title: bsgs_739


title: bsgs_742


title: bsgs_743


title: bsgs_734


title: bsgs_740

value: 13 yrs


title: bsgs_737


title: bsgs_736


title: bsgs_727


title: bsgs_738


title: bsgs_728


title: bsgs_731


title: bsgs_726


title: bsgs_730


title: bsgs_803


title: bsgs_725


title: bsgs_733


title: bsgs_724


title: bsgs_732

value: 43 yrs


title: bsgs_729


title: bsgs_723

value: 35 yrs


title: bsgs_717


title: bsgs_718


title: bsgs_735


title: bsgs_721


title: bsgs_716


title: bsgs_720


title: bsgs_719


title: bsgs_722


title: bsgs_715


title: bsgs_779


title: bsgs_714


title: bsgs_769


title: bsgs_707


title: bsgs_706


title: bsgs_712


title: bsgs_713


title: bsgs_709


title: bsgs_710


title: bsgs_708


title: bsgs_703


title: bsgs_704


title: bsgs_701


title: bsgs_702


title: bsgs_700


title: bsgs_711

value: 34 yrs


title: bsgs_705


title: bsgs_696


title: bsgs_697

value: 48 yrs


title: bsgs_691

value: F


title: bsgs_689

value: 17 yrs


title: bsgs_695

value: 18 yrs


title: bsgs_699

value: 15 yrs


title: bsgs_690

value: M


title: bsgs_694


title: bsgs_692

value: DZ


title: bsgs_693


title: bsgs_685

value: 47 yrs


title: bsgs_698

value: 12 yrs


title: bsgs_688


title: bsgs_681


title: bsgs_687


title: bsgs_679


title: bsgs_678


title: bsgs_674


title: bsgs_668


title: bsgs_684


title: bsgs_682


title: bsgs_671


title: bsgs_680


title: bsgs_675

value: 45 yrs


title: bsgs_662

value: MZ


title: bsgs_672


title: bsgs_666


title: bsgs_667


title: bsgs_673

value: 16 yrs


title: bsgs_663

value: 14 yrs


title: bsgs_670


title: bsgs_676

value: 11 yrs


title: bsgs_677


title: bsgs_664


title: bsgs_661


title: bsgs_669


title: bsgs_665


title: bsgs_660

value: 10 yrs


title: bsgs_657


title: bsgs_658


title: bsgs_654


title: bsgs_656


title: bsgs_653


title: bsgs_649


title: bsgs_648


title: bsgs_651


title: bsgs_655


title: bsgs_645


title: bsgs_650


title: bsgs_646


title: bsgs_644

value: 13 yrs


title: bsgs_642


title: bsgs_652


title: bsgs_647

value: 40 yrs


title: bsgs_641


title: bsgs_635


title: bsgs_643


title: bsgs_640


title: bsgs_639


title: bsgs_638


title: bsgs_634


title: bsgs_633


title: bsgs_636


title: bsgs_637


title: bsgs_632


title: bsgs_629


title: bsgs_628


title: bsgs_627


title: bsgs_630


title: bsgs_625


title: bsgs_624


title: bsgs_631


title: bsgs_686


title: bsgs_659

value: 39 yrs


title: bsgs_626


title: bsgs_622


title: bsgs_615


title: bsgs_623

value: F


title: bsgs_616


title: bsgs_621


title: bsgs_618


title: bsgs_619


title: bsgs_617


title: bsgs_683

value: 20 yrs


title: bsgs_620


title: bsgs_611


title: bsgs_609


title: bsgs_612


title: bsgs_605


title: bsgs_614

value: 24 yrs


title: bsgs_613

value: 17 yrs


title: bsgs_608

value: M


title: bsgs_603

value: DZ


title: bsgs_606


title: bsgs_607


title: bsgs_610


title: bsgs_601


title: bsgs_599


title: bsgs_604


title: bsgs_602


title: bsgs_590


title: bsgs_595


title: bsgs_593


title: bsgs_598

value: 18 yrs


title: bsgs_596

value: 15 yrs


title: bsgs_597


title: bsgs_600

value: 44 yrs


title: bsgs_591

value: MZ

value: 12 yrs


title: bsgs_589


title: bsgs_594


title: bsgs_588

value: 46 yrs


title: bsgs_585

value: 16 yrs


title: bsgs_592


title: bsgs_586


title: bsgs_583


title: bsgs_577

value: 49 yrs


title: bsgs_580


title: bsgs_584

value: 13 yrs


title: bsgs_576


title: bsgs_578

value: 19 yrs


title: bsgs_587

value: 10 yrs


title: bsgs_579

value: F


title: bsgs_574

value: 55 yrs


title: bsgs_582


title: bsgs_572


title: bsgs_575


title: bsgs_581

value: 11 yrs


title: bsgs_573


title: DU145 48 t 452a

city: Aarhus

first: Kasper

last: Thorsen

address: Brendstrupgaardsvej

country: Denmark

institute: Aarhus University Hospital

description: Gene expression data

hyb_protocol: Affymetrix hybridization kit, hybridize 16 hours at 45° at 60rpm to the GeneChip® Human Gene 1.0 ST Array

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneSpring GX 12.5. RMA16 algorithm was used for normalization

label: Biotin

source_name: DU145 cells transfected with miR-452 mimics, 48 h

label_protocol: 100 ng total RNA was labeled using the Ambion® WT Expression Kit (Ambion)

growth_protocol: Propagated in RPMI 1640 with L-glutamine (Invitrogen) supplemented with 10% heat-inactivated fetal calf serum (FCS), 100 U/ml penicillin and 100 μg/ml streptomycin at 37 °C in a humidified air atmosphere at 5% CO2.

extract_protocol: RNAeasy kit (Qiagen)

treatment_protocol: PC3 and DU145 cells were reverse transfected with 20 nM of each miRNA (miRNA mimics purchased from Applied Biosystems/Ambion) using LipofectamineTM 2000 reagent (Invitrogen). Medium was changed 6 hours post-transfection. RNA was extracted 48 hours post-transfection.

tag: cell line

tag: cell line origin

value: Prostate cancer brain metastasis

tag: miRNA mimic


title: DU145 48 t Scr2b

description: Gene expression data

source_name: DU145 cells transfected with scrampled miRNA, 48 h

value: Scrambled no. 2


title: DU145 48 t 452c

description: Gene expression data


title: DU145 48 t NTc

description: Gene expression data

source_name: DU145 cells without treatment, 48 h


title: DU145 48 t NTb

description: Gene expression data


title: PC3 48 t 452b

description: Gene expression data

source_name: PC3 cells transfected with miR-452 mimics, 48 h

value: Prostate cancer bone metastasis


title: DU145 48 t 224c

description: Gene expression data

source_name: DU145 cells transfected with miR-224 mimics, 48 h


title: PC3 48 t Scr2c

description: Gene expression data

source_name: PC3 cells transfected with scrampled miRNA, 48 h


title: PC3 48 t Scr2b

description: Gene expression data


title: PC3 48 t NTb

description: Gene expression data

source_name: PC3 cells without treatment, 48 h


title: PC3 48 t 452c

description: Gene expression data


title: DU145 48 t 224a

description: Gene expression data


title: bsgs_570

value: M


title: PC3 48 t NTc

description: Gene expression data


title: bsgs_569

value: DZ


title: PC3 48 t 224a

description: Gene expression data

source_name: PC3 cells transfected with miR-224 mimics, 48 h


title: bsgs_567


title: bsgs_565

value: 17 yrs


title: bsgs_564


title: bsgs_566

value: 54 yrs


title: bsgs_571

value: 12 yrs


title: bsgs_568

value: MZ


title: PC3 48 t 224b

description: Gene expression data


title: bsgs_560


title: bsgs_561


title: bsgs_563

value: 16 yrs


title: bsgs_562

value: 40 yrs


title: bsgs_559


title: bsgs_556


title: bsgs_557

value: 14 yrs


title: bsgs_552


title: bsgs_548


title: bsgs_554


title: bsgs_558


title: bsgs_551

value: 18 yrs


title: bsgs_549


title: bsgs_550

value: 15 yrs


title: bsgs_553


title: bsgs_543


title: bsgs_545

value: F


title: bsgs_546


title: bsgs_539


title: bsgs_555


title: bsgs_544


title: bsgs_547


title: bsgs_540


title: bsgs_537


title: bsgs_535

value: 51 yrs


title: bsgs_536


title: bsgs_534


title: bsgs_530


title: bsgs_542


title: bsgs_541

value: 58 yrs


title: bsgs_529


title: bsgs_523


title: bsgs_522


title: bsgs_524


title: bsgs_538

value: 47 yrs


title: bsgs_531

value: 75 yrs


title: bsgs_533


title: bsgs_526


title: bsgs_521


title: bsgs_518


title: bsgs_520


title: bsgs_519


title: bsgs_527


title: bsgs_528

value: 48 yrs


title: bsgs_517

value: M


title: bsgs_532

value: DZ


title: bsgs_525


title: bsgs_514

value: 46 yrs


title: bsgs_515

value: 17 yrs


title: bsgs_512

value: 59 yrs


title: bsgs_516

value: 49 yrs


title: bsgs_513

value: 16 yrs


title: bsgs_510


title: bsgs_507


title: bsgs_503


title: bsgs_511


title: bsgs_505


title: bsgs_497


title: bsgs_508


title: bsgs_509


title: bsgs_496

value: MZ


title: bsgs_501


title: bsgs_502


title: bsgs_498

value: 50 yrs


title: bsgs_500


title: bsgs_494

value: 20 yrs


title: bsgs_495

value: 14 yrs


title: bsgs_506

value: F


title: bsgs_492


title: bsgs_499


title: bsgs_489


title: bsgs_491

value: 18 yrs


title: bsgs_490


title: bsgs_486


title: bsgs_493

value: 12 yrs


title: bsgs_488


title: bsgs_485


title: bsgs_487

value: 43 yrs


title: bsgs_484


title: bsgs_483


title: bsgs_478


title: bsgs_481


title: bsgs_475


title: bsgs_482


title: bsgs_474


title: bsgs_477

value: 47 yrs


title: bsgs_480


title: bsgs_471


title: bsgs_473


title: bsgs_470


title: bsgs_468


title: bsgs_472


title: bsgs_469


title: bsgs_463


title: bsgs_476


title: bsgs_460


title: bsgs_465


title: bsgs_466


title: bsgs_479


title: bsgs_459

value: 13 yrs


title: bsgs_462


title: bsgs_457

value: M


title: bsgs_464

value: DZ


title: bsgs_451


title: bsgs_467

value: 15 yrs


title: bsgs_455

value: 19 yrs


title: bsgs_458


title: bsgs_454

value: 48 yrs


title: bsgs_461


title: bsgs_452

value: 44 yrs


title: bsgs_449


title: bsgs_456


title: bsgs_447


title: bsgs_450


title: bsgs_441


title: bsgs_444


title: bsgs_446


title: bsgs_445


title: bsgs_440


title: bsgs_438


title: bsgs_435


title: bsgs_437


title: bsgs_436


title: bsgs_439

value: 51 yrs


title: bsgs_442

value: MZ

value: 17 yrs


title: bsgs_434


title: bsgs_433


title: bsgs_431


title: bsgs_432


title: bsgs_425


title: bsgs_429


title: bsgs_426


title: bsgs_428


title: bsgs_423


title: bsgs_424


title: bsgs_421


title: bsgs_448


title: bsgs_427


title: bsgs_422


title: bsgs_419


title: bsgs_430


title: bsgs_418


title: bsgs_416


title: bsgs_420


title: bsgs_504

value: 16 yrs


title: bsgs_415

value: 14 yrs


title: bsgs_414

value: F


title: bsgs_409


title: bsgs_406


title: bsgs_412


title: bsgs_410


title: bsgs_407


title: bsgs_408


title: bsgs_413


title: bsgs_405


title: bsgs_395


title: bsgs_396


title: bsgs_403


title: bsgs_417


title: bsgs_404


title: bsgs_399


title: bsgs_398

value: 49 yrs


title: bsgs_402

value: 12 yrs


title: bsgs_393


title: bsgs_394


title: bsgs_411


title: bsgs_400


title: bsgs_392


title: bsgs_397


title: bsgs_390


title: bsgs_386


title: bsgs_389


title: bsgs_384


title: bsgs_391

value: 46 yrs


title: bsgs_387


title: bsgs_381


title: bsgs_382


title: bsgs_383


title: bsgs_385


title: bsgs_376


title: bsgs_388


title: bsgs_453


title: bsgs_443


title: bsgs_378

value: 54 yrs


title: bsgs_375


title: bsgs_379

value: 11 yrs


title: bsgs_371

value: M

value: 10 yrs


title: bsgs_368

value: DZ


title: bsgs_369


title: bsgs_366


title: bsgs_372


title: bsgs_373


title: bsgs_365


title: bsgs_367


title: bsgs_374


title: bsgs_377

value: 13 yrs


title: bsgs_370


title: bsgs_362


title: bsgs_360


title: bsgs_380


title: bsgs_363


title: bsgs_359


title: bsgs_357

value: 41 yrs


title: bsgs_361


title: bsgs_350


title: bsgs_355


title: bsgs_356


title: bsgs_348


title: bsgs_358


title: bsgs_352

value: 18 yrs


title: bsgs_353


title: bsgs_351


title: bsgs_354


title: bsgs_349


title: bsgs_342

value: 50 yrs


title: bsgs_347


title: bsgs_341


title: bsgs_364

value: 53 yrs


title: bsgs_346


title: bsgs_343


title: bsgs_344


title: bsgs_345


title: bsgs_340


title: bsgs_339


title: bsgs_337

value: 15 yrs


title: bsgs_336


title: bsgs_334

value: 17 yrs


title: bsgs_332

value: 16 yrs


title: bsgs_335


title: bsgs_333


title: bsgs_338

value: 14 yrs


title: bsgs_329

value: F


title: bsgs_330


title: bsgs_401


title: bsgs_331

value: MZ

value: 12 yrs


title: bsgs_321


title: bsgs_324


title: bsgs_327


title: bsgs_319


title: bsgs_326


title: bsgs_316


title: bsgs_317


title: bsgs_322


title: bsgs_318


title: bsgs_315


title: bsgs_320

value: 48 yrs


title: bsgs_325


title: bsgs_323


title: bsgs_328

value: 52 yrs


title: bsgs_311

value: M


title: bsgs_314


title: bsgs_308


title: bsgs_310


title: bsgs_307


title: bsgs_309


title: bsgs_305


title: bsgs_313


title: bsgs_303


title: bsgs_304


title: bsgs_312

value: 45 yrs


title: bsgs_301


title: bsgs_297

value: DZ


title: bsgs_288


title: bsgs_296

value: 13 yrs


title: bsgs_298


title: bsgs_293


title: bsgs_294

value: 10 yrs


title: bsgs_291


title: bsgs_306

value: 46 yrs


title: bsgs_300


title: bsgs_292


title: bsgs_295


title: bsgs_299


title: bsgs_287


title: bsgs_302


title: bsgs_286


title: bsgs_285


title: bsgs_290


title: bsgs_289


title: bsgs_284


title: bsgs_282


title: bsgs_280


title: bsgs_279


title: bsgs_276

value: 55 yrs


title: bsgs_283

value: 47 yrs


title: bsgs_277


title: bsgs_270


title: bsgs_273

value: 19 yrs


title: bsgs_278

value: 18 yrs


title: bsgs_271


title: bsgs_275

value: 40 yrs


title: bsgs_281


title: bsgs_269


title: bsgs_267

value: 37 yrs


title: bsgs_263


title: bsgs_274

value: F

value: 16 yrs


title: bsgs_268

value: 12 yrs


title: bsgs_262


title: bsgs_266


title: bsgs_261

value: 17 yrs


title: bsgs_272


title: bsgs_265

value: 52 yrs


title: bsgs_264

value: M


title: bsgs_260

value: 15 yrs


title: bsgs_259

value: 43 yrs


title: bsgs_258

value: DZ

value: 13 yrs


title: bsgs_257

value: 39 yrs


title: bsgs_256

value: 14 yrs


title: slide 345293

city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller University of Jena

description: comparison of antibiotic tagged synthetic wild type and ymdB E39Q point mutant at exponential phase

hyb_protocol: The protocol was performed as described in Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 PMID: 17183215

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing:
Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (den Hengst et al J. Biol. Chem. 280:34332-34342; PMID: 16040604). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.
Net{A} is the raw signal of channel A minus the local corner background signal of channel A
Net{B} is the raw signal of channel B minus the local corner background signal of channel B

organism: Bacillus subtilis

source_name: Net{A}

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using NucleoSpin Extract II columns

growth_protocol: B subtilis antibiotic tagged synthetic wild type (GP966) and its ymdB E39Q point mutant derivative strain (GP969) were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationer phase (OD600 ~2.2-2.4).  For both time points, 4 biological replicates were used, resulting 4 slides for both exponential and staioner phase.  RNA purification was performed on the samples.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 PMID: 17183215). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: strain

value: B subtilis GP966

tag: growth phase

value: exponential

source_name: Net{B}

value: B subtilis GP969


title: slide 345294


title: slide 345295

description: comparison of antibiotic tagged synthetic wild type and ymdB E39Q point mutant at stationer phase

value: stationer


title: bsgs_253

value: 49 yrs


title: slide 345298


title: bsgs_254

value: F


title: slide 345297


title: bsgs_249


title: bsgs_252

value: 50 yrs


title: slide 345296


title: slide 345292


title: slide 345291


title: bsgs_255

value: 12 yrs


title: bsgs_251


title: bsgs_250

value: MZ

value: 16 yrs


title: bsgs_246

value: M


title: bsgs_247


title: slide 342622

description: comparison of wild type and ymdB mutant at stationary phase

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (den Hengst et al J. Biol. Chem. 280:34332-34342; PMID: 16040604). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

growth_protocol: B subtilis wild type (168) and its ymdB derivative strain were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationary phase (OD600 ~2.2-2.4).  For both time points, 4 biological replicates were used, resulting 4 slides for both exponential and stationary phase.  RNA purification was performed on the samples.

treatment_protocol: no treatment

tag: phase

value: stationary

value: ymdB


title: bsgs_248


title: bsgs_243

value: DZ


title: bsgs_244


title: bsgs_242


title: slide 343652


title: bsgs_241


title: bsgs_245

value: 10 yrs


title: slide 343648


title: slide 343640

description: comparison of wild type and ymdB mutant at exponential phase


title: slide 343644


title: slide 343636


title: slide 344032


title: bsgs_240

value: 43 yrs


title: bsgs_237

value: 14 yrs


title: bsgs_232


title: bsgs_231

value: 11 yrs


title: slide s2

description: comparison of wild type (PY79) with yvfI mutant (TEK1)

data_processing:
Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (den Hengst et al J. Biol. Chem. 280:34332-34342; PMID: 16040604). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.
LN ratio (Target / Control = Mutant / Wild type) and grid based lowess normalisation
Net{A} is the raw signal of channel A minus the local corner background signal of channel A
Net{B} is the raw signal of channel B minus the local corner background signal of channel B

growth_protocol: B. subtilis wild type strain (PY79) and its yvfI mutant (TEK1) were grown in PA medium (Perry and Abraham, 1979) until they reached OD of 7 at 600 nm and  samples were taken


title: bsgs_238


title: bsgs_233

value: 13 yrs


title: bsgs_235


title: bsgs_234


title: slide t2


title: slide 344028

value: exponential


title: slide t1


title: bsgs_236


title: bsgs_239


title: bsgs_230


title: bsgs_229

value: 41 yrs


title: bsgs_227


title: bsgs_224


title: bsgs_223


title: bsgs_226

value: 46 yrs


title: bsgs_228

value: 58 yrs


title: bsgs_220

value: 50 yrs


title: bsgs_222

value: F

value: 15 yrs


title: bsgs_225

value: MZ


title: bsgs_217

value: M

value: 12 yrs


title: bsgs_221


title: bsgs_218


title: bsgs_215


title: bsgs_216

value: 48 yrs


title: bsgs_219

value: 40 yrs


title: bsgs_214

value: 16 yrs


title: bsgs_211

value: DZ


title: bsgs_212


title: bsgs_209


title: bsgs_208


title: bsgs_207


title: bsgs_213

value: 14 yrs


title: bsgs_206

value: 52 yrs


title: bsgs_205

value: 38 yrs


title: bsgs_210


title: GM03075_cDNA

city: Montreal

first: Tomi

middle: Markku

last: Pastinen

state: Quebec

address: 740, Dr. Penfield Avenue

country: Canada

institute: McGill University and Génome Québec Innovation Centre

description: Family 444,  father

hyb_protocol: according to manufacturer's instructions

data_processing: Using GenomeStudio from Illumina

label: Cy3 and Cy5

growth_protocol: The Fibroblast primary cell lines were grown in medium containing a-MEM (SigmaAldrich) supplemented with 2 mmol/l L-Glutamine, 100 U/mL penicillin, 100 mg/ml streptomycin, and 10% fetal bovine serum (SigmaAldrich) at 37°C with 5% CO2. At 70%-80% confluence, the cells were harvested.

extract_protocol: total RNA was extracted from cell lysates resuspended in 600 mL RLT lysis buffer using the Rneasy Mini Kit (Qiagen). DNA was extracted from cell lysates resuspended in 200 mL PBS using the GenElute DNA Miniprep Kit (SigmaAldrich).

value: Male

tag: cell type

value: primary skin fibroblast

tag: population

value: Caucasian


title: GM00439_cDNA

description: Family 1907,  mother

scan_protocol: according to manufacturer's instructions

value: Female


title: GM02639_cDNA

description: Family 236,  son

label_protocol: according to manufacturer's instructions


title: GM02640_cDNA

description: Family 236,  father


title: bsgs_204


title: GM02316_cDNA

description: Family 56,  father


title: bsgs_202

value: 47 yrs


title: bsgs_203

value: F

value: 13 yrs


title: GM02314_cDNA

description: Family 56,  daughter


title: GM02555_cDNA

description: Family 222,  mother


title: GM02641_cDNA

description: Family 236,  mother


title: GM02704_cDNA

description: Family 243,  father


title: GM02706_cDNA

description: Family 243,  mother


title: GM01516_cDNA

description: Family 208,  mother


title: GM02205_cDNA

description: Family 208,  father


title: GM02317_cDNA

description: Family 56,  mother


title: GM00438_cDNA

description: Family 1907, father


title: GM02455_cDNA

description: Family 222,  daughter


title: bsgs_201

value: 60 yrs


title: bsgs_200

value: M

value: 45 yrs


title: GM01391_cDNA

description: Family 42,  daughter


title: bsgs_199

value: MZ

value: 17 yrs


title: GM02173_cDNA

description: Family 111,  mother


title: GM02175_cDNA

description: Family 111,  father


title: bsgs_198


title: GM02149_cDNA

description: Family 108,  mother


title: bsgs_197

value: 16 yrs


title: GM01393_cDNA

description: Family 42,  father


title: GM01392_cDNA

description: Family 42,  mother


title: GM02147_cDNA

description: Family 108,  father


title: bsgs_195

value: 18 yrs


title: bsgs_194

value: DZ

value: 12 yrs


title: GM02456_cDNA

description: Family 222,  father


title: GM03073_cDNA

description: Family 444,  mother


title: GM01375_cDNA

description: Family 15,  mother


title: bsgs_193

value: 44 yrs


title: bsgs_196


title: bsgs_189


title: bsgs_192

value: 14 yrs


title: GM01376_cDNA

description: Family 15,  father

value: Male

value: primary skin fibroblast


title: bsgs_188


title: bsgs_191


title: bsgs_187


title: bsgs_190

value: 48 yrs


title: GM01095_cDNA

description: Family 50,  mother

value: Female

value: Caucasian


title: bsgs_185

value: F

value: 11 yrs


title: bsgs_186


title: bsgs_184


title: GM01096_cDNA

description: Family 50,  father


title: bsgs_183

value: M

value: 51 yrs


title: bsgs_182


title: bsgs_181


title: bsgs_179

value: 45 yrs


title: bsgs_180


title: GM00940_cDNA

description: Family 82,  mother


title: bsgs_178


title: GM00290_cDNA

description: Family 24,  mother


title: GM00292_cDNA

description: Family 24,  son


title: bsgs_177

value: 17 yrs


title: bsgs_176


title: GM00941_cDNA

description: Family 82,  father


title: GM00031_cDNA

description: Family 40,  mother


title: GM00289_cDNA

description: Family 24,  father


title: bsgs_175


title: WG2415_cDNA

description: Trio 20,  mother


title: bsgs_174


title: WG2121_cDNA

description: Trio 18,  mother


title: WG3465_cDNA

description: Trio 21,  father


title: WG3466_cDNA

description: Trio 21,  mother


title: GM00042_cDNA

description: Family 40,  father


title: WG2414_cDNA

description: Trio 20,  father


title: WG2843_cDNA

description: Trio 17,  father


title: WG2193_cDNA

description: Trio 19,  father


title: bsgs_173


title: bsgs_172


title: bsgs_169

value: 46 yrs


title: WG2194_cDNA

description: Trio 19,  mother


title: WG1226_cDNA

description: Trio 16,  son


title: bsgs_171

value: 49 yrs


title: WG2844_cDNA

description: Trio 17,  mother


title: bsgs_167

value: 57 yrs


title: bsgs_168

value: MZ

value: 12 yrs


title: WG2120_cDNA

description: Trio 18,  father


title: WG1084_cDNA

description: Trio 17,  son


title: WG1978_cDNA

description: Trio 15,  father


title: bsgs_166

value: DZ


title: WG1283_cDNA

description: Trio 16,  mother


title: WG1977_cDNA

description: Trio 15,  mother


title: bsgs_161

value: 13 yrs


title: bsgs_162

value: 14 yrs


title: bsgs_165


title: bsgs_163

value: 20 yrs


title: bsgs_170

value: 37 yrs


title: WG1310_cDNA

description: Trio 16,  mother

value: Female

value: primary skin fibroblast

value: Caucasian


title: bsgs_160

value: F


title: WG1309_cDNA

description: Trio 16,  father

value: Male


title: WG1656_cDNA

description: Trio 13,  son


title: WG1282_cDNA

description: Trio 16,  father


title: bsgs_164

value: 43 yrs


title: bsgs_158

value: 47 yrs


title: bsgs_159

value: M

value: 50 yrs


title: bsgs_157

value: 52 yrs


title: bsgs_155


title: bsgs_154

value: 48 yrs


title: bsgs_156

value: 45 yrs


title: WG1657_cDNA

description: Trio 13,  father


title: WG1722_cDNA

description: Trio 12,  mother


title: bsgs_151

value: 49 yrs


title: bsgs_152

value: MZ

value: 17 yrs


title: bsgs_153

value: 16 yrs


title: GM01653_cDNA

description: Family 165,  father


title: GM01650_cDNA

description: Family 165,  mother


title: GM00520_cDNA

description: Family 51,  father


title: WG1658_cDNA

description: Trio 13,  mother


title: WG1721_cDNA

description: Trio 12,  father


title: GM00016_cDNA

description: Family 491 ,  father


title: bsgs_149

value: 13 yrs


title: GM00022_cDNA

description: Family 491 ,  mother

value: Female


title: GM00519_cDNA

description: Family 51,  daughter

value: primary skin fibroblast


title: bsgs_147

value: 42 yrs


title: bsgs_148

value: F

value: 41 yrs


title: GM09255_cDNA

description: Family 2131,  father

value: Male

value: Caucasian


title: bsgs_150

value: M

value: DZ

value: 14 yrs


title: bsgs_146

value: 12 yrs


title: WG2064_cDNA

description: Trio 11,  daughter


title: bsgs_144


title: bsgs_145


title: WG1513_cDNA

description: Trio 14,  father


title: WG1983_cDNA

description: Family 51,  mother


title: bsgs_143


title: bsgs_142

value: 46 yrs


title: GM09256_cDNA

description: Family 2131,  mother


title: GM00935_cDNA

description: Family 51,  mother


title: WG1984_cDNA

description: Family 51,  father


title: bsgs_141


title: WG2065_cDNA

description: Trio 11,  mother


title: bsgs_140


title: GM00439_gDNA

description: Family 1907,  mother


title: WG2276_cDNA

description: Trio 10,  mother


title: WG2275_cDNA

description: Trio 10,  father


title: WG2066_cDNA

description: Trio 11,  father


title: bsgs_138

value: 49 yrs


title: bsgs_137

value: 10 yrs


title: bsgs_139


title: GM03073_gDNA

description: Family 444,  mother


title: GM00440_gDNA

description: Family 1907,  daughter


title: GM03075_gDNA

description: Family 444,  father


title: GM03071_gDNA

description: Family 444,  son


title: bsgs_135


title: bsgs_136

value: 55 yrs


title: bsgs_134


title: bsgs_132

value: 11 yrs


title: GM02708_gDNA

description: Family 243,  son


title: bsgs_131

value: MZ


title: bsgs_133

value: 47 yrs


title: bsgs_130

value: 17 yrs


title: WG1514_cDNA

description: Trio 14,  mother

value: Female

value: primary skin fibroblast


title: bsgs_129


title: bsgs_128

value: 51 yrs


title: GM02639_gDNA

description: Family 236,  son

value: Male


title: GM02641_gDNA

description: Family 236,  mother

value: Caucasian


title: bsgs_125

value: F


title: GM02455_gDNA

description: Family 222,  daughter


title: bsgs_126

value: M


title: GM02555_gDNA

description: Family 222,  mother


title: bsgs_124

value: DZ

value: 14 yrs


title: bsgs_127


title: GM02704_gDNA

description: Family 243,  father


title: bsgs_123

value: 12 yrs


title: bsgs_122


title: GM01516_gDNA

description: Family 208,  mother


title: GM02206_gDNA

description: Family 208,  daughter


title: bsgs_120


title: bsgs_121

value: 48 yrs


title: bsgs_119

value: 16 yrs


title: GM02317_gDNA

description: Family 56,  mother


title: GM02640_gDNA

description: Family 236,  father


title: GM02706_gDNA

description: Family 243,  mother


title: GM02205_gDNA

description: Family 208,  father


title: bsgs_118


title: GM02314_gDNA

description: Family 56,  daughter


title: bsgs_117

value: 44 yrs


title: GM02316_gDNA

description: Family 56,  father


title: GM02171_gDNA

description: Family 111,  daughter


title: bsgs_114


title: bsgs_115


title: GM02151_gDNA

description: Family 108,  daughter


title: GM01374_gDNA

description: Family 15,  daughter


title: bsgs_113

value: 49 yrs


title: GM01391_gDNA

description: Family 42,  daughter


title: GM02147_gDNA

description: Family 108,  father


title: GM02173_gDNA

description: Family 111,  mother


title: GM02456_gDNA

description: Family 222,  father


title: GM02175_gDNA

description: Family 111,  father


title: GM01393_gDNA

description: Family 42,  father


title: bsgs_110


title: bsgs_112


title: GM01375_gDNA

description: Family 15,  mother


title: bsgs_111

value: MZ


title: bsgs_116


title: bsgs_109


title: bsgs_108

value: 45 yrs


title: GM01094_gDNA

description: Family 50,  daughter


title: GM02149_gDNA

description: Family 108,  mother


title: bsgs_107


title: GM01095_gDNA

description: Family 50,  mother


title: GM01376_gDNA

description: Family 15,  father


title: bsgs_106

value: 19 yrs


title: bsgs_104


title: bsgs_105


title: bsgs_102


title: GM00940_gDNA

description: Family 82,  mother

value: Female


title: bsgs_103

value: 46 yrs


title: GM00292_gDNA

description: Family 24,  son

value: primary skin fibroblast


title: bsgs_101


title: GM00939_gDNA

description: Family 82,  daughter


title: bsgs_99


title: bsgs_100


title: GM01096_gDNA

description: Family 50,  father

value: Male


title: GM00941_gDNA

description: Family 82,  father

value: Caucasian


title: bsgs_97


title: GM01392_gDNA

description: Family 42,  mother


title: bsgs_96


title: bsgs_98


title: bsgs_94

value: F


title: GM00031_gDNA

description: Family 40,  mother


title: bsgs_95

value: 43 yrs


title: bsgs_92

value: M

value: DZ

value: 13 yrs


title: bsgs_93


title: GM00034_gDNA

description: Family 40,  daughter


title: GM00289_gDNA

description: Family 24,  father


title: GM00290_gDNA

description: Family 24,  mother


title: bsgs_89

value: 12 yrs


title: bsgs_91


title: WG2415_gDNA

description: Trio 20,  mother


title: bsgs_90


title: WG2194_gDNA

description: Trio 19,  mother


title: bsgs_88

value: 42 yrs


title: WG3189_gDNA

description: Trio 21,  son


title: WG2414_gDNA

description: Trio 20,  father


title: WG3466_gDNA

description: Trio 21,  mother


title: GM00042_gDNA

description: Family 40,  father


title: bsgs_87


title: WG2195_gDNA

description: Trio 19,  son


title: WG2413_gDNA

description: Trio 20,  daughter


title: genotype: ALLO_195 - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Wheat alloplasmic line-Genome donor CHRIS; Plasmon donor Aegilops squarrosa; Plasmon type (D) (May still include original submitter created erros/discrepancies)

scan_protocol: Affymetrix MAS 5.0 Standard Scanning at NASC

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

organism: Triticum aestivum

source_name: second fully expanded leaf (genotype: ALLO_195)

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: Trizol RNA extraction followed by RNeasy purification

tag: germplasm name

value: Conserved IAS-CSIC_Cordoba_Spain

value: second fully expanded leaf

tag: development stage

value: 14 days old seedling

tag: growth media

value: garden soil


title: WG2121_gDNA

description: Trio 18,  mother

tag: gender


title: WG2193_gDNA

description: Trio 19,  father


title: bsgs_85

tag: twin

tag: age

value: 40 yrs


title: WG2120_gDNA

description: Trio 18,  father


title: WG1084_gDNA

description: Trio 17,  son


title: WG1226_gDNA

description: Trio 16,  son


title: genotype: ALLO_195 - rep2

tag: tissue


title: bsgs_84


title: genotype: ALLO_183 - rep3

description: Wheat alloplasmic line-Genome donor CHRIS; Plasmon donor Aegilops uniaristata; Plasmon type (N) (May still include original submitter created erros/discrepancies)

source_name: second fully expanded leaf (genotype: ALLO_183)


title: bsgs_86

value: MZ


title: bsgs_83

value: 49 yrs


title: WG1282_gDNA

description: Trio 16,  father

value: primary skin fibroblast


title: WG2843_gDNA

description: Trio 17,  father

value: Male


title: genotype: ALLO_183 - rep2


title: genotype: ALLO_195 - rep1


title: WG2844_gDNA

description: Trio 17,  mother

value: Female

value: Caucasian


title: genotype: EU_CHRIS - rep3

description: wheat euplasmic line CHRIS (May still include original submitter created erros/discrepancies)

source_name: second fully expanded leaf (genotype: EU_CHRIS)

value: National small grain collection (USA)


title: genotype: ALLO_183 - rep1


title: genotype: ALLO_TH237 - rep3

description: Wheat alloplasmic line-Genome donor T20; Plasmon donor Hordeum chilense (H7) (May still include original submitter created erros/discrepancies)

source_name: second fully expanded leaf (genotype: ALLO_TH237)

tag: germplasm name/origin

value: Atienza et al., (2007). Plant Breeding, 126:5-8. Conserved IAS-CSIC_Cordoba_Spain


title: genotype: EU_CHRIS - rep2


title: bsgs_82

value: F

value: 15 yrs


title: bsgs_81

value: 46 yrs


title: WG3465_gDNA

description: Trio 21,  father


title: bsgs_80

value: M

value: 17 yrs


title: WG1283_gDNA

description: Trio 16,  mother


title: WG1310_gDNA

description: Trio 16,  mother


title: genotype: ALLO_TH237 - rep1

value: second fully expanded leaf


title: genotype: EU_CHRIS - rep1

value: 14 days old seedling


title: WG1311_gDNA

description: Trio 16,  son


title: genotype: EU_T20 - rep3

description: wheat euplasmic line T20 (May still include original submitter created erros/discrepancies)

source_name: second fully expanded leaf (genotype: EU_T20)

value: Dr. A. Refoyo Conserved:IAS-CSIC_Cordoba_Spain

value: garden soil


title: genotype: ALLO_TH237 - rep2


title: genotype: EU_T20 - rep2


title: WG1976_gDNA

description: Trio 15,  son


title: bsgs_78

value: 43 yrs


title: R26MER/MER MEFs, MSCV, 0.2%serum, 16h 4OHT-treatment, biological rep3

city: Berkeley

first: Lin

last: He

state: CA

address: 535 LSA, UC-Berkeley

institute: UC-Berkeley

description:
Gene expression data from R26MER/MER MEFs, infected with an empty retroviral vector, serum starved and treated with 4-OHT to activate c-myc.
R26MERMEF_MSCV-3

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Mouse430_2  Array. GeneChips were washed and stained in the Two GeneChip® Fluidic Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with GC-RMA package in R/BioConductor with default parameter setting.

organism: Mus musculus

source_name: R26MER/MER MEFs, infected with MSCV retroviral vector (empty vector), cultured in 0.2%serum, and treated with 4-OHT for 16h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

growth_protocol: MEFs were cultured in DMEM with 10% fetal bovine serum and were kept 60-70% confluent

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

treatment_protocol: Induced and serum starved MEFs were prepared by incubating the cells with DMEM with 0.2% fetal bovine serum and 100 nM of 4-hydroxytamoxifen for 16h before harvesting the cells.

value: R26MER/MER MEF

tag: genotype/variation

value: control


title: bsgs_79

source_name: whole blood, healthy

value: 42 yrs


title: R26MER/MER MEFs, MSCV, 0.2%serum, 16h 4OHT-treatment, biological rep2

description:
Gene expression data from R26MER/MER MEFs, infected with an empty retroviral vector, serum starved and treated with 4-OHT to activate c-myc.
R26MERMEF_MSCV-2


title: genotype: EU_T20 - rep1

value: Dr. A. Refoyo Conserved:IAS-CSIC _Cordoba_Spain


title: R26MER/MER MEFs, MSCV, 0.2%serum, 16h 4OHT-treatment, biological rep1

description:
Gene expression data from R26MER/MER MEFs, infected with an empty retroviral vector, serum starved and treated with 4-OHT to activate c-myc.
R26MERMEF_MSCV-1


title: bsgs_77

value: DZ

value: 12 yrs


title: WG2122_gDNA

description: Trio 18,  daughter

value: Female

value: primary skin fibroblast

value: Caucasian


title: R26MER/MER MEFs, MSCV-miR92, 0.2%serum, 16h 4OHT-treatment, biological rep3

description:
Gene expression data from R26MER/MER MEFs, infected with MSCV-miR92 retroviral vector, serum starved and treated with 4-OHT to activate c-myc.
R26MERMEF_MSCV-miR92-3

source_name: R26MER/MER MEFs, infected with MSCV-miR92 retroviral vector, cultured in 0.2%serum, and treated with 4-OHT for 16h

value: miR92 overexpression


title: bsgs_75

value: F


title: R26MER/MER MEFs, MSCV-miR92, 0.2%serum, 16h 4OHT-treatment, biological rep2

description:
Gene expression data from R26MER/MER MEFs, infected with MSCV-miR92 retroviral vector, serum starved and treated with 4-OHT to activate c-myc.
R26MERMEF_MSCV-miR92-2


title: R26MER/MER MEFs, MSCV-miR92, 0.2% serum, 16h 4OHT-treatment, biological rep1

description:
Gene expression data from R26MER/MER MEFs, infected with MSCV-miR92 retroviral vector, serum starved and treated with 4-OHT to activate c-myc.
R26MERMEF_MSCV-miR92-1


title: WG1978_gDNA

description: Trio 15,  father

value: Male


title: WG1513_gDNA

description: Trio 14,  father


title: Wnt3-/-_Wnt3a_36h

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

country: Japan

institute: Nara Medical University

description:
cytokine-stimulation by WNT3A (50ng/ml)
EA1107_23_36h_KO_Wnt3a+BMP4

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix)

data_processing: CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software (Dec17, 2010 build).  Data were normalized together with the default settings.  The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.

source_name: Wnt3-/- Epiblast-like cells (36h)

label_protocol: cDNAs were amplified as described in Kurimot et al., 2006, Nucreic Acids Research.  Biotinylated cRNA were prepared from amplified cDNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)

growth_protocol: mESCs maintained in N2B27medium supplemented with 2i (PD0325901, 0.4 uM: BioVision, Milpitas, CA; CHIR99021, 3 uM: BioVision) and LIF (1000 u/ml). They were induced into EpiLCs in a well of a 12-well plate coated with human plasma fibronectin (Merck Millipore) (16.7 ug/ml) in N2B27medium containing Activin A (20 ng/ml; Peprotech), bFGF (12 ng/ml; Invitrogen), and KSR (1%; Invitrogen). Medium was changed 24 hrs later, followed by another 24 hr-cultivation.

extract_protocol: Total RNA was isolated with Qianeg RNeasy Micro according to manufacture's instruction.

treatment_protocol: EpiLCs derived from mESCs were cultured by plating 2 x 10^3 cells in a well of a lipidure U-bottom 96-well plate and induced into floating aggregates in GMEM supplemented with 15% Knockout Serum Replacement (KSR; Invitrogen), leukemia inhibitory factor (LIF; 1000 u/ml; Merk Millipore), 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and 2 mM L-glutamine.

tag: strain background

value: Wnt3 Knockout; Wnt3 (-/-)

value: male

value: Wnt3 (-/-) mESCs bearing the BV transgenes

tag: cell subtype

value: Epiblast-like cells (EpiLCs)

tag: stimulated with

value: Wnt3a for 36h


title: WG1635_gDNA

description: Trio 14,  daughter


title: Wnt3-/-_BMP4+Wnt3a_36h

description:
cytokine-stimulation by BMP4 (500ng/ml) and WNT3A (50ng/ml)
EA1107_22_36h_KO_Wnt3a

value: BMP4+Wnt3a for 36h


title: WG1514_gDNA

description: Trio 14,  mother


title: bsgs_74

value: M

value: MZ


title: Wnt3-/-_BMP4_36h

description:
cytokine-stimulation by BMP4 (500ng/ml)
EA1107_21_36h_KO_BMP4

value: BMP4 for 36h


title: Wnt3+/+_BMP4_36h

description:
cytokine-stimulation by BMP4 (500ng/ml)
EA1107_18_36h_WT_BMP4

source_name: Wnt3+/+ Epiblast-like cells (36h)

value: wild type; Wnt3 (+/+)

value: Wnt3 (+/+) mESCs bearing the BV transgenes


title: Wnt3-/-_non_36h

description:
no additional cytokines
EA1107_20_36h_KO_non

value: none for 36h


title: Wnt3+/+_Wnt3a_36h

description:
cytokine-stimulation by WNT3A (50ng/ml)
EA1107_19_36h_WT_Wnt3a


title: Wnt3+/+_non_36h

description:
no additional cytokines
EA1107_17_36h_WT_non


title: bsgs_72

value: DZ

value: 15 yrs


title: Wnt3-/-_BMP4+Wnt3a_24h

description:
cytokine-stimulation by BMP4 (500ng/ml) and WNT3A (50ng/ml)
EA1107_15_24h_KO_Wnt3a

source_name: Wnt3-/- Epiblast-like cells (24h)

value: BMP4+Wnt3a for 24h


title: WG1656_gDNA

description: Trio 13,  son

value: primary skin fibroblast

value: Caucasian


title: bsgs_71

value: F

value: 44 yrs


title: Wnt3-/-_BMP4_24h

description:
cytokine-stimulation by BMP4 (500ng/ml)
EA1107_14_24h_KO_BMP4

value: Wnt3 Knockout; Wnt3 (-/-)

value: male

value: Wnt3 (-/-) mESCs bearing the BV transgenes

value: BMP4 for 24h


title: WG1977_gDNA

description: Trio 15,  mother

value: Female


title: Wnt3-/-_non_24h

description:
no additional cytokines
EA1107_13_24h_KO_non

value: Epiblast-like cells (EpiLCs)

value: none for 24h


title: Wnt3-/-_Wnt3a_24h

description:
cytokine-stimulation by WNT3A (50ng/ml)
EA1107_16_24h_KO_Wnt3a+BMP4

value: Wnt3a for 24h


title: WG1309_gDNA

description: Trio 16,  father

value: Male


title: bsgs_70

value: 12 yrs


title: WG1657_gDNA

description: Trio 13,  father


title: bsgs_73

value: DZ


title: WG1658_gDNA

description: Trio 13,  mother


title: bsgs_76


title: bsgs_69


title: WG1720_gDNA

description: Trio 12,  son


title: Wnt3+/+_BMP4_24h

description:
cytokine-stimulation by BMP4 (500ng/ml)
EA1107_11_24h_WT_BMP4

source_name: Wnt3+/+ Epiblast-like cells (24h)

value: wild type; Wnt3 (+/+)

value: Wnt3 (+/+) mESCs bearing the BV transgenes


title: Wnt3+/+_non_24h

description:
no additional cytokines
EA1107_10_24h_WT_non


title: WG1722_gDNA

description: Trio 12,  mother

value: primary skin fibroblast


title: WG1721_gDNA

description: Trio 12,  father

value: Caucasian


title: bsgs_67

value: M

value: 43 yrs


title: bsgs_68

value: 16 yrs


title: Wnt3-/-_Wnt3a_12h

description:
cytokine-stimulation by WNT3A (50ng/ml)
EA1107_09_12h_KO_Wnt3a+BMP4

source_name: Wnt3-/- Epiblast-like cells (12h)

value: Wnt3 Knockout; Wnt3 (-/-)

value: male

value: Wnt3a for 12h


title: bsgs_66

value: F


title: Wnt3-/-_BMP4+Wnt3a_12h

description:
cytokine-stimulation by BMP4 (500ng/ml) and WNT3A (50ng/ml)
EA1107_08_12h_KO_Wnt3a

value: Wnt3 (-/-) mESCs bearing the BV transgenes

value: Epiblast-like cells (EpiLCs)

value: BMP4+Wnt3a for 12h


title: GM01652_gDNA

description: Family 165,  daughter

value: Female


title: bsgs_64

value: 12 yrs


title: Wnt3-/-_non_12h

description:
no additional cytokines
EA1107_06_12h_KO_non

value: none for 12h


title: Wnt3+/+_Wnt3a_12h

description:
cytokine-stimulation by WNT3A (50ng/ml)
EA1107_05_12h_WT_Wnt3a

source_name: Wnt3+/+ Epiblast-like cells (12h)

value: wild type; Wnt3 (+/+)


title: GM01650_gDNA

description: Family 165,  mother


title: bsgs_63

value: DZ


title: Wnt3+/+_BMP4_12h

description:
cytokine-stimulation by BMP4 (500ng/ml)
EA1107_04_12h_WT_BMP4

value: Wnt3 (+/+) mESCs bearing the BV transgenes

value: BMP4 for 12h


title: 1000 ng/ml doxycycline B

city: London

first: Rodney

middle: P.

last: DeKoter

state: Ontario

address: 1151 Richmond Street

department: Microbiology & Immunology

institute: University of Western Ontario

description: mouse gene 2.0 ST

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: GeneChip Scanner 3000 (Affymetrix).

data_processing:
Data were analyzed using Partek Genomics Suite.
MoEx-1 0-st-v1.r2.pgf
MoGene-2_0-st-v1.na33.mm10.transcript.csv

source_name: Myeloid cells, induced

label_protocol: RNA was processed using the WT terminal labeling and hybridization kit (Affymetrix, Santa Clara, CA)

growth_protocol: Myeloid cells were grown in 1 ng/ml GM-CSF

extract_protocol: Total RNA was prepared from single cell suspensions using Trizol reagent (Life Technologies)

treatment_protocol: Cultured cells were treated with or without 1000 ng/ml doxycycline for 72 hours

value: myeloid cell

tag: treatment

value: PU.1 expression

value: Fetal Liver


title: Wnt3+/+_0h

source_name: Wnt3+/+ Epiblast-like cells (0h)

value: none for 0h


title: Wnt3-/-_0h

source_name: Wnt3-/- Epiblast-like cells (0h)

value: Wnt3 Knockout; Wnt3 (-/-)

value: male


title: 1000 ng/ml doxycycline C

description: mouse gene 2.0 ST


title: Wnt3-/-_BMP4_12h

description:
cytokine-stimulation by BMP4 (500ng/ml)
EA1107_07_12h_KO_BMP4


title: Wnt3+/+_Wnt3a_24h

description:
cytokine-stimulation by WNT3A (50ng/ml)
EA1107_12_24h_WT_Wnt3a

value: Wnt3a for 24h


title: Wnt3+/+_non_12h

description:
no additional cytokines
EA1107_03_12h_WT_non


title: bsgs_62

value: F

value: 42 yrs


title: uninduced C

description: mouse gene 2.0 ST

source_name: Myeloid cells, control

value: control


title: bsgs_61


title: bsgs_60

value: M

value: 15 yrs


title: uninduced B

description: mouse gene 2.0 ST


title: 1000 ng/ml doxycycline A

description: mouse gene 2.0 ST


title: GM01653_gDNA

description: Family 165,  father

value: Male

value: primary skin fibroblast

value: Caucasian


title: uninduced A

description: mouse gene 2.0 ST


title: GM00022_gDNA

description: Family 491 ,  mother

value: Female


title: bsgs_57

value: 14 yrs


title: bsgs_58

value: 44 yrs


title: GM00242_gDNA

description: Family 491 ,  daughter


title: bsgs_65

value: 17 yrs


title: T cell (CD3 positive)_medip_control_aggressivity.28

first: Moshe

last: Szyf

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

description:
control aggressivity trajectory
control aggressivity trajectory
comparison of T cell DNA methylation in individuals with different aggressivity trajectories

hyb_protocol: All the steps of hybridization, washing, and scanning were performed following the Agilent protocol for ChIP-on-chip analysis. Cot-1 DNA was added to the hybridization mix to minimize cross-hybridization between repetitive element.

scan_protocol: Scanning was performed using the Agilent Technologies Scanner G2505B.

data_processing: After microarray scanning, probe intensities were extracted from scan images using Agilent's Feature Extraction 9.5.3 Image Analysis Software. Quality control involved visual inspection of microarray scan images, scanning software reports and generation of MvA plots (i.e. plots of log(Cy5/Cy3) vs log(Cy5 x Cy3)) to identify microarrays with dye biases or low signal. Microarrays were normalized using background subtraction followed by quantile normalization of log2-ratios of bound (Cy5) and input (Cy3) channel intensities.

source_name: T cell (CD3 positive)_meDIP_control_aggressivity

label_protocol: The input and bound fractions were amplified using Whole Genome Amplification kit (Sigma) and labeled for microarray hybridization with either Cy3-dUTP or Cy5-dUTP (Perkin Elmer) respectively using the CGH labeling kit (Invitrogen) following the manufacturer's instructions. 2ug of each of the input and bound fractions were labeled.

extract_protocol: 20 ml of blood were drawn in EDTA coated-tubes for each subjects. PBMC (whole mononuclear cells from peripheral blood) and T cell isolation procedures were adapted from Current Protocols in Immunology (1997, sections 7.1 and 7.5.1-7.5.11). Briefly, PBMC isolation was done by centrifugation with Ficoll-Paque (GE healthcare) and washed twice with HBSS (Hanks balanced salt solution, GIBCO). T cells were isolated from the PBMCs by immunomagnetic positive selection using CD3 dynabeads (Dynal). The beads were washed 3 times and incubated with the PBMCs for 45 min on a rotator at 4C. Coated CD3+ cells with the dynabeads were isolated using a strong magnet (Steam Cell Technology) and washed 5 times with PBS/FBS. CD3+ cells coated with the dynabeads were then frozen at -80C until DNA extraction.  T cells DNA was extracted with Wizard Genomic DNA Purification kit (Promega) following the manufacturer's protocol. For MeDIP analysis, 2 ug of the T cells DNA were sonicated and methylated DNA was immunoprecipitated with 10ug of anti-5methylCytosine (Calbiochem, Cat. # NA81, Lot: D00048001). The input and bound fractions were then amplified in triplicate using the Whole Genome Amplification kit (Sigma).

value: female

value: T cell (CD3 positive)

tag: state

value: control aggressivity trajectory

tag: antibody

value: anti-5 methylcytosine antibody (Calbiochem, Cat. # NA81, Lot:D00048001)

source_name: T cell (CD3 positive)_input_DNA_control_aggressivity


title: bsgs_56


title: bsgs_54

value: DZ

value: 12 yrs


title: bsgs_55

value: F


title: T cell (CD3 positive)_medip_control_aggressivity.26

tag: cell type


title: T cell (CD3 positive)_medip_control_aggressivity.27


title: bsgs_53


title: T cell (CD3 positive)_medip_control_aggressivity.25


title: T cell (CD3 positive)_medip_control_aggressivity.24


title: bsgs_52

value: 52 yrs


title: bsgs_50

value: M

value: 49 yrs


title: bsgs_51


title: bsgs_49

value: 42 yrs


title: bsgs_48

value: 21 yrs


title: T cell (CD3 positive)_medip_control_aggressivity.23


title: GM09256_gDNA

description: Family 2131,  mother

value: primary skin fibroblast

tag: population

value: Caucasian


title: T cell (CD3 positive)_medip_chronic_aggressivity.10

description:
chronic aggressivity trajectory
chronic aggressivity trajectory
comparison of T cell DNA methylation in individuals with different aggressivity trajectories

source_name: T cell (CD3 positive)_meDIP_chronic_aggressivity

value: chronic aggressivity trajectory

source_name: T cell (CD3 positive)_input_DNA_chronic_aggressivity


title: T cell (CD3 positive)_medip_chronic_aggressivity.9


title: bsgs_59


title: T cell (CD3 positive)_medip_control_aggressivity.20


title: GM00935_gDNA

description: Family 51,  mother

value: Female


title: T cell (CD3 positive)_medip_control_aggressivity.22


title: WG2064_gDNA

description: Trio 11,  daughter


title: T cell (CD3 positive)_medip_control_aggressivity.19


title: GM00519_gDNA

description: Family 51,  daughter


title: bsgs_45


title: bsgs_46


title: T cell (CD3 positive)_medip_control_aggressivity.21


title: WG1926_gDNA

description: Family 51,  son

value: Male


title: GM00520_gDNA

description: Family 51,  father


title: T cell (CD3 positive)_medip_control_aggressivity.17

value: female


title: bsgs_44

value: 48 yrs


title: T cell (CD3 positive)_medip_control_aggressivity.18

value: T cell (CD3 positive)

value: control aggressivity trajectory


title: bsgs_42

value: DZ


title: bsgs_43

value: 38 yrs


title: T cell (CD3 positive)_medip_control_aggressivity.15

value: anti-5 methylcytosine antibody (Calbiochem, Cat. # NA81, Lot:D00048001)


title: bsgs_41

value: F

value: 12 yrs


title: WG1983_gDNA

description: Family 51,  mother


title: WG2065_gDNA

description: Trio 11,  mother


title: WG1984_gDNA

description: Family 51,  father


title: bsgs_40

value: M

value: MZ


title: bsgs_39

value: 50 yrs


title: GM09257_gDNA

description: Family 2131,  daughter

value: primary skin fibroblast


title: bsgs_47


title: T cell (CD3 positive)_medip_control_aggressivity.13


title: bsgs_38


title: T cell (CD3 positive)_medip_control_aggressivity.14


title: bsgs_36

value: 13 yrs


title: T cell (CD3 positive)_medip_chronic_aggressivity.8

value: chronic aggressivity trajectory


title: T cell (CD3 positive)_medip_chronic_aggressivity.7


title: T cell (CD3 positive)_medip_control_aggressivity.12


title: T cell (CD3 positive)_medip_control_aggressivity.16


title: bsgs_37

value: 43 yrs


title: bsgs_34

value: 41 yrs


title: T cell (CD3 positive)_medip_control_aggressivity.10

value: female


title: bsgs_33

value: 47 yrs


title: GM00016_gDNA

description: Family 491 ,  father

value: Male

value: Caucasian


title: T cell (CD3 positive)_medip_chronic_aggressivity.6

value: T cell (CD3 positive)


title: GM09255_gDNA

description: Family 2131,  father


title: bsgs_31

value: DZ


title: CIRM-BIA1-spentmedium-rep3

city: Rennes

first: Hélène

last: Falentin

address: 65 rue de St Brieuc

department: Microbiologie

country: France

institute: INRA

description: Sample name: C30_3

hyb_protocol: Hybridization was carried out for 17 hours at 65°C using a Microarray hybridization chamber (Agilent Technologies) in a rotating hybridization oven prior to washing according to Agilent protocol

scan_protocol: scanning with an Agilent Scanner (DNA Microarray Scanner, Agilent Technologies) using the standard parameters for a gene expression 8x15K oligoarray (5µm and 20bits). Data were then obtained with the Agilent Feature Extraction software (10.5.1.1) according to the appropriate GE protocol (GE1_105_Dec08).

data_processing:
Probes were considered valid when the corresponding spots were present in at least 80% of the replicates of each experimental condition after the flagging procedure (66 probes were thus omitted from the rest of the analysis). The remaining bad spots (less than 5% of the total) were imputed by the k-nearest neighborhood (k=4) approach. An analysis of the variability within and between piglets (N= 13770 probes) using matrix of parametric correlations allowed us to choose the 2 most reproducible replicates amongst 4 for each piglet (figure S2). Four independent signals (one by piglet) were then obtained by averaging the 2 selected signals from each piglet. For the YEL condition, 8 biological repeats amongst the 12 measures were randomly selected and averaged 2 by 2, establishing 4 independent measures.  The multiple signals corresponding to the same probes were averaged, and the log2-signals were subsequently scaled-normalized using the median value of each array[34] given a final data sets of 2229 genes.
Differential comparisons between groups were performed gene by gene using modified t-test with limma adjustment (Pvalue≤ 10-4) from the limma package of R software[35, 36], which Bayesian approach stays a very convenient and powerful tool when working  with a low number of biological replicates[37].
The increase of the type I error rate induced by the multiplicity of tests was controlled by the Benjamini-Hochberg adjustment from the False Discovery Rate family[38]. Genes were declared as differentially expressed (DE) with P ≤ 0.001  and |fold change|> 2.

organism: Propionibacterium freudenreichii

source_name: RNA from Propionibacterium freudenreichii CIRM-BIA1 after 24H in spent YEL medium

label_protocol: RNA were retrotranscribed into cDNA and labelled with cyanine with the One color microarray-based prokaryote analysis FairPlay III Labelling kit (Agilent Technologies) according to manufacturer instructions. Briefly, for each sample, 6 µg of total RNA were retrotranscribed into cDNA with incorporation of an amino-allyldUTP and labeled using CyDye Cy3 mono reactive (GE Healthcare, Orsay, France). Yield (> 650 ng of cDNA) and specific activity (> 40 pmol of Cy3 per µg of cDNA) of the Cy3-cDNA produced were checked with the Nanodrop.  600 ng of Cy3-cDNA was hybridized on a sub-array.

growth_protocol: P. freudenreichii strain CIRM BIA 1 was grown at 30°C in YEL broth in closed glass tubes without agitation

extract_protocol: 1 ml of each culture or of a 1/10 v:v PBS dilution of the content of the dialysis tubing was mixed to 2 volumes of RnaProtect (Qiagen, Hilden, Germany), left 5 min at room temperature and centrifuged (8,000  g, 10 min, at room temperature). The supernatant was removed and the pellet stored at -80°C until total RNA was extracted. Pellets were thawed on ice, suspended in 200 µl of lysis buffer (50 mM Tris-HCl, 1 mM EDTA; pH 8.0) containing 20 mg/mL lysozyme (MP Biomedicals, Illkirch, France) and 50 U.mL-1 mutanolysin (Sigma, Saint Quentin Fallavier, France), and incubated for 15 min at 24°C. The suspensions were then transferred to 2-mL tubes containing 50 mg of zirconium beads (diameter, 0.1 mm; BioSpec Products, Bartlesville, OK) and 100 µl of SDS (10%). The tubes were shaken twice for 90 s at 30 Hz with a bead beater (MM301; Retsch, Haan, Germany) with chilling on ice for 2 min between the shaking steps. RNA extraction was then performed using an RNeasy minikit (Qiagen) according to the instructions of the manufacturer and the Qiacube extraction robot (Qiagen). RNA were suspended in 50 µl ofRNase-free water and treated with DNase (DNA free; Ambion, Cambridgeshire,United Kingdom) accordingly to the instructions of the supplier, and thenstored at -80°C until use. Quantification of RNAwas performed and contamination of RNA by proteins was assessed spectrophotometrically using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies,Inc., Rockland, DE). RNA quality was evaluated using an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). All of the RNA samples had a RIN value greater than 7.5, indicating good integrity of the rRNA. The absence of genomic DNA was confirmed by quantitative PCR.

treatment_protocol: Cultures were stopped at an A650nmof 3 ; i.e. in early stationary phase. Half of the culture was kept in spent YEL culture medium for 24 hours. The other half was concentrated 5 times by centrifugation and resuspension in spent YEL culture medium prior to introduction into a dialysis tubing. The dialysis tubing was inserted into the colonic lumen through the cannula and left for 24 hrs with recommendations of the French law (2001-464 29/05/01) and EEC (86/609/CEE) for the care and use of laboratory animals

tag: strain

tag: growth conditions

value: control


title: CIRM-BIA1-24Hcolon-pigD

description: Sample name: CO_D

source_name: RNA from Propionibacterium freudenreichii CIRM-BIA1 after 24H in the colon of pig

value: 24H in the colon of pig


title: CIRM-BIA1-spentmedium-rep4

description: Sample name: C30_4


title: CIRM-BIA1-spentmedium-rep1

description: Sample name: C30_1


title: WG2276_gDNA

description: Trio 10,  mother

value: Female


title: bsgs_26

source_name: whole blood, healthy

value: M

value: 12 yrs


title: WG2274_gDNA

description: Trio 10,  daughter


title: bsgs_28

value: MZ


title: bsgs_29

value: 15 yrs


title: bsgs_27


title: T cell (CD3 positive)_medip_chronic_aggressivity.5

value: anti-5 methylcytosine antibody (Calbiochem, Cat. # NA81, Lot:D00048001)


title: T cell (CD3 positive)_medip_chronic_aggressivity.4

value: chronic aggressivity trajectory


title: T cell (CD3 positive)_medip_control_aggressivity.9

value: control aggressivity trajectory


title: CIRM-BIA1-spentmedium-rep2

description: Sample name: C30_2


title: T cell (CD3 positive)_medip_control_aggressivity.8


title: bsgs_25

value: 16 yrs


title: CIRM-BIA1-24Hcolon-pigB

description: Sample name: CO_B


title: CIRM-BIA1-24Hcolon-pigC

description: Sample name: CO_C


title: bsgs_30

value: 55 yrs


title: T cell (CD3 positive)_medip_control_aggressivity.11

value: female


title: bsgs_35

value: F


title: bsgs_32


title: WG2275_gDNA

description: Trio 10,  father

value: Male

value: primary skin fibroblast

value: Caucasian


title: bsgs_23

value: DZ

value: 13 yrs


title: T cell (CD3 positive)_medip_control_aggressivity.6

value: T cell (CD3 positive)


title: CIRM-BIA1-24Hcolon-pigA

description: Sample name: CO_A

value: 24H in the colon of pig


title: T cell (CD3 positive)_medip_control_aggressivity.7


title: bsgs_22

value: M

value: 47 yrs


title: T cell (CD3 positive)_medip_control_aggressivity.5


title: T cell (CD3 positive)_medip_chronic_aggressivity.3


title: Whole fly tissue: hatched and raised in earth gravity fungal infection biological rep 3

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: Gene expression data from a pool of 4-20 whole flies hatched and raised in earth gravity, infected with B. bassiana

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila mlanogaster 3' IVT arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Partek Genomics Suite

organism: Drosophila melanogaster

source_name: Whole homogenized drosophila infected with Beauveria bassiana

label_protocol: Biotinylated cRNA were prepared according to the standard protocols described in the Affymetrix Gene Expression Analysis Technical Manual

extract_protocol: RNA was extracted with the Qiagen Rneasy kit according to the manufacturer's instructions.

value: Oregon R

value: whole organism

tag: life stage

value: adult

tag: infection

value: infected with Beauveria bassiana


title: bsgs_21

tag: gender

tag: twin

value: 44 yrs


title: WG2066_gDNA

description: Trio 11,  father


title: bsgs_24

tag: age

value: 14 yrs


title: bsgs_19


title: Whole fly tissue: hatched and raised in earth gravity fungal infection biological rep 2

tag: tissue


title: T cell (CD3 positive)_medip_control_aggressivity.4

value: female

value: control aggressivity trajectory

value: anti-5 methylcytosine antibody (Calbiochem, Cat. # NA81, Lot:D00048001)


title: T cell (CD3 positive)_medip_control_aggressivity.2


title: bsgs_20

value: F

value: 40 yrs


title: T cell (CD3 positive)_medip_chronic_aggressivity.1

value: chronic aggressivity trajectory


title: T cell (CD3 positive)_medip_control_aggressivity.1


title: Whole fly tissue: hatched and raised in earth gravity fungal infection biological rep 1


title: T cell (CD3 positive)_medip_chronic_aggressivity.2


title: T cell (CD3 positive)_medip_control_aggressivity.3


title: bsgs_14


title: bsgs_17

value: 41 yrs


title: Whole fly tissue: hatched and raised in microgravity fungal infection biological rep 3

description: Gene expression data from a pool of 4-20 whole flies hatched and raised in microgravity, infected with B. bassiana


title: Whole fly tissue: hatched and raised in microgravity bacterial infection biological rep 2

description: Gene expression data from a pool of 4-20 whole flies hatched and raised in microgravity, infected with E. coli

source_name: Whole homogenized drosophila infected with Escherichia coli

value: infected with Escherichia coli


title: Whole fly tissue: hatched and raised in microgravity fungal infection biological rep 2


title: Whole fly tissue: hatched and raised in microgravity bacterial infection biological rep 1


title: bsgs_15

value: 15 yrs


title: bsgs_12

value: 52 yrs


title: Whole fly tissue: hatched and raised in microgravity bacterial infection biological rep 3


title: bsgs_18

value: 38 yrs


title: Whole fly tissue: hatched and raised in earth gravity bacterial infection biological rep 1

description: Gene expression data from a pool of 4-20 whole flies hatched and raised in earth gravity, infected with E. coli

value: Oregon R


title: Whole fly tissue: hatched and raised in microgravity fungal infection biological rep 1

value: whole organism


title: Whole fly tissue: hatched and raised in earth gravity bacterial infection biological rep 2

value: adult


title: bsgs_16

value: M

value: DZ

value: 12 yrs


title: Whole fly tissue: hatched and raised in earth gravity bacterial infection biological rep 3


title: bsgs_13


title: bsgs_11

value: 13 yrs


title: Whole fly tissue: hatched and raised in earth gravity uninfected biological rep 3

description: Gene expression data from a pool of 4-20 whole flies hatched and raised in earth gravity, uninfected

source_name: Whole homogenized uninfected drosophila


title: bsgs_9


title: male-CPA3 pool

description:
CPA aggressivity trajectory
pool male-CPA3 of T cell (CD3 positive) DNA methylation from CPA males

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol, except that 8ul of bisulfite converted material was used to initiate the amplification step.

scan_protocol: Arrays were scanned using the Illumina iScan Reader using standard recommended Illumina scanner settings.

data_processing: Data analysis was performed using the Methylation module (version 1.9.0) of the GenomeStudio software (Illumina; version 2011.1). Significant differences in methylation levels between CPA and control groups were obtained using the Illumina custom method with a False Discovery Rate (FDR) < 0.05. Beta-values with detection P-value > 0.001 were removed from the analysis since they are considered to fall below the minimum intensity and threshold. All the probes that contained a SNP within 10 bp of the CpG site were excluded from the analysis to ensure equal annealing efficiency between the samples.

label_protocol: Standard Illumina Infinium Assay Protocol

extract_protocol: T cells were isolated from the PBMCs by immunomagnetic positive selection using CD3 dynabeads (Dynal). T cells DNA was extracted with Wizard Genomic DNA Purification kit (Promega) following the manufacturers protocol.  Genomic DNA was quantified using Picogreen protocol (Quant-iT PicoGreen dsDNA Products, Invitrogen) and read on SpectraMAX GeminiXS Spectrophotometer. Bisulfite conversion was performed with 500 ng of genomic DNA using the EZ-96 DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer's instructions.

value: male

value: T cell (CD3 positive)

value: CPA aggressivity trajectory


title: bsgs_10


title: Whole fly tissue: hatched and raised in microgravity uninfected biological rep 2

description: Gene expression data from a pool of 4-20 whole flies hatched and raised in microgravity, uninfected


title: bsgs_6

value: F

value: 40 yrs


title: bsgs_5

value: 44 yrs


title: Whole fly tissue: hatched and raised in earth gravity uninfected biological rep 2


title: bsgs_8

value: 43 yrs


title: bsgs_4

value: 14 yrs


title: Whole fly tissue: hatched and raised in microgravity uninfected biological rep 3


title: Whole fly tissue: hatched and raised in earth gravity uninfected biological rep 1


title: bsgs_7


title: bsgs_3

value: 18 yrs


title: bsgs_2


title: Whole fly tissue: hatched and raised in microgravity uninfected biological rep 1


title: sleep HSCs

city: Stanford

first: Irv

last: Weissman

address: 265 Campus Dr. West

department: Stem Cell Institute

institute: Stanford University

description: control

data_processing:
The normalization of each miRNA was to U6.Target gene signals normalized to U6; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_U6)]
Matrix normalized worksheet reports normalized signal (against U6). Fold change worksheets report test/control (i.e., sleep deprived/sleep) ratio

label: FAM

source_name: mouse HSC

label_protocol: pcr analysis was perfored using Applied Biosystems Rodent MicroRNA Card A

extract_protocol: total RNA was extracted using Trizol (Invitrogen)

value: hematopoetic stem cells

tag: time

value: slept for 4 hours


title: bsgs_1


title: female-NPA2 pool

description:
NPA aggressivity trajectory
pool female-NPA2 of T cell (CD3 positive) DNA methylation from NPA females

value: female

value: NPA aggressivity trajectory


title: female-CPA2 pool

description:
CPA aggressivity trajectory
pool female-CPA2 of T cell (CD3 positive) DNA methylation from CPA females


title: Reference sample vs. Alveolar macrophages with LPS Replicate 2

city: CORDOBA

first: JUAN JOSE

middle: GARRIDO

last: PAVÓN

state: CORDOBA

address: Edificio Gregor Mendel (C5)

department: GENÉTICA

country: Spain

institute: UNIVERSITY OF CÓRDOBA

description: 10-12 week old castrate of Landrace/Yorkshire/Duroc from a high health herd

hyb_protocol: DIAS_pig_55K2 slides were pre-hybridized for 30 min and hybridized for 16h at 42ºC in a Lucidea Automated Slide Processor (Amersham Biosciencies) following the protocol with formamide, both according to the supplier´s instructions (Corning, NY, USA).

scan_protocol: Images were acquired by a dual laser scanning system, GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA), at a resolution of 5 µm. The scanned microarray images were analyzed using the histogram method with default setting in a GenePix Pro 4.1 Microarray Image Analysis (Molecular Devices).

data_processing:
Spots flagged below 0 using GenePix v6.0 software (Axon Instruments) and those whose signal intensity did not surpass 2X their background signal in both channels were discarded. Background correction was performed with the “normexp” method of the limma library. M value was defined as the base two logarithm of every expression ratio, computed as the ratio between the background-corrected foreground intensities of the Cy3 and Cy5 channels. Raw expression data were normalized for all sources of systematic variation with the print-tip loess. using the common assumption of considering the whole microarray expression as invariant. The Biobase v 2.0.1 of the Bioconductor package [Gentleman RC et al. Genome Biol 2004, 5:R80] was installed under R version 2.7.1 for all statistical analysis, mainly the limma v 2.14.5 [Smyth G. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor. Edited by Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W. New York: Springer; 2005: 397–420] and marray v 1.18.0 (http://www.bioconductor.org/packages/release/bioc/html/marray.html) libraries.
Statistical analysis was carried out in the R computing environment (version 2.15.3 for windows) using the package Linear Models for Microarray Analysis (Limma, version 2.10.7) (Smyth, 2004) which is part of the Bioconductor project (Gentleman et al., 2004). The log2-transformed ratios of Alexa-647 to Alexa-555 (not background corrected) were normalized within-slide using printtip-loess with default parameters as implemented in Limma and can be found in the “Value” column.

organism: Sus scrofa

source_name: Common reference

label_protocol: Superscript Indirect cDNA Labeling System (Invitrogen) and ARES cDNA labeling kit (Molecular Probes/Invitrogen)

extract_protocol: RNeasy Midi Kit with DNase treatment (Qiagen)

value: Mixture of total RNA purified from challenged and healthy alveolar macrophages

source_name: Total RNA from alveolar macrophages with LPS 2

value: alveolar macrophages


title: female-CPA3 pool

description:
CPA aggressivity trajectory
pool female-CPA3 of T cell (CD3 positive) DNA methylation from CPA females


title: Reference sample vs. Alveolar macrophages without LPS Replicate 1

source_name: Total RNA from alveolar macrophages without LPS 1


title: Reference sample vs. Alveolar macrophages with LPS Replicate 1

source_name: Total RNA from alveolar macrophages with LPS 1


title: Reference sample vs. Alveolar macrophages without LPS Replicate 2

source_name: Total RNA from alveolar macrophages without LPS 2


title: sleep deprived HSCs

description: test

value: sleep deprived for 4 hours


title: female-CPA1 pool

description:
CPA aggressivity trajectory
pool female-CPA1 of T cell (CD3 positive) DNA methylation from CPA females


title: male-NPA2 pool

description:
NPA aggressivity trajectory
pool male-NPA2 of T cell (CD3 positive) DNA methylation from NPA males


title: female-NPA3 pool

description:
NPA aggressivity trajectory
pool female-NPA3 of T cell (CD3 positive) DNA methylation from NPA females


title: E. coli MG1655-control-3

status: Public on Dec 10 2013

first: Laura

last: Jarboe

address: 3051 Sweeney Hall

department: Chemical & Biological Engineering

institute: Iowa State university

description: Gene expression data in MOPS minimal media

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit: Affymetrix kit, Expression Analysis Technical Manual, GeneChip Fluidics Station 450

scan_protocol: Affymetrix Microarray Suite/Affymetrix GeneChip Scanner 3000, Expression Analysis Technical Manual

data_processing: MATLAB v. R2012b program using GCRMA algorithm

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli MG1655-MOPS+2%Dextrose

label_protocol: GeneChip® DNA Labeling Reagent, Affymetrix kit, Expression Analysis Technical Manual

growth_protocol: E. coli MG1655 was grown in MOPS + 2 % Dextrose minimal media +- 10 mM octanoic acid (pH=7.0) from OD550 0.05 to ~0.8 and harvested at Midlog.

extract_protocol: Cells were centrifuged and the cell pellets were stored in RNA Later solution at -80ºC. The RNeasy Mini Kit (Qiagen, Venlo, Netherlands) was used to isolate total RNA. The samples were then incubated at 37ºC with RNaseOut (New England Biolabs) and DNaseI (New England Biolabs) according to the manufacture’s protocol for 1 hour. The samples were mixed with saturated phenol/chloroform (pH=4.5) (Life Technologies) and precipitated with ethanol and 30 µL, 3 M sodium acetate (pH=5.5) (Fisher Scientific), overnight at -80ºC. After precipitation, the tubes were centrifuged and the RNA pellet was washed twice with 70 % ethanol and dried under vacuum.

treatment_protocol: The treatment condition includes adding 10 mM octanoic acid during logarithmic growth.


title: E. coli MG1655-C8-1

description: Gene expression data in MOPS minimal media with 10 mM ocatnoic acid, pH=7.0

source_name: E. coli MG1655-MOPS+2%Dextrose+10mM C8


title: E. coli MG1655-C8-3


title: E. coli MG1655-control-2


title: ZH11 14-day old seeding, biological rep 2

city: wuhan

first: zhong

last: xiaochao

address: shizishan road No.1

country: China

institute: NCPGR

description: Gene expression data from 14 days seeding

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

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

data_processing: The data were analyzed with affylmGUI packages in R. RMA was used to nomalized the data. Using toptable to order different expression genes with 2-fold change and p-value<0.05

organism: Oryza sativa Japonica Group

source_name: 14 days seedling after germination under normal growth conditions

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

growth_protocol: transgenic, mutant and wild-type seedlings were grown in half-strength Murashige and Skoog medium under a 16-h-light/8-h-dark cycle at 30℃ for 14 d

value: seedling

tag: genotype/variation


title: colorectal cancer without liver metastasis_16

city: Guangzhou

first: Dong-liang

last: Chen

address: No.651 Dong Feng East Road

institute: Sun Yat-sen University Cancer Center

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
1381T

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000G.

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

treatment_protocol: Their primary CRC tissues (n = 99), adjacent normal tissues (n = 99) and corresponding matched liver metastatic tissues (n = 44) were obtained immediately after surgery and stored at -80 ºC until use

tag: disease state

value: CRC

tag: liver metastasis

value: without


title: HY 14-day old seeding, biological rep 2

value: HY


title: E. coli MG1655-control-1


title: JMJ705 overexpression 14-day old seeding, biological rep 2

value: jmj705 overexpressed


title: colorectal cancer without liver metastasis_12

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
1117T


title: HY 14-day old seeding, biological rep 1


title: colorectal cancer without liver metastasis_13

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
1125T


title: jmj705 mutant 14-day old seeding, biological rep 2

value: jmj705 mutant


title: colorectal cancer without liver metastasis_14

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
1136T


title: ZH11 14-day old seeding, biological rep 1


title: JMJ705 overexpression 14-day old seeding, biological rep 1


title: male-NPA1 pool

description:
NPA aggressivity trajectory
pool male-NPA1 of T cell (CD3 positive) DNA methylation from NPA males

value: male

value: T cell (CD3 positive)


title: colorectal cancer without liver metastasis_9

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
944T


title: male-CPA2 pool

description:
CPA aggressivity trajectory
pool male-CPA2 of T cell (CD3 positive) DNA methylation from CPA males

value: CPA aggressivity trajectory


title: male-CPA1 pool

description:
CPA aggressivity trajectory
pool male-CPA1 of T cell (CD3 positive) DNA methylation from CPA males


title: colorectal cancer without liver metastasis_7

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
861T


title: jmj705 mutant 14-day old seeding, biological rep 1


title: colorectal cancer without liver metastasis_15

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
1145T


title: colorectal cancer without liver metastasis_2

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
703T


title: colorectal cancer without liver metastasis_5

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
776T


title: colorectal cancer without liver metastasis_4

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
735T


title: colorectal cancer without liver metastasis_8

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
862T


title: colorectal cancer without liver metastasis_3

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
709T


title: colorectal cancer without liver metastasis_6

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
828T


title: colorectal cancer without liver metastasis_10

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
979T


title: colorectal cancer without liver metastasis_11

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
1114T


title: colorectal cancer with liver metastasis_13

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
487T

source_name: colorectal cancer with liver metastasis

value: with


title: female-NPA1 pool

description:
NPA aggressivity trajectory
pool female-NPA1 of T cell (CD3 positive) DNA methylation from NPA females


title: colorectal cancer with liver metastasis_14

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
531T


title: colorectal cancer with liver metastasis_8

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
392T


title: colorectal cancer with liver metastasis_7

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
387T


title: colorectal cancer without liver metastasis_1

description:
Gene expression data from human colorectal cancer tissue without liver metastasis
687T


title: colorectal cancer with liver metastasis_9

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
402T


title: colorectal cancer with liver metastasis_6

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
382T


title: colorectal cancer with liver metastasis_10

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
422T


title: colorectal cancer with liver metastasis_4

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
342T


title: colorectal cancer with liver metastasis_1

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
61T


title: colorectal cancer with liver metastasis_5

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
347T


title: colorectal cancer with liver metastasis_11

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
438T


title: colorectal cancer with liver metastasis_12

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
451T


title: colorectal cancer with liver metastasis_2

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
272T


title: colorectal cancer with liver metastasis_3

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
328T


title: HS5-D1B_01

city: Seattle

first: mineo

last: iwata

state: WA

address: 1100 Fairview Ave N

department: Transplantation Biology

institute: Fred Hutchinson Cancer Research Center

description:
Sample 5
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Signal intensities were quantile normalized using the Bioconductor package lumi.

label_protocol: Illumina TotalPrep RNA Amplification Kit

growth_protocol: HS5 cells were transfected with siRNA (as described in the treatment protocol) using  Lipofectamine RNAiMAX (Life Technologies) and cultured for 2 days in RPMI1640 medium containing 10% FCS

extract_protocol: Total RNA was extracted from the cells using RNeasy mini spin columns (QIAGEN) in accordance with the manufacturer's protocol. Quality control was performed with Agilent 2100 Bioanalyzer.

treatment_protocol: Non-transfected (HS5_01, HS5_02) or transfected with siRNA for CDCP1 (HS5-CDCP_01, 02), KDM3B (HS5-D1B_01, 02, 03), luciferase (HS5-lucif_01, 02) or SDC1 (HS5-SDK_01, 02)

tag: cell line

value: HS5 stromal cells

value: KDM3B KD


title: HS5-CDCP_02

description:
Sample 4
replicate 2

value: CDCP1 KD


title: HS5-D1B_02

description:
Sample 6
replicate 2


title: HS5-SDK_01

description:
Sample 10
replicate 1

value: SDC1 KD


title: HS5-lucif_01

description:
Sample 8
replicate 1

value: luciferase KD


title: HS5-D1B_03

description:
Sample 7
replicate 3


title: HS5_02

description:
Sample 2
replicate 2


title: HS5-CDCP_01

description:
Sample 3
replicate 1


title: HS5-SDK_02

description:
Sample 11
replicate 2


title: PreGM Cebpa ∆/∆ GFP-pos rep 3

city: Copenhagen N

first: Ewa

last: Ohlsson

address: Ole Maaløes vej 5

department: Finsen Laboratory/BRIC/DanStem

institute: University of Copenhagen

description:
Bone marrow cells, PreGMs
PreGM Cebpa ∆/∆ GFP-pos rep 3

hyb_protocol: Affymetrix EukGE-WS2v4_450 Hybridization protocol, according to manufacturers specifications

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

data_processing: The data was normalized and log2 transformed using the RMA software from Bioconductor.

source_name: GFP-pos PreGM  72h post  MLL-ENL transduction

label_protocol: 2.5ug of amplified cDNA was fragmentated and labeled using Encore Biotin Module V2 according to manufactures instructions. www.nugeninc.com/nugen/index.cfm/products/pl/target-preparation/encore-biotin-module/

growth_protocol: Murine bone marrow cells were enriched for cKit+, transduced with pMIG retroviral vector expressing the MLL-ENL-IRES-GFP and GFP-positive and -negative hematopoietic PreGM cells were sorted by FACS.

extract_protocol: Total RNA from sorted cells were isolated with RNeasy Micro Kit (Qiagen). Samples were prepared in triplicates for each genotype. 5 ul of total RNA was amplified using Ovation Pico WTA system V2 (Nugene)according to manufactures instructions. www.nugeninc.com/nugen/index.cfm/products/cs/microarrays-and-qpcr/ovation-pico-wta-system-v2/manufacturers instructions.

treatment_protocol: Female mice were injected with pIpC, at day 14 they were sacrificed and bones were dissected, bone marrow cells were isolated by crushing, enriched for c-Kit expression and transduced with pMig-MLL-ENL in RPMI medium supplemented with 20 % FCS, 1 % Penicillin/Streptomycin, WEHI-conditioned medium, SCF and IL-6 and GFP-positive or negative PreGM cells were sorted by FACS.

value: Bone marrow

value: pregranulocyte-macrophage (PreGM)

tag: genotype

value: Cebpa flox/flox; Mx1Cre+

tag: cell population

value: Lin- Sca1- Kit+ CD150- CD41- FcgRII/III- CD105-


title: HS5-lucif_02

description:
Sample 9
replicate 2


title: PreGM Cebpa ∆/∆ GFP-pos rep 2

description:
Bone marrow cells, PreGMs
PreGM Cebpa ∆/∆ GFP-pos rep 2

tag: cell type


title: PreGM Cebpa flox/flox GFP-neg rep 3

description:
Bone marrow cells, PreGMs
PreGM Cebpa flox/flox GFP-neg rep 3

source_name: GFP-neg PreGM 72h post  MLL-ENL transduction

value: Cebpa flox/flox; Mx1Cre-


title: PreGM Cebpa ∆/∆ GFP-pos rep 1

description:
Bone marrow cells, PreGMs
PreGM Cebpa ∆/∆ GFP-pos rep 1


title: PreGM Cebpa ∆/∆ GFP-neg rep 1

description:
Bone marrow cells, PreGMs
PreGM Cebpa ∆/∆ GFP-neg rep 1


title: PreGM Cebpa flox/flox GFP-pos rep 3

description:
Bone marrow cells, PreGMs
PreGM Cebpa flox/flox GFP-pos rep 3


title: PreGM Cebpa ∆/∆ GFP-neg rep 2

description:
Bone marrow cells, PreGMs
PreGM Cebpa ∆/∆ GFP-neg rep 2


title: PreGM Cebpa ∆/∆ GFP-neg rep 3

description:
Bone marrow cells, PreGMs
PreGM Cebpa ∆/∆ GFP-neg rep 3


title: PreGM Cebpa flox/flox GFP-neg rep 2

description:
Bone marrow cells, PreGMs
PreGM Cebpa flox/flox GFP-neg rep 2


title: PreGM Cebpa flox/flox GFP-pos rep 2

description:
Bone marrow cells, PreGMs
PreGM Cebpa flox/flox GFP-pos rep 2


title: PreGM Cebpa flox/flox GFP-neg rep 1

description:
Bone marrow cells, PreGMs
PreGM Cebpa flox/flox GFP-neg rep 1


title: HS5_01

description:
Sample 1
replicate 1


title: HSC flox/flox;Mx1Cre 18 day post pIC rep1

first: Marie

middle: S

last: Hasemann

address: Ole Maaløes Vej 5

department: Finsen Laboratory

institute: Rigshospitalet

scan_protocol: standard Affymetrix protocol

data_processing: Cell intesity files (CEL files) were generated in the Genechip Command Console Software (AGCC), (Affymetrix, Santa Clara, CA, USA). The data was normalized using the RMA function from the Bioconductor package affy in R.

source_name: Sorted HSCs (LSKCD150+CD48-) from bone marrow samples, 18 days post conditional gene knock out

growth_protocol: Murine bone marrow cells were enriched for cKit+ and hematopoietic stem cells were sorted by FACS.

extract_protocol: Total RNA from sorted cells were isolated with RNeasy Micro Kit (Qiagen). Samples were prepared in triplicates for each genotype. 20 ng of total RNA was amplified using Ovation Pico WTA system V2 (Nugene)according to manufactures instructions. www.nugeninc.com/nugen/index.cfm/products/cs/microarrays-and-qpcr/ovation-pico-wta-system-v2/manufacturers instructions.

treatment_protocol: Female mice were injected with pIC, at day 18 they were sacrifized and bones were dissected, bone marrow cells were isolated by crushing and HSCs were sorted by FACS.

tag: Sex

value: female

value: Bone marrow cells, HSCs

value: Cebpa flox/flox; Mx1Cre

value: HSC:Lin-, Sca1+, cKit+, CD150+, CD48-


title: PreGM Cebpa flox/flox GFP-pos rep 1

description:
Bone marrow cells, PreGMs
PreGM Cebpa flox/flox GFP-pos rep 1

tag: strain


title: HSC flox/flox;Mx1Cre 18 day post pIC rep4


title: HSC flox/flox;Mx1Cre 18 day post pIC rep2


title: HSC flox/flox 18 days post pIC rep1

value: Cebpa flox/flox


title: male-NPA3 pool

description:
NPA aggressivity trajectory
pool male-NPA3 of T cell (CD3 positive) DNA methylation from NPA males

value: male

value: T cell (CD3 positive)

tag: state

value: NPA aggressivity trajectory


title: Liver from STZ-treated mice, biological replicate 1

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description:
STZ_29
Gene expression data from liver of STZ-treated mice.

hyb_protocol: According to the Affymetrix expression protocol (HWS kit).

scan_protocol: According to the Affymetrix expression protocol.

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.2) including median polish and Sketch-Quantile normalisation.

source_name: liver, STZ-treated mice

label_protocol: WT Expression Kit (Ambion) and the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Animals were housed under spf conditions.

extract_protocol: miRNeasy Mini Kit (Qiagen) including DNase treatment.

treatment_protocol: To induce type 1 diabetes, 65 mg/kg of streptozotocin (STZ) was injected i.p. into 10- to 16-week-old mice on 5 consecutive days while respective controls were mock-injected with citrate buffer. Animals were sacrificed 9-11 weeks after this treatment.

value: wildtype

value: liver

value: 5-6 months

tag: treatment

value: streptozotocin


title: Liver from STZ-treated mice, biological replicate 3

description:
STZ_31
Gene expression data from liver of STZ-treated mice.


title: HSC flox/flox;Mx1Cre 18 day post pIC rep3


title: Liver from STZ-treated mice, biological replicate 4

description:
STZ_32
Gene expression data from liver of STZ-treated mice.


title: HSC flox/flox 18 days post pIC rep2


title: Liver from STZ-treated mice, biological replicate 5

description:
STZ_40
Gene expression data from liver of STZ-treated mice.


title: Liver from control mice, biological replicate 5

description:
Ctrl_05
Gene expression data from liver of control mice.

source_name: liver, ctrl mice

value: mock


title: Liver from STZ-treated mice, biological replicate 2

description:
STZ_30
Gene expression data from liver of STZ-treated mice.


title: Liver from control mice, biological replicate 6

description:
Ctrl_06
Gene expression data from liver of control mice.


title: Liver from STZ-treated mice, biological replicate 6

description:
STZ_42
Gene expression data from liver of STZ-treated mice.


title: Liver from control mice, biological replicate 1

description:
Ctrl_01
Gene expression data from liver of control mice.


title: Liver from control mice, biological replicate 7

description:
Ctrl_07
Gene expression data from liver of control mice.