title: pTH8618_HK_8mer_5710

source_name: NCU01871_HK design


title: pTH8598_HK_8mer_5854

status: Public on Aug 01 2014

type: protein

city: Cincinnati

first: Matthew

middle: Tyson

last: Weirauch

state: OH

address: 3333 Burnet Avenue

country: USA

institute: Cincinnati Children's Hospital

hyb_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate. After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 mM resolution.  Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low).  The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used.   Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: We provide several scores for each 8-mer in each experiment. Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots. Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

molecule: protein

organism: synthetic construct

source_name: nhr-86_HK design

label_protocol: DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned as SacI–BamHI fragments into pTH5325, a modified T7-driven GST expression vector, in most cases.  See paper supplemental web site (http://hugheslab.ccbr.utoronto.ca/supplementary-data/CisBP/) for exceptions.

tag: dbd

tag: platform_id_id design

value: HK

tag: dbd source organism


title: pTH8592_ME_8mer_5485

source_name: RAV1_ME design

extract_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate.

value: ME


title: pTH8591_HK_8mer_5703

source_name: BIM3_HK design

value: HLH


title: pTH8591_ME_8mer_5484

source_name: BIM3_ME design


title: pTH8610_ME_8mer_5602

source_name: NCU00155_ME design


title: pTH8594_HK_8mer_5748

source_name: HCAG_10227_HK design


title: pTH8587_HK_8mer_5747

source_name: Smp_170910_HK design


title: pTH8590_HK_8mer_5842

source_name: ARR2_HK design


title: pTH8611_ME_8mer_5603

source_name: NCU00902_ME design

value: GATA


title: pTH8585_ME_8mer_5590

source_name: kdm2aa_ME design

value: zf-CXXC


title: pTH8596_HK_8mer_5749

source_name: LOC_Os08g36920_HK design


title: pTH8610_HK_8mer_5752

source_name: NCU00155_HK design


title: pTH8590_ME_8mer_5483

source_name: ARR2_ME design


title: pTH8580_HK_8mer_5742

value: SBP


title: pTH8580_ME_8mer_5586


title: pTH8596_ME_8mer_5595

source_name: LOC_Os08g36920_ME design


title: pTH8585_HK_8mer_5745

source_name: kdm2aa_HK design


title: pTH8587_ME_8mer_5593

source_name: Smp_170910_ME design


title: pTH8624_HK_8mer_5827

source_name: nit-2_HK design


title: pTH8584_HK_8mer_5744

source_name: fgenesh1_pg.scaffold_37000071_HK design


title: pTH8592_HK_8mer_5843

source_name: RAV1_HK design


title: pTH8584_ME_8mer_5589

source_name: fgenesh1_pg.scaffold_37000071_ME design


title: pTH8577_ME_8mer_5583

source_name: KDM2B_ME design


title: pTH8577_HK_8mer_5740

source_name: KDM2B_HK design


title: pTH8574_ME_8mer_5618

source_name: PRKRIR_ME design

value: THAP


title: pTH8594_ME_8mer_5594

source_name: HCAG_10227_ME design


title: pTH8574_HK_8mer_5852

source_name: PRKRIR_HK design


title: pTH8570_HK_8mer_5738

source_name: FBXL19_HK design


title: pTH8569_HK_8mer_5737

source_name: PFL1085w_HK design


title: pTH8570_ME_8mer_5577

source_name: FBXL19_ME design


title: pTH8566_HK_8mer_5851

source_name: LIN54_HK design

value: CXC


title: pTH8569_ME_8mer_5545

source_name: PFL1085w_ME design


title: pTH8559_ME_8mer_5535

source_name: mll_ME design


title: pTH8565_ME_8mer_5540

source_name: TFCP2_CHICK_ME design


title: pTH8555_ME_8mer_5883

source_name: Hmg20b_ME design


title: pTH8626_ME_8mer_5567

source_name: NCU00340_ME design


title: pTH8560_ME_8mer_5536

source_name: naif1_ME design


title: pTH8558_HK_8mer_5731

source_name: ENSXETG00000014047_HK design


title: pTH8565_HK_8mer_5909

source_name: TFCP2_CHICK_HK design


title: pTH8562_ME_8mer_5538

source_name: jund_ME design


title: pTH8556_ME_8mer_5532

source_name: pax2_ME design

value: PAX


title: pTH8566_ME_8mer_5542

source_name: LIN54_ME design


title: pTH8560_HK_8mer_5848

source_name: naif1_HK design


title: pTH8558_ME_8mer_5534

source_name: ENSXETG00000014047_ME design


title: pTH8559_HK_8mer_5847

source_name: mll_HK design


title: pTH8562_HK_8mer_5849

source_name: jund_HK design


title: pTH8557_HK_8mer_5846

source_name: nfatc1_HK design

value: RHD


title: pTH8556_HK_8mer_5729

source_name: pax2_HK design


title: pTH8552_ME_8mer_5560


title: pTH8554_ME_8mer_5531

source_name: Gm98_ME design


title: pTH8554_HK_8mer_5728

source_name: Gm98_HK design


title: pTH8555_HK_8mer_5955

source_name: Hmg20b_HK design


title: pTH8552_HK_8mer_5727


title: pTH8547_ME_8mer_5616

source_name: bhlh112_ME design


title: pTH8550_HK_8mer_5793

source_name: Phf21a_HK design


title: pTH8550_ME_8mer_4815

source_name: Phf21a_ME design


title: pTH8489_HK_8mer_5722

source_name: estExt_gwp_gw1.C_70211_HK design

value: Homeobox


title: pTH8547_HK_8mer_5797

source_name: bhlh112_HK design


title: pTH8488_ME_8mer_5525

source_name: estExt_fgenesh1_pg.C_4800009_ME design


title: pTH8492_HK_8mer_5725

source_name: fgenesh1_pg.scaffold_70000111_HK design


title: pTH8490_ME_8mer_5527

source_name: fgenesh1_pg.scaffold_1000495_ME design


title: pTH8491_ME_8mer_5529


title: pTH8492_ME_8mer_5546

source_name: fgenesh1_pg.scaffold_70000111_ME design


title: pTH8491_HK_8mer_5724


title: pTH8489_ME_8mer_5526

source_name: estExt_gwp_gw1.C_70211_ME design


title: pTH8478_ME_8mer_5521

value: NAM


title: pTH8472_ME_8mer_5515

source_name: estExt_gwp_gw1.C_550163_ME design


title: pTH8478_HK_8mer_5840


title: pTH8488_HK_8mer_5830

source_name: estExt_fgenesh1_pg.C_4800009_HK design


title: pTH8467_ME_8mer_5510


title: pTH8490_HK_8mer_5844

source_name: fgenesh1_pg.scaffold_1000495_HK design


title: pTH8477_HK_8mer_5839


title: pTH8472_HK_8mer_5838

source_name: estExt_gwp_gw1.C_550163_HK design


title: pTH8469_HK_8mer_5695

source_name: estExt_fgenesh1_pg.C_370003_HK design

value: zf-Dof


title: pTH8469_ME_8mer_5512

source_name: estExt_fgenesh1_pg.C_370003_ME design


title: pTH8467_HK_8mer_5837


title: pTH8477_ME_8mer_5520


title: pTH8466_ME_8mer_5509


title: pTH8466_HK_8mer_6178


title: pTH8464_ME_8mer_5507


title: pTH8463_HK_8mer_5691


title: pTH8463_ME_8mer_5506


title: pTH8557_ME_8mer_5533

source_name: nfatc1_ME design


title: pTH8461_ME_8mer_5504

source_name: e_gw1.362.4.1_ME design


title: pTH8459_ME_8mer_5502


title: pTH8459_HK_8mer_5689


title: pTH8458_HK_8mer_5688


title: pTH9723_ME_8mer_7622

source_name: PK22320.1_ME design


title: pTH9731_ME_8mer_7844

source_name: NCU03110_ME design


title: pTH9700_ME_8mer_7937

source_name: NCU05411_ME design


title: pTH9719_ME_8mer_7619

description: PBM CONSTRUCTS

source_name: ENSMGAG00000004157_ME design


title: pTH9731_HK_8mer_7863

source_name: NCU03110_HK design


title: pTH9699_ME_8mer_7751

source_name: NCU03070_ME design


title: pTH9698_HK_8mer_7967

source_name: NCU02853_HK design


title: pTH8458_ME_8mer_5501


title: pTH8461_HK_8mer_5690

source_name: e_gw1.362.4.1_HK design


title: pTH9718_HK_8mer_7784

source_name: ATCBF3_HK design


title: pTH9695_ME_8mer_7747

source_name: NCU02724_ME design


title: pTH9695_HK_8mer_7782

source_name: NCU02724_HK design


title: pTH9719_HK_8mer_7702

description: PBM CONSTRUCTS

source_name: ENSMGAG00000004157_HK design


title: pTH9730_ME_8mer_7843

source_name: NCU08634_ME design


title: pTH9699_HK_8mer_7860

source_name: NCU03070_HK design


title: pTH9718_ME_8mer_7618

source_name: ATCBF3_ME design


title: pTH9724_HK_8mer_7788

source_name: PK22848.1_HK design


title: pTH9730_HK_8mer_7862

source_name: NCU08634_HK design


title: pTH8464_HK_8mer_5692


title: pTH9723_HK_8mer_7703

source_name: PK22320.1_HK design


title: pTH9724_ME_8mer_7623

source_name: PK22848.1_ME design


title: pTH9700_HK_8mer_7861

source_name: NCU05411_HK design


title: pTH9691_ME_8mer_7743

source_name: NCU00090_ME design


title: pTH9693_HK_8mer_7781

source_name: NCU02012_HK design


title: pTH9687_HK_8mer_7777

source_name: NCU07587_HK design

value: KilA-N


title: pTH9685_ME_8mer_7733

source_name: NCU07392_ME design


title: pTH9691_HK_8mer_7779

source_name: NCU00090_HK design


title: pTH9683_ME_8mer_7731

source_name: NCU06971_ME design


title: pTH9693_ME_8mer_7745

source_name: NCU02012_ME design


title: pTH9682_HK_8mer_7772

source_name: NCU06907_HK design


title: pTH9683_HK_8mer_7774

source_name: NCU06971_HK design


title: pTH9676_HK_8mer_7767

source_name: NCU03725_HK design


title: pTH9671_ME_8mer_7739

source_name: NCU02787_ME design


title: pTH9675_HK_8mer_7766

source_name: NCU03552_HK design


title: pTH9682_ME_8mer_7730

source_name: NCU06907_ME design


title: pTH9687_ME_8mer_7735

source_name: NCU07587_ME design


title: pTH9671_HK_8mer_7962

source_name: NCU02787_HK design


title: pTH9677_ME_8mer_7725

source_name: NCU03975_ME design


title: pTH9672_HK_8mer_7765

source_name: NCU02819_HK design


title: pTH9681_HK_8mer_7773

source_name: NCU05308_HK design


title: pTH9675_ME_8mer_7723

source_name: NCU03552_ME design


title: pTH9685_HK_8mer_7776

source_name: NCU07392_HK design


title: pTH9670_ME_8mer_7717

source_name: NCU02752_ME design


title: pTH9670_HK_8mer_7763

source_name: NCU02752_HK design


title: pTH9681_ME_8mer_7729

source_name: NCU05308_ME design


title: pTH9672_ME_8mer_7719

source_name: NCU02819_ME design


title: pTH9677_HK_8mer_7768

source_name: NCU03975_HK design


title: pTH9689_HK_8mer_7778

source_name: NCU08159_HK design


title: pTH9668_ME_8mer_7715

source_name: NCU02576_ME design


title: pTH9665_HK_8mer_7761

source_name: NCU02173_HK design


title: pTH9664_ME_8mer_7711

source_name: NCU01994_ME design


title: pTH9668_HK_8mer_7762

source_name: NCU02576_HK design


title: pTH9676_ME_8mer_7724

source_name: NCU03725_ME design


title: pTH9665_ME_8mer_7712

source_name: NCU02173_ME design


title: pTH9662_ME_8mer_7709

source_name: NCU01706_ME design


title: pTH9662_HK_8mer_7758

source_name: NCU01706_HK design


title: pTH9664_HK_8mer_7760

source_name: NCU01994_HK design


title: pTH9689_ME_8mer_7741

source_name: NCU08159_ME design


title: pTH9661_ME_8mer_7708

source_name: NCU01386_ME design


title: pTH9663_ME_8mer_7710

source_name: NCU01924_ME design


title: pTH9663_HK_8mer_7759

source_name: NCU01924_HK design


title: pTH9658_ME_8mer_7705

source_name: NCU00392_ME design


title: pTH9660_ME_8mer_7707

source_name: NCU01209_ME design


title: pTH9661_HK_8mer_7757

source_name: NCU01386_HK design


title: pTH9660_HK_8mer_7756

source_name: NCU01209_HK design


title: pTH9655_HK_8mer_7859

source_name: NCU00019_HK design


title: pTH9658_HK_8mer_7754

source_name: NCU00392_HK design


title: pTH9655_ME_8mer_7649

source_name: NCU00019_ME design


title: pTH9656_ME_8mer_7720

source_name: tah-1_ME design


title: pTH9653_ME_8mer_7935

source_name: PK28565.1_ME design


title: pTH9698_ME_8mer_7750

source_name: NCU02853_ME design


title: pTH9657_HK_8mer_7753

source_name: NCU00344_HK design


title: pTH9656_HK_8mer_7752

source_name: tah-1_HK design


title: pTH9653_HK_8mer_7638

source_name: PK28565.1_HK design


title: pTH9649_HK_8mer_7637

source_name: PK06103.1_HK design


title: pTH9657_ME_8mer_7704

source_name: NCU00344_ME design


title: pTH9644_ME_8mer_7835


title: pTH9647_ME_8mer_7943


title: pTH9644_HK_8mer_7858


title: pTH9609_HK_8mer_7485

source_name: PK19363.1_HK design


title: pTH9647_HK_8mer_7960


title: pTH9600_ME_8mer_7500

source_name: PK27213.1_ME design


title: pTH9605_HK_8mer_7371

source_name: TET1_HK design


title: pTH9610_ME_8mer_7395

source_name: PK19779.1_ME design


title: pTH9600_HK_8mer_7789

source_name: PK27213.1_HK design


title: pTH9605_ME_8mer_7360

source_name: TET1_ME design


title: pTH9610_HK_8mer_7786

source_name: PK19779.1_HK design


title: pTH9649_ME_8mer_7399

source_name: PK06103.1_ME design


title: pTH9592_HK_8mer_7483

source_name: PK23829.1_HK design


title: pTH9609_ME_8mer_7394

source_name: PK19363.1_ME design


title: pTH9604_HK_8mer_7370

source_name: WRKY29_HK design

value: WRKY


title: pTH9588_ME_8mer_7550

source_name: PK17526.1_ME design


title: pTH9586_ME_8mer_7412

source_name: PK14653.1_ME design

value: TCP


title: pTH9595_ME_8mer_7530

source_name: PK29550.1_ME design


title: pTH9589_ME_8mer_7415

source_name: PK18474.1_ME design


title: pTH9595_HK_8mer_7484

source_name: PK29550.1_HK design


title: pTH9589_HK_8mer_7482

source_name: PK18474.1_HK design


title: pTH9604_ME_8mer_7359

source_name: WRKY29_ME design


title: pTH9583_HK_8mer_7369

source_name: PK06791.1_HK design


title: pTH9592_ME_8mer_7551

source_name: PK23829.1_ME design


title: pTH9489_ME_8mer_7103

source_name: PK10342.1_ME design


title: pTH8457_ME_8mer_5500


title: pTH9487_HK_8mer_7279

source_name: PK00738.1_HK design


title: pTH9583_ME_8mer_7345

source_name: PK06791.1_ME design


title: pTH8456_ME_8mer_5499

source_name: gw1.8.141.1_ME design


title: pTH9588_HK_8mer_7481

source_name: PK17526.1_HK design


title: pTH8457_HK_8mer_5687


title: pTH8456_HK_8mer_5686

source_name: gw1.8.141.1_HK design


title: pTH9491_ME_8mer_7105

source_name: PK14402.1_ME design


title: pTH9488_ME_8mer_7392

source_name: PK08316.1_ME design


title: pTH9488_HK_8mer_7479

source_name: PK08316.1_HK design


title: pTH9473_ME_8mer_7833

source_name: NCU09033_ME design


title: pTH8406_ME_8mer_7822

source_name: LOC_Os02g57820_ME design


title: pTH9581_HK_8mer_7368

source_name: PK06182.1_HK design


title: pTH9485_HK_8mer_7278

source_name: TET1_HK design


title: pTH9579_ME_8mer_7341

source_name: PK02532.1_ME design


title: pTH9586_HK_8mer_7480

source_name: PK14653.1_HK design


title: pTH9581_ME_8mer_7817

source_name: PK06182.1_ME design


title: pTH8411_HK_8mer_5684

source_name: tbx-40_HK design

value: T-box


title: pTH9480_ME_8mer_7225

source_name: ces-2_ME design


title: pTH9579_HK_8mer_7367

source_name: PK02532.1_HK design

value: HK


title: pTH8411_ME_8mer_5478

source_name: tbx-40_ME design

value: ME


title: pTH9480_HK_8mer_7277

source_name: ces-2_HK design


title: pTH9489_HK_8mer_7280

source_name: PK10342.1_HK design


title: pTH9473_HK_8mer_7857

source_name: NCU09033_HK design


title: pTH9491_HK_8mer_7281

source_name: PK14402.1_HK design


title: pTH9485_ME_8mer_7155

source_name: TET1_ME design


title: pTH9487_ME_8mer_7831

source_name: PK00738.1_ME design


title: pTH8401_ME_8mer_5474

source_name: NFATC1_ME design


title: pTH8401_HK_8mer_5683

source_name: NFATC1_HK design


title: pTH8398_HK_8mer_5681

source_name: WRKY40_HK design


title: pTH8399_HK_8mer_5682

source_name: lin54_HK design


title: pTH8370_ME_8mer_5334

source_name: CNBG_2239_ME design


title: pTH8362_ME_8mer_5328

source_name: danr_ME design


title: pTH8366_HK_8mer_5677

source_name: BGIBMGA013198_HK design

value: CUT


title: pTH8398_ME_8mer_5471

source_name: WRKY40_ME design


title: pTH8397_HK_8mer_5680

source_name: NAP_HK design


title: pTH8368_HK_8mer_5678

source_name: Smp_174320_HK design

value: Runt


title: pTH8362_HK_8mer_5676

source_name: danr_HK design


title: pTH8399_ME_8mer_5472

source_name: lin54_ME design


title: pTH8352_HK_8mer_5673

source_name: LOC_Os02g45450_HK design


title: pTH8356_ME_8mer_5806

source_name: LOC_Os06g04090_ME design


title: pTH8368_ME_8mer_5332

source_name: Smp_174320_ME design


title: pTH8361_ME_8mer_5327

source_name: gcm2_ME design

value: GCM


title: pTH8406_HK_8mer_7957

source_name: LOC_Os02g57820_HK design


title: pTH8370_HK_8mer_5679

source_name: CNBG_2239_HK design


title: pTH8350_ME_8mer_5177

source_name: vad-5_ME design


title: pTH8356_HK_8mer_5674

source_name: LOC_Os06g04090_HK design


title: pTH8350_HK_8mer_5671

source_name: vad-5_HK design


title: pTH8349_ME_8mer_5176

source_name: ANIA_01425_ME design


title: pTH8352_ME_8mer_5318

source_name: LOC_Os02g45450_ME design


title: pTH8349_HK_8mer_5670

source_name: ANIA_01425_HK design


title: pTH8351_ME_8mer_5178

source_name: EFNCRG00000000350_ME design


title: pTH8366_ME_8mer_5330

source_name: BGIBMGA013198_ME design


title: pTH8361_HK_8mer_5675

source_name: gcm2_HK design


title: pTH8348_ME_8mer_5156

source_name: BC1G_11044_ME design


title: pTH8348_HK_8mer_5669

source_name: BC1G_11044_HK design


title: pTH8347_HK_8mer_5668

source_name: ANIA_09147_HK design


title: pTH8318_HK_8mer_5660

source_name: GMEB1_HK design

value: SAND


title: pTH8318_ME_8mer_5296

source_name: GMEB1_ME design


title: pTH8341_HK_8mer_5667

source_name: unc-86_HK design

value: Pou,Homeobox


title: pTH8319_HK_8mer_5661

source_name: PRKRIR_HK design

value: THAP


title: pTH8347_ME_8mer_5155

source_name: ANIA_09147_ME design


title: pTH8341_ME_8mer_5313

source_name: unc-86_ME design


title: pTH8332_ME_8mer_5304

source_name: LOC_Os03g03164_ME design


title: pTH8334_HK_8mer_5666

source_name: LOC_Os02g49560_HK design


title: pTH8351_HK_8mer_5672

source_name: EFNCRG00000000350_HK design


title: pTH8334_ME_8mer_5305

source_name: LOC_Os02g49560_ME design


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title: pTH6483_ME_8mer_2907

source_name: NOT-like_E_ME design


title: pTH6486_ME_8mer_2910

source_name: nhr-145_ME design


title: pTH6482_ME_8mer_2906

source_name: TLX2_ME design


title: pTH6492_HK_8mer_3487

source_name: CXR_HK design


title: pTH6483_HK_8mer_3404

source_name: NOT-like_E_HK design


title: pTH6462_ME_8mer_2886

source_name: PRH_ME design


title: pTH6482_HK_8mer_3489

source_name: TLX2_HK design


title: pTH6472_ME_8mer_2896

source_name: NK-like_5_ME design


title: pTH6461_ME_8mer_2885

source_name: ATWOX13_ME design


title: pTH6478_HK_8mer_3401

source_name: Lim3_HK design


title: pTH6455_HK_8mer_3118

source_name: CAGL0H02959g_HK design


title: pTH6454_ME_8mer_2846


title: pTH6461_HK_8mer_3324

source_name: ATWOX13_HK design


title: pTH6478_ME_8mer_2902

source_name: Lim3_ME design


title: pTH6462_HK_8mer_3327

source_name: PRH_HK design


title: pTH6472_HK_8mer_3399

source_name: NK-like_5_HK design


title: pTH6453_ME_8mer_2845

source_name: Duxbl_ME design


title: pTH6454_HK_8mer_3117


title: pTH6450_ME_8mer_2842

source_name: Ets21C_ME design


title: pTH6449_ME_8mer_2841

source_name: BARX1_ME design


title: pTH6453_HK_8mer_3116

source_name: Duxbl_HK design


title: pTH6450_HK_8mer_3115

source_name: Ets21C_HK design


title: pTH6448_HK_8mer_3113

source_name: NOBOX_HK design


title: pTH6447_HK_8mer_3112

source_name: CG34031_HK design


title: pTH6449_HK_8mer_3114

source_name: BARX1_HK design


title: pTH6429_ME_8mer_2821

source_name: AGAP010438_ME design


title: pTH6423_HK_8mer_2952

source_name: pha-2_HK design


title: pTH6445_HK_8mer_3111

source_name: CG15696_HK design


title: pTH6425_ME_8mer_2817

source_name: ENSTNIG00000018555_ME design


title: pTH6448_ME_8mer_2840

source_name: NOBOX_ME design


title: pTH6408_HK_8mer_2949

source_name: Cbr-irx-1_HK design


title: pTH6429_HK_8mer_3109

source_name: AGAP010438_HK design


title: pTH6423_ME_8mer_2815

source_name: pha-2_ME design


title: pTH6445_ME_8mer_2837

source_name: CG15696_ME design


title: pTH6408_ME_8mer_2800

source_name: Cbr-irx-1_ME design


title: pTH6406_HK_8mer_2948

source_name: PHO2_HK design


title: pTH6404_HK_8mer_2947

source_name: LBX1_HK design


title: pTH6425_HK_8mer_3108

source_name: ENSTNIG00000018555_HK design


title: pTH6406_ME_8mer_2798

source_name: PHO2_ME design


title: pTH6404_ME_8mer_2796

source_name: LBX1_ME design


title: pTH6401_ME_8mer_2793

source_name: AAEL012091_ME design


title: pTH6447_ME_8mer_2839

source_name: CG34031_ME design


title: pTH6392_HK_8mer_2945

source_name: hbx9_HK design


title: pTH6363_ME_8mer_2723

source_name: ECU03_1170_ME design


title: pTH6379_HK_8mer_2772

source_name: Sebox_HK design


title: pTH6379_ME_8mer_2739

source_name: Sebox_ME design


title: pTH6354_ME_8mer_2714

source_name: b2-1_ME design


title: pTH6363_HK_8mer_2776

source_name: ECU03_1170_HK design


title: pTH6401_HK_8mer_2946

source_name: AAEL012091_HK design


title: pTH6369_HK_8mer_2778

source_name: SNAPOd2T00003340001_HK design


title: pTH6378_ME_8mer_2738

source_name: LOC_Os09g35910_ME design


title: pTH6366_HK_8mer_2777

source_name: lim-4_HK design


title: pTH6381_ME_8mer_2741

source_name: YHP1_ME design


title: pTH6345_HK_8mer_2773

source_name: ELK4_HK design


title: pTH6353_ME_8mer_2713

source_name: NVHD143-TALE_ME design


title: pTH6381_HK_8mer_2782

source_name: YHP1_HK design


title: pTH6340_HK_8mer_2780

source_name: ATEG_00670_HK design


title: pTH6369_ME_8mer_2729

source_name: SNAPOd2T00003340001_ME design


title: pTH6340_ME_8mer_2700

source_name: ATEG_00670_ME design


title: pTH6339_ME_8mer_2699

source_name: Q1T448_ME design


title: pTH6329_ME_8mer_3683

source_name: FGSG_07914T0_ME design


title: pTH6366_ME_8mer_2726

source_name: lim-4_ME design


title: pTH6436_HK_8mer_3110

source_name: eve_HK design


title: pTH6436_ME_8mer_2828

source_name: eve_ME design


title: pTH6392_ME_8mer_2784

source_name: hbx9_ME design


title: pTH6378_HK_8mer_2781

source_name: LOC_Os09g35910_HK design


title: pTH6353_HK_8mer_2774

source_name: NVHD143-TALE_HK design


title: pTH6339_HK_8mer_2771

source_name: Q1T448_HK design


title: pTH6345_ME_8mer_2705

source_name: ELK4_ME design


title: pTH6328_ME_8mer_2688

source_name: GRMZM2G135447_ME design


title: pTH6354_HK_8mer_2769

source_name: b2-1_HK design


title: pTH6455_ME_8mer_2879

source_name: CAGL0H02959g_ME design


title: pTH6327_ME_8mer_2687

source_name: ceh-24_ME design


title: pTH6329_HK_8mer_3512

source_name: FGSG_07914T0_HK design


title: pTH6328_HK_8mer_2770

source_name: GRMZM2G135447_HK design


title: pTH6321_HK_8mer_2767

source_name: NK-like_21_HK design


title: pTH6299_HK_8mer_2761

source_name: Ci-Hox12_HK design


title: pTH6313_HK_8mer_2754

source_name: UM00578_HK design


title: pTH6321_ME_8mer_2680

source_name: NK-like_21_ME design


title: pTH6284_ME_8mer_2629

source_name: Ci-Prd-B_ME design


title: pTH6313_ME_8mer_2672

source_name: UM00578_ME design


title: pTH6287_ME_8mer_2632

source_name: eve_ME design


title: pTH6326_ME_8mer_2685

source_name: GSTENG00029951001_ME design


title: pTH6303_ME_8mer_2662

source_name: NK-like_10_ME design


title: pTH6326_HK_8mer_2768

source_name: GSTENG00029951001_HK design


title: pTH6301_HK_8mer_2762

source_name: HBX4_HK design


title: pTH6303_HK_8mer_2763

source_name: NK-like_10_HK design


title: pTH6308_ME_8mer_2667

source_name: Cnox3_ME design


title: pTH6287_HK_8mer_2759

source_name: eve_HK design


title: pTH6299_ME_8mer_2658

source_name: Ci-Hox12_ME design


title: pTH6291_HK_8mer_2760

source_name: vex1_HK design


title: pTH6308_HK_8mer_2764

source_name: Cnox3_HK design


title: pTH6291_ME_8mer_2636

source_name: vex1_ME design


title: pTH6281_HK_8mer_2757

source_name: NR2E1_HK design


title: pTH6271_ME_8mer_2617

source_name: GSTENG00028216001_ME design

value: SAND


title: pTH6327_HK_8mer_2775

source_name: ceh-24_HK design


title: pTH6281_ME_8mer_2626

source_name: NR2E1_ME design


title: pTH6284_HK_8mer_2758

source_name: Ci-Prd-B_HK design


title: pTH6301_ME_8mer_2660

source_name: HBX4_ME design


title: pTH6271_HK_8mer_2755

source_name: GSTENG00028216001_HK design


title: pTH6268_ME_8mer_2613

source_name: Noto_ME design


title: pTH6221_ME_8mer_2479

source_name: vsx2_ME design


title: pTH6267_HK_8mer_2753

source_name: FGSG_07909T0_HK design


title: pTH6268_HK_8mer_2766

source_name: Noto_HK design


title: pTH6174_HK_8mer_2640

source_name: Tr4/Tr2_HK design


title: pTH6195_ME_8mer_2453

source_name: Vsx2_ME design


title: pTH6267_ME_8mer_2612

source_name: FGSG_07909T0_ME design


title: pTH6201_ME_8mer_2459

source_name: AGAP006642_ME design


title: pTH6265_HK_8mer_2752

source_name: ECU04_0970_HK design


title: pTH6218_ME_8mer_2476

source_name: dve_ME design


title: pTH6174_ME_8mer_2432

source_name: Tr4/Tr2_ME design


title: pTH6265_ME_8mer_2610

source_name: ECU04_0970_ME design


title: pTH6221_HK_8mer_2650

source_name: vsx2_HK design


title: pTH6176_ME_8mer_2434

source_name: LHX3-like_ME design


title: pTH6201_HK_8mer_2647

source_name: AGAP006642_HK design


title: pTH6215_HK_8mer_2648

source_name: HOXF_HK design


title: pTH6195_HK_8mer_2646

source_name: Vsx2_HK design


title: pTH6164_HK_8mer_3507

source_name: MedPost_HK design


title: pTH6218_HK_8mer_2649

source_name: dve_HK design


title: pTH6251_HK_8mer_2751

source_name: labial_HK design


title: pTH6162_ME_8mer_2421

source_name: pv.1_ME design


title: pTH6163_ME_8mer_2422

source_name: mix-a_ME design


title: pTH6176_HK_8mer_3508

source_name: LHX3-like_HK design


title: pTH6251_ME_8mer_2564

source_name: labial_ME design


title: pTH6156_ME_8mer_2415

source_name: AANF_ME design


title: pTH6162_HK_8mer_2604

source_name: pv.1_HK design


title: pTH6164_ME_8mer_2423

source_name: MedPost_ME design


title: pTH6215_ME_8mer_2473

source_name: HOXF_ME design


title: pTH6163_HK_8mer_2605

source_name: mix-a_HK design


title: pTH6156_HK_8mer_2603

source_name: AANF_HK design


title: pTH6150_ME_8mer_2409

source_name: Q50-5_ME design


title: pTH6144_ME_8mer_2403

source_name: AmNR2_ME design


title: pTH6142_ME_8mer_2401

source_name: FBpp0087454_ME design


title: pTH6143_HK_8mer_2600

source_name: hoxd13a_HK design


title: pTH6140_ME_8mer_2399

source_name: Splox_ME design


title: pTH6150_HK_8mer_2602

source_name: Q50-5_HK design


title: pTH6135_HK_8mer_3475

source_name: K50-6_HK design


title: pTH6110_HK_8mer_2591

source_name: Cbr-nhr-184_HK design


title: pTH6132_ME_8mer_2391

source_name: ZC123.3_ME design


title: pTH6135_ME_8mer_2394

source_name: K50-6_ME design


title: pTH6142_HK_8mer_2599

source_name: FBpp0087454_HK design


title: pTH6144_HK_8mer_2601

source_name: AmNR2_HK design


title: pTH6115_HK_8mer_2592

source_name: MIMI_R749_HK design


title: pTH6140_HK_8mer_2597

source_name: Splox_HK design


title: pTH6143_ME_8mer_2402

source_name: hoxd13a_ME design


title: pTH6141_ME_8mer_2400

source_name: GRMZM2G038252_P01_ME design


title: pTH6108_HK_8mer_2590

source_name: FOXK1_HK design


title: pTH6132_HK_8mer_2593

source_name: ZC123.3_HK design


title: pTH6103_ME_8mer_2361

source_name: PaxD4_ME design


title: pTH6115_ME_8mer_2373

source_name: MIMI_R749_ME design


title: pTH6104_ME_8mer_2362

source_name: vab-7_ME design


title: pTH6136_HK_8mer_2595

source_name: cnox3-Pc_HK design


title: pTH6104_HK_8mer_2588

source_name: vab-7_HK design


title: pTH6141_HK_8mer_2598

source_name: GRMZM2G038252_P01_HK design


title: pTH6136_ME_8mer_2395

source_name: cnox3-Pc_ME design


title: pTH6108_ME_8mer_2366

source_name: FOXK1_ME design


title: pTH6110_ME_8mer_2368

source_name: Cbr-nhr-184_ME design


title: pTH6101_ME_8mer_2359

source_name: NK-like_3_ME design


title: pTH6101_HK_8mer_2586

source_name: NK-like_3_HK design


title: pTH6103_HK_8mer_2587

source_name: PaxD4_HK design


title: pTH6076_HK_8mer_2585

source_name: Os02g0706600_HK design


title: pTH6076_ME_8mer_2270

source_name: Os02g0706600_ME design


title: pTH6071_ME_8mer_2265

source_name: Rhox8_ME design


title: pTH6070_HK_8mer_2583

source_name: KLLA0D10043g_HK design


title: pTH6070_ME_8mer_2264

source_name: KLLA0D10043g_ME design


title: pTH6064_HK_8mer_2582

source_name: ENSTNIG00000017092_HK design


title: pTH6064_ME_8mer_2258

source_name: ENSTNIG00000017092_ME design


title: pTH6057_HK_8mer_2526

source_name: SPBC21B10.13c_HK design


title: pTH6071_HK_8mer_3474

source_name: Rhox8_HK design


title: pTH6057_ME_8mer_2248

source_name: SPBC21B10.13c_ME design


title: pTH6053_ME_8mer_2244

source_name: FBpp0073832_ME design


title: pTH6056_HK_8mer_2581

source_name: CIMG_06089T0_HK design


title: pTH6055_ME_8mer_2246

source_name: Estrogen_receptor_ME design


title: pTH6051_HK_8mer_2521

source_name: CG42234_HK design


title: pTH6050_HK_8mer_2525

source_name: Peml_HK design


title: pTH6047_ME_8mer_2239

source_name: SPAC32A11.03c_ME design


title: pTH6055_HK_8mer_2524

source_name: Estrogen_receptor_HK design


title: M9_rep3

type: RNA

city: Ede

first: Annereinou

last: Dijkstra

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

hyb_protocol: Co-hybridization of Cy5- and Cy3-labeled cDNA probes was performed on these oligonucleotide arrays at 65°C and 10 rpm for 17 h using GEX HI-RPM buffer (Agilent Technologies).

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: The raw expression data were Lowess normalized and scaled to normalized probe expression levels using MicroPreP (van Hijum, 2003). As in general multiple probes were designed for each ORF, the ORF expression level was calculated from the median of its probe signals.

molecule: total RNA

organism: Lactococcus cremoris subsp. cremoris MG1363

source_name: MG1363 fermentation 9

label_protocol: 5 µg of total RNA was used for cDNA synthesis and indirect labeling with cyanine 5 or cyanine 3

growth_protocol: Lactococcus lactis strain MG1363 was grown in chemically defined medium

extract_protocol: Cultures were lysed by bead-beating and total RNA was isolated by subsequent phenol/chloroform extraction.

treatment_protocol: Harvested cells were resuspended in cold TE buffer with phenol/chloroform, SDS, sodium acetate and zirconia beads, frozen in liquid nitrogen and stored at -80°C.

tag: fermentation conditions

value: 0 mM NaCl, pH 6.0, 35°C, shaken


title: pTH6051_ME_8mer_2242

source_name: CG42234_ME design


title: pTH6053_HK_8mer_2516

source_name: FBpp0073832_HK design


title: pTH6050_ME_8mer_2241

source_name: Peml_ME design


title: M7_rep2

source_name: MG1363 fermentation 7

value: 0 mM NaCl, pH 6.5, 30°C, shaken


title: M13_rep3

source_name: MG1363 fermentation 13

value: 100 mM NaCl, pH 6.5, 30°C, static


title: M13_rep2


title: M10_rep2

source_name: MG1363 fermentation 10

value: 100 mM NaCl, pH 6.5, 35°C, shaken


title: pTH6056_ME_8mer_2247

source_name: CIMG_06089T0_ME design


title: pTH6047_HK_8mer_2511

source_name: SPAC32A11.03c_HK design

value: HK


title: M12_rep2

source_name: MG1363 fermentation 12

value: 100 mM NaCl, pH 6.0, 35°C, static


title: M12_rep1


title: pTH6041_ME_8mer_2233

source_name: Prep_ME design

value: ME


title: M13_rep4


title: M11_rep1

source_name: MG1363 fermentation 11

value: 0 mM NaCl, pH 6.5, 35°C, static


title: M11_rep2


title: M10_rep1


title: M9_rep2


title: pTH6019_ME_8mer_2230

source_name: bhr-2_ME design


title: pTH6041_HK_8mer_2579

source_name: Prep_HK design


title: M9_rep1


title: pTH6016_ME_8mer_2227

source_name: pal-1_ME design


title: M8_rep2

source_name: MG1363 fermentation 8

value: 100 mM NaCl, pH 6.0, 30°C, shaken


title: pTH6016_HK_8mer_2347

source_name: pal-1_HK design


title: M8_rep1


title: M13_rep1


title: M7_rep1


title: pTH5996_HK_8mer_2342

source_name: MATALPHA2_HK design


title: M3_rep3

source_name: MG1363 fermentation 3

value: 0 mM NaCl, pH 6.5, 27°C, static


title: M6_rep3

source_name: MG1363 fermentation 6


title: pTH6014_ME_8mer_2225

source_name: FGSG_09047T0_ME design


title: pTH6003_ME_8mer_2197

source_name: Cbr-nhr-134_ME design


title: pTH6003_HK_8mer_2343

source_name: Cbr-nhr-134_HK design


title: pTH5986_HK_8mer_2339

source_name: Dux_HK design


title: pTH5996_ME_8mer_2190

source_name: MATALPHA2_ME design


title: pTH5994_ME_8mer_2188

source_name: LBX_ME design


title: pTH6013_HK_8mer_2346

source_name: CNBK3340_HK design


title: pTH6014_HK_8mer_2349

source_name: FGSG_09047T0_HK design


title: pTH5986_ME_8mer_2180

source_name: Dux_ME design


title: M6_rep4


title: M1_rep2

source_name: MG1363 fermentation 1

value: 0 mM NaCl, pH 6.0, 27°C, shaken


title: pTH5976_ME_8mer_2154

source_name: SNAPOd2T00005194001_ME design


title: pTH6013_ME_8mer_2224

source_name: CNBK3340_ME design


title: M4_rep1

source_name: MG1363 fermentation 4

value: 100 mM NaCl, pH 6.0, 27°C, static


title: M2_rep2

source_name: MG1363 fermentation 2

value: 100 mM NaCl, pH 6.5, 27°C, shaken


title: M3_rep2


title: M6_rep1


title: pTH5975_ME_8mer_2153

source_name: ECU10_1470_ME design


title: M6_rep2


title: M4_rep2


title: M3_rep1

source_name: MG1363 fermentation 3


title: M5_rep1

source_name: MG1363 fermentation 5

value: 0 mM NaCl, pH 6.0, 30°C, static


title: pTH5974_HK_8mer_2338

source_name: MATALPHA2_HK design


title: pTH5975_HK_8mer_2341

source_name: ECU10_1470_HK design


title: M1_rep1


title: M2_rep1


title: pTH5994_HK_8mer_2340

source_name: LBX_HK design


title: pTH5972_ME_8mer_2150

source_name: AC226150.2_ME design


title: pTH5976_HK_8mer_2344

source_name: SNAPOd2T00005194001_HK design


title: pTH5959_ME_8mer_2137

source_name: TVAG_451170_ME design


title: pTH5945_ME_8mer_2123

source_name: bap_ME design


title: pTH5932_HK_8mer_2332

source_name: UM04928_HK design


title: pTH5948_ME_8mer_2126

source_name: hbx7_ME design


title: pTH6019_HK_8mer_2348

source_name: bhr-2_HK design


title: pTH5932_ME_8mer_2116

source_name: UM04928_ME design


title: pTH5948_HK_8mer_2335

source_name: hbx7_HK design


title: pTH5972_HK_8mer_2337

source_name: AC226150.2_HK design


title: pTH5945_HK_8mer_2333

source_name: bap_HK design


title: pTH5928_ME_8mer_2112

source_name: six3_ME design


title: pTH5930_HK_8mer_2331

source_name: SNAPOd2T00006145001_HK design


title: pTH5922_ME_8mer_2106

source_name: Ci-Nkx-B_ME design


title: pTH5924_ME_8mer_2108

source_name: NR3C2_ME design


title: pTH5919_HK_8mer_2327

source_name: AGAP009986_HK design


title: pTH5928_HK_8mer_2330

source_name: six3_HK design


title: pTH5914_ME_8mer_2098

source_name: Sp110_ME design


title: pTH5922_HK_8mer_2328

source_name: Ci-Nkx-B_HK design


title: pTH5904_HK_8mer_2324

source_name: MSXB_HK design


title: pTH5930_ME_8mer_2114

source_name: SNAPOd2T00006145001_ME design


title: pTH5919_ME_8mer_2103

source_name: AGAP009986_ME design


title: pTH5916_HK_8mer_2326

source_name: efl-2_HK design


title: pTH5904_ME_8mer_2070

source_name: MSXB_ME design


title: pTH5891_ME_8mer_2055

source_name: nhr-49_ME design


title: pTH5903_ME_8mer_2069

source_name: CDA2_ME design


title: pTH5914_HK_8mer_2325

source_name: Sp110_HK design


title: pTH5916_ME_8mer_2100

source_name: efl-2_ME design


title: pTH5903_HK_8mer_2323

source_name: CDA2_HK design


title: pTH5924_HK_8mer_2329

source_name: NR3C2_HK design


title: pTH5897_HK_8mer_2322

source_name: ZHX1_HK design


title: pTH5897_ME_8mer_2061

source_name: ZHX1_ME design


title: pTH5959_HK_8mer_2336

source_name: TVAG_451170_HK design


title: pTH5891_HK_8mer_2321

source_name: nhr-49_HK design


title: pTH5974_ME_8mer_2152

source_name: MATALPHA2_ME design


title: pTH5887_HK_8mer_2320

source_name: HOXA2_HK design


title: pTH5871_ME_8mer_1822

source_name: ATEG_04171_ME design


title: pTH5883_ME_8mer_2047

source_name: ATHB22_ME design


title: pTH5882_ME_8mer_2046

source_name: nr2f2_ME design


title: pTH5887_ME_8mer_2051

source_name: HOXA2_ME design


title: pTH5882_HK_8mer_3461

source_name: nr2f2_HK design


title: pTH5877_HK_8mer_2089

source_name: Dpse\GA24899_HK design


title: pTH5877_ME_8mer_2041

source_name: Dpse\GA24899_ME design


title: pTH5871_HK_8mer_1887

source_name: ATEG_04171_HK design


title: pTH5883_HK_8mer_2093

source_name: ATHB22_HK design


title: pTH5869_HK_8mer_2021

source_name: EAT84071.1_HK design


title: M5_rep2

source_name: MG1363 fermentation 5


title: pTH5860_ME_8mer_1811

source_name: EAT80686.1_ME design


title: pTH5869_ME_8mer_1820

source_name: EAT84071.1_ME design


title: HCT116 3BKO  5-Aza-CdR D54

type: genomic

city: Los Angeles

first: Xiaojing

last: Yang

state: CA

address: 1441 Eastlake Ave, Room 7336

institute: USC/Norris Comprehensive Cancer Center

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with a genetic knockout of DNMT3B
SAMPLE 21

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation HM450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Colon

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified by phenol chloroform extractions

tag: gender

value: Male

tag: cell line

tag: genotype

value: DNMT3B KO

tag: treatment

tag: time


title: pTH5860_HK_8mer_1902

source_name: EAT80686.1_HK design

value: Homeobox


title: pTH5859_HK_8mer_1886

source_name: NCU03070_HK design


title: pTH5859_ME_8mer_1810

source_name: NCU03070_ME design


title: low-grade GIST

city: Heidelberg

first: Henri-Jacques

last: Delecluse

address: Im Neuenheimer Feld 242

department: Pathogenesis of virus-associated tumours

country: Germany

institute: German Cancer Research Center (DKFZ)

description: methylation data from a low-grade invasive gastro-intestinal stromal tumour

hyb_protocol: Sample was processed at genomics and proteomics core facility at German Cancer Research Center (DKFZ), Heidelberg according to manufactureres recommendations.

scan_protocol: llumina iScan System according to the manufacturer's protocol.

data_processing: The raw intensity values (two channels for each probe) were extracted from the Illumina .idat files using the LUMI software package for R. The standard signals available from Illumina and reported in Bibikova et. al., "High density DNA methylation array with single CpG site resolution", Genomics 98(4), 2011 were used for normalisation as follows. For every probe, the two color channels of the two reference samples (unmethylated and methylated DNA) define a 2x2 matrix, whose inverse was multiplied onto the measured signals. Thus, the reference unmethylated signal gets transformed into (1,0) and the methylated signal into (0,1). Probes where the two reference samples showed insufficient differences (e.g. the control probes) were not processed. To project onto a single value, the angle with the first axis was taken, with 90 degrees normalised to 1.

label: biotin/DNP

source_name: Gastro-intestinal stromal tumour, gastric resection

label_protocol: Illumina Protocol

extract_protocol: Tissue was homogenized and subsequently mixed with lysis buffer (700µl/g tissue) containing 2.1% (v/v) Proteinase K (10mg/ml) and 0.7% SDS in TE (pH 8.0). Samples were incubated o/n at 37°C. Phenol extraction followed by butanol treatment and ethanol precipitation was performed as described by Sambrook and Russell. 500ng of DNA was used for the assay.

value: male

tag: age

tag: tissue

value: stomach

tag: morphology

value: spindle

tag: kit

value: positive

tag: sdhb

tag: mitotic rate

value: 3 per 50 high-power fields


title: pTH5843_ME_8mer_1806

source_name: a2-1_ME design


title: HCT116 3BKO 5-Aza-CdR D68

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with a genetic knockout of DNMT3B
SAMPLE 22


title: HCT116 3BKO  5-Aza-CdR D5

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with a genetic knockout of DNMT3B
SAMPLE 16


title: HCT116 3BKO  5-Aza-CdR D42

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with a genetic knockout of DNMT3B
SAMPLE 20


title: pTH5843_HK_8mer_2018

source_name: a2-1_HK design

value: HK


title: HCT116 3BKO  5-Aza-CdR D10

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with a genetic knockout of DNMT3B
SAMPLE 17


title: HCT116 3BKO  5-Aza-CdR D14

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with a genetic knockout of DNMT3B
SAMPLE 18


title: HCT116 3BKO  5-Aza-CdR D24

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with a genetic knockout of DNMT3B
SAMPLE 19


title: pTH5833_ME_8mer_1796

source_name: FGSG_09043T0_ME design

value: ME


title: pTH5833_HK_8mer_1853

source_name: FGSG_09043T0_HK design


title: HCT116 1KO 5-Aza-CdR D68

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with homozygous deletions for DNMT1
SAMPLE 14


title: pTH5832_HK_8mer_2017

source_name: CDB2_HK design


title: pTH5828_ME_8mer_1791

source_name: nhr-84_ME design


title: pTH5832_ME_8mer_1795

source_name: CDB2_ME design


title: HCT116 1KO 5-Aza-CdR D5

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with homozygous deletions for DNMT1
SAMPLE 9


title: HCT116 3BKO Ctrl

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with a genetic knockout of DNMT3B
SAMPLE 15

value: control

value: baseline


title: HCT116 1KO 5-Aza-CdR D42

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with homozygous deletions for DNMT1
SAMPLE 12


title: HCT116 1KO 5-Aza-CdR D14

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with homozygous deletions for DNMT1
SAMPLE 10


title: pTH5828_HK_8mer_2028

source_name: nhr-84_HK design


title: pTH5822_ME_8mer_1785

source_name: GRF10_ME design


title: HCT116 1KO 5-Aza-CdR D54

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with homozygous deletions for DNMT1
SAMPLE 13


title: HCT116 5-Aza-CdR D54

description:
colorectal carcinoma cell line
SAMPLE 6


title: HCT116 1KO 5-Aza-CdR D24

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with homozygous deletions for DNMT1
SAMPLE 11


title: HCT116 1KO Ctrl

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with homozygous deletions for DNMT1
SAMPLE 8


title: HCT116 5-Aza-CdR D24

description:
colorectal carcinoma cell line
SAMPLE 4


title: HCT116 5-Aza-CdR D68

description:
colorectal carcinoma cell line
SAMPLE 7


title: HCT116 5-Aza-CdR D42

description:
colorectal carcinoma cell line
SAMPLE 5


title: HCT116 5-Aza-CdR D14

description:
colorectal carcinoma cell line
SAMPLE 3


title: MT.CRTS-22

city: daejeon

first: Jonglyul

last: Park

address: 52, Eoeun-dong, Yuseong-gu

department: Medical genomics

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

hyb_protocol: Amplified DNA was hybridized on the Infinium HumanMethylation 450 BeadChip (Illumina), following the Illumina Infinium HD Methylation protocol.

scan_protocol: The arrays were imaged using the Illumina HiScan SQ scanner, and image processing and extraction of intensity data were performed according to Illumina’s instructions.

data_processing: Each methylation signal was used to compute the β value, which is a quantitative measure of DNA methylation ranging from 0 (for completely unmethylated cytosines) to 1 (for completely methylated cytosines) (Bibikova et al., 2006).

source_name: rectal cancer tissue

extract_protocol: Genomic DNA (1 µg) from each sample was bisulfite converted using the EZ DNA methylation kit (Zymo Research), and 200 ng of the converted DNA was used for amplification.

tag: Sex

value: M

tag: er

tag: cr

tag: ryn


title: HCT116 5-Aza-CdR D5

description:
colorectal carcinoma cell line
SAMPLE 2


title: pTH5822_HK_8mer_2016

source_name: GRF10_HK design

tag: dbd

tag: platform_id_id design

tag: dbd source organism


title: pTH5818_ME_8mer_2037

source_name: ANIA_01217_ME design


title: pTH5818_HK_8mer_2014

source_name: ANIA_01217_HK design


title: pTH5821_HK_8mer_2015

source_name: Vsx1_HK design


title: MT.CRTS-21


title: MT.CRTS-20


title: pTH5816_ME_8mer_1781

source_name: GRMZM2G087741_ME design


title: pTH5808_ME_8mer_2036

source_name: HOXB13_ME design


title: pTH5812_ME_8mer_1777

source_name: LHX2_ME design


title: pTH5812_HK_8mer_1899

source_name: LHX2_HK design


title: pTH5805_ME_8mer_2035

source_name: SHOX_ME design


title: pTH5808_HK_8mer_1883

source_name: HOXB13_HK design


title: pTH5805_HK_8mer_2013

source_name: SHOX_HK design


title: pTH5802_HK_8mer_1850

source_name: NK-like_13_HK design


title: MT.CRTS-17


title: pTH5821_ME_8mer_1784

source_name: Vsx1_ME design


title: pTH5802_ME_8mer_1766

source_name: NK-like_13_ME design


title: pTH5791_ME_8mer_1755

source_name: Hbox10_ME design


title: MT.CRTS-19


title: MT.CRTS-15

value: F


title: pTH5791_HK_8mer_1898

source_name: Hbox10_HK design


title: MT.CRTS-18

source_name: rectal cancer tissue


title: pTH5784_HK_8mer_1882

source_name: TVAG_493070_HK design


title: MT.CRT 64


title: pTH5784_ME_8mer_1748

source_name: TVAG_493070_ME design


title: HCT116 Ctrl (2)

description:
colorectal carcinoma cell line
SAMPLE 1

source_name: Colon

tag: gender

tag: cell line


title: MT.CRTS-10


title: MT.CRT2-3


title: MT.CRTS-12


title: pTH5816_HK_8mer_1851

source_name: GRMZM2G087741_HK design


title: MT.CRTS-14


title: MT.CRTS-11


title: MT.CRTS-13


title: MT.CRT 63


title: pTH5782_ME_8mer_1746

source_name: DMBXd-paired_ME design


title: MT.CRT 9


title: pTH5782_HK_8mer_1866

source_name: DMBXd-paired_HK design


title: MT.CRTS-16


title: pTH5781_ME_8mer_1745

source_name: unc-62_ME design


title: pTH5781_HK_8mer_1849

source_name: unc-62_HK design


title: MT.CRT 8


title: MT.CRT2-10


title: pTH5778_ME_8mer_1742

source_name: CBG00023_ME design


title: pTH5763_ME_8mer_2034

source_name: Q6WL90_ME design


title: MT.CRT2-8


title: MT.CRT2-11


title: MT.CRT 1


title: pTH5759_HK_8mer_1865

source_name: Awh_HK design


title: MT.CRT 5


title: pTH5749_HK_8mer_1896

source_name: NK-like_2_HK design


title: MT.CRT2-7


title: pTH5746_ME_8mer_1720

source_name: Rhox11_ME design


title: MT.CRT2-2


title: MT.CRT2-5


title: pTH5778_HK_8mer_1897

source_name: CBG00023_HK design


title: pTH5737_HK_8mer_2576

source_name: CBG20542_HK design


title: pTH5749_ME_8mer_1723

source_name: NK-like_2_ME design


title: pTH5737_ME_8mer_1685

source_name: CBG20542_ME design


title: pTH5746_HK_8mer_2011

source_name: Rhox11_HK design


title: MT.CRT 69

source_name: rectal cancer tissue


title: MT.CRT 47


title: MT.CRT2-4


title: pTH5759_ME_8mer_1733

source_name: Awh_ME design


title: pTH5727_HK_8mer_1878

source_name: TVAG_062990_HK design


title: MT.CRT 48


title: pTH5727_ME_8mer_1615

source_name: TVAG_062990_ME design


title: MT.CRT 43


title: MT.CRT 41


title: pTH5724_ME_8mer_1612

source_name: CNBG1320_ME design


title: MT.CRT 37


title: pTH5724_HK_8mer_1862

source_name: CNBG1320_HK design


title: pTH5713_HK_8mer_2027

source_name: a2-1_HK design


title: pTH5714_HK_8mer_2029

source_name: tll_HK design


title: pTH5713_ME_8mer_1638

source_name: a2-1_ME design


title: pTH5709_HK_8mer_2022

source_name: FBpp0074853_HK design


title: pTH5709_ME_8mer_1567

source_name: FBpp0074853_ME design


title: pTH5707_HK_8mer_1843

source_name: e_gw1.38.2.1_HK design


title: pTH5707_ME_8mer_1565

source_name: e_gw1.38.2.1_ME design


title: MT.CRT 26


title: MT.CRT2-6


title: pTH5714_ME_8mer_1683

source_name: tll_ME design


title: MT.CRT 28


title: MT.CRT 27


title: pTH5701_ME_8mer_1576


title: pTH5698_ME_8mer_1573

source_name: HD2_ME design


title: pTH5763_HK_8mer_2012

source_name: Q6WL90_HK design


title: MT.CRT 29


title: MT.CRT 50


title: MT.CRT 22


title: E.albidus_experiment 2_Control_8d_rep4

city: Aveiro

first: Sara

last: Novais

address: Campus de Santiago, Department of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

description: E.albidus gene expression after 8 days under control conditions

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit . 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-030589 Custom Gene Expression Array for Enchytraeus albidus 8x15k, for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).

data_processing: Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies) using default parameters (protocol GE1_105_Dec08 and Grid: 030589_D_F_20101007) to obtain background subtracted intensities. The gBGSubSignal column was used for further analysis and intensities inferior to 1 were excluded from the analysis.

organism: Enchytraeus albidus

source_name: Enchytraeus albidus, experiment 2, control, 8 days, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Isolation of total RNA from each replicate was performed through the Trizol extraction method (Invitrogen, Belgium). This RNA followed a DNAse treatment (Fermentas, Germany) and further purification steps consisting of phenol/chloroform extractions. The quantity and purity of the isolated RNA were measured spectrophotometrically with nanodrop (NanoDrop ND-1000 Spectrophotometer) and its integrity was checked on a denaturing formaldehyde agarose gel electrophoresis.

treatment_protocol: Ten adult worms with well developed clitellum were introduced in the test vessels, each containing 25 g moist soil (control or spiked with acetone). The worms were exposed for 2 days in experiment 1 and for 2, 4 and 8 days in experiment 2 (at 20ºC and a 16:8h photoperiod). Further, organisms were sampled directly from the cultures (CULT – 10 adult worms for each of the three biological replicates) at day 0 of experiment 1. Three and four biological replicates per treatment  were used respectively in experiment 1 and 2. At test end, animals of each replicate were carefully removed, rinsed in deionised water, stored in RNA later (Ambion, USA) containing criotubes and frozen in liquid Nitrogen. All the samples were stored at -80ºC till further analysis.

value: Whole body extracts

tag: developmental stage

value: Adult organisms with well developed clitellum


title: pTH5701_HK_8mer_1844


title: E.albidus_experiment 2_Control_8d_rep2

source_name: Enchytraeus albidus, experiment 2, control, 8 days, replicate 2


title: MT.CRT 19

source_name: rectal cancer tissue


title: E.albidus_experiment 2_Control_8d_rep3

source_name: Enchytraeus albidus, experiment 2, control, 8 days, replicate 3


title: MT.CRT 25


title: treepeonybud_chilling_24d_rep1

city: Qingdao

first: Shu-Peng

last: Gai

state: Shandong Province

address: Changcheng Road 700

department: College of Life Science

country: China

institute: Qingdao Agricultural University

description: Gene expression in buds after 24 day chilling

hyb_protocol: Each Slide was hybridized with 1.65 μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings, Scan resolution=5 μm, PMT 100%, 10%.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.5.1 (Agilent technologies, Santa Clara, CA, US).

molecule: polyA RNA

organism: Paeonia ostii

source_name: buds,chilling, 24d, rep1

label_protocol: Total RNA was amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX,US), Cy3 NHS ester (Cat#PA13105,GE healthcare Biosciences, Pittsburgh, PA,US) followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Endo-dormancy plants were potted and placed in refrigeration house with temperature 0-4°C from 5 November to 30 December 2009 in Qingdao, Shandong, China.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (QIAGEN, GmBH, Germany).

treatment_protocol: Mixed buds, three buds for each individual, were collected after 0d, 6d, 12d, 15d, 18d and 24d chilling requirement fulfilling during the period of bud dormancy release. Three replications (3 plants/ replication) were harvested and immediately frozen in liquid nitrogen and stored at -80°C until use.

tag: development

value: eco-dormancy


title: E.albidus_experiment 2_Control_4d_rep4

description: E.albidus gene expression after 4 days under control conditions

source_name: Enchytraeus albidus, experiment 2, control, 4 days, replicate 4


title: treepeonybud_chilling_18d_rep3

description: Gene expression in buds after 18 day chilling

source_name: buds,chilling, 18d, rep3

value: endo-dormancy release

tag: age


title: pTH5698_HK_8mer_2025

source_name: HD2_HK design


title: MT.CRT 21


title: MT.CRT 23


title: treepeonybud_chilling_18d_rep2

source_name: buds,chilling, 18d, rep2


title: MT.CRT 20


title: pTH5696_HK_8mer_2023

source_name: TOS8_HK design


title: pTH5696_ME_8mer_1571

source_name: TOS8_ME design


title: pTH5690_HK_8mer_2010

source_name: so_HK design


title: treepeonybud_chilling_15d_rep1

description: Gene expression in buds after 15 day chilling

source_name: buds,chilling, 15d, rep1

value: endo-dormancy


title: treepeonybud_chilling_24d_rep2

source_name: buds,chilling, 24d, rep2


title: pTH5688_ME_8mer_1717

source_name: ZHX1_ME design

value: Homeobox


title: pTH5690_ME_8mer_1719

source_name: so_ME design


title: E.albidus_experiment 2_Control_4d_rep2

source_name: Enchytraeus albidus, experiment 2, control, 4 days, replicate 2

tag: tissue


title: E.albidus_experiment 2_Control_4d_rep3

source_name: Enchytraeus albidus, experiment 2, control, 4 days, replicate 3


title: treepeonybud_chilling_18d_rep1

source_name: buds,chilling, 18d, rep1


title: treepeonybud_chilling_12d_rep3

description: Gene expression in buds after 12 day chilling

source_name: buds,chilling, 12d, rep3


title: E.albidus_experiment 2_Control_8d_rep1

source_name: Enchytraeus albidus, experiment 2, control, 8 days, replicate 1


title: E.albidus_experiment 2_Control_2d_rep4

description: E.albidus gene expression after 2 days under control conditions

source_name: Enchytraeus albidus, experiment 2, control, 2 days, replicate 4


title: treepeonybud_chilling_15d_rep2

source_name: buds,chilling, 15d, rep2


title: treepeonybud_chilling_12d_rep2

source_name: buds,chilling, 12d, rep2


title: treepeonybud_chilling_12d_rep1

source_name: buds,chilling, 12d, rep1


title: E.albidus_experiment 2_Control_2d_rep3

source_name: Enchytraeus albidus, experiment 2, control, 2 days, replicate 3


title: treepeonybud_chilling_6d_rep3

description: Gene expression in buds after 6 day chilling

source_name: buds,chilling, 6d, rep3


title: rgg2 mutant at 5hrs, Biological replicate 3

city: Vermillion

first: SRIVISHNUPRIYA

last: ANBALAGAN

state: SD

address: 414 East Clark Street

department: Basic Biomedical Sciences

institute: University of South Dakota

description: rgg2 mutant exp-3_5hrs

hyb_protocol: Labeled aRNAwas hybridized and  detected according to the manufacturer’s instructions for antisense prokaryotic arrays (Affymetrix)

scan_protocol: Scanning was carried out according to  to the manufacturer’s instructions for antisense prokaryotic arrays (Affymetrix)

data_processing: The data from three biological replicates were normalized and analyzed using the Probe Logarithmic Intensity Error (PLIER) estimation algorithm in ArrayStar (DNAStar, Inc., Madison, WI).

label: biotin

organism: Streptococcus pyogenes M1 GAS

source_name: rgg2 mutant grown to 5hrs

label_protocol: Amplified and labeled using the MessageAmp II-Bacteria kit (Ambion) according to manufacturer's instructions

growth_protocol: Both wild-type and rgg2 mutant was grown at 37°C without agitation with Todd-Hewitt broth containing 0.2% (wt/vol) yeast extract either to mid-exponential or post-exponential phase of growth.

extract_protocol: RNA was isolated from 40 ml cultures of S. pyogenes in the middle-exponential and post-exponential phase corresponding to 2 hrs and 5 hrs of growth, respectively using an RNeasy Mini Kit (QIAGEN, Valencia, CA), as recommended by manufacturer

tag: genotype/variation

value: rgg2 mutant

tag: growth phase

value: Post-exponential phase


title: rgg2 mutant at 5hrs, Biological replicate 2

description: rgg2 mutant exp-2_5hrs


title: E.albidus_experiment 2_Control_2d_rep2

source_name: Enchytraeus albidus, experiment 2, control, 2 days, replicate 2


title: treepeonybud_chilling_0d_rep1

description: Gene expression in buds of 0 day chilling

source_name: buds,chilling, 0d, rep1


title: treepeonybud_chilling_6d_rep2

source_name: buds,chilling, 6d, rep2


title: treepeonybud_chilling_6d_rep1

source_name: buds,chilling, 6d, rep1


title: treepeonybud_chilling_24d_rep3

source_name: buds,chilling, 24d, rep3


title: E.albidus_experiment 2_Control_2d_rep1

source_name: Enchytraeus albidus, experiment 2, control, 2 days, replicate 1


title: rgg2 mutant at 5hrs, Biological replicate 1

description: rgg2 mutant exp-1_5hrs


title: treepeonybud_chilling_0d_rep3

source_name: buds,chilling, 0d, rep3


title: treepeonybud_chilling_0d_rep2

source_name: buds,chilling, 0d, rep2


title: pTH5685_ME_8mer_2033

source_name: Nanog_ME design


title: SF370 at 5hrs, Biological replicate 2

description: SF370 exp-2_5hrs

source_name: SF370 grown to 5hrs

value: wild type


title: pTH5688_HK_8mer_2026

source_name: ZHX1_HK design


title: SF370 at 5hrs, Biological replicate 1

description: SF370 exp-1_5hrs


title: E.albidus_experiment 1_Culture_0d_rep3

description: E.albidus gene expression directly sampled from the culture at day 0

source_name: Enchytraeus albidus, experiment 1, culture, day 0, replicate 3


title: pTH5685_HK_8mer_2009

source_name: Nanog_HK design


title: pTH5677_HK_8mer_1859

source_name: EMX1_HK design


title: pTH5673_HK_8mer_1842

source_name: ems_HK design


title: SF370 at 5hrs, Biological replicate 3

description: SF370 exp-3_5hrs


title: rgg2 mutant at 2hrs, Biological replicate 3

description: rgg2 mutant exp-3_2hrs

source_name: rgg2 mutant grown to 2hrs

value: Mid-exponential phase


title: treepeonybud_chilling_15d_rep3

source_name: buds,chilling, 15d, rep3


title: rgg2 mutant at 2hrs, Biological replicate 2

description: rgg2 mutant exp-2_2hrs


title: pTH5677_ME_8mer_1550

source_name: EMX1_ME design


title: E.albidus_experiment 1_Acetone_2d_rep3

description: E.albidus gene expression after 2 days exposed to acetone

source_name: Enchytraeus albidus, experiment 1, acetone, 2 days, replicate 3


title: E.albidus_experiment 1_Culture_0d_rep2

source_name: Enchytraeus albidus, experiment 1, culture, day 0, replicate 2


title: SF370 at 2hrs, Biological replicate 1

description: SF370 exp-1_2hrs

source_name: SF370 grown to 2hrs


title: pTH5673_ME_8mer_1545

source_name: ems_ME design


title: E.albidus_experiment 1_Control_2d_rep3

source_name: Enchytraeus albidus, experiment 1, control, 2 days, replicate 3


title: E.albidus_experiment 1_Culture_0d_rep1

source_name: Enchytraeus albidus, experiment 1, culture, day 0, replicate 1


title: E.albidus_experiment 1_Acetone_2d_rep2

source_name: Enchytraeus albidus, experiment 1, acetone, 2 days, replicate 2


title: pTH5672_ME_8mer_1544

source_name: Lbx-related_ME design


title: SF370 at 2hrs, Biological replicate 2

description: SF370 exp-2_2hrs


title: rgg2 mutant at 2hrs, Biological replicate 1

description: rgg2 mutant exp-1_2hrs


title: E.albidus_experiment 1_Control_2d_rep2

source_name: Enchytraeus albidus, experiment 1, control, 2 days, replicate 2


title: SF370 at 2hrs, Biological replicate 3

description: SF370 exp-3_2hrs


title: E.albidus_experiment 1_Acetone_2d_rep1

source_name: Enchytraeus albidus, experiment 1, acetone, 2 days, replicate 1


title: E.albidus_experiment 1_Control_2d_rep1

source_name: Enchytraeus albidus, experiment 1, control, 2 days, replicate 1


title: pTH5667_HK_8mer_1915

source_name: sex-1_HK design


title: pTH5667_ME_8mer_1539

source_name: sex-1_ME design


title: pTH5661_ME_8mer_1533

source_name: ceh-19_ME design


title: pTH5672_HK_8mer_1890

source_name: Lbx-related_HK design


title: pTH5666_ME_8mer_2032

source_name: SNAPOd2T00006620001_ME design


title: pTH5666_HK_8mer_2008

source_name: SNAPOd2T00006620001_HK design


title: muscle stem cells at 12wks old, biological rep2

city: Toyoake

first: Takahiko

last: Sato

state: Aichi

address: 1-98, Dengakugakubo, Kutsukakecho

country: Japan

institute: Fujita Health University

description: Adult MuSC_2

hyb_protocol: Hybridization was performed on GeneChip miRNA 2.0 arrays (Affymetrix) using standard protocols available at www.affymetrix.com. Standard Affymetrix protocols were also used for staining and washing of the arrays.

scan_protocol: Standard Affymetrix protocols was used for scanning of the arrays (available at www.affymetrix.com).

data_processing: Data files were analyzed with Affymetrix Expression Console (v.1.2.1.20) using RMA background correction and quantile normalization

organism: Mus musculus

source_name: GFP+RFP+ sorted cells_adultl mice

label_protocol: biotinylated cRNA were prepared with FlashTag Biotin HSR labelling kit (Genisphere) according to manufacture's protocol.

growth_protocol: Pax3-GFP; MyoD-RFP expressing compound mice were prepared at neonatal, juvenile and adult stages.

extract_protocol: total RNA was extracted with miRNeasy Micro kit (QIAGEN) according to manufacture's protocol

treatment_protocol: diaphragmic skeletal muscle tissue were dissected and homogenized with collagenase to collect single cells by FACs Aria2 (BD).

tag: strain background

value: expressing Pax3-GFP; MyoD-primed RFP

value: adultl (12wks)

value: diaphragmic skeletal muscle tissue

tag: cell type

value: GFP+RFP+ sorted cells


title: muscle stem cells at 2wks old, biological rep1

description: Juvenile MuSC_1

source_name: GFP+RFP+ sorted cells_juvenilel mice

value: juvenilel (2wks)