name: E-MTAB-2030:Ctbp2 knockdown - undifferentiated 1

characteristic: INSDC last update

text: public

characteristic: SRA accession

tag: Namespace:National Research Center for Epigenome Reprogramming Network

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: common name

text: Protocols: We purchased normal mouse embryonic stem cells (E14) from the Mutant Mouse Regional Resource Centers (MMRRC). We cultured stem cells in DMEM containing 15% (v/v) FBS (Hyclone), 2 mM L-glutamine, 1% (v/v) nonessential amino acids, 55uM-mercaptoethanol, antibiotics (all from Gibco) and 1,000 U ml-1of ESGRO (Chemicon) on gelatin-coated plates. ESC differentiation was induced by LIF withdrawal of ESC medium in monolayer cultures. PLKO-puro constructs expressing shRNAs were purchased from Sigma. The shRNA constructs targeting Ctbp2 are TRCN0000109335 and TRCN0000307495. Lentiviruses were produced with 293FT cell by co-transfection of 1 mg each of pMD2.G, pMDLg/pRRE, pRSV-rev, pLKO-shRNA using Lipofectamin (Invitrogen). 48 h after transfection, virus-containing medium was collected and filtered by 0.45 mm filters. Polybrene (10 mg ml-1) was added just before infection to target cells and infection was performed for 5 h. Puromysin selection (2 mg ml-1) was performed 48 h after infection for 2 days. As a control, we used pLKO.1 puro vector. RNA was isolated by Trizol reagent (Invitrogen). Sequencing library was prepared using Truseq RNA Sample Preparation kit v2 (IIIumina, CA, USA) according the manufacture's protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.

characteristic: description

text: undifferentiated

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain

text: Ctbp2 knockdown - undifferentiated 1


name: E-MTAB-2030:Control sample - undifferentiated 1

status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Research Center for Epigenome Reprogramming Network

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

text: undifferentiated

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: fresh specimen

text: Control sample - undifferentiated 1

characteristic: title

type: has member


name: E-MTAB-2030:Control sample - differentiated(-Lif day7) 1

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: common name

characteristic: description

text: 7-day differentiated

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen


name: E-MTAB-2030:Ctbp2 knockdown - differentiated(-Lif day7) 1

characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: 7-day differentiated

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NCMLS

characteristic: INSDC center name

text: public

text: ATCC

characteristic: biomaterial provider

text: Cell Line

characteristic: biomaterial type

text: human

text: K-562 Cell line

text: erythroleukemia type, CML patient, positive for the bcr:abl fusion gene

characteristic: differentiation method

text: Chronic Myelogenous Leukemia

characteristic: disease

characteristic: line

text: mesoderm

characteristic: lineage

text: RPMI1640 + glutamax 10% FCS and 1% pen/strep

characteristic: medium

text: genomic DNA

characteristic: molecule

text: Homo sapiens

text: +/- 11 after obtaining cells from ATCC

characteristic: passage

text: Homo sapiens

text: Female

characteristic: sex


text: Saccharomyces cerevisiae

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 2787STDY5607070-sc-2013-10-29T15:36:17Z-1710329

characteristic: Submitter Id

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

characteristic: organism

text: lane 2

characteristic: sample description

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: 2787STDY5607071-sc-2013-10-29T15:36:20Z-1710330

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

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text: 2787STDY5607072-sc-2013-10-29T15:36:21Z-1710331

text: baker's yeast

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text: lane 2

text: Saccharomyces cerevisiae


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text: 2787STDY5607073-sc-2013-10-29T15:36:22Z-1710332

text: baker's yeast

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text: Saccharomyces cerevisiae

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text: 2787STDY5607074-sc-2013-10-29T15:36:24Z-1710333

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


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text: 2787STDY5607075-sc-2013-10-29T15:36:25Z-1710334

text: baker's yeast

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text: 2787STDY5607076-sc-2013-10-29T15:36:26Z-1710335

text: baker's yeast

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text: lane 2

text: Saccharomyces cerevisiae


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text: 2787STDY5607077-sc-2013-10-29T15:36:28Z-1710336

text: baker's yeast

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text: 2787STDY5607078-sc-2013-10-29T15:36:30Z-1710337

text: baker's yeast

text: Saccharomyces cerevisiae

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text: 2787STDY5607079-sc-2013-10-29T15:36:32Z-1710338

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


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text: SC

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text: 2787STDY5607080-sc-2013-10-29T15:36:33Z-1710339

text: baker's yeast

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text: lane 2

text: Saccharomyces cerevisiae


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text: 2787STDY5607081-sc-2013-10-29T15:36:34Z-1710340

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

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text: 2787STDY5607082-sc-2013-10-29T15:36:35Z-1710341

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text: 2787STDY5607083-sc-2013-10-29T15:36:37Z-1710342

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text: lane 2

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text: 2787STDY5607084-sc-2013-10-29T15:36:38Z-1710343

text: baker's yeast

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text: lane 2

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text: 2787STDY5607085-sc-2013-10-29T15:36:40Z-1710344

text: baker's yeast

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text: lane 2

text: Saccharomyces cerevisiae


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text: 2787STDY5607086-sc-2013-10-29T15:36:41Z-1710345

text: baker's yeast

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text: lane 2

text: Saccharomyces cerevisiae


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text: 2787STDY5607087-sc-2013-10-29T15:36:42Z-1710346

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

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text: 2787STDY5607088-sc-2013-10-29T15:36:44Z-1710347

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

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text: 2787STDY5607089-sc-2013-10-29T15:36:45Z-1710348

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


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text: 2787STDY5607090-sc-2013-10-29T15:36:46Z-1710349

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


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text: 2787STDY5607091-sc-2013-10-29T15:36:47Z-1710350

text: baker's yeast

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text: lane 2

text: Saccharomyces cerevisiae


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text: 2787STDY5607092-sc-2013-10-29T15:36:48Z-1710351

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

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text: 2787STDY5607093-sc-2013-10-29T15:36:49Z-1710352

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


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text: 2787STDY5607094-sc-2013-10-29T15:36:50Z-1710353

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

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text: 2787STDY5607095-sc-2013-10-29T15:36:51Z-1710354

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

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text: 2787STDY5607096-sc-2013-10-29T15:36:52Z-1710355

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

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text: 2787STDY5607097-sc-2013-10-29T15:36:54Z-1710356

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

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text: 2787STDY5607098-sc-2013-10-29T15:36:55Z-1710357

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607099-sc-2013-10-29T15:36:56Z-1710358

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607102-sc-2013-10-29T15:37:00Z-1710361

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607103-sc-2013-10-29T15:37:01Z-1710362

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607104-sc-2013-10-29T15:37:02Z-1710363

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607105-sc-2013-10-29T15:37:03Z-1710364

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607106-sc-2013-10-29T15:37:04Z-1710365

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607107-sc-2013-10-29T15:37:05Z-1710366

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607108-sc-2013-10-29T15:37:06Z-1710367

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607109-sc-2013-10-29T15:37:07Z-1710368

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607110-sc-2013-10-29T15:37:08Z-1710369

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607111-sc-2013-10-29T15:37:10Z-1710370

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607112-sc-2013-10-29T15:37:11Z-1710371

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607113-sc-2013-10-29T15:37:12Z-1710372

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607114-sc-2013-10-29T15:37:13Z-1710373

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607115-sc-2013-10-29T15:37:14Z-1710374

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607116-sc-2013-10-29T15:37:16Z-1710375

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

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text: 2787STDY5607117-sc-2013-10-29T15:37:17Z-1710376

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


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text: SC

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text: 2787STDY5607118-sc-2013-10-29T15:37:18Z-1710377

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607119-sc-2013-10-29T15:37:19Z-1710378

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607120-sc-2013-10-29T15:37:21Z-1710379

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

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text: 2787STDY5607121-sc-2013-10-29T15:37:23Z-1710380

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

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text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

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text: 2787STDY5607123-sc-2013-10-29T15:37:25Z-1710382

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

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text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

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text: 2787STDY5607125-sc-2013-10-29T15:37:27Z-1710384

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

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text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607126-sc-2013-10-29T15:37:31Z-1710385

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

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text: Saccharomyces cerevisiae

text: SC

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text: 2787STDY5607127-sc-2013-10-29T15:37:33Z-1710386

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

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text: 2787STDY5607128-sc-2013-10-29T15:37:34Z-1710387

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607129-sc-2013-10-29T15:37:35Z-1710388

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

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text: 2787STDY5607130-sc-2013-10-29T15:37:36Z-1710389

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

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text: SC

text: public

text: 2787STDY5607131-sc-2013-10-29T15:37:37Z-1710390

text: baker's yeast

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text: lane 1

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text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607133-sc-2013-10-29T15:37:39Z-1710392

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

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text: 2787STDY5607134-sc-2013-10-29T15:37:40Z-1710393

text: baker's yeast

text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: 2787STDY5607135-sc-2013-10-29T15:37:41Z-1710394

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

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text: SC

text: public

text: 2787STDY5607136-sc-2013-10-29T15:37:43Z-1710395

text: baker's yeast

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text: lane 2

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text: 2787STDY5607137-sc-2013-10-29T15:37:44Z-1710396

text: baker's yeast

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text: lane 2

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text: baker's yeast

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text: baker's yeast

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text: baker's yeast

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text: baker's yeast

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text: 2787STDY5607142-sc-2013-10-29T15:37:49Z-1710401

text: baker's yeast

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text: baker's yeast

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text: baker's yeast

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text: baker's yeast

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text: baker's yeast

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text: baker's yeast

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text: baker's yeast

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text: baker's yeast

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text: baker's yeast

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text: lane 2

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text: baker's yeast

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text: 2787STDY5607152-sc-2013-10-29T15:38:00Z-1710411

text: baker's yeast

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text: baker's yeast

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text: lane 2

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text: Saccharomyces cerevisiae

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text: 2787STDY5607154-sc-2013-10-29T15:38:02Z-1710413

text: baker's yeast

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text: lane 2

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text: 2787STDY5607155-sc-2013-10-29T15:38:03Z-1710414

text: baker's yeast

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text: Saccharomyces cerevisiae

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text: 2787STDY5607156-sc-2013-10-29T15:38:04Z-1710415

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

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text: 2787STDY5607158-sc-2013-10-29T15:38:06Z-1710417

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


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text: 2787STDY5607159-sc-2013-10-29T15:38:07Z-1710418

text: baker's yeast

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text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

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text: 2787STDY5607160-sc-2013-10-29T15:38:08Z-1710419

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607161-sc-2013-10-29T15:38:09Z-1710420

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607162-sc-2013-10-29T15:38:10Z-1710421

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607163-sc-2013-10-29T15:38:11Z-1710422

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607164-sc-2013-10-29T15:38:12Z-1710423

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5607165-sc-2013-10-29T15:38:13Z-1710424

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: National Yang-Ming University

text: public

tag: Namespace:National Yang-Ming University

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: MCF7 cells were washed with 1X PBS and resuspended with cell lysis buffer. Cells were treated with 0.1 mg/mL of RNaseA for an hour at 37 degrees C and 0.3 mg/mL proteinase K for 12-16 hr at 55 degrees C. DNA was extracted with an equal volume of phenol/chloroform/isoamyl alcohol mixture (24:25:1). The extraction procedure was repeated until the interface is clean. An equal volume of chloroform was then added and the mixture centrifuged for 10 minutes at 13000x g. Finally, the aqueous phase was removed and precipitated with ethanol. After removal of the supernatant, the DNA pellet was washed with 70% ethanol, air-dried, and dissolved in triple distilled H2O. The integrity of the DNA extracted was checked by 1.2 % (w/v) agarose gel electrophoresis. The concentration of DNA was estimated by ultraviolet spectrophotometry. The genomic DNA of human adult normal breast and tumor tissues were purchased from BioChain (Hayward, CA): normal breast (Catalog No.: D1234086, Lot No.: B503025). BT089 (Catalog No.: D1235086-DC, Lot No.: A805089), BT126 (Catalog No.: D1235086, Lot No.: A808126) and BT198 (Catalog No.: D1235086, Lot No.: B410198). Bisulfite-seq library was prepared using a method based on Lister et al1. Briefly, 3-5 ug of DNA was fragmented by sonication with a Bioruptor (Diagenode, Sparta, NJ) following by adapter ligation using the Pair End DNA Sample Prep kit (Illumina Inc., USA) with the use of methylated adapter (Illumina Inc., USA) according to manufacturer's instruction. For each sample, four adapter-ligated DNA fragments of 200-250 bp, 250-300 bp, 300-350 bp and 350-400 bp were isolated by gel electrophoresis and subjected to bisulfite conversion and PCR enrichment independently to generate 4 separate libraries for each sample. Bisulfite treatment was performed using an EZ DNA Methylation-Gold Kit (Zymo Research) that converts unmethylated cytosines to uracils and leaves methylated cytosines unchanged. Four separate PCR were performed for each library using PfuTurbo(r) Cx Hotstart DNA polymerase (Stratagene) and then pooling the enrichment products following by gel purification. PCR-amplified library was quantified by quantitative PCR and the library size was determined on an Agilent 2100 Bioanalyzer with High Sensitivity DNA chip.

characteristic: description

text: breast cancer

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

text: National Yang-Ming University

text: public

text: ArrayExpress

characteristic: cell line

text: human breast cancer

characteristic: cell type

text: human

text: Protocols: MCF7 cells were cultured in RPMI1640 medium (GIBCO/BRL) supplemented with 10% (v/v) fetal bovine serum (GIBCO/BRL), 2.0 g/L sodium bicarbonate, and were incubated in a humidified 37 degrees C incubator with 5% CO2. MCF7 cells were washed with 1X PBS and resuspended with cell lysis buffer. Cells were treated with 0.1 mg/mL of RNaseA for an hour at 37 degrees C and 0.3 mg/mL proteinase K for 12-16 hr at 55 degrees C. DNA was extracted with an equal volume of phenol/chloroform/isoamyl alcohol mixture (24:25:1). The extraction procedure was repeated until the interface is clean. An equal volume of chloroform was then added and the mixture centrifuged for 10 minutes at 13000x g. Finally, the aqueous phase was removed and precipitated with ethanol. After removal of the supernatant, the DNA pellet was washed with 70% ethanol, air-dried, and dissolved in triple distilled H2O. The integrity of the DNA extracted was checked by 1.2 % (w/v) agarose gel electrophoresis. The concentration of DNA was estimated by ultraviolet spectrophotometry. The genomic DNA of human adult normal breast and tumor tissues were purchased from BioChain (Hayward, CA): normal breast (Catalog No.: D1234086, Lot No.: B503025). BT089 (Catalog No.: D1235086-DC, Lot No.: A805089), BT126 (Catalog No.: D1235086, Lot No.: A808126) and BT198 (Catalog No.: D1235086, Lot No.: B410198). Bisulfite-seq library was prepared using a method based on Lister et al1. Briefly, 3-5 ug of DNA was fragmented by sonication with a Bioruptor (Diagenode, Sparta, NJ) following by adapter ligation using the Pair End DNA Sample Prep kit (Illumina Inc., USA) with the use of methylated adapter (Illumina Inc., USA) according to manufacturer's instruction. For each sample, four adapter-ligated DNA fragments of 200-250 bp, 250-300 bp, 300-350 bp and 350-400 bp were isolated by gel electrophoresis and subjected to bisulfite conversion and PCR enrichment independently to generate 4 separate libraries for each sample. Bisulfite treatment was performed using an EZ DNA Methylation-Gold Kit (Zymo Research) that converts unmethylated cytosines to uracils and leaves methylated cytosines unchanged. Four separate PCR were performed for each library using PfuTurbo(r) Cx Hotstart DNA polymerase (Stratagene) and then pooling the enrichment products following by gel purification. PCR-amplified library was quantified by quantitative PCR and the library size was determined on an Agilent 2100 Bioanalyzer with High Sensitivity DNA chip.

text: breast cancer

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: sex


E-MTAB-2014:normal breast

text: National Yang-Ming University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2014:normal breast

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

text: normal breast


text: Larval: Day 5 ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: ZMP_phenotype_17_1_mutant-sc-2013-10-30T14:16:05Z-1747633

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 17 clutch 1. A 5 base indexing sequence (GAGGC) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph17

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval: Day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: ZMP_phenotype_17_1_sibling-sc-2013-10-30T14:16:08Z-1747634

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 17 clutch 1. A 5 base indexing sequence (AGAAG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph17

text: Danio rerio

text: mixed


text: Larval: Day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ZMP_phenotype_17_2_mutant-sc-2013-10-30T14:16:09Z-1747635

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 17 clutch 2. A 5 base indexing sequence (CAGAG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph17

text: Danio rerio

text: mixed


text: Larval: Day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ZMP_phenotype_17_2_sibling-sc-2013-10-30T14:16:11Z-1747636

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 17 clutch 2. A 5 base indexing sequence (GCACG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph17

text: Danio rerio

text: mixed


text: Larval: Day 5 ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_17_3_mutant-sc-2013-10-30T14:16:12Z-1747637

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 17 clutch 3. A 5 base indexing sequence (CGCAA) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph17

text: Danio rerio

text: mixed


text: Larval: Day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: ZMP_phenotype_17_3_sibling-sc-2013-10-30T14:16:13Z-1747638

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 17 clutch 3. A 5 base indexing sequence (CAAGA) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph17

text: Danio rerio

text: mixed


text: Larval - day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype31_2_mutant-sc-2013-10-30T14:21:10Z-1747639

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 31 clutch 2. A 5 base indexing sequence (GAGGC) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph31

text: Danio rerio

text: mixed


text: Larval - day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_31_2_sibling-sc-2013-10-30T14:21:13Z-1747640

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 31 clutch 2. A 5 base indexing sequence (AGAAG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph31

characteristic: sample description

text: Danio rerio

text: mixed


text: Larval - day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

text: ZMP_phenotype_31_2_mutant-sc-2013-10-30T14:21:14Z-1747641

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 31 clutch 3. A 5 base indexing sequence (CAGAG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph31

text: Danio rerio

text: mixed

characteristic: strain


text: Larval - day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: ZMP_phenotype_31_2_sibling-sc-2013-10-30T14:21:16Z-1747642

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 31 clutch 3. A 5 base indexing sequence (GCACG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph31

text: Danio rerio

text: mixed


text: Larval - day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: ZMP_phenotype_31_6_mutant-sc-2013-10-30T14:21:17Z-1747643

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 31 clutch 6. A 5 base indexing sequence (CGCAA) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph31

text: Danio rerio

text: mixed


text: Larval day 4 ZFS:0000036 - Larval day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ZMP_phenotype31_6_sibling-sc-2013-10-30T14:21:18Z-1747644

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 31 clutch 6. A 5 base indexing sequence (CAAGA) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph31

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ZMP_phenotype_31_7_mutant-sc-2013-10-30T14:21:20Z-1747645

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 31 clutch 7. A 5 base indexing sequence (GCCGA) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph31

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_31_7sibling-sc-2013-10-30T14:21:21Z-1747646

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 31 clutch 7. A 5 base indexing sequence (CGGCC) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph31

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: ZMP_phenotype_31_8_mutant-sc-2013-10-30T14:21:23Z-1747647

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 31 clutch 8. A 5 base indexing sequence (AACCG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph31

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_31_8_sibling-sc-2013-10-30T14:21:25Z-1747648

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 31 clutch 8. A 5 base indexing sequence (ACGGG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph31

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_31_10_mutant-sc-2013-10-30T14:21:26Z-1747649

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 31 clutch 10. A 5 base indexing sequence (CCAAC) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph31

characteristic: sample description

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

text: ZMP_phenotype_31_10_sibling-sc-2013-10-30T14:21:27Z-1747650

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 31 clutch 10. A 5 base indexing sequence (AGCGC) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph31

text: Danio rerio

text: mixed

characteristic: strain


name: E-MTAB-2034:TCF7L2 knockdown_Replicate 2 (passage 63)

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Lund University, Department of Clinical Science, Endocrinology and Diabetes

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: Norway rat

text: Protocols: 60uM siRNA against Tcf7l2 (rat), 48 hours incubation- Human Molecular Genetics, 2011 doi:10.1093/hmg/ddr454 Library preparation was preformed according to mRNA Sequencing Sample Preparation Guide (Illumina, TruSeq RNA sample preparation kit). Reagents were taken from the Illumina sample preparation kit (Illumina, TruSeq RNA sample prep kit). Illumina TrueSeqTM RNA Library preparation protocol, paired-end

characteristic: description

text: gene knock down

characteristic: genetic modification

text: TCF7L2 knock down

characteristic: genotype

text: Rattus norvegicus

text: Rattus norvegicus

characteristic: sampling time

text: Rattus norvegicus

characteristic: title


name: E-MTAB-2034:Control sample-Replicate 4 (passage 82)

characteristic: External Id

text: Lund University, Department of Clinical Science, Endocrinology and Diabetes

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: Norway rat

text: Control

text: Rattus norvegicus

text: Rattus norvegicus

text: Rattus norvegicus

text: Control sample-Replicate 4 (passage 82)


name: E-MTAB-2034:TCF7L2 knockdown_Replicate 1 (passage 62)

characteristic: ENA-CHECKLIST

text: public

characteristic: Submitter Id

text: ArrayExpress

text: Norway rat

characteristic: common name

text: gene knock down

text: TCF7L2 knock down

text: Rattus norvegicus

characteristic: organism

text: Rattus norvegicus

text: Rattus norvegicus


name: E-MTAB-2034:TCF7L2 knockdown_Replicate 4 (passage 82)

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

characteristic: broker name

text: Norway rat

text: gene knock down

text: TCF7L2 knock down

text: Rattus norvegicus

text: Rattus norvegicus

text: Rattus norvegicus

characteristic: strain


name: E-MTAB-2034:Control sample-Replicate 3 (passage 81)

text: public

text: ArrayExpress

characteristic: cell line

text: Norway rat

characteristic: description

text: Control

characteristic: genotype

text: Rattus norvegicus

text: Rattus norvegicus

text: Rattus norvegicus

text: Control sample-Replicate 3 (passage 81)


name: E-MTAB-2034:Control sample-Replicate 2 (passage 63)

characteristic: External Id

text: public

text: ArrayExpress

text: Norway rat

text: Control

text: Rattus norvegicus

text: Rattus norvegicus

characteristic: sampling time

text: Rattus norvegicus

text: Control sample-Replicate 2 (passage 63)

characteristic: title


name: E-MTAB-2034:TCF7L2 knockdown_Replicate 3 (passage 81)

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: Norway rat

text: gene knock down

characteristic: genetic modification

text: TCF7L2 knock down

text: Rattus norvegicus

text: Rattus norvegicus

text: Rattus norvegicus


name: E-MTAB-2034:Control sample-Replicate 1 (passage 62)

characteristic: ENA-CHECKLIST

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Norway rat

text: Control

text: Rattus norvegicus

text: Rattus norvegicus

text: Rattus norvegicus

text: Control sample-Replicate 1 (passage 62)


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: National Research Center for Epigenome Reprogramming Network

text: public

text: ArrayExpress

text: mouse embryonic stem cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: We purchased normal mouse embryonic stem cells (E14) from the Mutant Mouse Regional Resource Centers (MMRRC). We cultured stem cells in DMEM containing 15% (v/v) FBS (Hyclone), 2 mM L-glutamine, 1% (v/v) nonessential amino acids, 55uM-mercaptoethanol, antibiotics (all from Gibco) and 1,000 U ml-1of ESGRO (Chemicon) on gelatin-coated plates. Cells were cross-linked with 1% (v/v) formaldehyde for 10min at 37C and lysed with buffer containing 85mM KCl, 5mM PIPES (pH 8.0) and 0.5% (v/v) NP-40. After centrifugation, nuclear pellets were resuspended in buffer containing 10mM EDTA, 100mM Tris-Cl (pH 8.1) and 1% SDS. To solubilize and shear cross-linked DNA, lysates were sonicated. 10-fold diluted lysates in IP buffer containing 16.7mM Tris-Cl (pH 8.1), 167mM NaCl, 0.01% (w/v) SDS, 1.1% (v/v) Triton X-100 and 1.2mM EDTA were incubated overnight at 4C with protein A/G PLUS agarose and 1-2ug appropriate antibodies.(Ctbp2 antibody=BD Transduction Laboratories, cat#612044; normal mouse igG antibody = Santa Cruz, cat#sc-2025) Beads were washed with 1X 20mM Tris-Cl (pH 8.1), 150mM NaCl, 0.1% (w/v) SDS, 1% Triton X-100, 2mM EDTA, 1X 20mM Tris-Cl (pH 8.1), 150mM NaCl, 0.1% (w/v) SDS, 1% Triton X-100, 2mM EDTA, 1X 0.25M LiCl, 1% (v/v) NP40, 1% (v/v) Deoxycholate, 1mM EDTA, 10mM Tris-Cl (pH 8.1) and 2X with TE. Immune complexes were then eluted by adding 250ul of elution buffer containing 1% (w/v) SDS and 0.1M NaHCO3 two times. Cross-linking was reversed by adding of 20ul of 5M NaCl and incubated overnight at 65C. DNA was precipitated with ethanol and kept in -20C for the further use.

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state


text: Saccharomyces cerevisiae

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

text: public

text: 2787STDY5623198-sc-2013-10-31T13:56:14Z-1727417

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

characteristic: sample description

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

characteristic: INSDC center name

text: public

text: 2787STDY5623199-sc-2013-10-31T13:56:18Z-1727418

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

characteristic: INSDC first public

text: public

text: 2787STDY5623200-sc-2013-10-31T13:56:19Z-1727419

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

characteristic: INSDC last update

text: public

text: 2787STDY5623201-sc-2013-10-31T13:56:20Z-1727420

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623202-sc-2013-10-31T13:56:22Z-1727421

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623204-sc-2013-10-31T13:56:24Z-1727423

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623205-sc-2013-10-31T13:56:25Z-1727424

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623206-sc-2013-10-31T13:56:27Z-1727425

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623207-sc-2013-10-31T13:56:28Z-1727426

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623208-sc-2013-10-31T13:56:29Z-1727427

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623209-sc-2013-10-31T13:56:30Z-1727428

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623210-sc-2013-10-31T13:56:32Z-1727429

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623211-sc-2013-10-31T13:56:33Z-1727430

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623212-sc-2013-10-31T13:56:34Z-1727431

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623213-sc-2013-10-31T13:56:35Z-1727432

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623214-sc-2013-10-31T13:56:36Z-1727433

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623215-sc-2013-10-31T13:56:38Z-1727434

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623216-sc-2013-10-31T13:56:39Z-1727435

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623217-sc-2013-10-31T13:56:40Z-1727436

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623218-sc-2013-10-31T13:56:41Z-1727437

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623219-sc-2013-10-31T13:56:42Z-1727438

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623220-sc-2013-10-31T13:56:43Z-1727439

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623221-sc-2013-10-31T13:56:44Z-1727440

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623223-sc-2013-10-31T13:56:47Z-1727442

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623224-sc-2013-10-31T13:56:48Z-1727443

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623225-sc-2013-10-31T13:56:49Z-1727444

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5623226-sc-2013-10-31T13:56:50Z-1727445

text: baker's yeast

text: Saccharomyces cerevisiae

text: lane 2

text: Saccharomyces cerevisiae


E-MTAB-2045:iBF 42h

text: ICGEB at New Delhi

text: public

text: E-MTAB-2045:iBF 42h

tag: Namespace:ICGEB at New Delhi

text: 6 to 7 day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Asian malaria mosquito

text: Protocols: An. stephensi from laboratory stock were reared under controlled conditions at 28 + 2degreesC, 70 -75% humidity. Adult mosquitoes were fed with 2% sterile glucose solution and water soaked raisin.Samples were prepared from An. stephensi at 5 different conditions. 5-6 days old sugar fed adult female mosquitoes were collected. Blood fed and parasite infected mosquitoes were collected at two time points, at 42 hours and five days post blood feeding. Whole body of all mosquito samples were stored in Trizol (Invitrogen) until RNA extraction. Stock solution of Plasmodium vinckei petteri 279 BY was thawed and injected into 5 weeks old BALB/C mice. When gametocytemia reached 0.05%, naive 4-5 days old female mosquitoes were fed on infected mice. Midguts of mosquitoes on 5th day post infection (dpi) were dissected, stained in mercurochrome and observed for the presence of oocysts under microscope. Presence of oocysts confirmed infection of mosquitoes by Plasmodium parasite. BF 42h and BF 5d mosquitoes were fed on normal mice blood and were collected at specified time points. Total RNA enriched in small RNA population was extracted using miRNeasy kit (Qiagen) as per the manualﾒs protocol. Quality and quantity of RNA was checked by using Agilent 2100 Bioanalyzer RNA Nano 6000 kit. Illumina Truseq small RNA libraries were made as per the manufacturer's instructions (Illumina Inc). 1ug of total RNA was ligated with 3prime and 5prime adaptors followed by reverse transcription using RT primers. Following PCR amplification of the adaptor enriched fragments, population of small RNA within length 140-160 bps were ran and eluted from 6 % TBE PAGE gel. Eluted product was precipitated using sodium acetate and ethanol and was dissolved in RNAase free water. These RNA samples were sent for high throughput sequencing using Illumina Genome Analyzer II.

characteristic: description

text: wild type

characteristic: genotype

text: Anopheles stephensi

text: Anopheles stephensi

text: Anopheles stephensi

text: female

characteristic: sex

text: fresh specimen

text: iBF 42h

characteristic: title


E-MTAB-2045:BF 42h

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: ICGEB at New Delhi

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2045:BF 42h

characteristic: Submitter Id

text: 6 to 7 day

text: ArrayExpress

text: Asian malaria mosquito

text: wild type

text: Anopheles stephensi

text: Anopheles stephensi

text: Anopheles stephensi

text: female

text: fresh specimen

text: BF 42h


E-MTAB-2045:iBF 5d

characteristic: External Id

text: ICGEB at New Delhi

text: public

text: E-MTAB-2045:iBF 5d

text: 6 to 7 day

text: ArrayExpress

text: Asian malaria mosquito

characteristic: common name

text: wild type

text: Anopheles stephensi

characteristic: organism

text: Anopheles stephensi

text: Anopheles stephensi

text: female

text: fresh specimen

characteristic: specimen with known storage state

text: iBF 5d


text: ICGEB at New Delhi

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 6 to 7 day

text: ArrayExpress

text: Asian malaria mosquito

text: Protocols: An. stephensi from laboratory stock were reared under controlled conditions at 28 + 2degreesC, 70 -75% humidity. Adult mosquitoes were fed with 2% sterile glucose solution and water soaked raisin.Samples were prepared from An. stephensi at 5 different conditions. 5-6 days old sugar fed adult female mosquitoes were collected. Blood fed and parasite infected mosquitoes were collected at two time points, at 42 hours and five days post blood feeding. Whole body of all mosquito samples were stored in Trizol (Invitrogen) until RNA extraction. Total RNA enriched in small RNA population was extracted using miRNeasy kit (Qiagen) as per the manualﾒs protocol. Quality and quantity of RNA was checked by using Agilent 2100 Bioanalyzer RNA Nano 6000 kit. Illumina Truseq small RNA libraries were made as per the manufacturer's instructions (Illumina Inc). 1ug of total RNA was ligated with 3prime and 5prime adaptors followed by reverse transcription using RT primers. Following PCR amplification of the adaptor enriched fragments, population of small RNA within length 140-160 bps were ran and eluted from 6 % TBE PAGE gel. Eluted product was precipitated using sodium acetate and ethanol and was dissolved in RNAase free water. These RNA samples were sent for high throughput sequencing using Illumina Genome Analyzer II.

text: wild type

text: Anopheles stephensi

text: Anopheles stephensi

text: Anopheles stephensi

text: female

text: fresh specimen

text: SF


E-MTAB-2045:BF 5d

text: ICGEB at New Delhi

text: public

text: E-MTAB-2045:BF 5d

text: 6 to 7 day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Asian malaria mosquito

characteristic: description

text: wild type

text: Anopheles stephensi

text: Anopheles stephensi

text: Anopheles stephensi

text: female

text: fresh specimen

text: BF 5d


text: GIS

text: public

text: ArrayExpress

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: human

text: Protocols: The hESC lines H1 (WA-01) was used for this study. For routine culture of hESCs in TeSR1 (Stem cell technologies), cells were cultured feeder free on matri-gel (BD). Medium was changed daily. The hESCs were subcultured with 1 mg/ml Dispase (Stem cell technologies) every 5-7 days. For treatment with 3iL conditions, hESCs cultured in TeSR1 was treated with 3iL 48 hrs post-seeding. The cells are subsequently subcultured on mitomycin C inactivated mouse fibroblast. Cells are dissociated to single cells using TrypLE (Life technologies). 3iL medium was refreshed daily and cells were subcultured upon confluency. Crosslinking of protein and DNA was done at room temperature for 10 minutes using serum free media that contains 1% formaldehyde. The crosslinking reaction was quenched with 0.2M final concentration of glycine for 5 minutes. Cells were washed extensively with TBSE (20 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA), scraped and pelleted. The cells were lysed with 0.1% SDS buffer and collected nuclei were lysed with 1% SDS buffer. Pelleted chromatin was resuspended in the 0.1% SDS buffer (50 mM HEPES-KOH, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS) and the DNA was sheared with the probe sonicator (Branson digital sonifier S-450D) for 20 cycles of 30 seconds with 1 min intervals at amplitude 40. The chromatin sample was centrifuged at 20,000 rpm for 45 mins before the supernatant was harvested as chromatin extracts for ChIP. Chromatin extracts were pre-cleared with Protein G Dynal Magnetic Beads (Invitrogen) (2 h, 4C) and immunoprecipitated overnight at 4C using Protein G Dynal Magnetic Beads pre-coupled with antibodies against H3K4me3 (Millipore 04-745), H3K27me3 (Millipore 07-449) or H3K27ac (abcam ab4729). Beads were washed 3x with 0.1% SDS buffer, once with 0.1% SDS/ 0.35M NaCl buffer, once in 10 mM Tris-HCl, 0.25M LiCl, 1 mM EDTA, 0.5% deoxycholate, 0.5% NP-40, and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA). Immunoprecipitated material was eluted from the beads with 50 mM Tris-HCl, 10 mM EDTA, 1% SDS at 69C for 30 mins in a orbital shaker at 10000 rpm. Crosslinks were reversed by incubation with pronase for 2 h at 42C then 6 h at 67C. DNA was extracted by phenol/chloroform/isoamyl-alcohol followed by chloroform, then precipitated with ethanol and resuspended in TE buffer. ChIP-Seq library was prepared using the NEBNext ChIP-Seq Library kit (NEB Biolabs) according to the manufacturer’s instructions. Briefly, the DNA was end-repaired with exonucleases and an adaptor was ligated to the end. Size selection was performed using AMPure XP Beads prior to PCR amplification for 15-18 cycles. The amplified DNA was purified using AMPure XP Beads, multiplexed and sequenced with the HiSeq 2000 system (Illumina).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

characteristic: sex

text: hESCs

characteristic: title


E-MTAB-2041:3iL hESCs

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: GIS

text: public

characteristic: INSDC status

text: E-MTAB-2041:3iL hESCs

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

text: 3iL hESCs


text: female

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Oocyte

characteristic: sample description

text: Mus musculus


E-MTAB-2042:3iL hESCs

text: GIS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-2042:3iL hESCs

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

text: human

text: Protocols: For treatment with 3iL conditions, hESCs cultured in TeSR1 was treated with 3iL 48 hrs post-seeding. The cells are subsequently subcultured on mitomycin C inactivated mouse fibroblast. Cells are dissociated to single cells using TrypLE (Life technologies). 3iL medium was refreshed daily and cells were subcultured upon confluency. For treatment with 3iL conditions, hESCs cultured in TeSR1 was treated with 3iL 48 hrs post-seeding. The cells are subsequently subcultured on mitomycin C inactivated mouse fibroblast. Cells are dissociated to single cells using TrypLE (Life technologies). 3iL medium was refreshed daily and cells were subcultured upon confluency. Crosslinking of protein and DNA was done at room temperature for 10 minutes using serum free media that contains 1% formaldehyde. The crosslinking reaction was quenched with 0.2M final concentration of glycine for 5 minutes. Cells were washed extensively with TBSE (20 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA), scraped and pelleted. The cells were lysed with 0.1% SDS buffer and collected nuclei were lysed with 1% SDS buffer. Pelleted chromatin was resuspended in the 0.1% SDS buffer (50 mM HEPES-KOH, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS) and the DNA was sheared with the probe sonicator (Branson digital sonifier S-450D) for 20 cycles of 30 seconds with 1 min intervals at amplitude 40. The chromatin sample was centrifuged at 20,000 rpm for 45 mins before the supernatant was harvested as chromatin extracts for ChIP. Chromatin extracts were pre-cleared with Protein G Dynal Magnetic Beads (Invitrogen) (2 h, 4C) and immunoprecipitated overnight at 4C using Protein G Dynal Magnetic Beads pre-coupled with antibodies against Phospho-Stat3 (Cell Signalling Technology 9145). Beads were washed 3x with 0.1% SDS buffer, once with 0.1% SDS/ 0.35M NaCl buffer, once in 10 mM Tris-HCl, 0.25M LiCl, 1 mM EDTA, 0.5% deoxycholate, 0.5% NP-40, and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA). Immunoprecipitated material was eluted from the beads with 50 mM Tris-HCl, 10 mM EDTA, 1% SDS at 69C for 30 mins in a orbital shaker at 10000 rpm. Crosslinks were reversed by incubation with pronase for 2 h at 42C then 6 h at 67C. DNA was extracted by phenol/chloroform/isoamyl-alcohol followed by chloroform, then precipitated with ethanol and resuspended in TE buffer. ChIP-Seq library was prepared using the NEBNext ChIP-Seq Library kit (NEB Biolabs) according to the manufacturer’s instructions. Briefly, the DNA was end-repaired with exonucleases and an adaptor was ligated to the end. Size selection was performed using AMPure XP Beads prior to PCR amplification for 15-18 cycles. The amplified DNA was purified using AMPure XP Beads, multiplexed and sequenced with the HiSeq 2000 system (Illumina).

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: male

text: 3iL hESCs


E-MTAB-2044:3iL hESCs

text: GIS

text: public

text: E-MTAB-2044:3iL hESCs

text: ArrayExpress

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: human

text: Protocols: The hESC lines H1 (WA-01) was used for this study. For routine culture of hESCs in TeSR1 (Stem cell technologies), cells were cultured feeder free on matri-gel (BD). Medium was changed daily. The hESCs were subcultured with 1 mg/ml Dispase (Stem cell technologies) every 5-7 days. For treatment with 3iL conditions, hESCs cultured in TeSR1 was treated with 3iL 48 hrs post-seeding. The cells are subsequently subcultured on mitomycin C inactivated mouse fibroblast. Cells are dissociated to single cells using TrypLE (Life technologies). 3iL medium was refreshed daily and cells were subcultured upon confluency. Crosslinking of protein and DNA was done at room temperature for 10 minutes using serum free media that contains 1% formaldehyde. The crosslinking reaction was quenched with 0.2M final concentration of glycine for 5 minutes. Cells were washed extensively with TBSE (20 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA), scraped and pelleted. The cells were lysed with 0.1% SDS buffer and collected nuclei were lysed with 1% SDS buffer. Pelleted chromatin was resuspended in the 0.1% SDS buffer (50 mM HEPES-KOH, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS) and the DNA was sheared with the probe sonicator (Branson digital sonifier S-450D) for 20 cycles of 30 seconds with 1 min intervals at amplitude 40. The chromatin sample was centrifuged at 20,000 rpm for 45 mins before the supernatant was harvested as chromatin extracts for ChIP. Chromatin extracts were pre-cleared with Protein G Dynal Magnetic Beads (Invitrogen) (2 h, 4C) and immunoprecipitated overnight at 4C using Protein G Dynal Magnetic Beads pre-coupled with antibodies against Oct4 (Abcam ab19857), Nanog (R&D AF1997) or p300 (Santa Cruz sc585). Beads were washed 3x with 0.1% SDS buffer, once with 0.1% SDS/ 0.35M NaCl buffer, once in 10 mM Tris-HCl, 0.25M LiCl, 1 mM EDTA, 0.5% deoxycholate, 0.5% NP-40, and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA). Immunoprecipitated material was eluted from the beads with 50 mM Tris-HCl, 10 mM EDTA, 1% SDS at 69C for 30 mins in a orbital shaker at 10000 rpm. Crosslinks were reversed by incubation with pronase for 2 h at 42C then 6 h at 67C. DNA was extracted by phenol/chloroform/isoamyl-alcohol followed by chloroform, then precipitated with ethanol and resuspended in TE buffer. ChIP-Seq library was prepared using the NEBNext ChIP-Seq Library kit (NEB Biolabs) according to the manufacturer’s instructions. Briefly, the DNA was end-repaired with exonucleases and an adaptor was ligated to the end. Size selection was performed using AMPure XP Beads prior to PCR amplification for 15-18 cycles. The amplified DNA was purified using AMPure XP Beads, multiplexed and sequenced with the HiSeq 2000 system (Illumina).

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

characteristic: sex

text: 3iL hESCs

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: GIS

text: public

characteristic: INSDC status

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

text: hESCs


text: male

characteristic: ArrayExpress-Sex

text: Mouse

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

text: SC_GCIM5642974-sc-2013-11-04T08:37:30Z-1748579

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: SC_GCIM5642975-sc-2013-11-04T08:37:31Z-1748580

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_GCIM5642976-sc-2013-11-04T08:37:32Z-1748581

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_GCIM5642977-sc-2013-11-04T08:37:33Z-1748582

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mouse

text: SC

text: public

text: SC_GCIM5642978-sc-2013-11-04T08:37:37Z-1748583

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mouse

text: SC

text: public

text: SC_GCIM5642979-sc-2013-11-04T08:37:38Z-1748584

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mouse

text: SC

text: public

text: SC_GCIM5642980-sc-2013-11-04T08:37:39Z-1748585

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mouse

text: SC

text: public

text: SC_GCIM5642981-sc-2013-11-04T08:37:40Z-1748586

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mouse

text: SC

text: public

text: SC_GCIM5642982-sc-2013-11-04T08:37:42Z-1748587

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mouse

text: SC

text: public

text: SC_GCIM5642983-sc-2013-11-04T08:37:43Z-1748588

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mouse

text: SC

text: public

text: SC_GCIM5642984-sc-2013-11-04T08:37:44Z-1748589

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mouse

text: SC

text: public

text: SC_GCIM5642985-sc-2013-11-04T08:37:45Z-1748590

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mouse

text: SC

text: public

text: SC_GCIM5642986-sc-2013-11-04T08:37:46Z-1748591

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mouse

text: SC

text: public

text: SC_GCIM5642987-sc-2013-11-04T08:37:47Z-1748592

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mouse

text: SC

text: public

text: SC_GCIM5642988-sc-2013-11-04T08:37:48Z-1748593

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mouse

text: SC

text: public

text: SC_GCIM5642989-sc-2013-11-04T08:37:49Z-1748594

text: house mouse

text: Mus musculus

text: Mus musculus


text: Functional Genomics Group, PICB

text: public

tag: Namespace:Functional Genomics Group, PICB

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: Norway rat

text: Protocols: PC12 cells were plated on a Poly-L-lysine-coated dishes (Corning) and maintained in DMEM/F12 (Invitrogen) with 5% FBS(Biochrom), 5% horse serum (Gibco) and 1% penicillin/streptomycin at 37C in 5% CO2. Cells were cross-linked with formaldehyde and sonicated to generate chromatin fragments size enriches between 200-600 bp. Antibody against GATA3 (558686, BD PharmingenTM ) was used. Chromatin from 20 million cells was used for each ChIP experiment, which yielded approximately 10 ng of DNA. As input, 2% of sonicated chromatin was treated with proteinase K at 50C for 2 hr and purified using the QIAquick PCR Purification Kit (Qiagen Cat # 28106).

characteristic: description

text: Rattus norvegicus

text: Rattus norvegicus

text: Rattus norvegicus


characteristic: ENA-CHECKLIST

text: Functional Genomics Group, PICB

text: public

text: ArrayExpress

text: Norway rat

text: Protocols: PC12 cells were plated on a Poly-L-lysine-coated dishes (Corning) and maintained in DMEM/F12 (Invitrogen) with 5% FBS(Biochrom), 5% horse serum (Gibco) and 1% penicillin/streptomycin at 37C in 5% CO2. We used two different custom-made siRNAs against Gata3. siGATA3-1 (sense 5-GUACUACAAACUCCACAAUTT-3 and antisense 5-AUUGUGGAGUUU GUAGUACTT-3), siGATA3-2 (sense 5-CCGUAAGAUGUCUAGCAAATT-3 and antisense 5-UUUGCUAGACAUCUUACGGTT3) and negative controls (sense 5-UUCUCCGAACGUGUCACGUTT-3 and antisense 5-ACGUGAC ACGUUCGGAGAATT) were obtained from GenePharma (Shanghai). All siRNA experiments were at a final concentration of 50nM. Transfections were conducted using Lipofectamine RNAiMAX (Invitrogen). Total RNA was isolated from cells using Trizol (Invitrogen).

text: Rattus norvegicus

text: Rattus norvegicus

text: Rattus norvegicus

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: t(14;18) negative

text: NCMLS

text: public

text: DSMZ

characteristic: biomaterial provider

text: Cell Line

characteristic: biomaterial type

text: human

text: SU-DHL-5 Cell Line

text: Drexler HG chapter 16 Establishment and culture of leukemia-lymphoma cell in Cancer Cell Culture Methods and Protocols 2nd Edition Springer Berlin pp 181 to 200 in 2011

characteristic: differentiation method

text: B cell

characteristic: differentiation stage

text: Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma

characteristic: disease

characteristic: line

text: RPMI 1640 + 10%FBS + 1% Glutamine

characteristic: medium

text: total RNA

characteristic: molecule

text: Homo sapiens

text: Homo sapiens

text: Female

characteristic: sex


characteristic: External Id

text: NCMLS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: DSMZ

text: Cell Line

text: human

characteristic: common name

text: KARPAS-422 Cell Line

text: B cell

text: RPMI 1640 + 20%FBS + 1% Glutamine

text: genomic DNA

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: TGAC

text: public

text: thale cress

text: HMW DNA for Mate Pair testing

characteristic: description

text: Arabidopsis thaliana

text: Arabidopsis thaliana

characteristic: title


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught male

characteristic: latitude

characteristic: longitude

text: Heliconius erato

text: Heliconius erato

text: Jiggins 16302


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught male

text: Heliconius erato

text: Heliconius erato

text: Jiggins 16307


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught female

text: Heliconius erato

text: Heliconius erato

text: Jiggins 16314


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught male

text: Heliconius erato

text: Heliconius erato

text: Jiggins 16451


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught male

text: Heliconius erato

text: Heliconius erato

text: Jiggins 16457


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught male

text: Heliconius erato

text: Heliconius erato

text: Jiggins 16460


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught male

text: Heliconius erato

text: Heliconius erato

text: Jiggins 16634


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught male

text: Heliconius erato

text: Heliconius erato

text: Jiggins 16638


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught male

text: Heliconius erato

text: Heliconius erato

text: Jiggins 16640


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught female

text: Heliconius erato

text: Heliconius erato

text: Jiggins 16642


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught

text: Heliconius erato

text: Heliconius erato

text: McMillan_Counterman NCS0328


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught

text: Heliconius erato

text: Heliconius erato

text: McMillan_Counterman NCS0345


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught

text: Heliconius erato

text: Heliconius erato

text: McMillan_Counterman NCS0709


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught

text: Heliconius erato

text: Heliconius erato

text: McMillan_Counterman NCS0616


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught

text: Heliconius erato

text: Heliconius erato

text: McMillan_Counterman NCS0677


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught

text: Heliconius erato

text: Heliconius erato

text: McMillan_Counterman NCS0680


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught

text: Heliconius erato

text: Heliconius erato

text: McMillan_Counterman NCS0681


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught

text: Heliconius erato

text: Heliconius erato

text: McMillan_Counterman NCS0701


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught

text: Heliconius erato

text: Heliconius erato

text: McMillan_Counterman NCS0736


text: CAM

text: public

text: crimson-patched longwing

text: Pst1 RAD wild-caught

text: Heliconius erato

text: Heliconius erato

text: McMillan_Counterman NCS0864


E-MTAB-1896:one mouse

text: public

text: E-MTAB-1896:one mouse

tag: Namespace:Swiss Federal Institute of Technology Zurich

text: 8 week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Immunised with NP-CGG (chicken gamma globulin (CGG) conjugated to 4-hydroxy-3-nitrophenylacetyl)

characteristic: clinical information

text: house mouse

text: Protocols: All animal experiments were performed under the guidelines and protocols approved by the Basel-Stadt cantonal veterinary office (Basel-Stadt Kantonales VeterinŠramt Tierversuchsbewilligung #2582). Female BALB/c mice (n=10, Charles Rivers Laboratories) 6 to 8 weeks old were housed under specific pathogen-free conditions and were maintained on a normal chow diet. Single cell suspensions of total splenocytes and bone marrow were obtained as described previously 4. Briefly, tibiae, femora, and spleens were collected into RPMI plus 10 % fetal bovine serum (FBS, Sigma). Bone marrow cells were flushed out using a 26-gauge syringe (Braun) and spleens were disintegrated using syringe and forceps. Cells were filtered through a 70-uM cell strainer (BD) into 15 mL falcon tubes (Falcon, BD) and subsequently centrifuged at 1500 rpm for 10 min at 4 degrees C. Red blood cells were lysed for 3 min in red blood cell lysis buffer (eBioscience). Cell suspension was then washed once with 10 mL RPMI + 10% FBS. Finally, cells were resuspended in 1 mL PBS + 0.5 % bovine serum albumin (BSA) + 2 mM ethylenediaminetetracetic acid (EDTA, buffer 1). Bone marrow cells were depleted of CD45R-positive cells before plasma cell isolation by incubation with anti-CD45R-biotin antibody (eBioscience, 13-0452) for 15 min on ice. After washing the cell suspension twice in BSA-free PBS supplemented with 2 mM EDTA (buffer 2), 30 ul of washed streptavidin-coupled Dynabeads (M-280, Invitrogen) was added and incubated for 20 min on ice. Following magnetic selection, the negative fraction was used in the subsequent steps. For plasma cell enrichment, spleen and CD45R-depleted bone marrow cell fractions were incubated with anti-CD138-biotin antibody (BD, 553713) for 15 min on ice. Following two wash steps in buffer 2, 30 ul of Dynabeads were added and incubated for 20 min on ice as before. Bead-bound cells were manually counted on a Neubauer cell counter, buffer removed by separation on the magnet, and beads plus cells were lysed in 1 mL of TRIzol¨ reagent (Invitrogen) and stored at -80 degrees C until further usage. Following cell isolation, isolated spleen and bone marrow cells were combined from nine mice ('9M', ~2.5 x 107 ASCs) and one mouse ('1M', ~3 x 106 ASCs) samples.

text: Mus musculus

text: Mus musculus

text: spleen and bone marrow

characteristic: organism part

text: Mus musculus

text: Balb/c

characteristic: strain

text: one mouse


E-MTAB-1896:pool of nine mice

characteristic: External Id

text: Swiss Federal Institute of Technology Zurich

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-1896:pool of nine mice

text: 8 week

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: spleen and bone marrow

text: Mus musculus

text: Balb/c

text: pool of nine mice


characteristic: ENA-CHECKLIST

text: CAAS

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: large yellow croaker

characteristic: common name

text: gut microbiota

characteristic: environment (biome)

text: gut microbiota of large yellow croaker

characteristic: environment (feature)

text: gut microbiota of large yellow croaker

characteristic: environment (material)

text: China

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: Larimichthys crocea

characteristic: organism

text: gut microbiota of large yellow croaker

characteristic: project name

text: Larimichthys crocea

text: 454 GS FLX

characteristic: sequencing method

text: ut microbiota of large yellow croaker


SGTW

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BGI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: M. Deyholos

text: SGTW

text: maidenhair tree

text: Ginkgo biloba

text: developing shoots

characteristic: plant body site

text: RNA extract

characteristic: samp mat process

text: D. W. Stevenson

text: Ginkgo biloba

text: developing shoots

characteristic: tissue type

characteristic: title


WWSS

characteristic: ENA-CHECKLIST

text: BGI

text: public

characteristic: INSDC status

text: M. Deyholos

characteristic: SRA accession

text: WWSS

characteristic: Submitter Id

text: English yew

characteristic: common name

text: Taxus baccata

text: mature leaves and small woody branch

text: RNA extract

text: M. Deyholos

text: Taxus baccata

text: mature leaves and small woody branch


JPYU

text: BGI

text: public

text: M. Deyholos

text: JPYU

text: liverwort

text: Marchantia polymorpha

characteristic: organism

text: clean thalli without gemmules

text: RNA extract

text: M. Deyholos

text: Marchantia polymorpha

text: clean thalli without gemmules


UNPT

text: BGI

text: public

text: T. Kutchan

text: UNPT

text: California poppy

text: Eschscholzia californica

text: leaf

text: RNA extract

text: T. Kutchan

text: Eschscholzia californica

text: T. Kutchan 6173583 (MO)

text: leaf


NJKC

text: BGI

text: public

text: T. Kutchan

text: NJKC

text: California poppy

text: Eschscholzia californica

text: stem

text: RNA extract

text: T. Kutchan

text: Eschscholzia californica

text: T. Kutchan 6173583 (MO)

text: stem


RKGT

text: BGI

text: public

text: T. Kutchan

text: RKGT

text: California poppy

text: This sample was not analyzed for the 1KP publication [Nature 574, 679-685 (2019)] because it was identified as mislabeled and/or contaminated. We released the data nonetheless as some find even these data useful. More information is given at [GigaScience 8, giz126 (2019)], including estimates of which particular sequences might be problematic.

characteristic: details

text: Eschscholzia californica

text: root

text: RNA extract

text: T. Kutchan

text: Eschscholzia californica

text: T. Kutchan 6173583 (MO)

text: mislabelled or contaminated

characteristic: status

text: root


TUHA

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: BGI

text: public

text: T. Kutchan

text: TUHA

text: California poppy

text: Eschscholzia californica

text: flower bud

text: RNA extract

text: T. Kutchan

text: Eschscholzia californica

text: T. Kutchan 6173583 (MO)

text: flower bud

text: TUHA-Eschscholzia_californica-flower_bud


ERXG

characteristic: External Id

text: BGI

characteristic: INSDC center name

text: public

text: T. Kutchan

text: ERXG

text: California poppy

text: Eschscholzia californica

text: developing fruit

text: RNA extract

text: T. Kutchan

text: Eschscholzia californica

text: T. Kutchan 6173583 (MO)

text: developing fruit

text: ERXG-Eschscholzia_californica-developing_fruit


UDUT

text: BGI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: M. Deyholos

text: UDUT

text: creosote bush

text: Larrea tridentata

text: woody seedling including leaves and root

text: RNA extract

text: M. Deyholos

text: Larrea tridentata


UOYN

text: BGI

text: public

text: M. Deyholos

text: UOYN

text: Madagascar periwinkle

text: Catharanthus roseus

text: flower, floral buds, leaves and stem

characteristic: plant body site

text: RNA extract

characteristic: samp mat process

text: M. Deyholos

text: Catharanthus roseus

text: flower, floral buds, leaves and stem


FDMM

text: BGI

text: public

text: M. Deyholos

text: FDMM

text: rosemary

text: Rosmarinus officinalis

text: mature stem and leaves

text: RNA extract

text: M. Deyholos

text: Rosmarinus officinalis

text: mature stem and leaves

characteristic: tissue type

characteristic: title


VXKB

characteristic: ENA-CHECKLIST

text: BGI

text: public

characteristic: INSDC status

text: BGI

text: VXKB

text: common morning-glory

text: Ipomoea purpurea

text: leaf, stem, flower

text: frozen tissue

text: R. Baucom

text: Ipomoea purpurea

text: leaf, stem, flower


text: public

characteristic: SRA accession

text: E-MTAB-1994:cell_culture_Hypoxia_HIF-1a_siRNA_rep2

tag: Namespace:The Nuffield Department of Medicine, University of Oxford, Oxford, UK

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: Protocols: MCF-7 cells were cultured in Dulbecco's modified Eagles medium DMEM (Invitrogen). Media were supplemented with and 10% Fetal Bovine Serum (FBS) (Sigma-Aldrich). Cells were incubated for 24 hours in an In vivo2 Hypoxia Work Station (Ruskin Technologies) in an atmosphere of either normoxia (21% oxygen) or hypoxia (1% oxygen). In addtion, cells were treated with scramble control, HIF-1a and/or HIF-2a siRNAs as describes in paper and cultured in hypoxia for 24 hours. Total RNA was prepared using the mirVana miRNA Isolation Kit (Ambion) and treated with DNaseI (TURBO DNA-free, Ambion). Ribosomal RNAs were depleted using RiboMinus Locked Nucleic Acid probes (Invitrogen). Poly A selected RNA-seq libraries were papered according to TruSeq RNA Sample Prep Kit (Illumina), directional PolyA selected RNA libraries were prepared using the ScriptSeq v2 RNA-Seq kit (Epicentre) and ribosomal depleted strand specific total RNA-seq libraries were prepared according to optimised protocol described in the paper.

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: The Nuffield Department of Medicine, University of Oxford, Oxford, UK

text: public

text: ArrayExpress

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-1994:cell_culture_Scramble_siRNA_control_rep2

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-1994:cell_culture_Hypoxia_HIF-2a_siRNA_rep1

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

text: E-MTAB-1994:cell_culture_Hypoxia_HIF-1a&2a_siRNA_rep1

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

text: E-MTAB-1994:cell_culture_Hypoxia_HIF-1a&2a_siRNA_rep2

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

text: E-MTAB-1994:cell_culture_Scramble_siRNA_control_rep1

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

text: E-MTAB-1994:cell_culture_Hypoxia_HIF-1a_siRNA_rep1

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

text: E-MTAB-1994:cell_culture_Hypoxia_HIF-2a_siRNA_rep2

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: La Sapienza' University of Rome

text: public

text: E-MTAB-2056:HCT116_Dicer_EX5_cells_RIP_anti-Ago2

tag: Namespace:La Sapienza' University of Rome

text: ArrayExpress

text: human

text: Protocols: HCT 116 WT and DICER_Ex5 cells were grown in McCoy's 5A medium supplemented with 10% (v/v) fetal bovine serum, 2mM L-Glutamine and Penicillin-Streptomycin. Nuclei of 350 x 10E+6 HCT116 WT and DICER_Ex5 were lysed in IP-buffer supplemented with RNasin (Promega). Nuclear lysates were clarified and pre-cleared in the presence of Protein G-sepharose beads for 2 hr 4 degrees C under constant rotation and then filtered through a 0.45 um filter. Lysate aliquots were taken out as Input for RNA and protein isolation. Antibody anti-AGO2 (11A9, Ascenion) and isotype-matched IgG (mock_IP) were coupled to Protein G-sepharose beads for 2 h at 4 degrees C in IP-buffer containing 1 mg/ml heparin (Sigma). The pre-cleared nuclear lysate was incubated with antibody-coupled beads overnight at 4 degrees C under constant rotation. IP samples were washed once with IP-buffer for 5 min at 4 degrees C, and three times with IP-wash buffer (50 mM Tris-HCl, pH 7.5; 300 mM NaCl; 5 mM MgCl2; and 0.05% Nonidet P-40) at 4 degrees C. An aliquot was taken out for western blot in order to check immunoprecipitation efficiency. For RNA isolation, Input and IP samples were DNAseI- and Proteinase K-treated. Total RNA and co-precipitated RNA was extracted by phenol:chloroform:isopropyl alcohol and precipitated in ethanol. Small RNA libraries were constructed using the TruSeq SmallRNA Sample preparation kit (Illumina)

text: targeted mutation

characteristic: genetic modification

text: Dicer hypomorphic

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state


characteristic: ENA-CHECKLIST

text: La Sapienza' University of Rome

text: public

characteristic: INSDC status

text: E-MTAB-2056:HCT116_wt_cells_nuclear_input

text: ArrayExpress

text: human

text: wild type

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: frozen specimen

characteristic: title


text: La Sapienza' University of Rome

text: public

characteristic: SRA accession

text: E-MTAB-2056:HCT116_wt_cells_RIP_anti-IgG

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: wild type

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: frozen specimen


characteristic: ENA-FIRST-PUBLIC

text: La Sapienza' University of Rome

text: public

text: E-MTAB-2056:HCT116_wt_cells_RIP_anti-Ago2

text: ArrayExpress

characteristic: cell line

text: human

characteristic: description

text: wild type

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: frozen specimen


characteristic: ENA-LAST-UPDATE

text: La Sapienza' University of Rome

text: public

text: E-MTAB-2056:HCT116_Dicer_EX5_nuclear_input

text: ArrayExpress

text: human

characteristic: common name

text: targeted mutation

text: Dicer hypomorphic

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: frozen specimen


characteristic: External Id

text: La Sapienza' University of Rome

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-2056:HCT116_Dicer_EX5_cells_RIP_anti-IgG

text: ArrayExpress

text: human

text: targeted mutation

text: Dicer hypomorphic

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: frozen specimen


characteristic: INSDC last update

text: public

text: E-MTAB-1995:cell_culture_ Hypoxia_H3K4me3

text: ArrayExpress

text: human

text: Protocols: MCF-7 cells were cultured in Dulbeccos modified Eagle's medium 'DMEM' (Invitrogen). Media were supplemented with and 10% Fetal Bovine Serum (FBS) (Sigma-Aldrich). Cells were incubated for 24 hours in an In vivo2 Hypoxia Work Station (Ruskin Technologies) in an atmosphere of either normoxia (21% oxygen) or hypoxia (0.5% oxygen). Chromatin immunoprecipitation was performed as described in the paper. Libraries were prepared using the Illumina ChIP-Seq kit.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: cell_culture_ Hypoxia_H3K4me3


text: The Nuffield Department of Medicine, University of Oxford, Oxford, UK

text: public

text: E-MTAB-1995:cell_culture_Hypoxia_RNA-Pol2

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

text: E-MTAB-1995:cell_culture_ Normoxia_H3K4me3

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: cell_culture_ Normoxia_H3K4me3


text: public

text: E-MTAB-1995:cell_culture_Normoxia_RNA_Pol2

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Saccharomyces cerevisiae

characteristic: ArrayExpress-Species

text: SC

text: public

text: 2787STDY5644702-sc-2013-11-12T16:36:10Z-1751119

text: baker's yeast

text: Saccharomyces cerevisiae

text: Lane 1

characteristic: sample description

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

text: 2787STDY5644703-sc-2013-11-12T16:36:13Z-1751120

text: baker's yeast

text: Saccharomyces cerevisiae

text: Lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

characteristic: SRA accession

text: 2787STDY5644704-sc-2013-11-12T16:36:14Z-1751121

text: baker's yeast

text: Saccharomyces cerevisiae

text: Lane 1

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5644705-sc-2013-11-12T16:36:16Z-1751122

characteristic: Submitter Id

text: baker's yeast

text: Saccharomyces cerevisiae

text: Lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5644706-sc-2013-11-12T16:36:17Z-1751123

text: baker's yeast

text: Saccharomyces cerevisiae

text: Lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: 2787STDY5644707-sc-2013-11-12T16:36:18Z-1751124

text: baker's yeast

text: Saccharomyces cerevisiae

text: Lane 2

text: Saccharomyces cerevisiae


text: Danio rerio

text: TL/AB

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: SL6_12_A1-sc-2013-11-13T13:06:18Z-1757458

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB

characteristic: strain


text: Danio rerio

text: TL/AB

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: SL6_12_B1-sc-2013-11-13T13:06:21Z-1757459

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL6_12_C1-sc-2013-11-13T13:06:22Z-1757460

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL6_12_D1-sc-2013-11-13T13:06:23Z-1757461

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL6_12_A2-sc-2013-11-13T13:06:24Z-1757466

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL6_12_B2-sc-2013-11-13T13:06:26Z-1757467

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL6_12_C2-sc-2013-11-13T13:06:27Z-1757468

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL6_12_D2-sc-2013-11-13T13:06:28Z-1757469

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL6_12_A3-sc-2013-11-13T13:06:29Z-1757474

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL6_12_B3-sc-2013-11-13T13:06:30Z-1757475

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB