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text: Protocols: All mice were housed and procedures carried out at the WTCHG. Mice were maintained in a specific pathogen free facility in individually ventilated cages, and given food and water ad libitum. All experiments were carried out in accordance with U.K. national (Home Office) and institutional guidelines. Hippocampus and lung RNA was extracted from 30 mice from a reciprocal cross of C57BL/6J x B6(C)-H2bm12/KhEgJ. Total RNA was isolated from frozen lung using RNeasy(r) kit, and from frozen hippocampus using RNeasy(r) micro kit (Qiagen, Crawley, UK). RNA concentrations were determined using a NanoDrop spectrophotometer, and lung RNA quality, purity and integrity were assessed using an Agilent 2100 Bioanalyser (Agilent Technologies, Waldbronn, Germany). Hippocampus RNA quality was not routinely assessed on the Bioanalyser because the quantities were too low. Three or four mice from each combination of sex, F1 genotype and parental genotype were used. RNA was barcoded, pooled and sequenced on a lane of a Hiseq2000 using 51bp paired end reads. Total RNA quantity and integrity were assessed, using Quant-IT RiboGreen RNA Assay Kit (Invitrogen, Carlsbad, CA, USA) and Agilent Tapestation 2200 R6K. mRNA enrichment was achieved by processing 5ug of total RNA using the Magnetic mRNA Isolation Kit from NEB (S1550S) with minor modifications. Generation of double stranded cDNA and library construction were performed using NEBNext(r) Ultra(tm) Directional RNA Library Prep Kit for Illumina(r) (E7420L) according to manufacturer specifications. Upon ligation of Illumina Adapters (Multiplexing Sample Preparation Oliogonucleotide Kit) each library was size selected with two Ampure Bead bindings (firstly, 1:0.7x volume and secondly, the supernatant from the first bind was taken for a 1:1.7x volume clean-up). The following custom primers (25 uM each) were used for the PCR enrichment step: Multiplex PCR primer 1.0: 5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' Index primer: 5'-CAAGCAGAAGACGGCATACGAGAT[INDEX]CAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3' Indices used the eight bases tags developed by WTCHG (Lamble et al. in press). Amplified libraries were analysed for size distribution using the Agilent Tapestation 2200 D1K. Libraries were quantified by quantitative RT-PCR using Agilent qPCR Library Quantification Kit and a MX3005P instrument (Agilent) and relative volumes were pooled accordingly. Finally, a second quantitative RT-PCR was performed to measure the relative concentration of the pool compared to a previously sequenced mRNA library in order to determine the volume to use for sequencing.

characteristic: description

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text: Mus musculus

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text: house mouse

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characteristic: Submitter Id

text: house mouse

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text: sin_OSN_184-sc-2013-10-18T12:16:32Z-1728146

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text: sin_OSN_185-sc-2013-10-18T12:16:34Z-1728147

text: house mouse

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characteristic: Submitter Id

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characteristic: Submitter Id

text: house mouse

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characteristic: Submitter Id

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text: sin_OSN_232-sc-2013-10-18T12:17:32Z-1728194

characteristic: Submitter Id

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text: sin_OSN_233-sc-2013-10-18T12:17:33Z-1728195

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text: sin_OSN_234-sc-2013-10-18T12:17:34Z-1728196

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text: Mus musculus


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text: sin_OSN_235-sc-2013-10-18T12:17:35Z-1728197

text: house mouse

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text: sin_OSN_236-sc-2013-10-18T12:17:36Z-1728198

text: house mouse

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text: sin_OSN_237-sc-2013-10-18T12:17:38Z-1728199

text: house mouse

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text: sin_OSN_238-sc-2013-10-18T12:17:39Z-1728200

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text: sin_OSN_239-sc-2013-10-18T12:17:40Z-1728201

characteristic: Submitter Id

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text: Mus musculus


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characteristic: INSDC center name

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text: sin_OSN_240-sc-2013-10-18T12:17:41Z-1728202

text: house mouse

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text: sin_OSN_241-sc-2013-10-18T12:17:42Z-1728203

text: house mouse

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text: Mus musculus


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text: house mouse

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characteristic: ArrayExpress-Genotype

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text: sin_OSN_243-sc-2013-10-18T12:17:45Z-1728205

text: house mouse

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characteristic: organism

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text: sin_OSN_244-sc-2013-10-18T12:17:46Z-1728206

text: house mouse

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characteristic: sample description

text: Mus musculus


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text: Olfactory epithelium

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characteristic: ArrayExpress-StrainOrLine

characteristic: External Id

text: SC

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text: sin_OSN_245-sc-2013-10-18T12:17:47Z-1728207

text: house mouse

text: Mus musculus

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text: Mus musculus

characteristic: strain


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text: Olfactory epithelium

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characteristic: INSDC center name

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text: public

text: sin_OSN_246-sc-2013-10-18T12:17:48Z-1728208

characteristic: Submitter Id

text: house mouse

text: Mus musculus

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text: Mus musculus


text: OMP-GFP (+/-)

text: Olfactory epithelium

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characteristic: ENA-CHECKLIST

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text: sin_OSN_247-sc-2013-10-18T12:17:49Z-1728209

text: house mouse

characteristic: common name

text: Mus musculus

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text: Mus musculus


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text: Olfactory epithelium

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characteristic: ENA-FIRST-PUBLIC

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text: SC

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characteristic: INSDC status

text: sin_OSN_248-sc-2013-10-18T12:17:50Z-1728210

text: house mouse

text: Mus musculus

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text: Mus musculus


text: OMP-GFP (+/-)

characteristic: ArrayExpress-Genotype

text: Olfactory epithelium

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text: male

text: Mus musculus

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characteristic: SRA accession

text: sin_OSN_249-sc-2013-10-18T12:17:51Z-1728211

text: house mouse

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text: Mus musculus


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text: Olfactory epithelium

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characteristic: ArrayExpress-Sex

text: Mus musculus

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text: SC

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text: sin_OSN_250-sc-2013-10-18T12:17:52Z-1728212

text: house mouse

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characteristic: organism

text: library from single OSNs

text: Mus musculus


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text: Olfactory epithelium

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characteristic: ArrayExpress-StrainOrLine

characteristic: External Id

text: SC

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text: sin_OSN_251-sc-2013-10-18T12:17:54Z-1728213

text: house mouse

text: Mus musculus

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characteristic: sample description

text: Mus musculus


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text: Olfactory epithelium

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text: Mus musculus

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characteristic: INSDC center name

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text: public

text: sin_OSN_252-sc-2013-10-18T12:17:55Z-1728214

text: house mouse

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text: Mus musculus

characteristic: strain


text: OMP-GFP (+/-)

text: Olfactory epithelium

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text: Mus musculus

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

text: sin_OSN_253-sc-2013-10-18T12:17:56Z-1728215

characteristic: Submitter Id

text: house mouse

text: Mus musculus

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text: Mus musculus


text: OMP-GFP (+/-)

text: Olfactory epithelium

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characteristic: ENA-FIRST-PUBLIC

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text: SC

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text: sin_OSN_254-sc-2013-10-18T12:17:57Z-1728216

text: house mouse

characteristic: common name

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text: Mus musculus


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text: Olfactory epithelium

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text: male

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characteristic: INSDC status

text: sin_OSN_255-sc-2013-10-18T12:17:58Z-1728217

text: house mouse

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text: Mus musculus


text: OMP-GFP (+/-)

text: Olfactory epithelium

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characteristic: ArrayExpress-Sex

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text: SC

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characteristic: SRA accession

text: sin_OSN_256-sc-2013-10-18T12:17:59Z-1728218

text: house mouse

text: Mus musculus

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text: Mus musculus


text: OMP-GFP (+/-)

text: Olfactory epithelium

text: male

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characteristic: ArrayExpress-StrainOrLine

characteristic: External Id

text: SC

text: public

text: sin_OSN_257-sc-2013-10-18T12:18:00Z-1728219

text: house mouse

text: Mus musculus

characteristic: organism

text: library from single OSNs

text: Mus musculus


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text: Olfactory epithelium

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characteristic: INSDC center name

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text: public

text: sin_OSN_258-sc-2013-10-18T12:18:01Z-1728220

text: house mouse

text: Mus musculus

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characteristic: sample description

text: Mus musculus


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text: Olfactory epithelium

text: male

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characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

text: sin_OSN_259-sc-2013-10-18T12:18:05Z-1728221

text: house mouse

text: Mus musculus

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characteristic: strain


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text: Olfactory epithelium

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characteristic: ENA-FIRST-PUBLIC

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text: SC

text: public

text: sin_OSN_260-sc-2013-10-18T12:18:07Z-1728222

characteristic: Submitter Id

text: house mouse

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text: Mus musculus


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characteristic: ArrayExpress-Genotype

text: Olfactory epithelium

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text: male

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text: sin_OSN_261-sc-2013-10-18T12:18:08Z-1728223

text: house mouse

characteristic: common name

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text: Mus musculus


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text: Olfactory epithelium

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characteristic: ArrayExpress-Sex

text: Mus musculus

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text: SC

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characteristic: INSDC status

text: sin_OSN_262-sc-2013-10-18T12:18:09Z-1728224

text: house mouse

text: Mus musculus

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text: Mus musculus


text: OMP-GFP (+/-)

text: Olfactory epithelium

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text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

characteristic: External Id

text: SC

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characteristic: SRA accession

text: sin_OSN_263-sc-2013-10-18T12:18:10Z-1728225

text: house mouse

text: Mus musculus

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text: Mus musculus


text: OMP-GFP (+/-)

text: Olfactory epithelium

text: male

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characteristic: INSDC center name

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text: public

text: sin_OSN_264-sc-2013-10-18T12:18:11Z-1728226

text: house mouse

text: Mus musculus

characteristic: organism

text: library from single OSNs

text: Mus musculus


text: male

text: Mouse

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

text: SC_mskintumour5622238-sc-2013-10-21T08:46:27Z-1726388

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: SC_mskintumour5622239-sc-2013-10-21T08:46:31Z-1726389

text: house mouse

text: Mus musculus

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text: male

text: Mouse

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: SC_mskintumour5622240-sc-2013-10-21T08:46:32Z-1726390

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622241-sc-2013-10-21T08:46:33Z-1726391

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622242-sc-2013-10-21T08:46:35Z-1726392

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622244-sc-2013-10-21T08:46:37Z-1726394

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622245-sc-2013-10-21T08:46:39Z-1726395

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622246-sc-2013-10-21T08:46:40Z-1726396

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622247-sc-2013-10-21T08:46:41Z-1726397

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622248-sc-2013-10-21T08:46:43Z-1726398

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622249-sc-2013-10-21T08:46:44Z-1726399

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622250-sc-2013-10-21T08:46:46Z-1726400

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622251-sc-2013-10-21T08:46:47Z-1726401

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622252-sc-2013-10-21T08:46:48Z-1726402

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622253-sc-2013-10-21T08:46:49Z-1726403

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622254-sc-2013-10-21T08:46:51Z-1726404

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622255-sc-2013-10-21T08:46:52Z-1726405

text: house mouse

text: Mus musculus

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text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622256-sc-2013-10-21T08:46:53Z-1726406

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622257-sc-2013-10-21T08:46:54Z-1726407

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622258-sc-2013-10-21T08:46:55Z-1726408

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622259-sc-2013-10-21T08:46:56Z-1726409

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622260-sc-2013-10-21T08:46:57Z-1726410

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622261-sc-2013-10-21T08:46:59Z-1726411

text: house mouse

text: Mus musculus

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text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622262-sc-2013-10-21T08:47:00Z-1726412

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622263-sc-2013-10-21T08:47:02Z-1726413

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622264-sc-2013-10-21T08:47:03Z-1726414

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622265-sc-2013-10-21T08:47:04Z-1726415

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622266-sc-2013-10-21T08:47:05Z-1726416

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622267-sc-2013-10-21T08:47:06Z-1726417

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622269-sc-2013-10-21T08:47:09Z-1726419

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622270-sc-2013-10-21T08:47:10Z-1726420

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622271-sc-2013-10-21T08:47:12Z-1726421

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622272-sc-2013-10-21T08:47:13Z-1726422

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622273-sc-2013-10-21T08:47:14Z-1726423

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622274-sc-2013-10-21T08:47:15Z-1726424

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622275-sc-2013-10-21T08:47:17Z-1726425

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622276-sc-2013-10-21T08:47:18Z-1726426

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622277-sc-2013-10-21T08:47:19Z-1726427

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622278-sc-2013-10-21T08:47:20Z-1726428

text: house mouse

text: Mus musculus

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text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622279-sc-2013-10-21T08:47:21Z-1726429

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622280-sc-2013-10-21T08:47:22Z-1726430

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622281-sc-2013-10-21T08:47:23Z-1726431

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622282-sc-2013-10-21T08:47:24Z-1726432

text: house mouse

text: Mus musculus

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text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622283-sc-2013-10-21T08:47:25Z-1726433

text: house mouse

text: Mus musculus

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text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622284-sc-2013-10-21T08:47:26Z-1726434

text: house mouse

text: Mus musculus

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text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622285-sc-2013-10-21T08:47:28Z-1726435

text: house mouse

text: Mus musculus

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text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622286-sc-2013-10-21T08:47:29Z-1726436

text: house mouse

text: Mus musculus

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text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622287-sc-2013-10-21T08:47:30Z-1726437

text: house mouse

text: Mus musculus

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text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622288-sc-2013-10-21T08:47:32Z-1726438

text: house mouse

text: Mus musculus

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text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622289-sc-2013-10-21T08:47:33Z-1726439

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622290-sc-2013-10-21T08:47:35Z-1726440

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622291-sc-2013-10-21T08:47:39Z-1726441

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622292-sc-2013-10-21T08:47:40Z-1726442

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622293-sc-2013-10-21T08:47:41Z-1726443

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622294-sc-2013-10-21T08:47:42Z-1726444

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622295-sc-2013-10-21T08:47:43Z-1726445

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622296-sc-2013-10-21T08:47:45Z-1726446

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622297-sc-2013-10-21T08:47:46Z-1726447

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622298-sc-2013-10-21T08:47:47Z-1726448

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622299-sc-2013-10-21T08:47:48Z-1726449

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622300-sc-2013-10-21T08:47:49Z-1726450

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622301-sc-2013-10-21T08:47:50Z-1726451

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622302-sc-2013-10-21T08:47:51Z-1726452

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622303-sc-2013-10-21T08:47:52Z-1726453

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622304-sc-2013-10-21T08:47:53Z-1726454

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622305-sc-2013-10-21T08:47:55Z-1726455

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622306-sc-2013-10-21T08:47:56Z-1726456

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622307-sc-2013-10-21T08:47:57Z-1726457

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622308-sc-2013-10-21T08:47:58Z-1726458

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622309-sc-2013-10-21T08:47:59Z-1726459

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622310-sc-2013-10-21T08:48:00Z-1726460

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622311-sc-2013-10-21T08:48:01Z-1726461

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622312-sc-2013-10-21T08:48:02Z-1726462

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622313-sc-2013-10-21T08:48:03Z-1726463

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622314-sc-2013-10-21T08:48:05Z-1726464

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622315-sc-2013-10-21T08:48:06Z-1726465

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622316-sc-2013-10-21T08:48:07Z-1726466

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622318-sc-2013-10-21T08:48:09Z-1726468

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622319-sc-2013-10-21T08:48:11Z-1726469

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622320-sc-2013-10-21T08:48:12Z-1726470

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622321-sc-2013-10-21T08:48:13Z-1726471

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622322-sc-2013-10-21T08:48:14Z-1726472

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622334-sc-2013-10-21T08:48:15Z-1726484

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622335-sc-2013-10-21T08:48:16Z-1726485

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622336-sc-2013-10-21T08:48:17Z-1726486

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622337-sc-2013-10-21T08:48:18Z-1726487

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622338-sc-2013-10-21T08:48:19Z-1726488

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622339-sc-2013-10-21T08:48:21Z-1726489

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622340-sc-2013-10-21T08:48:22Z-1726490

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622341-sc-2013-10-21T08:48:23Z-1726491

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622342-sc-2013-10-21T08:48:24Z-1726492

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622343-sc-2013-10-21T08:48:25Z-1726493

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622344-sc-2013-10-21T08:48:26Z-1726494

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622345-sc-2013-10-21T08:48:27Z-1726495

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622346-sc-2013-10-21T08:48:28Z-1726496

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622347-sc-2013-10-21T08:48:29Z-1726497

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622348-sc-2013-10-21T08:48:30Z-1726498

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622349-sc-2013-10-21T08:48:31Z-1726499

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622350-sc-2013-10-21T08:48:32Z-1726500

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622351-sc-2013-10-21T08:48:34Z-1726501

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622352-sc-2013-10-21T08:48:35Z-1726502

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622353-sc-2013-10-21T08:48:36Z-1726503

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622354-sc-2013-10-21T08:48:37Z-1726504

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622356-sc-2013-10-21T08:48:39Z-1726506

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622359-sc-2013-10-21T08:48:43Z-1726509

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622360-sc-2013-10-21T08:48:45Z-1726510

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622361-sc-2013-10-21T08:48:46Z-1726511

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622362-sc-2013-10-21T08:48:47Z-1726512

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622363-sc-2013-10-21T08:48:48Z-1726513

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622364-sc-2013-10-21T08:48:49Z-1726514

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622365-sc-2013-10-21T08:48:51Z-1726515

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622366-sc-2013-10-21T08:48:52Z-1726516

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622367-sc-2013-10-21T08:48:53Z-1726517

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622368-sc-2013-10-21T08:48:54Z-1726518

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622369-sc-2013-10-21T08:48:55Z-1726519

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mouse

text: SC

text: public

text: SC_mskintumour5622370-sc-2013-10-21T08:48:56Z-1726520

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622371-sc-2013-10-21T08:48:57Z-1726521

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: SC_mskintumour5622372-sc-2013-10-21T08:48:58Z-1726522

text: house mouse

text: Mus musculus

text: Mus musculus


text: University of Manchester

text: public

tag: Namespace:University of Manchester

text: 3-3.5 hour

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: Protocols: The Decepentaplegic receptor Thickviens (Tkv) was over-expressed using the UASp-GAL4 system. pUASp-tkvQD was obtained from this original stock yw;pUASpTkvQD/TM6B (Casanueva and Ferguson, 2004; Development, 131(9): 1881-90). Gal4-Tub:VP16 was obtained from the original stock, Bloomington 7062. At the 3-3.5h time point after egg lay (AEL) embryos over-expressing TkvQD, derived from Gal4-Tub:VP16/+ ; P{UASp-TkvQD}/+ adults were collected. As an experimental control, 3-3.5h embryos derived from Gal4-Tub:VP16/+ ; + were also collected. RNA was extracted from 30ul of Drosophila embryos per sample using Trizol (Invitrogen) SOLiDTM Total RNA-Seq Kit (PN 4445374)

characteristic: description

text: larval stage

characteristic: developmental stage

text: Gal4-Tub:VP16/+ ; P{UASp-TkvQD}/+

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

characteristic: title


text: University of Manchester

text: public

characteristic: INSDC status

text: 3-3.5 hour

text: ArrayExpress

text: fruit fly

characteristic: common name

text: larval stage

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster


E-MTAB-1961:MCF7 cells

characteristic: External Id

text: VGH-YM Genome Research Center

text: public

characteristic: SRA accession

text: E-MTAB-1961:MCF7 cells

tag: Namespace:VGH-YM Genome Research Center

text: ArrayExpress

characteristic: cell line

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 37C incubator with 5% CO2. MCF7 cells were grown to 85% confluence in 6 cm tissue culture dish. Each 6 cm dish was rinsed twice with 1X PBS. Total RNA was extracted using TRIreagent (Invitrogen) protocol. The integrity of the RNA extract was checked by 1.2% (w/v) agarose gel electrophoresis and the concentration of RNA was estimated by ultraviolet spectrophotometry. The normal breast tissue mRNA were purchased from Origene (Catalog No.: CR559104 and CR561898). The sequencing library for mRNA-seq was prepared using TruSeq RNA Sample Preparation Kit (Illumina Inc., USA) as per manufacturers instruction. Briefly, total RNA with RIN (RNA integrity number) greater than 7.5 was subjected for poly-A mRNA isolation using poly-T oligo-attached magnetic beads. The poly-A mRNA was fragmented and first-strand cDNA was synthesized using random hexamers following by second-strand cDNA synthesis, end repair, addition of a single A base and adapter ligation. The adapter-ligated cDNA library was sized-selected by agarose gel and amplified by PCR.

text: breast adenocarcinoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: sex

text: MCF7 cells


characteristic: ENA-CHECKLIST

text: VGH-YM Genome Research Center

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: female


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Uppsala University, Uppsala, Sweden and Broad Institute, Boston, MA

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: dog

text: Protocols: Genomic DNA was prepared from whole blood QIAamp DNA Midi kit For each sample, 3 ug of genomic dna was sonicated to 200-800 bp and library preparation was performed using the Illumina paired end kit. Fragments were blunt ended, a 3' adonesine overhang was added followed by ligation of adapters. Ligated fragments were enriched using 11-15 cycles of adapter specific PCR using a high-fidelity polymerase (Phusion, Finnzymes).1 ug of cleaned PCR product was hybridized on the Roche Nimblegen Sequence Capture array with 385,000 probes. The array was customized to target 95% of the 5 Mb target region. Enriched DNA samples were sequenced using paired-end sequencing.

text: osteosarcoma

characteristic: individual

text: Canis lupus familiaris

text: Canis familiaris

text: blood

characteristic: organism part

text: Canis lupus familiaris

text: female

text: frozen specimen

characteristic: specimen with known storage state


characteristic: External Id

text: Uppsala University, Uppsala, Sweden and Broad Institute, Boston, MA

text: public

characteristic: INSDC status

text: ArrayExpress

text: dog

characteristic: common name

characteristic: description

text: normal

text: Canis lupus familiaris

text: Canis familiaris

text: blood

text: Canis lupus familiaris

text: female

text: frozen specimen

characteristic: title


characteristic: ENA-CHECKLIST

text: public

characteristic: SRA accession

text: ArrayExpress

text: dog

text: normal

characteristic: disease

text: Canis lupus familiaris

text: Canis familiaris

text: blood

text: Canis lupus familiaris

text: male

characteristic: sex

text: frozen specimen


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: dog

text: Protocols: Genomic DNA was prepared from whole blood QIAamp DNA Midi kit For each sample 1 ug of genomic DNA was fragmented and prepared according to the Illumina 12 plex multiplexing protocol. After ligation of adapters a unique barcode was introduced to each sample with the PCR enrichment step. After cleaning of the PCR product and quantification using Qubit fluorometric quantification, equimolar amounts of DNA from the 12 samples were pooled together and 5 ug of DNA hybridized to a single Sequence Capture array. Eluted DNA was amplified with 18 cycles of PCR. Enriched DNA samples were sequenced using paired-end sequencing

text: osteosarcoma

text: Canis lupus familiaris

characteristic: organism

text: Canis familiaris

text: blood

text: Canis lupus familiaris

text: female

text: frozen specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: dog

text: osteosarcoma

text: Canis lupus familiaris

text: Canis familiaris

text: blood

text: Canis lupus familiaris

text: male

text: frozen specimen


characteristic: External Id

text: public

text: ArrayExpress

text: dog

text: osteosarcoma

characteristic: individual

text: Canis lupus familiaris

text: Canis familiaris

text: blood

characteristic: organism part

text: Canis lupus familiaris

text: frozen specimen

characteristic: specimen with known storage state


text: public

characteristic: INSDC status

text: ArrayExpress

text: dog

characteristic: common name

characteristic: description

text: osteosarcoma

text: Canis lupus familiaris

text: Canis familiaris

text: blood

text: Canis lupus familiaris

text: female

text: frozen specimen

characteristic: title


characteristic: ENA-CHECKLIST

text: public

characteristic: SRA accession

text: ArrayExpress

text: dog

text: osteosarcoma

characteristic: disease

text: Canis lupus familiaris

text: Canis familiaris

text: blood

text: Canis lupus familiaris

text: male

characteristic: sex

text: frozen specimen


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: dog

text: normal

text: Canis lupus familiaris

characteristic: organism

text: Canis familiaris

text: blood

text: Canis lupus familiaris

text: female

text: frozen specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EBC

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: Tissue and total RNA samples from two fetal frontal cortex tissues, 38 weeks female (Sample 1) and 23/24 weeks male (Sample 2) were purchased from Capital Biosciences. The commercial adult frontal lobe polyA+ RNA sample with two rounds of polyA+ selection was acquired from Clontech (Catalogue number: 636165). Cytoplasmic RNA, nuclear RNA, total RNA and PolyA+ RNA was extracted from each of the samples. A novel protocol for cytoplasmic and nuclear RNA extraction was developed, based on the Norgen purification kit. The SOLiD RNA-seq protocol was used to prepare RNA libraries

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: frozen specimen


characteristic: ArrayExpress-CellType

text: Homo sapiens

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

text: public

text: HCC38_RNA_5-sc-2013-10-23T08:41:18Z-1732108

text: human

text: Homo sapiens

text: single cell Whole Transcriptome Amplification Product

characteristic: sample description

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

characteristic: INSDC status

text: HCC38_RNA_6-sc-2013-10-23T08:41:21Z-1732109

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: SRA accession

text: HCC38_RNA_7-sc-2013-10-23T08:41:22Z-1732110

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_RNA_8-sc-2013-10-23T08:41:24Z-1732111

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_RNA_10-sc-2013-10-23T08:41:25Z-1732112

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_RNA_11-sc-2013-10-23T08:41:26Z-1732113

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_RNA_12-sc-2013-10-23T08:41:27Z-1732114

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_RNA_13-sc-2013-10-23T08:41:29Z-1732115

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_RNA_14-sc-2013-10-23T08:41:30Z-1732116

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_RNA_15-sc-2013-10-23T08:41:32Z-1732117

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_RNA_16-sc-2013-10-23T08:41:33Z-1732118

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_DNA_5-sc-2013-10-23T08:41:34Z-1732119

text: human

text: Homo sapiens

text: single cell Whole Genome Amplification Product

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_DNA_6-sc-2013-10-23T08:41:35Z-1732120

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_DNA_7-sc-2013-10-23T08:41:37Z-1732121

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_DNA_8-sc-2013-10-23T08:41:38Z-1732122

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_DNA_10-sc-2013-10-23T08:41:39Z-1732123

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_DNA_11-sc-2013-10-23T08:41:41Z-1732124

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_DNA_12-sc-2013-10-23T08:41:42Z-1732125

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_DNA_13-sc-2013-10-23T08:41:43Z-1732126

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_DNA_14-sc-2013-10-23T08:41:44Z-1732127

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_DNA_15-sc-2013-10-23T08:41:45Z-1732128

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

text: SC

text: public

text: HCC38_DNA_16-sc-2013-10-23T08:41:47Z-1732129

text: human

text: Homo sapiens

text: Homo sapiens


text: University of California, Riverside

text: public

tag: Namespace:University of California, Riverside

text: ArrayExpress

characteristic: cell line

text: human

text: Protocols: U2OS cells were maintained in McCoys 5A media (Invitrogen) 20 J/m2 UVC irradiation treatment for 0, 8 or 16 hr Formaldehyde Cross-linking and chromatin immunoprecipitation assays for this experiment were performed as described by Boyd and Farnham (MCB 29:8389-8299) and Y. Shang et al. (Cell 103:843-852) with some modifications. Formaldehyde concentration used was 1% for 10 minutes. Antibody used for immunoprecipitation was Rabbit p53 (Santa Cruz FL-393) Purified ChIP DNA was used to prepare Illumina multiplexed sequencing libraries. Libraries for Illumina sequencing were prepared following the Illumina-compatible NEXTflex ChIP-Seq Kit (Bioo Scientific).

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: Mus musculus

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


name: E-MTAB-1990:in vitro human pancreatic progenitor cells (PP2)

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Hospital Clinic de Barcelona

text: public

tag: Namespace:Hospital Clinic de Barcelona

text: ArrayExpress

text: embryonic stem cell

characteristic: cell type

text: human

text: Protocols: The differentiation protocol is described in Cho, C.H. et al. Inhibition of activin/nodal signalling is necessary for pancreatic differentiation of human pluripotent stem cells. Diabetologia 55, 3284-3295 (2012) In vitro human pancreatic progenitor cells were fixed, sonicated and processed for ChIP as described (van Arensbergen, J. et al. Genome Res 20:722, 2010) using 1-1.5ug of the following antibodies: rabbit anti-H3K4me1 (ab-8895), goat anti-Pdx1 (Chris Wright, BCBC AB2027), goat anti-FOXA2 (sc-6554), rabbit anti-GATA6 (sc-9055X), rabbit anti-HNF1B(sc-22840-X), rabbit anti-ONECUT1 (sc-13050). The immunoprecipitated DNA was modified for sequencing following the Illumina sequencing following the manufacturer protocol (Preparing Sample for ChIP Sequencing of DNA (11257047 Rev A)).

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


name: E-MTAB-1990:in vitro human pancreatic progenitor cells (PP3)

text: Hospital Clinic de Barcelona

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


name: E-MTAB-1990:in vitro human pancreatic progenitor cells (PP4)

characteristic: External Id

text: Hospital Clinic de Barcelona

text: public

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: NCMLS

text: public

characteristic: INSDC status

text: DSMZ

characteristic: biomaterial provider

text: Cell Line

characteristic: biomaterial type

text: human

text: JVM-2 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: Mantle Cell Lymphoma

characteristic: disease

characteristic: line

text: RPMI 1640 + 10%FBS

characteristic: medium

text: total RNA

characteristic: molecule

text: Homo sapiens

text: Homo sapiens

text: Female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: NCMLS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: DSMZ

text: Cell Line

text: human

characteristic: common name

text: BL-2 Cell Line

characteristic: description

text: B cell

text: Sporadic Burkitt lymphoma

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

text: total RNA

text: Homo sapiens

text: Homo sapiens

text: Male

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: t(14;18) negative

text: NCMLS

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: DSMZ

characteristic: biomaterial provider

text: Cell Line

characteristic: biomaterial type

text: human

text: SU-DHL-5 Cell Line

text: B cell

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

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

text: total RNA

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Female


E-MTAB-2031:3iL hESCs

text: GIS

text: public

text: E-MTAB-2031:3iL hESCs

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell resembling native pluripotent cell

characteristic: cell type

text: human

text: Protocols: The hESC lines H1 (WA-01, passage 28) 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. hESCs cultured in TeSR1 were treated with 3iL 48hrs 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 is refreshed daily and cells are subcultured upon confluency. For expression analysis, total RNA from the cells was extracted using the TRIzol reagent (Invitrogen). Total RNA was extracted with chloroform and precipitated with isopropanol. The precipitated RNA was centrifuged at 13000rpm at 4 degrees C for 10mins. The RNA pellet was washed with 70% ethanol and subsequently reconstituted with DEPC-treated water (AMBION). DNA contaminants were digested with DNASE I (Ambion) at 37 degrees C for 30 min. The total RNA was further purified by column (Purelink RNA Mini kit, Ambion). RNA-Seq libraries were prepared using 4 ug of total RNA according to the manufacturer (TruSeq RNA Sample Preparation Kit v2, Illumina). Briefly, mRNA was obtained using two rounds of purification with poly-T oligo-attached magnetic beads. The mRNA was then fragmented and subjected to the first strand and second strand cDNA synthesis, then end-repaired, adenylated, adaptor ligated and finally subjected to 15 cycles of PCR.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

characteristic: sex

text: 3iL hESCs


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: GIS

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

text: hESCs