title: Hormad1-/-, rep1

city: Pittsburgh

first: Aleksandar

last: Rajkovic

state: PA

address: 204 Craft Ave. Suite A230

department: Dept. of Obstetrics, Gynecology & Reproductive Sciences

institute: Magee-Womens Research Institute

description:
Replicate 1 of 3.
5130656003_D

hyb_protocol: Standard Illumina hybridization protocol. The appropriate mass of cRNA was mixed with GEX-HYB hybridization buffer (supplied by Illumina) and nuclease-free water as needed to normalize the volume. BeadChips were hybridized overnight at 55C with rotation.  Following hybridization, the BeadChips were washed with manufacturer-supplied wash buffer.  Blocking was performed at room temperature using supplied blocking solution and the BeadChips were stained with strepdavidin–Cy3 for 10 minutes.  Excess stain solution was washed off with provided wash buffer and Beadchips dried via centrifugation.

scan_protocol: Illumina Bead Array Reader.

data_processing: The data were normalized using cubic spline with Illumina’s GenomeStudio application version 3.4.0.

source_name: testes, Hormad1-/-

label_protocol: Samples are prepared and biotin-labeled for Illumina BeadChip® analysis using the Ilumina TotalPrep® RNA amplification kit (Ambion).

extract_protocol: RNA was extracted with mirVANA miRNA extraction kit, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: genotype

tag: age

value: 2 weeks

value: testes


title: NT-5

status: Public on Apr 27 2010

type: RNA

city: Boston

first: Matthias

last: Stadtfeld

state: MA

address: 185 Cambridge Street

country: USA

institute: MGH

hyb_protocol: Biotinylated cRNA was cleaned up, fragmented and hybridized to GeneChip HT Array Plates (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip H Scanner (Affymetrix).

data_processing: Normalization of the array data was done using the "mean normalize" function in GeneSifter.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: NT-ESC from Adeno-2, subclone 2

label_protocol: Biotinylated cRNA was prepared from total RNA using the GeneChip HT IVT Labeling Kit (Affymetrix).

growth_protocol: All cells were cultured in standard ESC media (15% FBS, LIF) on irradiated MEFs.

extract_protocol: Total RNA was extracted using the QIAGEN miRNeasy kit.

treatment_protocol: Cells were trypsinized and preplated for 45 minutes to remove MEFs.

tag: origin

value: cloned blastocyst

tag: cell type

value: embryonic stem cell


title: iPSC-48

source_name: iPSC, clone 48

value: TTFs, chimera 2

value: induced pluripotent stem cell


title: wild-type, rep1

description:
Replicate 1 of 3.
5130656003_A

source_name: testes, wild-type

tag: strain

value: wild-type

tag: tissue


title: iPSC-45

source_name: iPSC, clone 45


title: NT-6

source_name: NT-ESC from Adeno-2, subclone 3


title: Hormad1-/-, rep2

description:
Replicate 2 of 3.
5130656003_E


title: wild-type, rep2

description:
Replicate 2 of 3.
5130656003_B


title: iPSC-46

source_name: iPSC, clone 46


title: Hormad1-/-, rep3

description:
Replicate 3 of 3.
5130656003_F


title: iPSC-47

source_name: iPSC, clone 47


title: iPSC-41

source_name: iPSC, clone 41

value: Granulocytes, chimera 2


title: iPSC-42

source_name: iPSC, clone 42


title: iPSC-43

source_name: iPSC, clone 43


title: iPSC-35

source_name: iPSC, clone 35

value: HSCs, chimera 2


title: iPSC-39

source_name: iPSC, clone 39

value: GMPs, chimera 2


title: iPSC-34

source_name: iPSC, clone 34

value: PFs, mouse 2


title: iPSC-36

source_name: iPSC, clone 36


title: iPSC-32

source_name: iPSC, clone 32


title: iPSC-30

source_name: iPSC, clone 30

value: Granulocytes, mouse 2


title: iPSC-28

source_name: iPSC, clone 28

value: GMPs, mouse 2


title: iPSC-31

source_name: iPSC, clone 31


title: iPSC-33

source_name: iPSC, clone 33


title: iPSC-27

source_name: iPSC, clone 27


title: iPSC-24

source_name: iPSC, clone 24

value: HSCs, mouse 2


title: iPSC-38

source_name: iPSC, clone 38


title: iPSC-29

source_name: iPSC, clone 29


title: iPSC-37

source_name: iPSC, clone 37


title: iPSC-25

source_name: iPSC, clone 25


title: iPSC-21

source_name: iPSC, clone 21


title: iPSC-22

source_name: iPSC, clone 22


title: iPSC-26

source_name: iPSC, clone 26


title: iPSC-23

source_name: iPSC, clone 23


title: iPSC-40

source_name: iPSC, clone 40


title: Co-twin/sibling_810_813, direct comparison replicate 1

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

hyb_protocol: The two differentially labeled probes (Alexa 647 or Alexa 555) were mixed and dried down in the presence of Human CotI DNA in a SpeedVac to a volume less than 5 µl.  80µl of DIG Easy hybridization buffer and 4µl of yeast tRNA (10mg/mL) was added to each sample and denatured at 65ºC for 2 minutes.  Each sample was hybridized onto 8.1K CpG island microarrays (UHN Microarray Centre, University of Toronto, Canada) overnight at 37ºC.

scan_protocol: Scanned on an Axon GenePix 4000B scanner.  Images were quantified using TIGR Spotfinder.

data_processing: Analysis of raw intensity data was performed using the TIGR TM4 Software Suite.  Raw intensity data were normalized and filtered using LOWESS normalization and standard deviation (variance) regularization programs contained with TIGR MIDAS.  The  normalized intensities were then uploaded into TIGR MeV and a 70% data filter was applied to remove CpG island regions for which log2 intensity values are missing in >30% of the samples before statistical analyses of the data. Differentially methylated CpG islands were identified using the Significance Analysis of Microarrays (SAM) module within TIGR MeV, which also provided false discovery rates (FDR) for each analysis.  A 1-class analysis identified differential methylation between discordant monozygotic twins as well as across both twins in comparison to unaffected control siblings.

label: Alexa 647

organism: Homo sapiens

source_name: Cell line HI0813

label_protocol: Enriched and unenriched MIRA (methyl-CpG island recovery assay) fractions derived from each individual were  indirectly labeled with aminoallyl-dUTP, and conjugated with either Alexa 647 or Alexa 555 fluors (Invitrogen, Carlsbad, CA).

growth_protocol: LCL were cultured in RPMI 1640 + L-glutamine media supplemented with 15% fetal bovine serum and 1% penicillin/streptomycin in a humidified incubator under 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad,CA) according to the manufacturer’s protocol.

tag: cell line

tag: gender

value: Male

tag: status

value: Unaffected

value: Lymphoblastoid cell lines

label: Alexa 555

source_name: Cell line HI0810

value: Broad Spectrum


title: Co-twin/sibling_810_813, indirect comparison replicate 2

description: 13496752.mev = 810 indirect comparison  13718705.mev = 813 indirect comparison

label: 813 Input=Alexa 647  813 MIRA enriched = Alexa555

label: 810 Input=Alexa 647  810 MIRA enriched = Alexa555


title: iPSC-20

source_name: iPSC, clone 20

value: PFs, mouse 1


title: Col-0 control, biological rep 1

city: Acton

first: Jed

last: Christianson

state: ACT

address: Clunies Ross Road

country: Australia

institute: CSIRO Plant Industry

description: Col-0 1

hyb_protocol: Following fragmentation, cRNA was hybridized to the ATH1 Arabidopsis Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data was analysed using the limma Bioconductor package in R. Array data was normalized using the EXPRESSO function (Gautier et al., 2005). A robust multi-chip average was calculated using quantile normalization, background correction and the median polish method as recommended by (Bolstad et al., 2003) and (Irizarry et al., 2003).

organism: Arabidopsis thaliana

source_name: Root tissue from three-week-old Arabidopsis plants, control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Plants were kept in a growth room at 22°C with a day:night period of 16:8-hrs and fluorescent lighting levels of ~75uE. Plants were grown on MS media with 3% sucrose and 0.8% agar and transferred to liquid MS media containing 3% sucrose one day prior to sampling.

extract_protocol: Root tissue was excised from plants and was flash frozen and ground in liquid nitrogen. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Plants in the low oxygen treatment group were placed in anaerobic microbial chambers (Oxoid, Adelaide, SA, Australia) and the chambers were flushed with a gas mixture of 0.1% oxygen, balance nitrogen at a flow rate of ~10L/min. for 20 minutes. Chambers were then sealed, and plants were left in the 0.1% oxygen atmosphere for five hours. Plants in the control group were placed in cannisters that were left unsealed.

tag: ecotype

value: 3 weeks

value: root

tag: treatment

value: normal oxygen


title: Col-0 control, biological rep 2

description: Col-0 2


title: Col-0 low oxygen treated, biological rep 1

description: Col-0 1 LO

source_name: Root tissue from three-week-old Arabidopsis plants, low oxygen

value: low oxygen


title: Co-twin/sibling_810_813, indirect comparison replicate 1

description: 13490046b_MDS.mev = 810 indirect comparison  13490047a_MDS.mev = 813 indirect comparison


title: Co-twin/sibling_810_813, direct comparison replicate 2


title: Co-twin/sibling_809_813, indirect comparison replicate 2

description: 13718706.mev = 809 indirect comparison  13718705.mev = 813 indirect comparison

label: 809 Input=Alexa 647  809 MIRA enriched = Alexa555

source_name: Cell line HI0809

value: Autism


title: Col-0 low oxygen treated, biological rep 2

description: Col-0 2 LO


title: Co-twin/sibling_2368_2357, indirect comparison replicate 2

description: 13714302.mev.mev = 2368 indirect comparison  13714304.mev = 2357 indirect comparison

label: 2368 Input=Alexa 647  2368 MIRA enriched = Alexa555

source_name: Cell line HI2368

value: NQA

label: 2357 Input=Alexa 647  2357 MIRA enriched = Alexa555

source_name: Cell line HI2357


title: iPSC-17

source_name: iPSC, clone 17

value: Granulocytes, mouse 1

value: induced pluripotent stem cell


title: iPSC-13

source_name: iPSC, clone 13

value: GMPs, mouse 1


title: iPSC-15

source_name: iPSC, clone 15


title: iPSC-12

source_name: iPSC, clone 12


title: iPSC-16

source_name: iPSC, clone 16


title: Co-twin/sibling_2368_2357, direct comparison replicate1


title: Co-twin/sibling_2369_2357, indirect comparison replicate 2

description: 13714303.mev.mev = 2369 indirect comparison  13714304.mev = 2357 indirect comparison

label: 2369 Input=Alexa 647  2369 MIRA enriched = Alexa555

source_name: Cell line HI2369


title: iPSC-14

source_name: iPSC, clone 14


title: Co-twin/sibling_2368_2357, indirect comparison replicate1

description: 13496656a_MDS.mev = 2368 indirect comparison  13496654a_MDS.mev = 2357 indirect comparison


title: Co-twin/sibling_809_813, direct comparison replicate 1


title: Co-twin/sibling_809_813, direct comparison replicate 2


title: Co-twin/sibling_809_813, indirect comparison replicate 1

description: 13490049b_MDS.mev = 809 indirect comparison  13490047a_MDS.mev = 813 indirect comparison


title: iPSC-19

source_name: iPSC, clone 19


title: iPSC-9

source_name: iPSC, clone 9

value: HSCs, mouse 1


title: iPSC-10

source_name: iPSC, clone 10


title: iPSC-11

source_name: iPSC, clone 11


title: Co-twin/sibling_2369_2357, indirect comparison replicate1

description: 13496655b_MDS.mev = 2369 indirect comparison  13496654a_MDS.mev = 2357 indirect comparison


title: iPSC-8

source_name: iPSC, clone 8


title: Co-twin/sibling_2369_2357, direct comparison replicate 2


title: Co-twin/sibling_2369_2357, direct comparison replicate1


title: Discordant MZ twins_2369_2368, indirect comparison replicate 2

description: 13714303.mev.mev = 2369 indirect comparison  13714302.mev.mev = 2368 indirect comparison


title: iPSC-5

source_name: iPSC, clone 5

value: MEFs, chimera 1


title: iPSC-6

source_name: iPSC, clone 6


title: Discordant MZ twins_2369_2368, indirect comparison replicate 1

description: 13496655b_MDS.mev = 2369 indirect comparison  13496656a_MDS.mev = 2368 indirect comparison


title: Discordant MZ twins_2369_2368, direct comparison replicate 2


title: Discordant MZ twins_2369_2368, direct comparison replicate 1


title: iPSC-4

source_name: iPSC, clone 4


title: iPSC-7

source_name: iPSC, clone 7


title: ESC-3

source_name: ESC, clone 3

value: KH2 ESC, targeted

value: embryonic stem cell


title: iPSC-2

source_name: iPSC, clone 2


title: iPSC-3

source_name: iPSC, clone 3


title: Discordant MZ twins_809_810, indirect comparison replicate 2

description: 13718706.mev = 809 indirect comparison  13496752.mev = 810 indirect comparison

source_name: Cell line HI0809

value: Male

source_name: Cell line HI0810


title: Discordant MZ twins_809_810, direct comparison replicate 2

value: Lymphoblastoid cell lines


title: ESC-4

source_name: ESC, clone 4


title: iPSC-1

source_name: iPSC, clone 1


title: wild-type, rep3

description:
Replicate 3 of 3.
5130656003_C

source_name: testes, wild-type

value: wild-type

value: 2 weeks

value: testes


title: Discordant MZ twins_360_361, indirect comparison replicate 2

description: 13718689.mev.mev = 361 indirect comparison  13718691_rescan.mev.mev = 360 indirect comparison

label: 360 Input=Alexa 647  360 MIRA enriched = Alexa555

source_name: Cell line HI0360

value: Broad Spectrum

label: 361 Input=Alexa 647  361 MIRA enriched = Alexa555

source_name: Cell line HI0361


title: ESC-1

source_name: ESC, clone 1


title: Discordant MZ twins_360_361, direct comparison replicate 2


title: ESC-2

source_name: ESC, clone 2


title: Discordant MZ twins_360_361, indirect comparison replicate 1

description: 13496653a.mev = 361 indirect comparison  13496659b.mev = 360 indirect comparison


title: Discordant MZ twins_809_810, indirect comparison replicate 1

description: 13490049b_MDS.mev = 809 indirect comparison  13490046b_MDS.mev = 810 indirect comparison


title: Discordant MZ twins_809_810, direct comparison replicate 1


title: Discordant MZ twins_360_361, direct comparison replicate 1


title: Unaffected MZ twins, indirect comparison replicate 2

description: 13718704.mev = 2744 indirect comparison  13718703.mev = 2745 indirect comparison

label: 2744 Input=Alexa 647  2744 MIRA enriched = Alexa555

source_name: Cell line HI2744

value: Unaffected

label: 2745 Input=Alexa 647  2745 MIRA enriched = Alexa555

source_name: Cell line HI2745


title: Unaffected MZ twins, direct comparison replicate 2


title: iPSC-44

source_name: iPSC, clone 44

value: TTFs, chimera 2


title: Unaffected MZ twins, direct comparison replicate 1


title: Unaffected MZ twins, indirect comparison replicate 1

description: 13490035b.mev = 2744 indirect comparison  13490034b.mev = 2745 indirect comparison


title: HeLa_PHF8-knockdown_rep3

city: Barcelona

first: Klaus

last: Fortschegger

address: C/ Dr. Aiguader 88

department: Gene Regulation

country: Spain

institute: Center for Genomic Regulation

description: HM__3000251485045839__Cy5_NTshRep3_Cy5_PHF8shARep3.txt

hyb_protocol: 825 ng of fragmented labeled cRNA from each of the two samples were co-hybridized for 17h at 65°C with in situ hybridization buffer (Agilent) and subsequently washed with Gene Expression Wash buffers 1 & 2 (Agilent).

scan_protocol: Arrays were scanned on a G2565BA scanner (Agilent) at 5µm resolution.

data_processing: Features were extracted using GenePix Pro 6.0. Intensities were background corrected and normalized using global lowess method. Probes spotted several times were averaged.

source_name: HeLa, PHF8-shA, 3d post transfection, Rep3

label_protocol: 500 ng total RNA were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy5- or Cy3-CTP using Quick Amp Labeling kit (Agilent) and purified using RNeasy kit (Qiagen).

growth_protocol: HeLa S3 cells were grown in DMEM medium supplemented with 10% fetal calf serum and antibiotics.

extract_protocol: Total RNA was extracted using Trizol reagent according to manufacturer's protocol (Invitrogen). Quality check was performed on a Bioanalyzer 2100 (Agilent).

treatment_protocol: Cells were transfected with shRNA vector pRetroSuperPuro expressing PHF8-shA or control NT-sh using Metafectene Pro reagent (Biontex). One day post transfection puromycin selection was performed at 2.5µg/ml for two more days.

value: HeLa S3

tag: shrna

source_name: HeLa, control shRNA, 3d post transfection, Rep3

value: control NT-sh


title: HeLa_PHF8-knockdown_dyeswap_rep3

description:
HM__2000251485045839__Cy5_PHF8shARep3_Cy3_NTshRep3_DS.txt
Dye Swap


title: HeLa_PHF8-knockdown_dyeswap_rep2

description:
HM__4000251485045839__Cy5_PHF8shARep2_Cy3_NTshRep2_DS.txt
Dye Swap

source_name: HeLa, control shRNA, 3d post transfection, Rep2

source_name: HeLa, PHF8-shA, 3d post transfection, Rep2


title: glioma 709

status: Public on Apr 26 2010

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

description: Gene expression analysis.

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 450.

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

data_processing: Expression levels of 17,527 genes were extracted from Affymetrix HU133 Plus 2.0 arrays using updated array annotation (Dai et al., 2005) based on reorganizing probes to gene specific probe sets, excluding inaccurate or wrongly annotated probes.

source_name: brain tissue, glioma

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

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

value: brain

tag: histology

value: PA (grade I)

tag: age at diagnosis


title: glioma 704

description: Gene expression analysis.

value: GBM (grade IV)


title: HeLa_PHF8-knockdown_rep1

description: HM__4000251485045961__Cy5_NTshRep1_Cy3_PHF8shARep1.txt

source_name: HeLa, PHF8-shA, 3d post transfection, Rep1

source_name: HeLa, control shRNA, 3d post transfection, Rep1


title: glioma 670

description: Gene expression analysis.

value: Female

value: OA (grade III)


title: HeLa_PHF8-knockdown_dyeswap_rep1

description:
HM__3000251485045961__Cy5_PHF8shARep1_Cy3_NTshRep1_DS.txt
Dye Swap


title: glioma 656

description: Gene expression analysis.


title: glioma 648

description: Gene expression analysis.

value: OD (grade III)


title: glioma 649

description: Gene expression analysis.


title: glioma 657

description: Gene expression analysis.


title: HeLa_PHF8-knockdown_rep2

description: HM__2000251485045961__Cy5_NTshRep2_Cy3_PHF8shARep2.txt


title: glioma 635

description: Gene expression analysis.


title: glioma 651

description: Gene expression analysis.


title: glioma 712

description: Gene expression analysis.


title: glioma 652

description: Gene expression analysis.


title: glioma 711

description: Gene expression analysis.


title: glioma 697

description: Gene expression analysis.


title: glioma 662

description: Gene expression analysis.


title: glioma 691

description: Gene expression analysis.


title: glioma 636

description: Gene expression analysis.


title: glioma 629

description: Gene expression analysis.


title: glioma 631

description: Gene expression analysis.


title: glioma 619

description: Gene expression analysis.


title: glioma 627

description: Gene expression analysis.


title: glioma 615

description: Gene expression analysis.


title: glioma 612

description: Gene expression analysis.


title: glioma 585

description: Gene expression analysis.


title: glioma 547

description: Gene expression analysis.


title: glioma 603

description: Gene expression analysis.


title: glioma 601

description: Gene expression analysis.


title: glioma 610

description: Gene expression analysis.


title: glioma 564

description: Gene expression analysis.


title: glioma 536

description: Gene expression analysis.

value: OA (grade II)


title: glioma 568

description: Gene expression analysis.


title: glioma 584

description: Gene expression analysis.


title: glioma 569

description: Gene expression analysis.

value: Male


title: glioma 535

description: Gene expression analysis.


title: glioma 545

description: Gene expression analysis.

value: A (grade II)


title: glioma 540

description: Gene expression analysis.


title: glioma 634

description: Gene expression analysis.


title: glioma 566

description: Gene expression analysis.


title: glioma 609

description: Gene expression analysis.


title: glioma 543

description: Gene expression analysis.


title: glioma 567

description: Gene expression analysis.


title: glioma 538

description: Gene expression analysis.

value: OD (grade II)


title: glioma 565

description: Gene expression analysis.


title: glioma 532

description: Gene expression analysis.


title: glioma 533

description: Gene expression analysis.


title: glioma 537

description: Gene expression analysis.


title: glioma 525

description: Gene expression analysis.


title: glioma 529

description: Gene expression analysis.


title: glioma 514

description: Gene expression analysis.


title: glioma 510

description: Gene expression analysis.


title: glioma 515

description: Gene expression analysis.


title: glioma 500

description: Gene expression analysis.


title: glioma 509

description: Gene expression analysis.


title: glioma 497

description: Gene expression analysis.

value: A (grade III)


title: glioma 520

description: Gene expression analysis.


title: glioma 473

description: Gene expression analysis.


title: glioma 488

description: Gene expression analysis.


title: glioma 485

description: Gene expression analysis.


title: glioma 489

description: Gene expression analysis.


title: glioma 519

description: Gene expression analysis.


title: glioma 494

description: Gene expression analysis.


title: glioma 487

description: Gene expression analysis.


title: glioma 468

description: Gene expression analysis.


title: glioma 524

description: Gene expression analysis.


title: glioma 628

description: Gene expression analysis.


title: glioma 499

description: Gene expression analysis.


title: glioma 465

description: Gene expression analysis.


title: glioma 512

description: Gene expression analysis.


title: glioma 496

description: Gene expression analysis.


title: glioma 495

description: Gene expression analysis.


title: glioma 490

description: Gene expression analysis.


title: glioma 466

description: Gene expression analysis.


title: glioma 467

description: Gene expression analysis.


title: glioma 463

description: Gene expression analysis.


title: glioma 483

description: Gene expression analysis.


title: glioma 462

description: Gene expression analysis.


title: glioma 461

description: Gene expression analysis.


title: glioma 449

description: Gene expression analysis.


title: glioma 446

description: Gene expression analysis.


title: glioma 445

description: Gene expression analysis.


title: glioma 440

description: Gene expression analysis.


title: glioma 437

description: Gene expression analysis.


title: glioma 436

description: Gene expression analysis.


title: glioma 432

description: Gene expression analysis.


title: glioma 442

description: Gene expression analysis.


title: glioma 452

description: Gene expression analysis.


title: glioma 451

description: Gene expression analysis.


title: glioma 433

description: Gene expression analysis.


title: glioma 434

description: Gene expression analysis.


title: glioma 420

description: Gene expression analysis.


title: glioma 421

description: Gene expression analysis.


title: glioma 455

description: Gene expression analysis.


title: glioma 441

description: Gene expression analysis.


title: glioma 443

description: Gene expression analysis.


title: glioma 427

description: Gene expression analysis.


title: glioma 428

description: Gene expression analysis.


title: glioma 431

description: Gene expression analysis.


title: glioma 411

description: Gene expression analysis.


title: glioma 458

description: Gene expression analysis.


title: glioma 425

description: Gene expression analysis.


title: glioma 415

description: Gene expression analysis.


title: glioma 416

description: Gene expression analysis.


title: glioma 406

description: Gene expression analysis.


title: glioma 417

description: Gene expression analysis.


title: glioma 444

description: Gene expression analysis.


title: glioma 395

description: Gene expression analysis.


title: glioma 388

description: Gene expression analysis.


title: glioma 384

description: Gene expression analysis.


title: glioma 387

description: Gene expression analysis.


title: control 344

description: Gene expression analysis.

source_name: brain tissue, control

value: control


title: glioma 360

description: Gene expression analysis.


title: glioma 393

description: Gene expression analysis.


title: glioma 376

description: Gene expression analysis.


title: glioma 362

description: Gene expression analysis.


title: glioma 368

description: Gene expression analysis.


title: glioma 372

description: Gene expression analysis.


title: glioma 336

description: Gene expression analysis.


title: glioma 389

description: Gene expression analysis.


title: control 343

description: Gene expression analysis.


title: control 345

description: Gene expression analysis.


title: glioma 378

description: Gene expression analysis.


title: glioma 380

description: Gene expression analysis.


title: control 346

description: Gene expression analysis.


title: glioma 351

description: Gene expression analysis.


title: glioma 352

description: Gene expression analysis.


title: glioma 333

description: Gene expression analysis.


title: glioma 337

description: Gene expression analysis.


title: glioma 405

description: Gene expression analysis.


title: glioma 332

description: Gene expression analysis.


title: glioma 353

description: Gene expression analysis.


title: glioma 319

description: Gene expression analysis.


title: glioma 308

description: Gene expression analysis.


title: glioma 299

description: Gene expression analysis.


title: glioma 710

description: Gene expression analysis.


title: glioma 295

description: Gene expression analysis.


title: glioma 310

description: Gene expression analysis.


title: glioma 285

description: Gene expression analysis.


title: glioma 328

description: Gene expression analysis.


title: control 278

description: Gene expression analysis.


title: glioma 258

description: Gene expression analysis.


title: glioma 293

description: Gene expression analysis.


title: glioma 300

description: Gene expression analysis.


title: control 269

description: Gene expression analysis.


title: glioma 291

description: Gene expression analysis.


title: glioma 286

description: Gene expression analysis.


title: glioma 271

description: Gene expression analysis.


title: glioma 294

description: Gene expression analysis.


title: glioma 256

description: Gene expression analysis.


title: glioma 260

description: Gene expression analysis.


title: glioma 284

description: Gene expression analysis.


title: glioma 306

description: Gene expression analysis.


title: glioma 255

description: Gene expression analysis.


title: glioma 257

description: Gene expression analysis.


title: glioma 252

description: Gene expression analysis.


title: glioma 253

description: Gene expression analysis.


title: glioma 254

description: Gene expression analysis.


title: glioma 251

description: Gene expression analysis.


title: glioma 270

description: Gene expression analysis.


title: glioma 283

description: Gene expression analysis.


title: glioma 250

description: Gene expression analysis.


title: glioma 244

description: Gene expression analysis.


title: glioma 247

description: Gene expression analysis.


title: glioma 638

description: Gene expression analysis.


title: glioma 243

description: Gene expression analysis.


title: glioma 230

description: Gene expression analysis.


title: glioma 229

description: Gene expression analysis.


title: glioma 218

description: Gene expression analysis.


title: glioma 225

description: Gene expression analysis.


title: glioma 223

description: Gene expression analysis.


title: glioma 237

description: Gene expression analysis.


title: glioma 224

description: Gene expression analysis.


title: glioma 216

description: Gene expression analysis.


title: glioma 228

description: Gene expression analysis.


title: glioma 210

description: Gene expression analysis.


title: glioma 246

description: Gene expression analysis.


title: glioma 201

description: Gene expression analysis.


title: glioma 227

description: Gene expression analysis.


title: glioma 222

description: Gene expression analysis.


title: glioma 240

description: Gene expression analysis.


title: glioma 219

description: Gene expression analysis.


title: glioma 214

description: Gene expression analysis.


title: glioma 206

description: Gene expression analysis.


title: glioma 233

description: Gene expression analysis.


title: glioma 207

description: Gene expression analysis.


title: glioma 203

description: Gene expression analysis.


title: glioma 209

description: Gene expression analysis.


title: glioma 199

description: Gene expression analysis.


title: glioma 198

description: Gene expression analysis.


title: glioma 189

description: Gene expression analysis.


title: glioma 196

description: Gene expression analysis.


title: glioma 204

description: Gene expression analysis.


title: glioma 194

description: Gene expression analysis.


title: glioma 188

description: Gene expression analysis.


title: glioma 190

description: Gene expression analysis.


title: glioma 185

description: Gene expression analysis.


title: glioma 187

description: Gene expression analysis.


title: glioma 171

description: Gene expression analysis.


title: glioma 186

description: Gene expression analysis.


title: glioma 158

description: Gene expression analysis.


title: glioma 183

description: Gene expression analysis.


title: glioma 172

description: Gene expression analysis.


title: glioma 173

description: Gene expression analysis.


title: glioma 163

description: Gene expression analysis.


title: glioma 161

description: Gene expression analysis.


title: glioma 169

description: Gene expression analysis.


title: glioma 164

description: Gene expression analysis.


title: glioma 178

description: Gene expression analysis.


title: glioma 168

description: Gene expression analysis.


title: glioma 176

description: Gene expression analysis.


title: glioma 162

description: Gene expression analysis.


title: glioma 155

description: Gene expression analysis.


title: glioma 157

description: Gene expression analysis.


title: glioma 180

description: Gene expression analysis.


title: glioma 170

description: Gene expression analysis.


title: glioma 174

description: Gene expression analysis.


title: glioma 149

description: Gene expression analysis.


title: glioma 150

description: Gene expression analysis.


title: glioma 143

description: Gene expression analysis.


title: glioma 148

description: Gene expression analysis.


title: glioma 144

description: Gene expression analysis.


title: glioma 152

description: Gene expression analysis.


title: glioma 141

description: Gene expression analysis.


title: glioma 120

description: Gene expression analysis.


title: glioma 134

description: Gene expression analysis.


title: glioma 130

description: Gene expression analysis.


title: glioma 136

description: Gene expression analysis.


title: glioma 131

description: Gene expression analysis.


title: glioma 132

description: Gene expression analysis.


title: glioma 123

description: Gene expression analysis.


title: glioma 142

description: Gene expression analysis.


title: glioma 133

description: Gene expression analysis.


title: glioma 101

description: Gene expression analysis.


title: glioma 139

description: Gene expression analysis.


title: glioma 90

description: Gene expression analysis.


title: glioma 98

description: Gene expression analysis.


title: glioma 315

description: Gene expression analysis.


title: glioma 119

description: Gene expression analysis.


title: glioma 126

description: Gene expression analysis.


title: glioma 111

description: Gene expression analysis.


title: glioma 138

description: Gene expression analysis.


title: glioma 112

description: Gene expression analysis.


title: glioma 105

description: Gene expression analysis.


title: glioma 107

description: Gene expression analysis.


title: glioma 92

description: Gene expression analysis.


title: glioma 83

description: Gene expression analysis.


title: glioma 104

description: Gene expression analysis.


title: glioma 99

description: Gene expression analysis.


title: glioma 89

description: Gene expression analysis.


title: glioma 82

description: Gene expression analysis.


title: glioma 81

description: Gene expression analysis.


title: glioma 67

description: Gene expression analysis.


title: glioma 73

description: Gene expression analysis.


title: glioma 87

description: Gene expression analysis.


title: glioma 64

description: Gene expression analysis.


title: glioma 72

description: Gene expression analysis.


title: glioma 62

description: Gene expression analysis.


title: glioma 80

description: Gene expression analysis.


title: glioma 77

description: Gene expression analysis.


title: glioma 56

description: Gene expression analysis.


title: glioma 63

description: Gene expression analysis.


title: glioma 55

description: Gene expression analysis.


title: glioma 23

description: Gene expression analysis.


title: glioma 25

description: Gene expression analysis.


title: control 7

description: Gene expression analysis.


title: glioma 9

description: Gene expression analysis.


title: glioma 40

description: Gene expression analysis.


title: glioma 20

description: Gene expression analysis.


title: glioma 53

description: Gene expression analysis.


title: glioma 8

description: Gene expression analysis.


title: glioma 60

description: Gene expression analysis.


title: glioma 21

description: Gene expression analysis.


title: glioma 11

description: Gene expression analysis.


title: cy5_10_Pyr_G20

status: Public on Apr 25 2010

city: Raleigh

first: Stan

last: Martin

state: NC

address: 1404 Crete Dr.

institute: Science Apps, L3C

hyb_protocol: Described in J. Bacteriology 188:1817-1828

data_processing:
Normalized with JMP Genomics 4.0 using standard normalization procedure, ie, JMP Genomics simply takes the log2 transformed value of the raw data, mean centers at 0 and divides by the standard deviation.
There were some cases where the signal was 0 so the division came up with a blank value. These were filtered out of the data set. There were also some empty spots that had no value that were filtered.

organism: Oleidesulfovibrio alaskensis G20

growth_protocol: Anaerobically grown in defined medium

tag: substrate

value: Pyruvate

tag: tecrep

tag: biorep


title: cy5_5_Lac_G20

scan_protocol: Described in J. Bacteriology 188:1817-1828

value: Lactate


title: cy5_11_Pyr_G20

label_protocol: Described in J. Bacteriology 188:1817-1828


title: cy5_21_Lac_I2

extract_protocol: Described in J. Bacteriology 188:1817-1828


title: cy5_7_Lac_G20


title: cy5_23_Pyr_I2


title: cy5_6_Lac_G20


title: cy5_8_Lac_G20


title: cy5_22_Lac_I2


title: cy5_17_Lac_I2


title: cy5_12_Pyr_G20


title: glioma 179

description: Gene expression analysis.


title: cy5_19_Lac_I2


title: cy5_3_Lac_G20


title: cy5_20_Lac_I2


title: cy5_4_Lac_G20


title: cy5_9_Pyr_G20


title: cy5_18_Lac_I2


title: NRG Melan-Ink4a #3

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

hyb_protocol: Hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Mouse GeneChipÒ 1.0 ST chips according to Affymetrix protocols.Chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix.

scan_protocol: Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays. Gene expression intensities were calculated using the Gene Chip Operating software 1.2 (GCOS 1.2; Affymetrix).

data_processing: Cel files generated by the Affymetrix GCOS program were imported in the Affymetrix Expression Consol program and RMA (Robust Microarray Analysis) normalization was performed to generate the .Chp files.

source_name: skin derived melanocyte cell line_21day NRG1 treated

label_protocol: 200 ng of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip 1.0 ST chips.

growth_protocol: All cells were grown at 37°C with 10% CO2 in RPMI medium 1640 supplemented with 10% FBS (Gibco, Scotland, UK), 200 nM 12-O-Tetradecanoylphorbol 13-acetate (TPA) (Sigma- Aldrich, St Louis, MO, USA) and 200 pM cholera toxin (CT) (Sigma- Aldrich). Medium was changed thrice a week. Total RNA was isolated from 90% confluent cells.

extract_protocol: Total RNA was isolated from 90% confluent cells as reported by Loftus et al. (2002) with one modification: following the Trizol reagent (Invitrogen, Carlsbad, CA, USA) lysis of the cell, a 5 min, 65°C incubation was added.

treatment_protocol: Melan-Ink4a cells stimulated with 10 nM NRG1-b1 (NRG1) (No. 377-HB; R&D Systems, Minneapolis, MN, USA) for 21 days.

value: skin

value: melanocyte

tag: genotype/variation

value: Ink4a-ARF1 null


title: monocytes_ischemia_rep3

city: Saint Louis

first: Alyssa

middle: D

last: Gregory

state: MO

address: 660 S Euclid Ave.

department: Medicine

institute: Washington University in St. Louis

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Bone marrow CX3CR1-GFP+ monocytes

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit

extract_protocol: Extract using Trizol; clean using QIAGEN RNEasy mini kit

tag: stress

value: hindlimb ischemia

tag: pair


title: cy5_1_Lac_G20


title: monocytes_ischemia_rep2


title: Untreated Melan-Ink4a #2

source_name: skin derived melanocyte cell line

tag: cell type


title: NRG Melan-Ink4a #2

tag: strain


title: cy5_2_Lac_G20


title: monocytes_basal_rep3


title: Untreated Melan-Ink4a #1

tag: tissue


title: Untreated Melan-Ink4a #3


title: NRG Melan-Ink4a #1


title: monocytes_basal_rep2


title: monocytes_basal_rep1


title: cy5_24_Pyr_I2


title: monocytes_ischemia_rep1


title: Normal Cell line GM36 4 Gy

status: Public on Apr 24 2010

city: Jefferson

first: Rohan

last: Kulkarni

state: AR

address: 3900 NCTR Road

department: Div. of Genetic and Reproductive Toxicology

institute: National Center for Toxicological Research

data_processing:
Sham-irradiated samples were used as a control. All reactions were performed in duplicate and the mean Ct value was used for calculations. We compared the relative expression between the normal and mitochondrial mutant cells.
For the data analysis of the genes involved in apoptosis, we used the software package available on the SuperArray website, RT² Profiler PCR Array Data Analysis Template v3.0. Two-sided p-values were calculated, and p<0.05 was considered significant. This analysis was also based upon the 2-ΔΔCt method (Livak and Schmittgen 2001).

label: SYBR Green

source_name: EBV transformed B-lymphoblastoid

label_protocol: For each reaction, a final volume of 25 µl was used which contained 12.5 µl of SYBR® GREEN Master Mix (Applied Biosystems, Foster City, CA), 11.5 µl of nuclease free water and 1 µl of template DNA (1 µg of total RNA). The thermal profile used for the reaction included a 10-min heat activation of the enzyme at 95°C, followed by 40 cycles of 95°C (10 sec.) and 60°C for 1 min followed by melt curve analysis.

growth_protocol: The culture medium was comprised of RPMI 1640 (GIBCO, Paisley, UK) supplemented with 15% fetal bovine serum (Hyclone, Logan, Utah), penicillin-streptomycin (100 units/ml penicillin G sodium, 100 µg/ml streptomycin in 0.85% saline) (GIBCO, Paisley, UK), 2.5 µg/ml Hyq® amphotericin B (Hyclone, Logan, Utah), and 2 mM L-glutamine (GIBCO, Paisley, UK). The cells were grown in suspension in a fully humidified incubator with 5% CO2 at 37°C in T25 culture flasks (Corning). The initial seeding was done at 1.0 X 105 cells/ml.

extract_protocol: After 24 hours of incubation following exposure, the cells were harvested by transferring them into 15-ml Falcon tubes followed by centrifugation at 3000 rpm for 5 minutes. After discarding the supernatant, the cell pellet was flash-frozen using dry ice and was stored at -80°C. Later, total RNA was isolated from the cell pellet using the RNeasy Mini RNA isolation kit (Qiagen, Valencia, CA). We used the Ready-To-Go You-Prime Kit (Amersham Biosciences) to reverse transcribe one microgram of RNA with random hexamers (IDTDNA Inc., Iowa). This cDNA was then used as a template for real-time PCR along with the cDNA obtained from the sham-irradiated cells, which were used as a control.

treatment_protocol: The two mitochondrial mutant cell lines along with the normal cells were irradiated in T-25 flasks after reaching a density of 1.0 X 106 cells/ml in a total volume of 10 mL. The cells were radiated with 0 (control), 0.5, 1, 2, 3 and 4 Gy X-rays at a dose rate of 0.85 Gy/min using a 160 kVp Faxitron X-ray unit. These doses were selected based on our previous results in which we demonstrated that following ionizing radiation exposure, these mutant cells exhibited increased frequencies of chromosome aberrations at doses up to 2 Gy compared to the normal cells. Normal cells showed a 7-fold increase in chromosomal aberrations at 2 Gy compared to the unirradiated cells, whereas mutants cells showed 10-fold and 9-fold increases in aberrations at 2 Gy in the Leigh cells and Leber cells, respectively, compared to normal cells exposed to the same dose. For doses above 2 Gy, increased cell killing was observed (Kulkarni et al. 2009). We also observed differences in ATP levels between normal and mutant cells at these doses (Kulkarni et al. 2010). Once irradiated, the cells were returned to the incubator for 24 hours before harvesting for total RNA without changing the original media. We selected the 24 hour time point based upon our earlier studies in which we performed a time course experiment for 1, 4, 8, 12 and 24 hours after exposure to assess gene expression and ATP levels as a function of time (Kulkarni et al. 2010). These studies show that 24 hours after exposure, the ATP and expression levels in the genes involved in ATP synthesis in the normal cell lines were increased compared to control levels whereas the mutant cell lines showed a decrease. Since we were interested in the effect of ATP and gene expression levels on apoptosis and DNA damage repair, we used the 24 hour post exposure time point in the present study.

value: EBV transformed B-lymphoblastoid

tag: cell line

tag: patient disease status

value: Normal

value: normal mitochondrial DNA

tag: treatment group

value: 4 Gy

value: 0 Gy


title: Normal Cell line GM36 2 Gy

value: 2 Gy


title: Leigh Syndrome cells GM40 2 Gy

value: Leigh Syndrome

value: mitochondrial DNA mutant (Mutation in ATP6)


title: negative control

type: genomic

city: Tucson

first: Virginia

middle: Isabel

last: Rich

state: AZ

address: 1041 E. Lowell St.

institute: University of Arizona

description: Cy5 for co-spot oligo complement used for gridding purposes

hyb_protocol: Hybridizations were performed as in (Rich et al., 2008), by labeling randomly-amplified sample DNA with a single fluorophore (Cy3) for hybridization, with a few modifications. All samples were hybridized to at least three replicate arrays, and 1 pmol of Cy5-labeled co-spot complement oligo was added to each hybridization for spot localization purposes (modified from (Urisman et al., 2005).   After labeling, Cy3 sample labeling reactions were cleaned in ExcelaPure 96-well plates. Each sample was combined with 280ul TE and transferred to the Excela-Pure plate. After vacuum flow-through, samples were washed 2x300ul TE. The hood was kept dark and the sample plate covered with aluminum foil while under vacuum, to preserve the fluorophore. The cospot complement oligo was cleaned using a Microcon-30, in 480ul of TE and with 2x500ul TE washes. Labeled sample DNA was concentrated to 20 ul per array (so 63ul for a triplicate hybridization) in TE. For triplicate hybridizations, we combined: 61.5ul of Cy3-DNA, 3.1ul of Cy5-cospot-complement oligo (at 1pmol/ul), 13.92ul 20X SSX, 1.92ul 1M HEPES, ph 7.0, 6.94ul nuclease-free water (Ambion); this was mixed thoroughly and then combined with 3.78ul 10mg/ml polyA and 1.92ul 10% SDS.  This produced a ﬁnal volume of 30ul per array. Samples were denatured 4 min at 100°C, then pipetted onto the arrays. Arrays were hybridized overnight at 65°C in a heating oven (Model, 2000 Micro Hybridization Incubator, Robbins Scientiﬁc, Sunnyvale, CA), then washed at room temperature, ﬁrst vigorously for 30 s in 0.6X SSC, 0.03% SDS, and second in 0.06X SSC vigorously for 30 s then gently for 5 min.

scan_protocol: Hybridized arrays were scanned using an Axon Instruments4000B scanner (Foster City, CA), and the associated GenePix software was used for image capture.

data_processing: Data were pre-processed as in (Rich et al., 2008), with minor modifications. Briefly, poorly-performing arrays, defined as those with less than half the positive control probes brighter than the standard deviation of the negative control probes, were removed from further analysis. Within each remaining array, bad spots (those with areas of poly-L-lysine peeling or excessive background fluorescence) were manually flagged and removed from further analysis. Background-subtracted spot intensities were negative-control-subtracted and normalized to each array’s mean positive control value, then replicate spots of a given probe were pooled across replicate arrays and the median was taken as the value for that probe.   Finally, the signal for each targeted genotype was calculated. To be considered present, at least 40% of its probes were required to be above the standard deviation of the negative control probe set (rather than above twice the mean negative control value, as in Rich et al., 2008), or the targeted genotype was considered “absent” and its value set to zero. This was done to remove erroneous target abundances due to uninformative single-gene cross-hybridizations. For targets that passed this thresh-holding step, the mean or tukey biweight (TBW) across each probe set was taken, as in (Rich et al., 2008). We did not examine which probes for each organism showed signal, since probes were not designed to distinguish particular genes; i.e., no alignments were used to target conserved or variable parts of given genes, but instead the probe was chosen purely on hybridization characteristics.

molecule: genomic DNA

organism: unidentified

label_protocol: Labeling was performed as in Rich et al 2008, with minor modifications for higher throughput. Target DNA was ampliﬁed and labelled using A/B/C random ampliﬁcation (Wang et al., 2003, with the modiﬁcation that the initial reverse transcription step was omitted). Brieﬂy, random-primed ampliﬁcation was carried out in three reactions: round A used Sequenase to extend primer A (GTT TCC CAG TCA CGA TCN NNN NNN NN); round B used 20 rounds of PCR to amplify the resulting fragments, using primer B (GTT TCC CAG TCA CGA TC); and round C used 10 rounds of PCR to incorporate amino-allyl-deoxyuridine triphosphates (aa-dUTP). All A/B/C reactions were performed in triplicate and pooled, and were performed in 96 well plates for higher throughput. Ampliﬁcation products were cleaned through ExcelaPure 96-well plates (Edge Biosystems, Gaithersburg); the vacuum was run at ~10”Hg and products were washed once with 300ul nuclease-free water (Ambion), and concentrated/resuspended in ~30ul of nuclease-free water. These were transferred to V-bottom 96-well plates and dried down using a vacuum centrifuge with a plate-compatible rotor. Products were then resuspended directly in 0.1M NaHCO3 (allowed to sit at ~60 deg C for 10”, thevortexed gently and spun down). Products were labeled with Cy3 by combining 10 ml aa-DNA in 0.1M NaHCO3 with 5 ml Cy3 dye (33 mg in DMSO), and incubating at room temperature in the dark for 1 h.  All co-spot complement oligo required for each batch of hybridizations was labeled in a single separate labeling reaction using Cy5, allowing ~1pmol of cospot complement oligo per hybridization. After 1 hour, 2ul of 4M hydroxylamine was added to each reaction, mixed, and allowed to sit in the dark for 15”.

extract_protocol: DNA was extracted from all 0m and 200m filters available from 2000 JD271 through 2004 JD167, and all 30m samples available from 2000 JD271 through 2002 JD070. In this location, 0m is in the photic zone, 30m is generally below the mixed layer, and 200m is below the photic zone. All MB DNA extractions were performed simultaneously in 96-well format to minimize extraction variability, as in (Rich et al., 2008). Briefly, cell lysis was performed by incubating each filter with 242ml lysis buffer (lysis buffer: 40 mM EDTA, 50 mM Tris pH 8.3, 0.73 M sucrose, 1.15 mg ml-1 lysozyme, 200 mg ml-1 RNase, 0.2 mm-ﬁlter-sterilized) in a microcentrifuge tube at 37°C for 30 min, rotating. Protein degradation was accomplished by adding SDS to 1%, and 13.5ml Proteinase K solution (10 mg ml-1 in 40 mM EDTA, 50 mM Tris pH 8.3, 0.73 M sucrose), and incubating overnight at 55°C, rotating. DNA was then extracted with the DNeasy 96 Tissue kit (Qiagen, Valencia, CA), using modifications of the manufacturer’s protocol. Each tube was vortexed with 300ml of Buffer AL and incubated at 70°C for 10 min, then vortexed with 300ml of 99% ethanol and pipetted onto a 96-well spin plate. The plate was sealed with an airpore sheet (supplied with kit) and spun at 40°C, 4612 x g in a Sorvall Legend RT centrifuge (Kendro Laboratory Products, Newtown, CT). After a 10 min spin 500 ml Buffer AW1 was added to each well, the plate was re-sealed and spun 5 min, then 500 ml Buffer AW2 was added to each well, and the plate was re-sealed and spun 5 min. Columns were then incubated for 15 min at 70°C atop a new rack of elution microtubes RS (supplied with kit). DNA was eluted with 2 x 200 ml Buffer AE preheated to 70°C, incubated 1 min, and spun 2 min. Finally, DNA was concentrated by Excela-Pure 96-well PCR puriﬁcation kits (Edge BioSystems, Gaithersburg, MD), following the manufacturer’s protocol. DNA was rinsed with 100 ml nuclease-free water, resuspended in 20 ml dilute TE (1 mM Tris pH 8, 0.1 mM EDTA pH 8), and transferred to a clean 96-well plate. Extracted DNAs were quantified spectrophotometrically (Nanodrop, Thermo Scientific) and stored at -80°C until use. Yields averaged ~470 ng per liter of seawater for 200m samples (range 177-903 ng) and ~1460 ng per liter of seawater for 0m and 30m samples (range 484-3804 ng).

treatment_protocol: Samples were collected from Station M1 (36.747˚ N, 122.022˚ W) in Monterey Bay at approximately monthly intervals, with several longer gaps, between JD271 in 2000 and JD167 in 2004. 2L of seawater from each of eight depths (0, 20, 30, 40, 80, 100, 150 and 200m) were filtered through a 45mm GF-A 1.6μm-pore prefilter (Whatman) and concentrated onto a 25mm Supor-200 0.2μm-pore filter (Pall Corp, Ann Arbor, MI), using a MasterFlex peristaltic pump system (Cole-Parmer Instrument Company, Vernon Hills, IL) at ≤15psi. Filters were stored dry in 2ml screw-cap tubes, immediately placed in a -20°C freezer shipboard, and transferred on ice to a -80°C freezer upon landfall.

tag: depth

value: negative control


title: Leigh Syndrome cells GM40 4 Gy


title: Leber optic atrophy cells GM44 2 Gy

value: Leber optic atrophy


title: 30m depth, Year 2002, Julian Day 070

organism: marine metagenome

source_name: marine microbial community, Monterey Bay, station M1

tag: year

tag: julian day


title: 30m depth, Year 2002, Julian Day 053


title: 30m depth, Year 2001, Julian Day 312


title: 30m depth, Year 2001, Julian Day 331


title: 30m depth, Year 2001, Julian Day 352


title: 30m depth, Year 2001, Julian Day 058


title: 30m depth, Year 2001, Julian Day 115


title: 30m depth, Year 2001, Julian Day 248


title: 30m depth, Year 2000, Julian Day 271


title: 30m depth, Year 2001, Julian Day 017


title: 30m depth, Year 2000, Julian Day 321


title: 30m depth, Year 2000, Julian Day 355


title: 200m depth, Year 2004, Julian Day 146


title: 200m depth, Year 2004, Julian Day 123


title: cy5_26_Pyr_I2


title: 200m depth, Year 2004, Julian Day 091


title: 200m depth, Year 2004, Julian Day 070


title: 200m depth, Year 2003, Julian Day 322


title: type 2 diabetes 9_microRNA

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

description: replicate 9

hyb_protocol: hybridized on miRCURY LNA™ Arrays, using MAUI® hybridization system

scan_protocol: Chips were scanned on Innopsys Scan 700, microarray scanner at 532 nm

data_processing: miRNA microarray data were analyzed by subtracting the mean background signal (B532nm) from the test signal (F532nm)

source_name: blood

label_protocol: LNA-modified oligonucleotide (Exiqon) probes for human, mouse and rat miRNAs annotated in miRBase version 11.0 were used in the microarray. Total RNA (1 μg) was 3’-end –labeled with Cy3 dye using the miRCURY LNA ™ Power Labeling Kit (Exiqon)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: patient type

value: type 2 diabetes 9

tag: gender

value: male


title: 200m depth, Year 2004, Julian Day 021


title: Leber optic atrophy cells GM44 4 Gy


title: type 2 diabetes 7_microRNA

description: replicate 7

value: type 2 diabetes 7


title: 200m depth, Year 2003, Julian Day 294


title: 30m depth, Year 2001, Julian Day 289


title: type 2 diabetes 8_microRNA

description: replicate 8

value: type 2 diabetes 8


title: 200m depth, Year 2003, Julian Day 281


title: type 2 diabetes 5_microRNA

description: replicate 5

value: type 2 diabetes 5


title: type 2 diabetes 6_microRNA

description: replicate 6

value: type 2 diabetes 6


title: type 2 diabetes 4_microRNA

description: replicate 4

value: type 2 diabetes 4


title: type 2 diabetes 2_microRNA

description: replicate 2

value: type 2 diabetes 2


title: 200m depth, Year 2001, Julian Day 352


title: type 2 diabetes 3_microRNA

description: replicate 3

value: type 2 diabetes 3


title: 200m depth, Year 2002, Julian Day 053


title: type 2 diabetes 8

description: replicate 8

data_processing: The signal intensity was background subtracted and subsequently used for analysis

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


title: 200m depth, Year 2001, Julian Day 331


title: type 2 diabetes 7

description: replicate 7


title: type 2 diabetes 5

description: replicate 5


title: type 2 diabetes 9

description: replicate 9


title: type 2 diabetes 1_microRNA

description: replicate 1

value: type 2 diabetes 1


title: 200m depth, Year 2001, Julian Day 289


title: 200m depth, Year 2001, Julian Day 248


title: 200m depth, Year 2001, Julian Day 135


title: impaired fasting glucose 6_microRNA

description: replicate 6

value: impaired fasting glucose 6


title: 200m depth, Year 2002, Julian Day 070


title: impaired fasting glucose 7_microRNA

description: replicate 7

value: impaired fasting glucose 7


title: 200m depth, Year 2001, Julian Day 017


title: type 2 diabetes 6

description: replicate 6


title: 200m depth, Year 2001, Julian Day 058


title: 200m depth, Year 2000, Julian Day 355


title: 200m depth, Year 2001, Julian Day 312


title: 200m depth, Year 2000, Julian Day 321


title: 200m depth, Year 2001, Julian Day 115


title: 200m depth, Year 2000, Julian Day 298


title: impaired fasting glucose 4_microRNA

description: replicate 4

value: impaired fasting glucose 4


title: type 2 diabetes 2

description: replicate 2


title: impaired fasting glucose 3_microRNA

description: replicate 3

value: impaired fasting glucose 3


title: 0m depth, Year 2004, Julian Day 167


title: 0m depth, Year 2004, Julian Day 146


title: impaired fasting glucose 5_microRNA

description: replicate 5

value: impaired fasting glucose 5


title: type 2 diabetes 4

description: replicate 4


title: impaired fasting glucose 1_microRNA

description: replicate 1

value: impaired fasting glucose 1


title: type 2 diabetes 3

description: replicate 3


title: impaired fasting glucose 7

description: replicate 7


title: 0m depth, Year 2004, Julian Day 091


title: 0m depth, Year 2004, Julian Day 021


title: control 10_microRNA

value: control 10


title: 0m depth, Year 2004, Julian Day 070


title: 200m depth, Year 2000, Julian Day 271


title: impaired fasting glucose 6

description: replicate 6


title: type 2 diabetes 1

description: replicate 1


title: 0m depth, Year 2002, Julian Day 070


title: 0m depth, Year 2003, Julian Day 294


title: impaired fasting glucose 2_microRNA

description: replicate 2

value: impaired fasting glucose 2


title: control 9_microRNA

value: control 9

value: male


title: control 8_microRNA

value: control 8


title: 0m depth, Year 2002, Julian Day 053


title: impaired fasting glucose 5

description: replicate 5


title: 0m depth, Year 2001, Julian Day 312


title: 0m depth, Year 2001, Julian Day 352


title: 0m depth, Year 2001, Julian Day 331


title: 0m depth, Year 2003, Julian Day 322


title: 0m depth, Year 2001, Julian Day 289


title: cy5_25_Pyr_I2

tag: substrate

value: Pyruvate


title: 0m depth, Year 2001, Julian Day 135


title: impaired fasting glucose 3

description: replicate 3


title: impaired fasting glucose 2

description: replicate 2


title: 0m depth, Year 2001, Julian Day 058


title: impaired fasting glucose 4

description: replicate 4


title: control 6_microRNA

value: control 6


title: control 5_microRNA

value: control 5


title: control 7_microRNA

value: control 7


title: 0m depth, Year 2001, Julian Day 017


title: control 4_microRNA

value: control 4


title: 0m depth, Year 2000, Julian Day 355


title: 0m depth, Year 2000, Julian Day 321


title: control 3_microRNA

value: control 3


title: 0m depth, Year 2001, Julian Day 115


title: control 8


title: impaired fasting glucose 1

description: replicate 1


title: control 2_microRNA

value: control 2


title: control 7


title: control 1_microRNA

value: control 1


title: 0m depth, Year 2000, Julian Day 298


title: 0m depth, Year 2000, Julian Day 271


title: control 5


title: control 6


title: control 4


title: control 2


title: control 3


title: control 1


title: rpd3Δ mutant thermo-responsive gene expression replicate 3

status: Public on Apr 23 2010

first: Eulalia

last: de Nadal

address: Aiguader 88

department: CEXS

institute: UPF

description: Biological replicate 3 of 3

hyb_protocol: The labeled cRNA was hybridized to the Agilent Yeast 4x44k 60-mer oligo microarray according to the manufacturer's protocol. The arrays were washed and dried.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT and 5 um resolution. Images were quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular spot finding option

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization, followed by scaling across chips. Differential expression analysis was performed using SAM (Significance Analysis of Microarrays, Tusher et al. 2001).

organism: Saccharomyces cerevisiae

source_name: rpd3Δ mutant 25º

label_protocol: RNA (500 ng) was labeled using Agilent's Low Input RNA Labeling Kit, which involves reverse transcribing the mRNA in the presence of T7-oligo-dT primer to produce cDNA and then in vitro transcribing with T7 RNA polymerase in the presence of Cy3-CTP and Cy5-CTP to produce labeled cRNA

growth_protocol: Three independent 200 ml cultures of wild-type (BY4741) and rpd3Δ mutant strains were grown to mid-log phase in YPD rich medium.

extract_protocol: RNA was extracted with hot phenol (Körher K and Domdey H. Methods in Enzymology 194:398-405. 1991). Hybridizations were performed between stressed and control conditions by triplicate. Results were analyzed comparing thermo-responsive gene expression respect to the control in each individual strain.

treatment_protocol: Wild-type and rpd3Δ mutant strains were grown at 25ºC (control) or at 39 ºC for 20 min (heat stressed).

tag: temperature

tag: genotype

value: rpd3Δ mutant

tag: genetic background

tag: treatment protocol

value: heat stress at 25ºC for 20 minutes

tag: growth protocol

source_name: rpd3Δ mutant 39º

value: heat stress at 39ºC for 20 minutes


title: rpd3Δ mutant thermo-responsive gene expression replicate 2

description: Biological replicate 2 of 3

value: grown to mid-log phase in YPD rich medium

tag: cell type


title: rpd3Δ mutant thermo-responsive gene expression replicate 1

description: Biological replicate 1 of 3


title: Wild type thermo-responsive gene expression replicate 3

description: Biological replicate 3 of 3

source_name: BY wild type 25º

value: wild type

source_name: BY wild type 39º


title: Reh_shCBFA2T3_IKK_2

city: Berlin

first: Karl

last: Koechert

address: Robert-Roessle-Str. 10

country: Germany

institute: Max-Delbrueck-Centre for Molecular Medicine

description: Biological replicate 2 of 2.

hyb_protocol: Hybridization was done according to the manufacturer's recommendations (Affymetrix).

scan_protocol: Scanning was done according to the manufacturer's recommendations (Affymetrix). Scanner Model was GeneChip® Scanner 3000 7G. GeneChip® Command Console® 2.0 was used as software.

data_processing: Raw data were background corrected with RMA and normalized using quantile normalization. All processing was done in R/Bioconductor.

source_name: Reh, transient knockdown of CBFA2T3 and transient expression of IKKb(EE)

label_protocol: Labeling was done according to the manufacturer's recommendations (Affymetrix).

extract_protocol: Total RNA was extracted using the RNeasy Mini-Kit from QIAGEN according to the manufacturer's recommendations.

value: Reh

tag: transfection

value: CBFA2T3 shRNA, IKKb(EE)

tag: malignancy

value: non-Hodgkin lymphoma


title: Wild type thermo-responsive gene expression replicate 2

description: Biological replicate 2 of 3


title: Wild type thermo-responsive gene expression replicate 1

description: Biological replicate 1 of 3


title: Reh_IKK_1

description: Biological replicate 1 of 2.

source_name: Reh, transient expression of IKKb(EE)

tag: cell line

value: IKKb(EE)


title: Reh_shCBFA2T3_IKK_1

description: Biological replicate 1 of 2.


title: Reh_shCBFA2T3_2

description: Biological replicate 2 of 2.

source_name: Reh, transient knockdown of CBFA2T3

value: CBFA2T3 shRNA


title: Reh_shCBFA2T3_1

description: Biological replicate 1 of 2.


title: Reh_mock2

description: Biological replicate 2 of 2.

source_name: Reh, control

value: control shRNA


title: control, biological rep8

first: Kusum

middle: Vijay

last: Pandit

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

institute: University of Pittsburgh

description: Lung tissue samples obtained from the University of Pittsburgh Health Sciences Tissue Bank. miRNA expression data from a lung with usual interstitial pneumonia.

hyb_protocol: Labeled RNA was hybridized for 20 hr at 55C on Agilent 8X15K microRNA array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Scanned on an Agilent G2505A Scanner

data_processing: Agilent Feature Extraction v9.5.3, default miRNA parameters

source_name: normal Lung tissue, control, biological rep8

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 100ng total RNA

extract_protocol: Total RNA extracted using miRNeasy mini kit according to the manufacturer's instructions.

tag: Normal lung tissues obtained from the disease free margins with normal histology of lung cancer resection


title: control, biological rep10

source_name: normal Lung tissue, control, biological rep10


title: control, biological rep2

source_name: normal Lung tissue, control, biological rep2


title: control, biological rep4

source_name: normal Lung tissue, control, biological rep4


title: control, biological rep5

source_name: normal Lung tissue, control, biological rep5


title: control, biological rep6

source_name: normal Lung tissue, control, biological rep6


title: control, biological rep1

source_name: normal Lung tissue, control, biological rep1


title: control, biological rep9

source_name: normal Lung tissue, control, biological rep9


title: control, biological rep7

source_name: normal Lung tissue, control, biological rep7


title: Reh_mock1

description: Biological replicate 1 of 2.


title: Cyclin D1b transfected multiple myeloma  LP-1 cell replicate 1

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

hyb_protocol: Each Cy3 Labelled probe was co-hybridized with the Cy5 reference probe on a 25K mouse oligonucleotide microarray in a G2545A oven (Agilent, Massy, France) at 60°C for 18 h. Microarrays were washed (10 minutes in 6X SSC, 0.005% Triton, 5 minutes in 0.1X SSC, 0.0025% Triton)

scan_protocol: microarrays were scanned using XDR with a G2565B Agilent scanner.

data_processing: Raw data were extracted from scanned microarray images (.tif) using Feature Extraction Software v9.5 (Agilent) and normalized using the Quantile method adapted to bicolour microarrays. To each array corresponds to one .txt format file (e.g. T804_01_346218_LP-1Cl1.txt for sample LP-1cl1_01). Log ratios in the raw data file are in base 10.

source_name: LP-1D1b cell line replicate 1

label_protocol: Total RNAs (200 ng) were amplified by linear PCR and labelled with Cy3 using Bioprime Array CGH Genomic Labelling System Kit (Invitrogen, Carlsbad, CA). Total RNA from one culture of LP-1cl1 cells was similarly amplified, labelled with Cy5 and used as a reference probe for hybridization.

growth_protocol: cells were maintained in RPMI 1640 containing 10% fetal calf serum, L-glutamine and antibiotics (Lonza Verviers SPRL)

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

treatment_protocol: LP-1 cells were transfected by electroporation with pcDNA3-flagged cyclin K, pcDNA3-c-Myc and pcDNA3-cyclin D1b, selected with 500 µg/ml G418, cloned by limiting dilution in 96-well plates. Single clones were individually tested for exogenous protein expression. After three months in culture without loss of transgene expression, G418 was first reduced and finally removed

tag: cell lines

value: Multiple myeloma LP-1 expressing cyclin D1b

source_name: LP-1cl1 cell line replicate 1

value: Multiple myeloma LP-1


title: UIP, biological rep9

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep9

tag: Tissue from a patient with pathological diagnosis of usual interstitial pneumonia.


title: control, biological rep3

source_name: normal Lung tissue, control, biological rep3


title: Reh_IKK_2

description: Biological replicate 2 of 2.


title: Cyclin D1b transfected multiple myeloma  LP-1 cell replicate 2

source_name: LP-1D1b cell line replicate 2


title: Cyclin D1b transfected multiple myeloma  LP-1 cell replicate 4

source_name: LP-1D1b cell line replicate 4


title: UIP, biological rep8

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep8


title: UIP, biological rep6

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep6


title: UIP, biological rep7

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep7


title: UIP, biological rep5

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep5


title: Cyclin D1b transfected multiple myeloma  LP-1 cell replicate 3

source_name: LP-1D1b cell line replicate 3


title: Light-dark comparison, replicate 4

city: Kansas City

first: Alexander

last: Idnurm

address: 5007 Rockhill Road

department: School of Biological Sciences

institute: University of Missouri-Kansas City

description: Light-treated cells compared to darkness-treated cells.

hyb_protocol: C. neoformans 70-mer microarray slides containing 7,936 probes, comprised primarily of genes annotated from the serotype D genome sequence, were spotted by the Duke University Microarray Facility (Durham, NC).  Slides were prehybridized at 42°C in 60 ml of prehybridization buffer (42.4 ml water, 2 ml 30% bovine serum albumin, 600 µl 10% sodium dodecyl sulfate, 15 ml 20x SSC [3 M NaCl, 0.3 M sodium citrate]), washed with distilled water and isopropanol, and dried by brief centrifugation.  The Cy3- and Cy5-labeled cDNA samples were combined, concentrated through a Microcon30 filter, and vacuum dried.  The dried cDNA samples were resuspended with 24 µl of 1x hybridization buffer (250 µl 50% formamide, 125 µl 20x SSC, 5 µl 10% SDS, 120 µl distilled water, for a total of 500 µl), added with 1 µl poly(A) tail DNA (Sigma) and incubated at 100°C for 3 min.  The microarray slides were cooled to room temperature and placed in DieTech hybridization chambers, with the slides covered by Lifterslips (Erie Scientific).  The Cy3- and Cy5-labeled cDNA samples were applied, and co-hybridization conducted for 16 h at 42°C.  After hybridization, the microarray slides were washed three times at 42°C: wash buffer 1, 10 ml 20x SSC, 600 µl 10% SDS, 189.4 ml dH2O; wash buffer 2, 3.5 ml 20x SSC, 346.5 ml dH2O; and wash buffer 3, 0.88 ml 20x SSC, 349.12 ml dH2O.

scan_protocol: Images were scanned on a GenePix 4000B scanner.

data_processing: LOWESS-normalized, background-subtracted data obtained from log2 of processed Red signal/processed Green signal. GenePix Pro version 4.0 and BRB Array Tools.

organism: Cryptococcus deneoformans

source_name: Yeast cells, light

label_protocol: The protocol is as reported in Ko et al. (2009) Eukaryotic Cell 8: 1197-1217 (PMID 19542307).  For cDNA synthesis, 15 µl of total RNA was mixed with 1 µl of 5 µg/µl oligo(dT) (5'-TTTTTTTTTTTTTTTTTTTTV-3')-pdN6 (Amersham) and incubated at 70°C for 10 min.  15 µl of cDNA synthesis mixture was added [3 µl 0.1 M dithiothreitol, 0.5 µl RNasin, 0.6 µl aa-dUTP [5-(3-aminoallyl)-2'-deoxyuridine 5'-triphosphate]-dNTPs (a mixture of 6 µl dTTP, 4 µl aa-dUTP, 10 µl dATP, 10 µl dCTP, and 10 µl dGTP at 100 mM each) 1.5 µl AffinityScript reverse transcriptase (Stratagene), 3 µl AffinityScript buffer, and 7 µl water] and incubated at 42°C for 2 h.  10 µl of 1 M NaOH and 10 µl of 0.5 M EDTA (pH 8.0) were added and incubated at 65°C for 15 min to stop the reaction, followed by the addtion of 25 µl of 1 M HEPES buffer (pH 8.0) and 450 µl water.  The mixture was concentrated through a Microcon30 filter and vacuum dried.  For cyanine dye labeling, Cy3 and Cy5 dyes (Amersham) were dissolved in dimethyl sulfoxide and added to cDNAs prepared as described above that were re-dissolved in 9 µl of 50 mM Na-bicarbonate (pH 8.0).  The cDNAs derived from cells grown in complete darkness were labeled with Cy3, and the cDNAs derived from cells exposed to light with Cy5.  Each mixture was further at room temperature for 1 h in the dark and purified with the QIAquick PCR purification kit.

growth_protocol: Cells were grown overnight in liquid YPD medium, then plated onto 15 cm diameter YPD agar plates.  Plates were parafilmed and wrapped in aluminum foil, and incubated at room temperature for 24 hours.

extract_protocol: Total RNA was extracted from lyophilized cells using TRIzol reagent (Invitrogen) according to manufacturer's guidelines.

treatment_protocol: For each light-dark comparison, the aluminum foil was removed from one plate, and this plate was exposed to white fluorescent light (1,600 lux).  The other plate was incubated for 24 hr in darkness and harvested under red light. Cells were scraped from the plate surfaces under safe light conditions.

tag: strain

tag: mating type

value: MAT a

tag: treatment

value: light

source_name: Yeast cells, dark

value: darkness


title: UIP, biological rep10

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep10


title: UIP, biological rep3

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep3


title: Cyclin K transfected multiple myeloma  LP-1 cell replicate 2

source_name: LP-1K cell line replicate 2

value: Multiple myeloma LP-1 expressing cyclin K


title: Cyclin K transfected multiple myeloma  LP-1 cell replicate 3

source_name: LP-1K cell line replicate 3


title: UIP, biological rep4

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep4


title: Light-dark comparison, replicate 6


title: Cyclin K transfected multiple myeloma  LP-1 cell replicate 4

source_name: LP-1K cell line replicate 4

source_name: LP-1cl1 cell line replicate 1


title: Light-dark comparison, replicate 5


title: UIP, biological rep2

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep2


title: UIP, biological rep1

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep1


title: Light-dark comparison, replicate 3

value: MAT alpha


title: Light-dark comparison, replicate 1


title: Cyclin K transfected multiple myeloma  LP-1 cell replicate 1

source_name: LP-1K cell line replicate 1


title: Light-dark comparison, replicate 2


title: Control multiple myeloma LP-1 cell replicate 1


title: Adult human bone marrow-metamylocyte-2

status: Public on Apr 22 2010

first: Su Ming

last: Sun

address: Dr. Molewaterplein 50

department: Hematology

institute: Erasmus University Medical Center

hyb_protocol: not applicable

scan_protocol: cDNA was quantified with realtime PCR, with specific primers and Taqman probes in so called Taqman Low Density Arrays (TLDA) according to protocol (Applied Biosystems)

data_processing: Ct values, obtained with RQ manager v 1.2, with threshold set to 1.0 and baseline correction set to automatic. Ct value represents -- Cycle which produced by amplied product crosses set threshold. After removal of the Undetermined and values above 35. Relative comparative quantification method (2^(-ddCT)) can be used to quantify expression. RNU48 can be used as endogenous control.

label: Not applicable

source_name: sorted from human bone marrow

label_protocol: Specific cDNA was made using specific Reversed Transcriptase- stem loop primers, divided over 8 multiplex reactions. 100 ng of RNA was used for each multiplex reaction according to protocol (Applied Biosystems)

growth_protocol: not applicable

extract_protocol: Total RNA was extracted using Trizol.

treatment_protocol: Bone marrow cells were extracted using standard clinical procedures, Cells were isotonic lysed to remove red blood cells and the different differention stages were sorted using the cell markers CD10, CD11b, CD34, CD45, CD117 and CD36

tag: developmental stage

value: Metamyelocyte


title: Control multiple myeloma LP-1 cell replicate 4

source_name: LP-1cl1 cell line replicate 4


title: Adult human bone marrow-neutrophil-1

value: Neutrophils


title: Adult human bone marrow-metamylocyte-3


title: Adult human bone marrow-metamylocyte-1


title: Adult human bone marrow-metamylocyte-4


title: Adult human bone marrow-neutrophil-2


title: Adult human bone marrow-neutrophil-3


title: LR552 (two biological replicates)

city: Seattle

first: Lakshmi

last: Rajagopal

state: WA

address: 1900 9th Ave

department: Pediatric Infectious Disease

institute: Seattle Children's Hospital Research Institute

description: 2 biological replicates

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Staphylococcus aureus

source_name: Newman D stk1

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Total prokaryotic RNA was extracted from post exponential phase (O.D 600nm=3.0) cultures of S. aureus grown in Tryptic Soy Broth at 37C. Two biological replicates of each strain were used on two four plex chips, with average values reported here.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at both Seattle Childrens Research Institute and Nimblegen.

treatment_protocol: Labeling was performed by NimbleGen Inc. using Cy3.

tag: genotype variation

value: stk1 deletion mutant

value: Newman


title: Adult human bone marrow-myeloblast&promyelocyte-1

value: Myeloblast & Promyelocytes


title: Adult human bone marrow-myeloblast&promyelocyte-3


title: Adult human bone marrow-myeloblast&promyelocyte-2


title: Adult human bone marrow-myeloblast-2

value: Myeloblast


title: Adult human bone marrow-myeloblast&promyelocyte-4


title: LR525 (two biological replicates)

description: 2 biolgoical replicates

source_name: Newman D stp1

value: stp1 deletion mutant


title: Control multiple myeloma LP-1 cell replicate 3

source_name: LP-1cl1 cell line replicate 3


title: Adult human bone marrow-myeloblast-1


title: Newman WT (two biological replicates)

description: 2 biological replicates

source_name: Newman WT

value: wild type


title: Control multiple myeloma LP-1 cell replicate 2

source_name: LP-1cl1 cell line replicate 2


title: 27665402

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

hyb_protocol: Samples were co-hybridized with a MAUI hybridization system (BioMicro Systems).

scan_protocol: The arrays were scanned using a 5 µm scanner, and Nimblescan software (Roche Nimblegen, Madison, WI) was used to retrieve fluorescent intensity raw data from the scanned images of the oligonucleotide tiling arrays.

data_processing: First, spatial correction was applied to adjust position-dependent non-uniformity of signals across the array. Specifically, locally weighted polynomial regression (loess) was used to adjust signal intensities based on X,Y feature position. Normalization was then performed using the q-spline method, followed by segmentation using the segMNT CNV calling algorithm.

organism: Bos taurus

source_name: genomic DNA from bovine cattle

label_protocol: According to manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Genomic DNA was purified from blood by salt precipitation. The precipitation was performed by adding 2.36volumes of cold 96% ethanol and 0.16volumes of 3M sodium acetate (pH 4.8). After 20 minutes of centrifugation at 4 degrees Celsius and 13.000 rpm, the precipitated DNA was washed with 70% ethanol, re-precipitated by 5 minutes of centrifugation at 4 degrees Celsius and 13.000 rpm. After precipitation, the isolated DNA was resuspended in 16TE-buffer. Following the isolation of the genomic DNA samples, the DNA quality was assessed by measuring the concentration and the purity on the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). DNA integrity and purity were also assessed by gel electrophoresis on a 1% agarose gel (SeaKemH GTGH Agarose, Cambrex Bio Science, and 16TBE buffer, Invitrogen) containing 0.15 mg/mL ethidium bromide.

tag: breed

value: Simmental

tag: tissue

value: Blood

tag: gender

value: Male

tag: id

value: Holstein

value: blood


title: 27626802


title: 27662702


title: 27666602


title: 27666002


title: 27664802


title: 24138002


title: 24133202


title: 27659602


title: 27621302


title: 27621902


title: 24138302


title: 24137702


title: 27626502

value: Hereford


title: 27020902


title: 27733802

value: Red Danish


title: 27633302


title: 24139902


title: 27019702


title: 24134102


title: 27627102


title: 27021202


title: 27020302


title: 21202402


title: 27017102


title: Control diet, biological rep 3

city: Kanagawa

first: Asuka

last: Kamei

address: LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi

department: Project for development of food functionality assessment methods

country: Japan

institute: Kanagawa Academy of Science and technology

description: No additional information

hyb_protocol: Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with the distribution free weighted method (DFW) using the statistical language R (http://www.r-project.org/), version 2.7.1.

label: Biotin

organism: Rattus norvegicus

source_name: Liver of rat fed control diet

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Male 3-week-old Sprague Dawley rats were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room conditioned at 24 ± 1°C and 40 ± 5% humidity with a 12-h light-dark cycle (lights on at 08:00). The rats were given a control diet and water for 24 h ad libitum. Diets for rats were obtained from Research Diets, Inc. (New Brunswick, NJ, USA). The composition of the control diet was based on the AIN93G diet , except that cellulose was replaced by Avicel, since cellulose is an ingredient of variable iron content. The iron-deficient diet was prepared by removal of iron (ferric citrate) from the control diet. At day 8, rats were divided into two groups comprising animals of similar body weights. One group (n = 6) was fed the control diet and the other group (n = 7) was fed the iron-deficient diet (iron-deficient diet group). After iron-deficient diet feeding was started, blood hemoglobin levels were measured every two days. Blood samples for hemoglobin measurements were collected from the tail vein, and hemoglobin levels were measured by using the Wako Hemoglobin B test (Wako Pure Chemical Industries, Osaka, Japan). On day 12 of the iron-deficient diet treatment, diets were removed at 17:00, and feeding was conducted between 09:00 and 17:00 for another 4 days. This protocol was intended to synchronize the rats’ feeding behavior. On day 17 of the iron-deficient diet treatment, rats were fed for 1.5 h prior to sacrifice under anesthesia.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Livers were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).

value: male

tag: age

value: 7 weeks

value: liver


title: Control diet, biological rep 4

description: No additional information


title: Iron-deficient diet, biological rep 3

description: No additional information

source_name: Liver of rat fed iron-deficient diet


title: Iron-deficient diet, biological rep 1

description: No additional information


title: Control diet, biological rep 2

description: No additional information


title: Control diet, biological rep 1

description: No additional information


title: 24133502


title: Control_12month_C1302_old

city: Jyväskylä

first: Eija

last: Pöllänen

address: PO Box 35/Viveca

department: Department of Health Sciences

country: Finland

institute: University of Jyväskylä

description: replicate 1

data_processing: The data were normalised using quantile normalisation with Affy-package in R; prior to normalization data from GPL2700 and GPL2507 platforms were combined and only probes present in boths platforms were used in further analysis

source_name: placebo: 12month

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Bio-Lab laboratories Experion.

value: female

value: postmenopausal

value: m. vastus lateralis


title: Control_12month_C440_old

description: replicate 1


title: Control_12month_C94_old

description: replicate 1


title: Iron-deficient diet, biological rep 2

description: No additional information


title: Control_0month_A94_old

description: replicate 1

source_name: placebo: 0month


title: 24134402


title: Control_0month_A268_old

description: replicate 1


title: Control_12month_C1296_old

description: replicate 1


title: Control_12month_C268_old

description: replicate 1


title: HRT_12month_C1216_old

description: replicate 1

source_name: hormone replacement therapy: 12month


title: HRT_12month_C1057_old

description: replicate 1


title: HRT_12month_C13_old

description: replicate 1


title: HRT_0month_A13_old

description: replicate 1

source_name: hormone replacement therapy: 0month


title: HRT_12month_C937_old

description: replicate 1


title: HRT_12month_C551_old

description: replicate 1


title: HRT_12month_C370_old

description: replicate 1


title: HRT_12month_C824_old

description: replicate 1


title: Control_0month_A1296_old

description: replicate 1


title: HRT_12month_C941_old

description: replicate 1


title: HRT_12month_C1092_old

description: replicate 1


title: HRT_0month_A1092_old

description: replicate 1


title: HRT_0month_A1216_old

description: replicate 1


title: Control_0month_A440_old

description: replicate 1


title: Control_0month_A1302_old

description: replicate 1


title: HRT_0month_A551_old

description: replicate 1


title: HRT_0month_A1057_old

description: replicate 1


title: HRT_0month_A145_old

description: replicate 1


title: 27673702


title: Control_12month_C880_new

description: replicate 1


title: Control_0month_A440_new

description: replicate 2


title: HRT_0month_A941_old

description: replicate 1


title: HRT_0month_A370_old

description: replicate 1


title: Control_12month_C144_new

description: replicate 1


title: HRT_0month_A937_old

description: replicate 1


title: Control_0month_A144_new

description: replicate 1


title: Control_12month_C241_new

description: replicate 1


title: Control_12month_C440_new

description: replicate 2


title: HRT_0month_A824_old

description: replicate 1


title: Control_0month_A411_new

description: replicate 1


title: Control_12month_C268_new

description: replicate 2


title: Control_0month_A1296_new

description: replicate 2


title: Control_0month_A880_new

description: replicate 1


title: HRT_12month_C145_old

description: replicate 1


title: Control_0month_A268_new

description: replicate 2


title: Iron-deficient diet, biological rep 4

description: No additional information


title: Control_12month_C1296_new

description: replicate 2


title: Control_0month_A241_new

description: replicate 1


title: 27665102


title: PT_12month_C1230_new

description: replicate 1

source_name: power training: 12month


title: 27017402


title: PT_0month_A807_new

description: replicate 1

source_name: power training: 0month


title: PT_0month_A768_new

description: replicate 1


title: PT_0month_A809_new

description: replicate 1


title: PT_0month_A96_new

description: replicate 1


title: PT_12month_C96_new

description: replicate 1


title: PT_12month_C636_new

description: replicate 1


title: PT_12month_C809_new

description: replicate 1


title: PT_0month_A1230_new

description: replicate 1


title: PT_0month_A636_new

description: replicate 1


title: PT_12month_C807_new

description: replicate 1


title: PT_0month_A683_new

description: replicate 1


title: PT_12month_C522_new

description: replicate 1


title: PT_12month_C768_new

description: replicate 1


title: PT_12month_C683_new

description: replicate 1


title: 19688602


title: PT_0month_A522_new

description: replicate 1


title: Control_12month_C411_new

description: replicate 1


title: 19631102


title: 19630802


title: 19628302


title: 19628002


title: 19651002


title: Gracilis muscle: ischemia 4h reperfusion 4h 1

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: Experimental replicate 1 of Gracilis muscle after ischemia 4h and reperfusion 4h

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.9.5.3).

data_processing: Agilent Feature Extraction Software (v 9.5.3) was used for background subtraction and LOWESS normalization.

source_name: Gracilis muscle

label_protocol: The RNA from the experimental and control gracilis muscle was labeled with Cy3.

growth_protocol: The harvested muscles were frozen in isopentane chilled in liquid nitrogen and stored at -80°C.

extract_protocol: 0.5 μg of total RNA was amplified using a Fluorescent Linear Amplification Kit (Agilent Technologies) and labeled with Cy3-CTP

treatment_protocol: Total RNA was extracted using the mirVana miRNA Isolation kit (Ambion, Austin, TX, USA) following manufacturer's instructions

value: Sprague-Dawley

value: Gracilis muscle

value: ischemia 4h reperfusion 4h


title: Gracilis muscle: ischemia 4h reperfusion 4h 2

description: Experimental replicate 2 of Gracilis muscle after ischemia 4h and reperfusion 4h


title: Gracilis muscle: ischemia-reperfusion sham operation control 2

description: Biological replicate 2 of Gracilis muscle as sham operation control


title: Gracilis muscle: ischemia-reperfusion sham operation control 1

description: Biological replicate 1 of Gracilis muscle as sham operation control


title: Piau 515 vs Piau 386

city: East Lansing

first: Catherine

middle: W.

last: Ernst

state: MI

address: 3330 Anthony Hall

department: Animal Science

institute: Michigan State University

description: The tissue samples compared on this array are part of an experiment to study muscle development at 40 and 70 days of gestation in a Brazilian local pig breed and crossbred pigs from the US using the swine protein-annotated oligonucleotide microarray.

hyb_protocol: Labeled aRNAs were purified and combined with 65 µl of Slide Hyb #1 solution (Ambion, Inc.) and denatured at 70C for 5 min. Hybridizations were performed in sealed hybridization cassettes (ArrayIt, TeleChem International, Inc., Sunnyvale, CA, USA) for 18 h at a humid 54C. Following hybridization, slides were washed in 2X SSC/0.5% SDS and 0.1X SSC/0.1% SDS solutions for 10 min each. The slides were rinsed in a 0.1X SSC solution and nuclease-free water and dried by centrifugation.

scan_protocol: Fluorescent images were detected by a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) and fluorescence intensity data were collected using GenePix software (Molecular Devices) after spot alignment. Median intensity values for each dye channel were stored as comma-separated values data files.

data_processing: Loess normalized log-ratio of Cy5 versus Cy3 intensities. No background correction.

organism: Sus scrofa

source_name: Skeletal muscle Piau 515

label_protocol: One µg of total RNA was reverse transcribed with a T7 oligo(dT) primer using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion Inc., Austin, TX, USA) according to the manufacturer’s instructions. Following first-strand and second-strand synthesis and purification, the cDNAs were in vitro transcribed to synthesize multiple copies of amino allyl-modified aRNAs. After purification, aRNAs were labeled with N-hydroxysuccinate (NHS) ester Cy3 (GE Healthcare, UK).

extract_protocol: Total RNA from 30 mg of tissue was extracted using RNeasy Mini kit with on-column RNase-free DNase digestion (Qiagen, Valencia, CA) according to the manufacturer’s instructions. RNA concentration and quality were determined with an RNA 6000 Pico LabChip® kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Palo Alto, CA, USA).

tag: breed type

value: Piau

tag: tissue type

value: Skeletal muscle – Longissimus dorsi

value: 70 days of gestation

source_name: Skeletal muscle Piau 386

label_protocol: One µg of total RNA was reverse transcribed with a T7 oligo(dT) primer using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion Inc., Austin, TX, USA) according to the manufacturer’s instructions. Following first-strand and second-strand synthesis and purification, the cDNAs were in vitro transcribed to synthesize multiple copies of amino allyl-modified aRNAs. After purification, aRNAs were labeled with N-hydroxysuccinate (NHS) ester Cy5 (GE Healthcare, UK).

value: 40 days of gestation


title: SF7259 p53 WT pten WT Map250kSty

city: South San Francisco

first: Anthony

middle: Steve

last: Guerrero

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech

description: SRCID:SRC107485,PRBID:PRB16798,SRCNAME:7259,RAWFILE:16798_7259_GBMTumors_SPR460_Map250kSty.CEL

hyb_protocol: According to manufacturer's protocol (Affymetrix)

data_processing: The genotyping copy number data were generated with Affymetrix's CNAT algorithm, version 4.  Nsp and Sty copy number data were also estimated using the dChip algorithm (2006 version, build Dec 22, 2005), normalized against normal hapmap samples (downloaded from affymetrix). Segmentation of copy number data was performed with GLAD, version: 1.16.0.

label_protocol: Affymetrix 500K Human Mapping 500K array manual

extract_protocol: Qiagen's  AllPrep DNA/RNA extraction kit (Catalog #80204) was used to extract DNA and RNA according to manufacturer's protocol

tag: source

value: UCSF

tag: sample id

tag: genome/variation

value: p53 exon 4-8 mutation status:wt

value: pten exon 5-6 mutation status:wt


title: SF7223 p53 WT pten MT Map250kSty

description: SRCID:SRC107481,PRBID:PRB16790,SRCNAME:7223,RAWFILE:16790_7223_GBMTumors_SPR460_Map250kSty.CEL

scan_protocol: According to manufacturer's protocol (Affymetrix)

value: pten exon 5-6 mutation status:HOMSUB.130R>G


title: 19651302

value: Red Danish

value: Blood

value: Male

value: Holstein

value: blood


title: SF7227 p53 WT pten WT Map250kSty

description: SRCID:SRC107483,PRBID:PRB16794,SRCNAME:7227,RAWFILE:16794_7227_GBMTumors_SPR460_Map250kSty.CEL


title: SF7192 p53 MT pten WT Map250kSty

description: SRCID:SRC107478,PRBID:PRB16784,SRCNAME:7192,RAWFILE:16784_7192_GBMTumors_SPR460_Map250kSty.CEL

value: p53 exon 4-8 mutation status:HETSUB.220Y>H

value: pten exon 5-6 mutation status:WT


title: SF7194 p53 WT pten WT Map250kSty

description: SRCID:SRC107479,PRBID:PRB16786,SRCNAME:7194,RAWFILE:16786_7194_GBMTumors_SPR460_Map250kSty.CEL


title: SF7101 p53 WT pten MT Map250kSty

description: SRCID:SRC107472,PRBID:PRB16772,SRCNAME:7101,RAWFILE:16772_7101_GBMTumors_SPR460_Map250kSty.CEL

value: pten exon 5-6 mutation status:HOMSUB.173R>C


title: SF7276 p53 WT pten MT Map250kSty

description: SRCID:SRC107486,PRBID:PRB16800,SRCNAME:7276,RAWFILE:16800_7276_GBMTumors_SPR460_Map250kSty.CEL

value: pten exon 5-6 mutation status:HETSUB.133V>I


title: SF7186 p53 WT pten WT Map250kSty

description: SRCID:SRC107477,PRBID:PRB16782,SRCNAME:7186,RAWFILE:16782_7184_GBMTumors_SPR460_Map250kSty.CEL