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characteristic: latitude

characteristic: longitude

text: gut metagenome

text: Purdue

text: True

text: Singapore Zoo

characteristic: provenance

text: True

characteristic: public

text: completed

text: feces

characteristic: sample type

text: sequenced (16S)

text: gut metagenome

text: gut metagenome

text: male

characteristic: sex

characteristic: year of birth


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: False

text: UBERON:feces

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:feces

characteristic: body site

text: 5/1/12 0:00

text: gut metagenome

characteristic: common name

text: GAZ:Singapore

characteristic: country

characteristic: depth

text: Javan Langur feces

characteristic: description

text: herbivore

characteristic: diet

text: True

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

text: feces

text: host-associated

text: True

text: FTA

text: China

text: Javan Langur

text: Trachypithecus auratus

text: gut metagenome

characteristic: organism

text: Purdue

text: True

text: Singapore Zoo

text: True

text: completed

text: feces

text: sequenced (16S)

text: gut metagenome

text: gut metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: years

text: False

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: 5/1/12 0:00

text: gut metagenome

text: GAZ:Singapore

text: Eastern Black and White Colubus feces

text: herbivore

text: True

text: urban biome

text: animal-associated habitat

characteristic: env feature

text: feces

characteristic: env matter

text: host-associated

characteristic: env package

text: True

characteristic: extracted DNA avail now

text: FTA

text: China

characteristic: geo loc name

text: Eastern Black and White Colubus

characteristic: host common name

text: Colobus Guereza

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: gut metagenome

text: Purdue

text: True

text: Singapore Zoo

characteristic: provenance

text: True

characteristic: public

text: completed

text: feces

characteristic: sample type

text: sequenced (16S)

text: gut metagenome

text: gut metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: False

text: UBERON:feces

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:feces

characteristic: body site

text: 5/1/12 0:00

text: gut metagenome

characteristic: common name

text: GAZ:Singapore

characteristic: country

characteristic: depth

text: Red shanked Douc Langur feces

characteristic: description

text: herbivore

characteristic: diet

text: True

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

text: feces

text: host-associated

text: True

text: FTA

text: China

text: Red shanked Douc Langur

text: Pygathrix nemaeus nemaeus

text: gut metagenome

characteristic: organism

text: Purdue

text: True

text: Singapore Zoo

text: True

text: completed

text: feces

text: sequenced (16S)

text: gut metagenome

text: gut metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: years

text: False

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: 11/2/12 0:00

text: gut metagenome

text: GAZ:United States of America

text: Spider monkey feces

text: herbivore

text: fruits, vegatables, primate biscuits

text: True

text: urban biome

text: animal-associated habitat

characteristic: env feature

text: feces

characteristic: env matter

text: host-associated

characteristic: env package

text: True

characteristic: extracted DNA avail now

text: freeze

text: China

characteristic: geo loc name

text: Spider monkey

characteristic: host common name

text: Ateles geoffroyi

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: gut metagenome

text: Purdue

text: True

text: Columbian Park Zoo

characteristic: provenance

text: True

characteristic: public

text: completed

text: feces

characteristic: sample type

text: sequenced (16S)

text: gut metagenome

text: gut metagenome

text: sun


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: False

text: UBERON:feces

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:feces

characteristic: body site

text: 11/2/12 0:00

text: gut metagenome

characteristic: common name

text: GAZ:United States of America

characteristic: country

characteristic: depth

text: Spider monkey feces

characteristic: description

text: herbivore

characteristic: diet

text: fruits, vegatables, primate biscuits

text: True

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

text: feces

text: host-associated

text: True

text: freeze

text: China

text: Spider monkey

text: Ateles geoffroyi

text: gut metagenome

characteristic: organism

text: Purdue

text: True

text: Columbian Park Zoo

text: True

text: completed

text: feces

text: sequenced (16S)

text: gut metagenome

text: gut metagenome

text: sun

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: years

text: False

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: 11/3/12 0:00

text: gut metagenome

text: GAZ:United States of America

text: Spider monkey feces

text: herbivore

text: fruits, vegatables, primate biscuits

text: True

text: urban biome

text: animal-associated habitat

characteristic: env feature

text: feces

characteristic: env matter

text: host-associated

characteristic: env package

text: True

characteristic: extracted DNA avail now

text: freeze

text: China

characteristic: geo loc name

text: Spider monkey

characteristic: host common name

text: Ateles geoffroyi

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: gut metagenome

text: Purdue

text: True

text: Columbian Park Zoo

characteristic: provenance

text: True

characteristic: public

text: completed

text: feces

characteristic: sample type

text: sequenced (16S)

text: gut metagenome

text: gut metagenome

text: sun


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: False

text: UBERON:feces

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:feces

characteristic: body site

text: 11/2/12 0:00

text: gut metagenome

characteristic: common name

text: GAZ:United States of America

characteristic: country

characteristic: depth

text: Spider monkey feces

characteristic: description

text: herbivore

characteristic: diet

text: fruits, vegatables, primate biscuits

text: True

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

text: feces

text: host-associated

text: True

text: freeze

text: China

text: Spider monkey

text: Ateles geoffroyi

text: gut metagenome

characteristic: organism

text: Purdue

text: True

text: Columbian Park Zoo

text: True

text: completed

text: feces

text: sequenced (16S)

text: gut metagenome

text: gut metagenome

text: shade

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: years

text: False

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: 11/2/12 0:00

text: gut metagenome

text: GAZ:United States of America

text: Spider monkey feces

text: herbivore

text: fruits, vegatables, primate biscuits

text: True

text: urban biome

text: animal-associated habitat

characteristic: env feature

text: feces

characteristic: env matter

text: host-associated

characteristic: env package

text: True

characteristic: extracted DNA avail now

text: freeze

text: China

characteristic: geo loc name

text: Spider monkey

characteristic: host common name

text: Ateles geoffroyi

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: gut metagenome

text: Purdue

text: True

text: Columbian Park Zoo

characteristic: provenance

text: True

characteristic: public

text: completed

text: feces

characteristic: sample type

text: sequenced (16S)

text: gut metagenome

text: gut metagenome

text: shade


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: False

text: UBERON:feces

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:feces

characteristic: body site

text: 11/3/12 0:00

text: gut metagenome

characteristic: common name

text: GAZ:United States of America

characteristic: country

characteristic: depth

text: Spider monkey feces

characteristic: description

text: herbivore

characteristic: diet

text: fruits, vegatables, primate biscuits

text: True

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

text: feces

text: host-associated

text: True

text: freeze

text: China

text: Spider monkey

text: Ateles geoffroyi

text: gut metagenome

characteristic: organism

text: Purdue

text: True

text: Columbian Park Zoo

text: True

text: completed

text: feces

text: sequenced (16S)

text: gut metagenome

text: gut metagenome

text: shade

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: years

text: False

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: 11/3/12 0:00

text: gut metagenome

text: GAZ:United States of America

text: Spider monkey feces

text: herbivore

text: fruits, vegatables, primate biscuits

text: True

text: urban biome

text: animal-associated habitat

characteristic: env feature

text: feces

characteristic: env matter

text: host-associated

characteristic: env package

text: True

characteristic: extracted DNA avail now

text: freeze

text: China

characteristic: geo loc name

text: Spider monkey

characteristic: host common name

text: Ateles geoffroyi

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: gut metagenome

text: Purdue

text: True

text: Columbian Park Zoo

characteristic: provenance

text: True

characteristic: public

text: completed

text: feces

characteristic: sample type

text: sequenced (16S)

text: gut metagenome

text: gut metagenome

text: shade


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UDEC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: Flavobacterium psychrophilum

characteristic: organism

text: Flavobacterium psychrophilum

characteristic: strain

text: Planktonic NCMB1947

characteristic: title


text: UDEC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Flavobacterium psychrophilum

text: Flavobacterium psychrophilum

text: Planktonic LM02FP


text: UDEC

text: public

text: Flavobacterium psychrophilum

text: Flavobacterium psychrophilum

text: Biofilm NCIMB1947


text: UDEC

text: public

text: Flavobacterium psychrophilum

text: Flavobacterium psychrophilum

text: Biofilm LM02FP


text: CEES

text: public

text: Atlantic cod

characteristic: common name

text: Gadus morhua

text: Gadus morhua

text: Atlantic cod sex-locus

type: has member


text: INSTITUT DE GENETIQUE ET MICROBIOLOGIE

text: public

tag: Namespace:INSTITUT DE GENETIQUE ET MICROBIOLOGIE

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: sequencing reads for phage P3P1


text: INSTITUT DE GENETIQUE ET MICROBIOLOGIE

text: public

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: sequencing reads for phage PII10A


text: Middle east technical university

text: public

tag: Namespace:Middle east technical university

text: human

text: Homo sapiens

text: Homo sapiens

text: METUADNA


text: IVF-CAAS-China

text: public

text: Bemisia tabaci

text: Bemisia tabaci

text: antennal

characteristic: tissue type

text: BTA


text: Escherichia coli

characteristic: ArrayExpress-Species

text: SC

text: public

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli


text: EMBL

text: public

text: ArrayExpress

characteristic: broker name

text: 46c ES

characteristic: cell line

text: house mouse

text: Protocols: 46c mouse ES cells were grown feeder-free on 0.2% gelatinized cell culture plates in 2i-media. The 2i-media contained DMEM/F12 media for SILAC (Pierce, 88215) supplemented 100 mg/ml of Lysine (Sigma, L8662), 100 mg/ml of Arginine (Sigma, A6969) and 100 mg/ml of Proline (Sigma, P5607), 100 microM MEM non-essential amino acids (Life technologies, 11140-050), 1xGlutamax (Life technologies, 35050-061), 1x penicillin and streptomycin (Life technologies, 15140-122), 100 microM of 2-mercaptoethanol (Sigma, M7522), 0.5mg/ml of BSA (Sigma, A3059), 200ng/ml of LIF (EMBL, protein expression core facility), 1microM of PD0325901(Reagents Direct, 39-C68), 3 microM of CHIR99021 (Reagents Direct, 27-H76). The cells were cultured using the 2i-media at least for 10 days, and passaged 4 times. The knock down (KD) was carried out by lentiviral transduction of : non-targeting shRNA, shTrim24 (TRCN0000088518), shTrp53 (TRCN0000310844), and the mixture of the last two shRNAs. For each knock down, 3 independent transductions was perfomed. For the details of virus production and infection please refer to PMID: 23260666. 48 hours after the viral treatment of the mouse ES cells, the cells were lysed, and RNA was extracted to be analyzed by qPCR and mRNA-seq RNA was extracted by Qiagen kit (RNeasy mini kit) mRNA-Seq libraries (from polyA+ cytoplasmic RNA) were created according to the standard Illumina TruSeq protocol.

characteristic: description

text: transfection

characteristic: genetic modification

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC center name

text: public

text: ArrayExpress

text: 46c ES

text: house mouse

text: transfection

text: Trim24/Trp53 Knock Down

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: EMBL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: ArrayExpress

text: 46c ES

text: house mouse

text: transfection

text: Trim24 Knock Down

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus


text: EMBL

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: 46c ES

text: house mouse

characteristic: common name

text: transfection

text: Trp53 Knock Down

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title


text: UNIVERSITY OF HELSINKI

text: public

tag: Namespace:UNIVERSITY OF HELSINKI

characteristic: collection date

text: second hand

text: human

characteristic: environment (biome)

text: skin

characteristic: environment (feature)

text: skin

characteristic: environment (material)

text: Finland

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-skin

characteristic: human skin environmental package

text: mimarks-survey

characteristic: investigation type

text: human skin metagenome

text: Human skin microbiome

characteristic: project name

text: human skin metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Human skin microbiome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: DTU2016-1569-PRJ1066-RD-Sewage-94_S10_L001

tag: Namespace:Centre for Genomic Epidemiology, National Food Institute, Technical University of Denmark (DTU), Denmark

characteristic: Submitter Id

text: DTU-GE

characteristic: broker name

text: Denmark

text: metagenome

text: Renseanlæg Damhusåen

characteristic: name of the sampling site

text: wastewater metagenome

text: wastewater metagenome

text: Waste water treament plant

characteristic: sewage type

text: Danish sewage


text: Centre for Genomic Epidemiology, National Food Institute, Technical University of Denmark (DTU), Denmark

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DTU2016-1570-PRJ1066-RL-Sewage-95_S11_L001

text: DTU-GE

characteristic: collection date

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome

text: Renseanlæg Lynetten

text: wastewater metagenome

characteristic: organism

text: wastewater metagenome

text: Waste water treament plant

text: Danish sewage

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: DTU2016-1571-PRJ1066-RD-Sewage-96_S12_L001

text: DTU-GE

text: Denmark

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Renseanlæg Damhusåen

text: wastewater metagenome

text: wastewater metagenome

text: Waste water treament plant

text: Danish sewage


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: DTU2016-1578-PRJ1066-RD-Sewage-103_S19_L001

text: DTU-GE

text: Denmark

text: metagenome

text: Renseanlæg Damhusåen

text: wastewater metagenome

text: wastewater metagenome

text: Waste water treament plant

text: Danish sewage


text: Max Rubner-Institut

characteristic: INSDC last update

text: public

tag: Namespace:Max Rubner-Institut

characteristic: Submitter Id

text: Klebsiella phage PMBT1

text: Klebsiella phage PMBT1


text: CEBITEC

text: public

characteristic: INSDC status

text: Draft genome sequence of Xanthomonas translucens pv. graminis ART-Xtg29

characteristic: description

text: grass

characteristic: environment (biome)

text: grass

characteristic: environment (feature)

text: grass

characteristic: environment (material)

text: Switzerland

text: mimarks-survey

characteristic: isolate

text: plant-associated

characteristic: plant-associated environmental package

characteristic: project name

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: ABERSYTWYTH UNIVERSITY

text: public

characteristic: SRA accession

tag: Namespace:ABERSYTWYTH UNIVERSITY

characteristic: collection date

unit: m

characteristic: depth

text: sediment

text: cave sediment

text: granular sediment

text: Portugal

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: cave metagenome

characteristic: organism

text: Labirinto Cave Metagenomes

text: cave metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina

characteristic: title


E-MTAB-4879:Sample 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-4879:Sample 1

tag: Namespace:Musculoskeletal Biology, Institute of Ageing and Chronic Disaese, Leahurst, Chester High Road, Neston, Wirral, CH647TE

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: osteocyte

characteristic: cell type

text: human

characteristic: common name

text: Protocols: MScs purchased from young and old human donors miRNAeasy kit for RNA extraction Total RNA samples were ribosomal RNA depleted using the Human, mouse, rat low inputRibozero kit from Epicentre. 1ug of RNA (or the max amount available) was mixed with the low input kit baits and allowed to anneal. This was then mixed with the magnetic microspheres which bind the ribosomal complexes and subsequently pulled out with a magnet. The remaining RNA was purified with RNA clean beads and analysed with the Agilent Bioanalyser with a RNA pico chip. Recovery was generally less than 1% of the original starting material. All of this material was used in the script seq reaction (Epicentre). Samples were denatured and annealed to cDNA primers and cDNA was generated. This was amplified with indexed primers for 15 cycles to make the library for sequencing. Libraries were checked on the Agilent Bioanalyser with a High sensitivity chip and quantities determined with Qubit DNA High sensitivity reagents.

characteristic: description

text: young adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 1


E-MTAB-4879:Sample 10

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Musculoskeletal Biology, Institute of Ageing and Chronic Disaese, Leahurst, Chester High Road, Neston, Wirral, CH647TE

text: public

characteristic: SRA accession

text: E-MTAB-4879:Sample 10

text: ArrayExpress

text: chondrocyte

text: human

text: young adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 10


E-MTAB-4879:Sample 11

text: public

text: E-MTAB-4879:Sample 11

text: ArrayExpress

text: chondrocyte

text: human

text: young adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Sample 11


E-MTAB-4879:Sample 13

text: public

text: E-MTAB-4879:Sample 13

text: ArrayExpress

text: chondrocyte

text: human

text: old adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 13

characteristic: title


E-MTAB-4879:Sample 14

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-4879:Sample 14

text: ArrayExpress

text: chondrocyte

text: human

text: old adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 14


E-MTAB-4879:Sample 16

characteristic: External Id

text: public

text: E-MTAB-4879:Sample 16

text: ArrayExpress

text: chondrocyte

text: human

text: old adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 16


E-MTAB-4879:Sample 17

characteristic: INSDC center name

text: public

text: E-MTAB-4879:Sample 17

text: ArrayExpress

text: tenocyte

text: human

text: young adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 17


E-MTAB-4879:Sample 18

characteristic: INSDC first public

text: public

text: E-MTAB-4879:Sample 18

text: ArrayExpress

text: tenocyte

text: human

text: young adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 18


E-MTAB-4879:Sample 19

characteristic: INSDC last update

text: public

text: E-MTAB-4879:Sample 19

text: ArrayExpress

text: tenocyte

text: human

text: young adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 19


E-MTAB-4879:Sample 2

text: public

characteristic: INSDC status

text: E-MTAB-4879:Sample 2

text: ArrayExpress

text: osteocyte

text: human

text: young adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 2


E-MTAB-4879:Sample 20

text: public

text: E-MTAB-4879:Sample 20

characteristic: Submitter Id

text: ArrayExpress

text: tenocyte

text: human

text: young adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 20


E-MTAB-4879:Sample 21

text: public

text: E-MTAB-4879:Sample 21

text: ArrayExpress

characteristic: broker name

text: tenocyte

text: human

text: old adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 21


E-MTAB-4879:Sample 22

text: public

text: E-MTAB-4879:Sample 22

text: ArrayExpress

text: tenocyte

characteristic: cell type

text: human

text: old adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 22


E-MTAB-4879:Sample 23

text: public

text: E-MTAB-4879:Sample 23

text: ArrayExpress

text: tenocyte

text: human

characteristic: common name

text: old adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 23


E-MTAB-4879:Sample 24

text: public

text: E-MTAB-4879:Sample 24

text: ArrayExpress

text: tenocyte

text: human

characteristic: description

text: old adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 24


E-MTAB-4879:Sample 25

text: public

text: E-MTAB-4879:Sample 25

text: ArrayExpress

text: mesenchymal stem cell

text: human

text: young adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 25


E-MTAB-4879:Sample 26

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-4879:Sample 26

text: ArrayExpress

text: mesenchymal stem cell

text: human

text: young adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 26


E-MTAB-4879:Sample 27

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-4879:Sample 27

text: ArrayExpress

text: mesenchymal stem cell

text: human

text: young adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 27


E-MTAB-4879:Sample 28

text: public

characteristic: SRA accession

text: E-MTAB-4879:Sample 28

text: ArrayExpress

text: mesenchymal stem cell

text: human

text: young adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 28


E-MTAB-4879:Sample 29

text: public

text: E-MTAB-4879:Sample 29

text: ArrayExpress

text: mesenchymal stem cell

text: human

text: old adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Sample 29


E-MTAB-4879:Sample 3

text: public

text: E-MTAB-4879:Sample 3

text: ArrayExpress

text: osteocyte

text: human

text: young adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 3

characteristic: title


E-MTAB-4879:Sample 30

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-4879:Sample 30

text: ArrayExpress

text: mesenchymal stem cell

text: human

text: old adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 30


E-MTAB-4879:Sample 31

characteristic: External Id

text: public

text: E-MTAB-4879:Sample 31

text: ArrayExpress

text: mesenchymal stem cell

text: human

text: old adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 31


E-MTAB-4879:Sample 32

characteristic: INSDC center name

text: public

text: E-MTAB-4879:Sample 32

text: ArrayExpress

text: mesenchymal stem cell

text: human

text: old adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 32


E-MTAB-4879:Sample 4

characteristic: INSDC first public

text: public

text: E-MTAB-4879:Sample 4

text: ArrayExpress

text: osteocyte

text: human

text: young adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 4


E-MTAB-4879:Sample 5

characteristic: INSDC last update

text: public

text: E-MTAB-4879:Sample 5

text: ArrayExpress

text: osteocyte

text: human

text: old adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 5


E-MTAB-4879:Sample 6

text: public

characteristic: INSDC status

text: E-MTAB-4879:Sample 6

text: ArrayExpress

text: osteocyte

text: human

text: old adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 6


E-MTAB-4879:Sample 7

text: public

text: E-MTAB-4879:Sample 7

characteristic: Submitter Id

text: ArrayExpress

text: osteocyte

text: human

text: old adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 7


E-MTAB-4879:Sample 8

text: public

text: E-MTAB-4879:Sample 8

text: ArrayExpress

characteristic: broker name

text: osteocyte

text: human

text: old adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 8


E-MTAB-4879:Sample 9

text: public

text: E-MTAB-4879:Sample 9

text: ArrayExpress

text: chondrocyte

characteristic: cell type

text: human

text: young adult

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 9


text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1HW8ACXX_13s002413_Pekowska_lane713s002413_ESC1

tag: Namespace:EMBL Heidelberg

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: common name

text: Protocols: Buffers for the procedure, Lysis buffer: 10 mM HEPES pH=8, 10 mM NaCl, 0.2percent NP-40, Wash buffer: 50 mM Tris-HCl pH = 8, 50 mM NaCl, 1 mM EDTA, EZ-Link Iodoacetyl PEG2 Biotin resuspension buffer - EZ RB: 50 mM Tris-HCl, 5 mM EDTA, pH = 8 - 8.3, Dialysis buffer: 10 mM Tris HCl pH = 8, 1 mM EDTA, PBST: PBS, 0.01 percent of Tween, Beads wash buffer 10 mM Tris-HCl pH = 8, 50 mM NaCl, 0.4 percent Triton X-100, Klenow Wash Buffer: 50 mM Tris-HCl pH = 7.4, 0.4 percent Triton X-100, 0.1 mM EDTA, DNA extraction buffer: 50 mM Tris-HCl pH = 8, 0.2 percent SDS, 1 mM EDTA, 100 mM NaCl, DNA resuspension solution: 10 mM Tris-HCl pH = 8, Bind and Wash Buffer: 2x : 10 mM Tris-HCl pH = 7.5, 1mM EDTA, 2 M NaCl, Cell crossling protocol: Put 100 million cell pellet in 45 ml of fresh medium and add 1.25 ml of 37 percent formaldehyde, Incubate 10 min at RT, Add 2.5 ml of 2.5M glycine , Incubate 5 min at RT, Incubate 15 min on ice, Divide the cell mixture into 4 equal parts, Centrifuge at 1500 rpm for 5 min. at 4 degrees and store the pellets if needed. To start the TCC procedure, Lyse the cells in 550 ul lysis buffer completed with PIC using a homogenizer , Incubate on ice at least 15 minutes , Lyse the cells using the Dounce homogenizer by moving the pestile A up and down 10 times, Incubate on ice for 1 minutes , Apply 10 more strokes of the pestile, Transfer the sample to 2ml tube, Wash the cells twice with the wash buffer, spin conditions: 2500g for 5 minutes, V = 250 ul, Re suspend the cell pellet in 250 ul of wash buffer, Add 95 ul of 2percent SDS and incubate at 65 degreeC for 10 min, Prepare the EZ link Iodoacetyl-PEG2-Biotin For two reactions, Equilibrate the powder to RT to reduce humidification of the reagen, take 3 mg of the EZ link Iodoacetyl-PEG2-Biotin and re suspend in 220 ul of EZ RB in an amber tube, Cool the chromatin suspension to RT, Mix the suspension with 105ul of 25 mM EZlink Iodoacetyl-PEG2-Biotin (IPB), Rock at the room temperature for 1 hour, protect from light, Mix the chromatin with 1300 ul of 1x NEB Buffer 2, Incubate on ice for 5 minutes, Mix the sample with 225 ul of 10 percent triton X-100, Incubate on ice for 10 min , Incubate at 37degree C for 10 minutes, Now the sample is ready to be digested to this end, add, 100 ul of 10x NEB buffer 2, 350 ul of water, 5 ul of 1M DTT, 20 ul of HindIIII (100U/ul), dispose the sample to two tubes and incubate the digestion reaction OVN at 37 degreeC with overhead shaking.Place the mixture in a 20 kD cutoff Slide-A-Lyser Cassette, dialyse it against 1L of dialysis buffer for 3 hours, Renew the buffer and dialyze for an additional hour, Transfer the dialyzed sample (ca 2.5 ml) to a 15 ml falcon tube, During the last step, prepare the T1 beads. Take 400 ul of beads per chromatin sample, Wash the beads 3 times with PBST, Re suspend the beads in 2 ml of PBST, Divide the chromatin after dialysis into 5 equal parts, put them into 1.5 ml eppendorf tubes and add 400 ul of the above-mentioned bead suspension to these 5 aliquots of chromatin, Rock the chromatin with beads at RT for 30 minutes, During this time prepare the neutralized IPB solution - nIPB, take 0.750 mg IPB and add 52.5 ul of the resuspension buffer , add 7.75 mili-mols of bME - 9 ul of bME stock (14.3 Molar solution), Mix each aliquot of chromatin with 5 ul of nIPB, Incubate with rotation for 15 minutes at RT, Wash the beads once with 600 ul of TPBS, Wash the beads with 600 ul of Beads Wash Buffer, Re-suspend the beads in 100 ul of Beads Wash Buffer, add 69 ul of water, 1.1 ul of 1M MgCl2, 11 ul of 10x NEB buffer 2, 0.77 ul of 10 uM dATP, 0.77 ul of 10 uM dTTP, 0.77ul of 10 uM dGTPαS, 16.5 ul 0.4 mM Biotin-14-dCTP, 4.4 ul of 10 percent Triton-X100, 5 ul of 5U/ul Klenow. Fill in the overhangs by 40 minute rocking incubation at RT with 100 ul of the above-mentioned mix, After the incubation with Klenow add 5ul of 0.5 M EDTA to the suspension, Wash the beads twice with 600 ul of Klenow Wash Buffer, Re-suspend the beads in 500 ul of Klenow wash buffer and transfer them all in a new 50 ml falcon tube (V = 2.5 ml), Prepare the ligation mix (0.275 ul 10X NEB T4 Ligase buffer, 4.3 ml water, 198 ul 10percent triton X-100, 110 ul 1 M Tris-Hcl, pH=7.4, 55ul 10mg/ml BSA, 2ul Qucik Ligase NEB), Rock the mix for 4 hours at 16 degreeC , Stop the ligation by adding 200 ul of 0.5 M EDTA, Place the bead suspension on the magnet and aspirate the supernatant, Reverse the crosslinks: resuspend the beads in 400 ul of an extraction buffer, Add 20 ul of 20 mg/ml proteinase K, Incubate at 65 degreeC OVN , Add 5 ul of 20 mg/ml proteinase K, Incubate for 2 additional hours at 65 degreeC, Transfer the supernatant to a new tube and extract the DNA twice with, phenol : chloroform : isoamyl alcohol, Once with an equal volume of chloroform, Mix the resulting aqueous phase with , NaCl (final concentration: 200 mM), Glycogen (final concentration: 25 ug/ul), Add 900 ul of 98 percent ethanol, Incubate at -20 ovn or at -80 for 1 hour, Centrifuge for 20 minutes at 4 degreeC at max speed, Wash the pellet with 80 percent ethanol, Resuspend the pellet in 20 ul of DNA resuspension solution and pull the 5 samples, Mix the solution with 1 ul of RNase A and incubate for 30 minutes at 37 degreeC Isolate the DNA by phenol chloroform isolation and ethnol precipitation Resuspend the pellet in water. ExoIII treatment: take 5 ug of the purified DNA and resuspend it in a total volume of 90 ul of 1x NEB buffer 1 Add 300 U of ExoIII, Incubate for 1 hour at 37 degreeC, Stop the reaction by adding 2 ul of 0.5 M EDTA and 2 ul of 5 M NaCl, Incubate the reaction at 70 degreeC for 20 minutes, Add water to 100 ul and shear on Covaris S2 apparatus to an average size of 100-400 bp:, duty cycle: 5percent, intensity: 5, cycles/burst: 200, time: 180 seconds, Purify the DNA by Ampure bead solution, elute in 90 ul of water, End repair the sample for 30 minutes at 20 degrees: add 10 ul of 10x T4 ligase buffer supplemented with ATP and DTT, add 1.6 ul of 25 mM dNTP mix, 5 U of Klenow - 1ul, 15 U T4 polymerase - 5 ul, 50 U of PNK - 5ul, Purify the DNA by Quiaquick/Ampure beads, elute in 44 ul of water Add the A-overhangs incubate for 30 minutes at 37 degrees with :, add 5 ul of water, 5 ul of 10x NEB Buffer 2, 1 ul of 10 mM dATP solution , 3 ul of exo-Klenow, Stop the reaction by adding 1 ul of 0.5 EDTA, Wash 50 ul of MyOne Streptavidin C1 beads twice with 500 ul of 1x Wash and Bind buffer in DNA Lo-Bind tubes, Re suspend the beads in 50 ul of 2x, Wash and bind buffer, Mix the beads with the A-added DNA sample and rock the mixture for 30 min at RT, After the incubation, wash the beads once with 500 ul of supplemented bind Wash buffer., Wash the beads once in DNA resuspension solution, Now we would like to add sequencing adapters to this end re-suspend the beads in the following mix: 50 ul 2x rapid ligation mix, 3 ul of sequencing adapters (5uM), 47 ul of water, add 1 ul of rapid ligase, incubate at RT with mixing for 20 minutes, Stop the reaction by adding 6 ul of 0.5 M EDTA/100 ul of ligation mix, Wash the beads twice with 1x Bind and wash buffer, Wash the beads once with TE, Resuspend the beads in 30 ul of water Perform the PCR amplification and size excision. Prepare Phusion mix: 0.5 ul of primer, 5 ul of beads, 25 ul of Phusion MM, 19.5 ul of water. Buffers for the procedure, Lysis buffer: 10 mM HEPES pH=8, 10 mM NaCl, 0.2percent NP-40, Wash buffer: 50 mM Tris-HCl pH = 8, 50 mM NaCl, 1 mM EDTA, EZ-Link Iodoacetyl PEG2 Biotin resuspension buffer - EZ RB: 50 mM Tris-HCl, 5 mM EDTA, pH = 8 - 8.3, Dialysis buffer: 10 mM Tris HCl pH = 8, 1 mM EDTA, PBST: PBS, 0.01 percent of Tween, Beads wash buffer 10 mM Tris-HCl pH = 8, 50 mM NaCl, 0.4 percent Triton X-100, Klenow Wash Buffer: 50 mM Tris-HCl pH = 7.4, 0.4 percent Triton X-100, 0.1 mM EDTA, DNA extraction buffer: 50 mM Tris-HCl pH = 8, 0.2 percent SDS, 1 mM EDTA, 100 mM NaCl, DNA resuspension solution: 10 mM Tris-HCl pH = 8, Bind and Wash Buffer: 2x : 10 mM Tris-HCl pH = 7.5, 1mM EDTA, 2 M NaCl, Cell crossling protocol: Put 100 million cell pellet in 45 ml of fresh medium and add 1.25 ml of 37 percent formaldehyde, Incubate 10 min at RT, Add 2.5 ml of 2.5M glycine , Incubate 5 min at RT, Incubate 15 min on ice, Divide the cell mixture into 4 equal parts, Centrifuge at 1500 rpm for 5 min. at 4 degrees and store the pellets if needed. To start the TCC procedure, Lyse the cells in 550 ul lysis buffer completed with PIC using a homogenizer , Incubate on ice at least 15 minutes , Lyse the cells using the Dounce homogenizer by moving the pestile A up and down 10 times, Incubate on ice for 1 minutes , Apply 10 more strokes of the pestile, Transfer the sample to 2ml tube, Wash the cells twice with the wash buffer, spin conditions: 2500g for 5 minutes, V = 250 ul, Re suspend the cell pellet in 250 ul of wash buffer, Add 95 ul of 2percent SDS and incubate at 65 degreeC for 10 min, Prepare the EZ link Iodoacetyl-PEG2-Biotin For two reactions, Equilibrate the powder to RT to reduce humidification of the reagen, take 3 mg of the EZ link Iodoacetyl-PEG2-Biotin and re suspend in 220 ul of EZ RB in an amber tube, Cool the chromatin suspension to RT, Mix the suspension with 105ul of 25 mM EZlink Iodoacetyl-PEG2-Biotin (IPB), Rock at the room temperature for 1 hour, protect from light, Mix the chromatin with 1300 ul of 1x NEB Buffer 2, Incubate on ice for 5 minutes, Mix the sample with 225 ul of 10 percent triton X-100, Incubate on ice for 10 min , Incubate at 37degree C for 10 minutes, Now the sample is ready to be digested to this end, add, 100 ul of 10x NEB buffer 2, 350 ul of water, 5 ul of 1M DTT, 20 ul of HindIIII (100U/ul), dispose the sample to two tubes and incubate the digestion reaction OVN at 37 degreeC with overhead shaking.Place the mixture in a 20 kD cutoff Slide-A-Lyser Cassette, dialyse it against 1L of dialysis buffer for 3 hours, Renew the buffer and dialyze for an additional hour, Transfer the dialyzed sample (ca 2.5 ml) to a 15 ml falcon tube, During the last step, prepare the T1 beads. Take 400 ul of beads per chromatin sample, Wash the beads 3 times with PBST, Re suspend the beads in 2 ml of PBST, Divide the chromatin after dialysis into 5 equal parts, put them into 1.5 ml eppendorf tubes and add 400 ul of the above-mentioned bead suspension to these 5 aliquots of chromatin, Rock the chromatin with beads at RT for 30 minutes, During this time prepare the neutralized IPB solution - nIPB, take 0.750 mg IPB and add 52.5 ul of the resuspension buffer , add 7.75 mili-mols of bME - 9 ul of bME stock (14.3 Molar solution), Mix each aliquot of chromatin with 5 ul of nIPB, Incubate with rotation for 15 minutes at RT, Wash the beads once with 600 ul of TPBS, Wash the beads with 600 ul of Beads Wash Buffer, Re-suspend the beads in 100 ul of Beads Wash Buffer, add 69 ul of water, 1.1 ul of 1M MgCl2, 11 ul of 10x NEB buffer 2, 0.77 ul of 10 uM dATP, 0.77 ul of 10 uM dTTP, 0.77ul of 10 uM dGTPαS, 16.5 ul 0.4 mM Biotin-14-dCTP, 4.4 ul of 10 percent Triton-X100, 5 ul of 5U/ul Klenow. Fill in the overhangs by 40 minute rocking incubation at RT with 100 ul of the above-mentioned mix, After the incubation with Klenow add 5ul of 0.5 M EDTA to the suspension, Wash the beads twice with 600 ul of Klenow Wash Buffer, Re-suspend the beads in 500 ul of Klenow wash buffer and transfer them all in a new 50 ml falcon tube (V = 2.5 ml), Prepare the ligation mix (0.275 ul 10X NEB T4 Ligase buffer, 4.3 ml water, 198 ul 10percent triton X-100, 110 ul 1 M Tris-Hcl, pH=7.4, 55ul 10mg/ml BSA, 2ul Qucik Ligase NEB), Rock the mix for 4 hours at 16 degreeC , Stop the ligation by adding 200 ul of 0.5 M EDTA, Place the bead suspension on the magnet and aspirate the supernatant, Reverse the crosslinks: resuspend the beads in 400 ul of an extraction buffer, Add 20 ul of 20 mg/ml proteinase K, Incubate at 65 degreeC OVN , Add 5 ul of 20 mg/ml proteinase K, Incubate for 2 additional hours at 65 degreeC, Transfer the supernatant to a new tube and extract the DNA twice with, phenol : chloroform : isoamyl alcohol, Once with an equal volume of chloroform, Mix the resulting aqueous phase with , NaCl (final concentration: 200 mM), Glycogen (final concentration: 25 ug/ul), Add 900 ul of 98 percent ethanol, Incubate at -20 ovn or at -80 for 1 hour, Centrifuge for 20 minutes at 4 degreeC at max speed, Wash the pellet with 80 percent ethanol, Resuspend the pellet in 20 ul of DNA resuspension solution and pull the 5 samples, Mix the solution with 1 ul of RNase A and incubate for 30 minutes at 37 degreeC Isolate the DNA by phenol chloroform isolation and ethnol precipitation Resuspend the pellet in water. ExoIII treatment: take 5 ug of the purified DNA and resuspend it in a total volume of 90 ul of 1x NEB buffer 1 Add 300 U of ExoIII, Incubate for 1 hour at 37 degreeC, Stop the reaction by adding 2 ul of 0.5 M EDTA and 2 ul of 5 M NaCl, Incubate the reaction at 70 degreeC for 20 minutes, Add water to 100 ul and shear on Covaris S2 apparatus to an average size of 100-400 bp:, duty cycle: 5percent, intensity: 5, cycles/burst: 200, time: 180 seconds, Purify the DNA by Ampure bead solution, elute in 90 ul of water, End repair the sample for 30 minutes at 20 degrees: add 10 ul of 10x T4 ligase buffer supplemented with ATP and DTT, add 1.6 ul of 25 mM dNTP mix, 5 U of Klenow - 1ul, 15 U T4 polymerase - 5 ul, 50 U of PNK - 5ul, Purify the DNA by Quiaquick/Ampure beads, elute in 44 ul of water Add the A-overhangs incubate for 30 minutes at 37 degrees with :, add 5 ul of water, 5 ul of 10x NEB Buffer 2, 1 ul of 10 mM dATP solution , 3 ul of exo-Klenow, Stop the reaction by adding 1 ul of 0.5 EDTA, Wash 50 ul of MyOne Streptavidin C1 beads twice with 500 ul of 1x Wash and Bind buffer in DNA Lo-Bind tubes, Re suspend the beads in 50 ul of 2x, Wash and bind buffer, Mix the beads with the A-added DNA sample and rock the mixture for 30 min at RT, After the incubation, wash the beads once with 500 ul of supplemented bind Wash buffer., Wash the beads once in DNA resuspension solution, Now we would like to add sequencing adapters to this end re-suspend the beads in the following mix: 50 ul 2x rapid ligation mix, 3 ul of sequencing adapters (5uM), 47 ul of water, add 1 ul of rapid ligase, incubate at RT with mixing for 20 minutes, Stop the reaction by adding 6 ul of 0.5 M EDTA/100 ul of ligation mix, Wash the beads twice with 1x Bind and wash buffer, Wash the beads once with TE, Resuspend the beads in 30 ul of water Perform the PCR amplification and size excision. Prepare Phusion mix: 0.5 ul of primer, 5 ul of beads, 25 ul of Phusion MM, 19.5 ul of water.

text: Mus musculus

text: Mus musculus

text: biological replicate1

characteristic: replicate

text: Mus musculus


text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1HW8ACXX_13s002413_Pekowska_lane713s002413_ESC2

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: description

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


characteristic: ENA-CHECKLIST

text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1HW8ACXX_13s002413_Pekowska_lane713s002413_NSC1

text: ArrayExpress

text: neural stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1HW8ACXX_13s002413_Pekowska_lane713s002413_NSC2

text: ArrayExpress

text: neural stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


text: EMBL Heidelberg

text: public

characteristic: SRA accession

text: E-MTAB-4870:C1HW8ACXX_13s002413_Pekowska_lane813s002413_ESC1

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1HW8ACXX_13s002413_Pekowska_lane813s002413_ESC2

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: biological replicate2

text: Mus musculus


text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1HW8ACXX_13s002413_Pekowska_lane813s002413_NSC1

text: ArrayExpress

text: neural stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus

characteristic: title


characteristic: ENA-LAST-UPDATE

text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1HW8ACXX_13s002413_Pekowska_lane813s002413_NSC2

text: ArrayExpress

text: neural stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


characteristic: External Id

text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane512s008032_ESC1

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus