text: FGCZ

text: public

text: human

characteristic: common name

text: Bladder wall biopsy from male patient with acontractile obstructed bladder, 86 years old

text: Homo sapiens

text: Homo sapiens

text: Acontractile Obstructed Bladder #1


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: FGCZ

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Bladder wall biopsy from male patient with acontractile obstructed bladder, 83 years old

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Acontractile Obstructed Bladder #2

characteristic: title


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from male patient with acontractile obstructed bladder, 74 years old

text: Homo sapiens

text: Homo sapiens

text: Acontractile Obstructed Bladder #3


text: FGCZ

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Acontractile Obstructed Bladder #4


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from male patient with acontractile obstructed bladder, 68 years old

text: Homo sapiens

text: Homo sapiens

text: Acontractile Obstructed Bladder #5


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from male patient with acontractile obstructed bladder, 69 years old

text: Homo sapiens

text: Homo sapiens

text: Acontractile Obstructed Bladder #6


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from male patient with bladder outlet obstruction without detrusor overactivity, 60 years old

text: Homo sapiens

text: Homo sapiens

text: Bladder Outlet Obstruction #1


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from male patient with bladder outlet obstruction without detrusor overactivity, 63 years old

text: Homo sapiens

text: Homo sapiens

text: Bladder Outlet Obstruction #2


text: FGCZ

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Bladder Outlet Obstruction #3


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from male patient with bladder outlet obstruction without detrusor overactivity, 76 years old

text: Homo sapiens

text: Homo sapiens

text: Bladder Outlet Obstruction #4


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from male patient with bladder outlet obstruction without detrusor overactivity, 73 years old

text: Homo sapiens

text: Homo sapiens

text: Bladder Outlet Obstruction #5


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from male patient with bladder outlet obstruction without detrusor overactivity, 67 years old

text: Homo sapiens

text: Homo sapiens

text: Bladder Outlet Obstruction #6


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from male patient with bladder outlet obstruction wiht detrusor overactivity, 55 years old

text: Homo sapiens

text: Homo sapiens

text: Over Active obstructed Bladder#1


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from male patient with bladder outlet obstruction wiht detrusor overactivity, 71 years old

text: Homo sapiens

text: Homo sapiens

text: Over Active obstructed Bladder#2


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from male patient with bladder outlet obstruction wiht detrusor overactivity, 69 years old

text: Homo sapiens

text: Homo sapiens

text: Over Active obstructed Bladder#3


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from male patient with bladder outlet obstruction wiht detrusor overactivity, 63 years old

text: Homo sapiens

text: Homo sapiens

text: Over Active obstructed Bladder#4


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from male patient with bladder outlet obstruction wiht detrusor overactivity, 60 years old

text: Homo sapiens

text: Homo sapiens

text: Over Active obstructed Bladder#5


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from male patient with bladder outlet obstruction wiht detrusor overactivity, 62 years old

text: Homo sapiens

text: Homo sapiens

text: Over Active obstructed Bladder#6


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from female patient with bladder pain syndrome

text: Homo sapiens

text: Homo sapiens

text: Bladder Pain Syndrome #1


text: FGCZ

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Bladder Pain Syndrome #2


text: FGCZ

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Bladder Pain Syndrome #3


text: FGCZ

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Bladder Pain Syndrome #4


text: FGCZ

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Bladder Pain Syndrome #5


text: FGCZ

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Bladder Pain Syndrome #6


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from normal male patient without any obstruction, 55 years old

text: Homo sapiens

text: Homo sapiens

text: Control Normal Bladder #1


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from normal male patient without any obstruction, 45 years old

text: Homo sapiens

text: Homo sapiens

text: Control Normal Bladder #2


text: FGCZ

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Control Normal Bladder #3


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from normal male patient without any obstruction, 51 years old

text: Homo sapiens

text: Homo sapiens

text: Control Normal Bladder #4


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from normal female patient without any obstruction, 73 years old

text: Homo sapiens

text: Homo sapiens

text: Control Normal Bladder #5


text: FGCZ

text: public

text: human

text: Bladder wall biopsy from normal female patient without any obstruction, 50 years old

text: Homo sapiens

text: Homo sapiens

text: Control Normal Bladder #6


text: macrophages

characteristic: ArrayExpress-CellType

text: Wildtype

characteristic: ArrayExpress-Genotype

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: E14_iCreiFlp_ESC_derived_macrophage_uninfected_1-sc-2168811

text: house mouse

text: Mus musculus

text: RNA from macrophages derived from murine embryonic stem cells

characteristic: sample description

text: Mus musculus


text: macrophages

text: Wildtype

text: Mus musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: E14_iCreiFlp_ESC_derived_macrophage_uninfected_2-sc-2168812

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: macrophages

text: Wildtype

text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: E14_iCreiFlp_ESC_derived_macrophage_uninfected_3-sc-2168813

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Traf2 mutant

text: Mus musculus

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: E14_iCreiFlp_ESC_derived_macrophage_infected_1-sc-2168814

text: house mouse

text: Mus musculus

text: RNA from macrophages derived from murine embryonic stem cells infected with Salmonella Typhimurium

text: Mus musculus


text: macrophages

text: Traf2 mutant

text: Mus musculus

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E14_iCreiFlp_ESC_derived_macrophage_infected_2-sc-2168815

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Traf2 mutant

text: Mus musculus

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E14_iCreiFlp_ESC_derived_macrophage_infected_3-sc-2168816

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Wildtype

text: Mus musculus

text: SC

text: public

text: Traf2_mutant_E14_iCreiFlp_ESC_derived_macrophage_uninfected_1-sc-2168817

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Wildtype

text: Mus musculus

text: SC

text: public

text: Traf2_mutant_E14_iCreiFlp_ESC_derived_macrophage_uninfected_2-sc-2168818

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus


text: macrophages

text: Wildtype

text: Mus musculus

text: SC

text: public

text: Traf2_mutant_E14_iCreiFlp_ESC_derived_macrophage_uninfected_3-sc-2168819

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Traf2 mutant

text: Mus musculus

text: SC

text: public

text: Traf2_mutant_E14_iCreiFlp_ESC_derived_macrophage_infected_1-sc-2168820

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Traf2 mutant

text: Mus musculus

text: SC

text: public

text: Traf2_mutant_E14_iCreiFlp_ESC_derived_macrophage_infected_2-sc-2168821

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Traf2 mutant

text: Mus musculus

text: SC

text: public

text: Traf2_mutant_E14_iCreiFlp_ESC_derived_macrophage_infected_3-sc-2168822

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Wildtype

text: Mus musculus

text: SC

text: public

text: E14_iCreiFlp_ESC_derived_macrophage_uninfected_1-sc-2168823

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Wildtype

text: Mus musculus

text: SC

text: public

text: E14_iCreiFlp_ESC_derived_macrophage_uninfected_2-sc-2168824

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Wildtype

text: Mus musculus

text: SC

text: public

text: E14_iCreiFlp_ESC_derived_macrophage_uninfected_3-sc-2168825

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Traf2 mutant

text: Mus musculus

text: SC

text: public

text: E14_iCreiFlp_ESC_derived_macrophage_infected_1-sc-2168826

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Traf2 mutant

text: Mus musculus

text: SC

text: public

text: E14_iCreiFlp_ESC_derived_macrophage_infected_2-sc-2168827

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Traf2 mutant

text: Mus musculus

text: SC

text: public

text: E14_iCreiFlp_ESC_derived_macrophage_infected_3-sc-2168828

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Wildtype

text: Mus musculus

text: SC

text: public

text: Traf2_mutant_E14_iCreiFlp_ESC_derived_macrophage_uninfected_1-sc-2168829

text: house mouse

text: Mus musculus

text: RNA from macrophages derived from murine embryonic stem cells

text: Mus musculus


text: macrophages

text: Wildtype

text: Mus musculus

text: SC

text: public

text: Traf2_mutant_E14_iCreiFlp_ESC_derived_macrophage_uninfected_2-sc-2168830

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Wildtype

text: Mus musculus

text: SC

text: public

text: Traf2_mutant_E14_iCreiFlp_ESC_derived_macrophage_uninfected_3-sc-2168831

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Traf2 mutant

text: Mus musculus

text: SC

text: public

text: Traf2_mutant_E14_iCreiFlp_ESC_derived_macrophage_infected_1-sc-2168832

text: house mouse

text: Mus musculus

text: RNA from macrophages derived from murine embryonic stem cells infected with Salmonella Typhimurium

text: Mus musculus


text: macrophages

text: Traf2 mutant

text: Mus musculus

text: SC

text: public

text: Traf2_mutant_E14_iCreiFlp_ESC_derived_macrophage_infected_2-sc-2168833

text: house mouse

text: Mus musculus

text: Mus musculus


text: macrophages

text: Traf2 mutant

text: Mus musculus

text: SC

text: public

text: Traf2_mutant_E14_iCreiFlp_ESC_derived_macrophage_infected_3-sc-2168834

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: DNA libraries made by the addition of tailed oligos in a second round of PCR.

text: Danio rerio


text: MDC

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: Protocols: Human embryonic kidney (HEK) 293 cells with tetracycline-inducible expression of FLAG/HA-tagged RBM20 have been described previously (5). For PAR-CLIP, we essentially followed the protocol as described (13). The libraries were sequenced on an Illumina Genome Analyzer GAII using the 50 bp single read protocol. 4 ug of total RNA was used for library preparation with the TruSeq RNA Sample Preparation Kit (Illumina).

characteristic: description

text: PAR-CLIP 2

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title

type: has member


characteristic: ENA-CHECKLIST

text: MDC

text: public

text: ArrayExpress

text: myocyte

characteristic: cell type

text: Norway rat

characteristic: common name

text: Protocols: Neonatal rat ventricular myocytes (NRVMs) were isolated from SD rats using a modification of the Kasten's technique as described (37). 48 h past isolation, cardiomyocytes were irradiated one time for 400mJ/cm and additional 200 mJ/cm with 254 nm UV light, and lysed in NP40 lysis buffer. After DNAse and RNase T1 treatment, the lysate was immunoprecipitated using RBM20 antibody (5) covalently coupled to Protein G Dynabeads (Invitrogen). Radiolabeling of immunoprecipitated RNA, protein-RNA complexes separation, sequencing library preparation and sequencing was done following the PAR-CLIP protocol 4 ug of total RNA was used for library preparation with the TruSeq RNA Sample Preparation Kit (Illumina).

text: HITS-CLIP 3

text: Rattus norvegicus

text: Rattus norvegicus

text: Rattus norvegicus

text: frozen specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MDC

text: public

text: ArrayExpress

text: human

text: PAR-CLIP 3

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: frozen specimen


text: MDC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: myocyte

text: Norway rat

text: HITS-CLIP 4

text: Rattus norvegicus

text: Rattus norvegicus

text: Rattus norvegicus

text: frozen specimen


text: MDC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: myocyte

text: Norway rat

text: HITS-CLIP 2

text: Rattus norvegicus

text: Rattus norvegicus

text: Rattus norvegicus

text: frozen specimen


text: MDC

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: PAR-CLIP 1

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: frozen specimen


text: MDC

text: public

text: ArrayExpress

text: myocyte

text: Norway rat

characteristic: description

text: HITS-CLIP 1

characteristic: individual

text: Rattus norvegicus

text: Rattus norvegicus

text: Rattus norvegicus

text: frozen specimen

characteristic: specimen with known storage state


text: mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: Mouse v2 library plasmid with B

characteristic: sample description

text: Mus musculus


text: Mus musculus

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Mus musculus

text: Mouse v2 library plasmid with M

text: Mus musculus


text: adult

characteristic: ArrayExpress-DevelopmentalStage

text: head

characteristic: ArrayExpress-OrganismPart

text: female

characteristic: ArrayExpress-Sex

text: Haemonchus contortus

text: New 1

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: barber pole worm

text: Haemonchus contortus

text: Whole genome amplified from a single Haemonchus contortus female head

text: Haemonchus contortus

text: New 1

characteristic: strain


text: adult

text: head

text: female

text: Haemonchus contortus

text: New 9

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: barber pole worm

text: Haemonchus contortus

characteristic: organism

text: Haemonchus contortus

text: New 9


text: adult

text: head

text: female

text: Haemonchus contortus

characteristic: ArrayExpress-Species

text: Lahore 16

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: barber pole worm

text: Haemonchus contortus

text: Haemonchus contortus

text: Lahore 16


text: whole

text: Haemonchus contortus

text: Farm 101

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: barber pole worm

characteristic: common name

text: Haemonchus contortus

text: Whole genome amplified from a single Haemonchus contortus L1 DNA lysate

characteristic: sample description

text: Haemonchus contortus

text: Farm 101


text: Human

text: PhiX DNA spike-in at 50%

characteristic: ArrayExpress-Treatment

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: human

text: Homo sapiens

text: DNA library from AML cell lines after CRISPR/CAS9 screens

text: Homo sapiens


text: Forward

characteristic: Direction of read

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: Sequence file sample contained in

tag: Namespace:UNIVERSITY OF MANCHESTER

text: TCTACGTAGC

characteristic: barcode seq

text: Graery threadfin seabass

text: Stool, day 41, Naive Mouse albendazole treated 4.2

characteristic: description

text: CGTATCGCCTCCCTCGCGCCATCAG(MID)CAGGCCTAACACATGCAAGTC

characteristic: forward primer

text: mus musculus C57BL/13

characteristic: host

text: Fresh Stool sample

characteristic: isolation source

text: University of Manchester

characteristic: lab host

text: environmental samples

text: CTATGCGCCTTGCCAGCCCGCTCAGATTACCGCGGCTGCTGG

characteristic: reverse primer

text: environmental samples

text: Male

characteristic: sex

text: DNA extracted from Stool sample

characteristic: title


text: Forward

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ACGACTACAG

text: blue hamlet

text: Stool, day 41, Naive Mouse albendazole treated 4.3

text: mus musculus C57BL/14

text: Fresh Stool sample

text: University of Manchester

text: environmental samples

characteristic: organism

text: environmental samples

text: Male

text: DNA extracted from Stool sample


text: Forward

characteristic: Direction of read

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

text: public

characteristic: Sequence file sample contained in

text: CGTAGACTAG

characteristic: barcode seq

text: camotillo

characteristic: common name

text: Stool, day 41, Naive Mouse albendazole treated 4.4

characteristic: description

text: mus musculus C57BL/15

text: Fresh Stool sample

text: University of Manchester

text: environmental samples

text: environmental samples

text: Male

text: DNA extracted from Stool sample


text: Forward

text: UNIVERSITY OF MANCHESTER

text: public

text: TACGAGTATG

text: parrot sand bass

text: Stool, day 41, Naive Mouse albendazole treated 4.5

characteristic: forward primer

text: mus musculus C57BL/16

characteristic: host

text: Fresh Stool sample

characteristic: isolation source

text: University of Manchester

characteristic: lab host

text: environmental samples

characteristic: reverse primer

text: environmental samples

text: Male

characteristic: sex

text: DNA extracted from Stool sample

characteristic: title


text: Forward

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: TACTCTCGTG

text: goldspotted sand bass

text: Stool, day 41, T.muris infected Mouse 7.1

text: mus musculus C57BL/17

text: Fresh Stool sample

text: University of Manchester

text: environmental samples

text: environmental samples

text: Male

text: DNA extracted from Stool sample


text: Forward

characteristic: Direction of read

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

text: public

characteristic: Sequence file sample contained in

characteristic: Submitter Id

text: TAGAGACGAG

characteristic: barcode seq

text: vieja

text: Stool, day 41, T.muris infected Mouse 7.2

text: mus musculus C57BL/18

text: Fresh Stool sample

text: University of Manchester

text: environmental samples

characteristic: organism

text: environmental samples

text: Male

text: DNA extracted from Stool sample


text: Forward

text: UNIVERSITY OF MANCHESTER

text: public

text: ACATACGCGT

text: black seabass

characteristic: common name

text: Stool, day 41, T.muris infected Mouse 7.4

characteristic: description

characteristic: forward primer

text: mus musculus C57BL/20

characteristic: host

text: Fresh Stool sample

characteristic: isolation source

text: University of Manchester

characteristic: lab host

text: environmental samples

characteristic: reverse primer

text: environmental samples

text: Male

text: DNA extracted from Stool sample


text: Forward

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ACGCGAGTAT

text: lantern bass

text: Stool, day 41, T.muris infected Mouse 7.5

text: mus musculus C57BL/21

text: Fresh Stool sample

text: University of Manchester

text: environmental samples

text: environmental samples

text: Male

characteristic: sex

text: DNA extracted from Stool sample

characteristic: title


text: Forward

characteristic: Direction of read

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Sequence file sample contained in

characteristic: Submitter Id

text: ACTACTATGT

text: Peruvian rock seabass

text: Stool, day 41, T.muris infected Mouse albendazole treated 9.1

text: mus musculus C57BL/22

text: Fresh Stool sample

text: University of Manchester

text: environmental samples

text: environmental samples

text: Male

text: DNA extracted from Stool sample


text: Forward

text: UNIVERSITY OF MANCHESTER

text: public

text: AGACTATACT

characteristic: barcode seq

text: inshore sand perch

characteristic: common name

text: Stool, day 41, T.muris infected Mouse albendazole treated 9.3

characteristic: description

characteristic: forward primer

text: mus musculus C57BL/24

characteristic: host

text: Fresh Stool sample

characteristic: isolation source

text: University of Manchester

text: environmental samples

characteristic: organism

text: environmental samples

text: Male

text: DNA extracted from Stool sample


text: Forward

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: AGCGTCGTCT

text: southern rock bass

text: Stool, day 41, T.muris infected Mouse albendazole treated 9.4

text: mus musculus C57BL/25

text: Fresh Stool sample

text: University of Manchester

characteristic: lab host

text: environmental samples

characteristic: reverse primer

text: environmental samples

text: Male

text: DNA extracted from Stool sample


text: Forward

characteristic: Direction of read

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CGTCTAGTAC

text: popeye catalufa

text: Stool, day 91, Naive Mouse 3.1

text: mus musculus C57BL/27

text: Fresh Stool sample

text: University of Manchester

text: environmental samples

text: environmental samples

text: Male

characteristic: sex

text: DNA extracted from Stool sample

characteristic: title


text: Forward

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: Sequence file sample contained in

characteristic: Submitter Id

text: TGTACTACTC

characteristic: barcode seq

text: giant sea bass

characteristic: common name

text: Stool, day 91, Naive Mouse 3.3

characteristic: description

characteristic: forward primer

text: mus musculus C57BL/29

characteristic: host

text: Fresh Stool sample

text: University of Manchester

text: environmental samples

text: environmental samples

text: Male

text: DNA extracted from Stool sample


text: Forward

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: TACGAGTATG

text: chain pickerel

text: Stool, day 91, Naive Mouse 3.5

text: mus musculus C57BL/31

text: Fresh Stool sample

characteristic: isolation source

text: University of Manchester

text: environmental samples

characteristic: organism

text: environmental samples

text: Male

text: DNA extracted from Stool sample


text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: Mus musculus


characteristic: ArrayExpress-DevelopmentalStage

text: whole

characteristic: ArrayExpress-OrganismPart

text: Haemonchus contortus

text: SC

text: public

characteristic: Submitter Id

text: barber pole worm

text: Haemonchus contortus

characteristic: sample description

text: Haemonchus contortus


E-MTAB-3084:SUMO2 FBS

text: University of Manchester

text: public

text: E-MTAB-3084:SUMO2 FBS

tag: Namespace:University of Manchester

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: osteosarcoma

characteristic: cell type

text: human

characteristic: common name

text: Protocols: The U2OS cells were grown in DMEM supplement with 10% foetal bovine serum. Cells were cross-linked with Formaldehyde for 10 minutes. After reverse cross-link and protein digestion with Proteinase K (Roche), DNA was purified using Qiaquick, PCR purification kit (Qiagen) following the manufacturer’s instructions. ChIP-seq was performed as described in Schmidt et al., 2009, using 3 x 10^6 U2OS. Immuno-precipitation was performed overnight at 4° C by incubating the shared DNA-protein complex with3 micro-gram of anti-SUMO2 (Life technologies) antibody previously coupled to Dynabeads protein A (Invitrogen). Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. (2009) ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48: 240-248. Libraries were generated following manufacturer's protocol.

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: sex

text: SUMO2 FBS

characteristic: title


E-MTAB-3084:Input DNA

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Manchester

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3084:Input DNA

text: ArrayExpress

text: osteosarcoma

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: female

text: Input DNA


text: mixed

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: Amplicon sequencing SNV confirmation

text: Mus musculus


text: IDIBAPS and IFIBYNE-CONICET

text: public

tag: Namespace:IDIBAPS and IFIBYNE-CONICET

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: polyA+ RNA Protocols: Human embryos were collected with informed consent following approval from the North West Regional Ethics Committee, UK (08/H1010/28) following termination of pregnancy and staged immediately by stereomicroscopy according to the Carnegie classification38. The collection, use and storage of material followed guidelines from the UK Polkinghorne Committee, legislation of the Human Tissue Act 2004 and the Codes of Practice of the Human Tissue Authority, UK. The analysis of human embryonic tissue was also approved by the Comitè Ètic d’Investigació Clínica del Centre de Medicina Regenerativa de Barcelona and Departament de Salut, Generalitat de Catalunya. Human embryonic pancreas and liver were dissected at Carnegie Stage (CS) 16-18, which correlates to ~37-45 days post-conception. These stages were the earliest at which the pancreatic epithelial cells could be efficiently dissected away from surrounding mesenchyme with minimal contamination. After isolation, pancreatic and liver tissues were rinsed with phosphate buffered saline 3 times, formaldehyde was added to a final concentration of 1%, and samples were incubated at room temperature for 10 min. Glycine was added to 125 mM for 5 min, tissue was next rinsed 3 times with phosphate-buffered saline containing protease inhibitor cocktail (Roche) at 4ºC, and then snap-frozen and stored at -80ºC. Total embryonic pancreas RNA was extracted from unfixed tissue using Trizol and then treated with DNase I. RNA was extracted usign TRIzol. Total RNA quality was confirmed using Bioanalyzer 2100. All analyzed samples had RIN values greater than 9. RNA-seq for in vivo and in vitro MPCs was generated from DNase I-treated PolyA+ RNA samples from a CS17 pancreatic bud or from a pool of 3 in vitro pancreatic MPC differentiation experiments. Libraries were contructed using Illumina standard recommended procedures.

text: Carnegie Stage 17

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: pancreatic bud

characteristic: organism part

text: Homo sapiens


text: IDIBAPS and IFIBYNE-CONICET

text: public

text: ArrayExpress

text: In vitro-derived pancreatic progenitors

characteristic: cell type

text: human

characteristic: common name

text: H3K27ac ChIP-seq Protocols: Human ESCs (H9 from WiCell, Maddison, WI, USA) were imported under the guidelines of the UK Stem Cell Bank Steering Committee (authorization SCSC10-44). Cells were passaged and used for in vitro differentiation of pancreatic MPCs as described previously17. In brief, definitive endoderm (DE) was induced by growing hESCs in CDM-PVA + Activin-A (100 ng/mL), BMP4 (10 ng/mL), bFGF (20 ng/mL) and LY (10 µM) (AFBLy). The CDM-PVA AFBLy cocktail was replenished daily, and daily media changes were made until day 10 of differentiation. After the DE stage (days 1-3), cells were cultured in Advanced DMEM (Invitrogen) supplemented with SB-431542 (10 µM; Tocris), FGF10 (50 ng/ml; Autogen Bioclear), all-trans retinoic acid (RA, 2 µM; Sigma) and Noggin (150 ng/ml; R-and-D Systems) for 3 days (days 4-6). For the next stage (days 7-9), the cells were cultured in Advanced DMEM supplemented with human FGF10 (50 ng/ml; Autogen Bioclear), all-trans retinoic acid (RA, 2 uM; Sigma), KAAD-cyclopamine (0.25 µM; Toronto Research Chemicals) and Noggin (150 ng/ml; R-and-D Systems). For the last stage (days 10-12), the cells were cultured in human FGF10 (50 ng/ml; R-and-D Systems). Human embryos were collected with informed consent following approval from the North West Regional Ethics Committee, UK (08/H1010/28) following termination of pregnancy and staged immediately by stereomicroscopy according to the Carnegie classification38. The collection, use and storage of material followed guidelines from the UK Polkinghorne Committee, legislation of the Human Tissue Act 2004 and the Codes of Practice of the Human Tissue Authority, UK. The analysis of human embryonic tissue was also approved by the Comitè Ètic d’Investigació Clínica del Centre de Medicina Regenerativa de Barcelona and Departament de Salut, Generalitat de Catalunya. Human embryonic pancreas and liver were dissected at Carnegie Stage (CS) 16-18, which correlates to ~37-45 days post-conception. These stages were the earliest at which the pancreatic epithelial cells could be efficiently dissected away from surrounding mesenchyme with minimal contamination. After isolation, pancreatic and liver tissues were rinsed with phosphate buffered saline 3 times, formaldehyde was added to a final concentration of 1%, and samples were incubated at room temperature for 10 min. Glycine was added to 125 mM for 5 min, tissue was next rinsed 3 times with phosphate-buffered saline containing protease inhibitor cocktail (Roche) at 4ºC, and then snap-frozen and stored at -80ºC. Total embryonic pancreas RNA was extracted from unfixed tissue using Trizol and then treated with DNase I. Either 7 human CS16-18 pancreatic buds, 4 CS16-18 liver buds, or ~10 million cells from a pool of 3 pancreatic progenitor in vitro differentiation experiments, were pooled in 1 mL of lysis buffer containing protease inhibitor cocktail (Roche) and sonicated 10-15 cycles. We verified that a substantial portion of chromatin fragments were in the 200-600 bp range by gel electrophoresis. ChIP was performed with 50-300 µL of sonicated chromatin. Chromatin was diluted with ChIP dilution buffer (0.75% Triton X-100, 140 mM NaCl, 0.1% sodium deoxycholate, 50 mM Hepes at pH8.0, 1 mM EDTA, 1X protease inhibitor cocktail) to achieve a final SDS concentration of 0.2%, pre-cleared with A/G sepharose beads (GEHealthcare) for 1 hour, and incubated overnight at 4ºC with 1-1.5µg of the following antibodies: rabbit anti-H3K27ac (ab-4729), rabbit anti-H3K4me1 (ab-8895), goat anti-Pdx1 (BCBC AB2027, Chris Wright, Vanderbilt University), goat anti-FOXA2 (sc-6554), rabbit anti-GATA6 (sc-9055X), rabbit anti-HNF1β (sc-22840-X), rabbit anti-ONECUT1 (sc-13050), mouse anti-TEAD1 (BD610922) or rabbit anti-YAP (Cell Signaling). Samples were then rotated 2 hours at 4ºC with A/G sepharose beads and then sequentially washed with Low salt wash buffer (1% Triton X-100, 0.1 % SDS, 150 mM NaCl, 2mM EDTA, 20 mM Tris-HCl pH 8.0), High salt wash buffer (1% Triton X-100, 0.1 % SDS, 500 mM NaCl, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), LiCl wash buffer (1% NP40, 0.25 M LiCl, 1 mM EDTA, 1% deoxycholate sodium, 10 mM Tris-HCl pH 8.0), TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Immune complexes were eluted from the beads by adding IP elution buffer (1% SDS, 0.1M NaHCO3). Next, chromatin was sequentially treated with RNAse (greater than 5 hr at 65 degrees C) and Proteinase K (overnight at 45 degrees C). Finally, DNA was extracted with phenol-chloroform followed by ethanol precipitation. For all libraries 5-10 ng of DNA were used to prepare ChIP libraries according to Illumina protocols, and sequencing of ~25 million (for transcription factors and H3K27ac) or ~50 million (for H3K4me1) single-end reads was performed on Illumina HiSeq2000 platform using standard recommended procedures.

characteristic: description

text: day 12

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: IDIBAPS and IFIBYNE-CONICET

characteristic: INSDC first public

text: public

text: ArrayExpress

text: human

text: FOXA2 ChIP-seq Protocols: Human embryos were collected with informed consent following approval from the North West Regional Ethics Committee, UK (08/H1010/28) following termination of pregnancy and staged immediately by stereomicroscopy according to the Carnegie classification38. The collection, use and storage of material followed guidelines from the UK Polkinghorne Committee, legislation of the Human Tissue Act 2004 and the Codes of Practice of the Human Tissue Authority, UK. The analysis of human embryonic tissue was also approved by the Comitè Ètic d’Investigació Clínica del Centre de Medicina Regenerativa de Barcelona and Departament de Salut, Generalitat de Catalunya. Human embryonic pancreas and liver were dissected at Carnegie Stage (CS) 16-18, which correlates to ~37-45 days post-conception. These stages were the earliest at which the pancreatic epithelial cells could be efficiently dissected away from surrounding mesenchyme with minimal contamination. After isolation, pancreatic and liver tissues were rinsed with phosphate buffered saline 3 times, formaldehyde was added to a final concentration of 1%, and samples were incubated at room temperature for 10 min. Glycine was added to 125 mM for 5 min, tissue was next rinsed 3 times with phosphate-buffered saline containing protease inhibitor cocktail (Roche) at 4ºC, and then snap-frozen and stored at -80ºC. Total embryonic pancreas RNA was extracted from unfixed tissue using Trizol and then treated with DNase I. Either 7 human CS16-18 pancreatic buds, 4 CS16-18 liver buds, or ~10 million cells from a pool of 3 pancreatic progenitor in vitro differentiation experiments, were pooled in 1 mL of lysis buffer containing protease inhibitor cocktail (Roche) and sonicated 10-15 cycles. We verified that a substantial portion of chromatin fragments were in the 200-600 bp range by gel electrophoresis. ChIP was performed with 50-300 µL of sonicated chromatin. Chromatin was diluted with ChIP dilution buffer (0.75% Triton X-100, 140 mM NaCl, 0.1% sodium deoxycholate, 50 mM Hepes at pH8.0, 1 mM EDTA, 1X protease inhibitor cocktail) to achieve a final SDS concentration of 0.2%, pre-cleared with A/G sepharose beads (GEHealthcare) for 1 hour, and incubated overnight at 4ºC with 1-1.5µg of the following antibodies: rabbit anti-H3K27ac (ab-4729), rabbit anti-H3K4me1 (ab-8895), goat anti-Pdx1 (BCBC AB2027, Chris Wright, Vanderbilt University), goat anti-FOXA2 (sc-6554), rabbit anti-GATA6 (sc-9055X), rabbit anti-HNF1β (sc-22840-X), rabbit anti-ONECUT1 (sc-13050), mouse anti-TEAD1 (BD610922) or rabbit anti-YAP (Cell Signaling). Samples were then rotated 2 hours at 4ºC with A/G sepharose beads and then sequentially washed with Low salt wash buffer (1% Triton X-100, 0.1 % SDS, 150 mM NaCl, 2mM EDTA, 20 mM Tris-HCl pH 8.0), High salt wash buffer (1% Triton X-100, 0.1 % SDS, 500 mM NaCl, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), LiCl wash buffer (1% NP40, 0.25 M LiCl, 1 mM EDTA, 1% deoxycholate sodium, 10 mM Tris-HCl pH 8.0), TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Immune complexes were eluted from the beads by adding IP elution buffer (1% SDS, 0.1M NaHCO3). Next, chromatin was sequentially treated with RNAse (greater than 5 hr at 65 degrees C) and Proteinase K (overnight at 45 degrees C). Finally, DNA was extracted with phenol-chloroform followed by ethanol precipitation. For all libraries 5-10 ng of DNA were used to prepare ChIP libraries according to Illumina protocols, and sequencing of ~25 million (for transcription factors and H3K27ac) or ~50 million (for H3K4me1) single-end reads was performed on Illumina HiSeq2000 platform using standard recommended procedures.

text: Carnegie Stage 16-18

text: Homo sapiens

text: Homo sapiens

text: liver bud

text: Homo sapiens


text: IDIBAPS and IFIBYNE-CONICET

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: Carnegie Stage 16-18

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: pancreatic bud

text: Homo sapiens


characteristic: External Id

text: IDIBAPS and IFIBYNE-CONICET

characteristic: INSDC center name

text: public

text: ArrayExpress

text: In vitro-derived pancreatic progenitors

text: human

text: TEAD1 ChIP-seq Protocols: Human ESCs (H9 from WiCell, Maddison, WI, USA) were imported under the guidelines of the UK Stem Cell Bank Steering Committee (authorization SCSC10-44). Cells were passaged and used for in vitro differentiation of pancreatic MPCs as described previously17. In brief, definitive endoderm (DE) was induced by growing hESCs in CDM-PVA + Activin-A (100 ng/mL), BMP4 (10 ng/mL), bFGF (20 ng/mL) and LY (10 µM) (AFBLy). The CDM-PVA AFBLy cocktail was replenished daily, and daily media changes were made until day 10 of differentiation. After the DE stage (days 1-3), cells were cultured in Advanced DMEM (Invitrogen) supplemented with SB-431542 (10 µM; Tocris), FGF10 (50 ng/ml; Autogen Bioclear), all-trans retinoic acid (RA, 2 µM; Sigma) and Noggin (150 ng/ml; R-and-D Systems) for 3 days (days 4-6). For the next stage (days 7-9), the cells were cultured in Advanced DMEM supplemented with human FGF10 (50 ng/ml; Autogen Bioclear), all-trans retinoic acid (RA, 2 uM; Sigma), KAAD-cyclopamine (0.25 µM; Toronto Research Chemicals) and Noggin (150 ng/ml; R-and-D Systems). For the last stage (days 10-12), the cells were cultured in human FGF10 (50 ng/ml; R-and-D Systems). Human embryos were collected with informed consent following approval from the North West Regional Ethics Committee, UK (08/H1010/28) following termination of pregnancy and staged immediately by stereomicroscopy according to the Carnegie classification38. The collection, use and storage of material followed guidelines from the UK Polkinghorne Committee, legislation of the Human Tissue Act 2004 and the Codes of Practice of the Human Tissue Authority, UK. The analysis of human embryonic tissue was also approved by the Comitè Ètic d’Investigació Clínica del Centre de Medicina Regenerativa de Barcelona and Departament de Salut, Generalitat de Catalunya. Human embryonic pancreas and liver were dissected at Carnegie Stage (CS) 16-18, which correlates to ~37-45 days post-conception. These stages were the earliest at which the pancreatic epithelial cells could be efficiently dissected away from surrounding mesenchyme with minimal contamination. After isolation, pancreatic and liver tissues were rinsed with phosphate buffered saline 3 times, formaldehyde was added to a final concentration of 1%, and samples were incubated at room temperature for 10 min. Glycine was added to 125 mM for 5 min, tissue was next rinsed 3 times with phosphate-buffered saline containing protease inhibitor cocktail (Roche) at 4ºC, and then snap-frozen and stored at -80ºC. Total embryonic pancreas RNA was extracted from unfixed tissue using Trizol and then treated with DNase I. Either 7 human CS16-18 pancreatic buds, 4 CS16-18 liver buds, or ~10 million cells from a pool of 3 pancreatic progenitor in vitro differentiation experiments, were pooled in 1 mL of lysis buffer containing protease inhibitor cocktail (Roche) and sonicated 10-15 cycles. We verified that a substantial portion of chromatin fragments were in the 200-600 bp range by gel electrophoresis. ChIP was performed with 50-300 µL of sonicated chromatin. Chromatin was diluted with ChIP dilution buffer (0.75% Triton X-100, 140 mM NaCl, 0.1% sodium deoxycholate, 50 mM Hepes at pH8.0, 1 mM EDTA, 1X protease inhibitor cocktail) to achieve a final SDS concentration of 0.2%, pre-cleared with A/G sepharose beads (GEHealthcare) for 1 hour, and incubated overnight at 4ºC with 1-1.5µg of the following antibodies: rabbit anti-H3K27ac (ab-4729), rabbit anti-H3K4me1 (ab-8895), goat anti-Pdx1 (BCBC AB2027, Chris Wright, Vanderbilt University), goat anti-FOXA2 (sc-6554), rabbit anti-GATA6 (sc-9055X), rabbit anti-HNF1β (sc-22840-X), rabbit anti-ONECUT1 (sc-13050), mouse anti-TEAD1 (BD610922) or rabbit anti-YAP (Cell Signaling). Samples were then rotated 2 hours at 4ºC with A/G sepharose beads and then sequentially washed with Low salt wash buffer (1% Triton X-100, 0.1 % SDS, 150 mM NaCl, 2mM EDTA, 20 mM Tris-HCl pH 8.0), High salt wash buffer (1% Triton X-100, 0.1 % SDS, 500 mM NaCl, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), LiCl wash buffer (1% NP40, 0.25 M LiCl, 1 mM EDTA, 1% deoxycholate sodium, 10 mM Tris-HCl pH 8.0), TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Immune complexes were eluted from the beads by adding IP elution buffer (1% SDS, 0.1M NaHCO3). Next, chromatin was sequentially treated with RNAse (greater than 5 hr at 65 degrees C) and Proteinase K (overnight at 45 degrees C). Finally, DNA was extracted with phenol-chloroform followed by ethanol precipitation. For all libraries 5-10 ng of DNA were used to prepare ChIP libraries according to Illumina protocols, and sequencing of ~25 million (for transcription factors and H3K27ac) or ~50 million (for H3K4me1) single-end reads was performed on Illumina HiSeq2000 platform using standard recommended procedures.

text: day 12

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: IDIBAPS and IFIBYNE-CONICET

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: In vitro-derived pancreatic progenitors

text: human

text: polyA+ RNA Protocols: Human ESCs (H9 from WiCell, Maddison, WI, USA) were imported under the guidelines of the UK Stem Cell Bank Steering Committee (authorization SCSC10-44). Cells were passaged and used for in vitro differentiation of pancreatic MPCs as described previously17. In brief, definitive endoderm (DE) was induced by growing hESCs in CDM-PVA + Activin-A (100 ng/mL), BMP4 (10 ng/mL), bFGF (20 ng/mL) and LY (10 µM) (AFBLy). The CDM-PVA AFBLy cocktail was replenished daily, and daily media changes were made until day 10 of differentiation. After the DE stage (days 1-3), cells were cultured in Advanced DMEM (Invitrogen) supplemented with SB-431542 (10 µM; Tocris), FGF10 (50 ng/ml; Autogen Bioclear), all-trans retinoic acid (RA, 2 µM; Sigma) and Noggin (150 ng/ml; R-and-D Systems) for 3 days (days 4-6). For the next stage (days 7-9), the cells were cultured in Advanced DMEM supplemented with human FGF10 (50 ng/ml; Autogen Bioclear), all-trans retinoic acid (RA, 2 uM; Sigma), KAAD-cyclopamine (0.25 µM; Toronto Research Chemicals) and Noggin (150 ng/ml; R-and-D Systems). For the last stage (days 10-12), the cells were cultured in human FGF10 (50 ng/ml; R-and-D Systems). Human embryos were collected with informed consent following approval from the North West Regional Ethics Committee, UK (08/H1010/28) following termination of pregnancy and staged immediately by stereomicroscopy according to the Carnegie classification38. The collection, use and storage of material followed guidelines from the UK Polkinghorne Committee, legislation of the Human Tissue Act 2004 and the Codes of Practice of the Human Tissue Authority, UK. The analysis of human embryonic tissue was also approved by the Comitè Ètic d’Investigació Clínica del Centre de Medicina Regenerativa de Barcelona and Departament de Salut, Generalitat de Catalunya. Human embryonic pancreas and liver were dissected at Carnegie Stage (CS) 16-18, which correlates to ~37-45 days post-conception. These stages were the earliest at which the pancreatic epithelial cells could be efficiently dissected away from surrounding mesenchyme with minimal contamination. After isolation, pancreatic and liver tissues were rinsed with phosphate buffered saline 3 times, formaldehyde was added to a final concentration of 1%, and samples were incubated at room temperature for 10 min. Glycine was added to 125 mM for 5 min, tissue was next rinsed 3 times with phosphate-buffered saline containing protease inhibitor cocktail (Roche) at 4ºC, and then snap-frozen and stored at -80ºC. Total embryonic pancreas RNA was extracted from unfixed tissue using Trizol and then treated with DNase I. RNA was extracted usign TRIzol. Total RNA quality was confirmed using Bioanalyzer 2100. All analyzed samples had RIN values greater than 9. RNA-seq for in vivo and in vitro MPCs was generated from DNase I-treated PolyA+ RNA samples from a CS17 pancreatic bud or from a pool of 3 in vitro pancreatic MPC differentiation experiments. Libraries were contructed using Illumina standard recommended procedures.

text: day 12

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: IDIBAPS and IFIBYNE-CONICET

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: H3K4me1 ChIP-seq Protocols: Human embryos were collected with informed consent following approval from the North West Regional Ethics Committee, UK (08/H1010/28) following termination of pregnancy and staged immediately by stereomicroscopy according to the Carnegie classification38. The collection, use and storage of material followed guidelines from the UK Polkinghorne Committee, legislation of the Human Tissue Act 2004 and the Codes of Practice of the Human Tissue Authority, UK. The analysis of human embryonic tissue was also approved by the Comitè Ètic d’Investigació Clínica del Centre de Medicina Regenerativa de Barcelona and Departament de Salut, Generalitat de Catalunya. Human embryonic pancreas and liver were dissected at Carnegie Stage (CS) 16-18, which correlates to ~37-45 days post-conception. These stages were the earliest at which the pancreatic epithelial cells could be efficiently dissected away from surrounding mesenchyme with minimal contamination. After isolation, pancreatic and liver tissues were rinsed with phosphate buffered saline 3 times, formaldehyde was added to a final concentration of 1%, and samples were incubated at room temperature for 10 min. Glycine was added to 125 mM for 5 min, tissue was next rinsed 3 times with phosphate-buffered saline containing protease inhibitor cocktail (Roche) at 4ºC, and then snap-frozen and stored at -80ºC. Total embryonic pancreas RNA was extracted from unfixed tissue using Trizol and then treated with DNase I. Either 7 human CS16-18 pancreatic buds, 4 CS16-18 liver buds, or ~10 million cells from a pool of 3 pancreatic progenitor in vitro differentiation experiments, were pooled in 1 mL of lysis buffer containing protease inhibitor cocktail (Roche) and sonicated 10-15 cycles. We verified that a substantial portion of chromatin fragments were in the 200-600 bp range by gel electrophoresis. ChIP was performed with 50-300 µL of sonicated chromatin. Chromatin was diluted with ChIP dilution buffer (0.75% Triton X-100, 140 mM NaCl, 0.1% sodium deoxycholate, 50 mM Hepes at pH8.0, 1 mM EDTA, 1X protease inhibitor cocktail) to achieve a final SDS concentration of 0.2%, pre-cleared with A/G sepharose beads (GEHealthcare) for 1 hour, and incubated overnight at 4ºC with 1-1.5µg of the following antibodies: rabbit anti-H3K27ac (ab-4729), rabbit anti-H3K4me1 (ab-8895), goat anti-Pdx1 (BCBC AB2027, Chris Wright, Vanderbilt University), goat anti-FOXA2 (sc-6554), rabbit anti-GATA6 (sc-9055X), rabbit anti-HNF1β (sc-22840-X), rabbit anti-ONECUT1 (sc-13050), mouse anti-TEAD1 (BD610922) or rabbit anti-YAP (Cell Signaling). Samples were then rotated 2 hours at 4ºC with A/G sepharose beads and then sequentially washed with Low salt wash buffer (1% Triton X-100, 0.1 % SDS, 150 mM NaCl, 2mM EDTA, 20 mM Tris-HCl pH 8.0), High salt wash buffer (1% Triton X-100, 0.1 % SDS, 500 mM NaCl, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), LiCl wash buffer (1% NP40, 0.25 M LiCl, 1 mM EDTA, 1% deoxycholate sodium, 10 mM Tris-HCl pH 8.0), TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Immune complexes were eluted from the beads by adding IP elution buffer (1% SDS, 0.1M NaHCO3). Next, chromatin was sequentially treated with RNAse (greater than 5 hr at 65 degrees C) and Proteinase K (overnight at 45 degrees C). Finally, DNA was extracted with phenol-chloroform followed by ethanol precipitation. For all libraries 5-10 ng of DNA were used to prepare ChIP libraries according to Illumina protocols, and sequencing of ~25 million (for transcription factors and H3K27ac) or ~50 million (for H3K4me1) single-end reads was performed on Illumina HiSeq2000 platform using standard recommended procedures.

text: Carnegie Stage 16-18

text: Homo sapiens

text: Homo sapiens

text: pancreatic bud

text: Homo sapiens


characteristic: ArrayExpress-DevelopmentalStage

text: Haemonchus contortus

characteristic: ArrayExpress-Species

text: SC

text: public

text: barber pole worm

text: Haemonchus contortus

text: Pool of 26 ddRADseq libraries: Hc1_F101_414989 (adp24), Hc2_F101_414989 (adp25), Hc3_F101_414989 (adp26), Hc4_F101_414989 (adp27), Hc5_F101_414989 (adp7), Hc6_F101_414989 (adp8), Hc7_F101_414989 (adp9), Hc8_F101_414989 (adp10), Hc9_F101_414989 (adp11), Hc11_F101_414989 (adp12), Hc1_F5_414989 (adp13), Hc2_F5_414989 (adp14), Hc4_F5_414989 (adp15), Hc6_F5_414989 (adp16), Hc14_F5_414989 (adp17), Hc9_F66_414989 (adp17+), Hc10_F66_414989 (adp18), Hc11_F66_414989 (adp19), Hc12_F66_414989 (adp20), Hc14_F66_414989 (adp22), Hc15_F86_414989 (adp1) Hc16_F86_414989 (adp2), Hc17_F86_414989 (adp3), Hc18_F86_414989 (adp4), Hc19_F86_414989 (adp5), Hc20_F86_414989 (adp6)

characteristic: sample description

text: Haemonchus contortus


text: Haemonchus contortus

text: SC

text: public

text: barber pole worm

characteristic: common name

text: Haemonchus contortus

text: Pool of 27 ddRADseq libraries: Hc3_F5_414989 (adp34), Hc5_F5_414989 (adp35), Hc7_F5_414989 (adp36), Hc8_F5_414989 (adp37), Hc10_F5_414989 (adp39), Hc11_F5_414989 (adp40), Hc12_F5_414989 (adp41), Hc13_F5_414989 (adp42), Hc15_F5_414989 (adp43), Hc1_F66_414989 (adp44), Hc2_F66_414989 (adp45), Hc3_F66_414989 (adp46), Hc4_F66_414989 (adp47), Hc5_F66_414989 (adp15), Hc6_F66_414989 (adp16), Hc8_F66_414989 (adp17+), Hc1_F86_414989 (adp1), Hc2_F86_414989 (adp31), Hc3_F66_414989 (adp3), Hc4_F66_414989 (adp4), Hc5_F86_414989 (adp28) Hc6_F86_414989 (adp29), Hc7_F86_414989 (adp30), Hc8_F86_414989 (adp2), Hc9_F86_414989 (adp32), Hc11_F86_414989 (adp11), Hc11_F86_414989 (adp12).

text: Haemonchus contortus


text: Haemonchus contortus

text: SC

text: public

text: barber pole worm

text: Haemonchus contortus

text: Pool of 19 ddRADseq libraries: Hc12_F101_414989 (adp21), Hc22_F101_414989 (adp22), Hc23_F101_414989 (adp23), Hc24_F101_414989 (adp24), Hc25_F101_414989 (adp25), Hc26_F101_414989 (adp26), Hc27_F101_414989 (adp27), Hc28_F101_414989 (adp28), Hc29_F101_414989 (adp29), Hc30_F101_414989 (adp30), Hc16_F5_414989 (adp31), Hc17_F5_414989 (adp32), Hc7_F5_414989 (adp33), Hc13_F66_414989 (adp34), Hc15_F66_414989 (adp35), Hc16_F66_414989 (adp36), Hc21_F86_414989 (adp18), Hc22_F86_414989 (adp19), Hc23_F86_414989 (adp20).

text: Haemonchus contortus


E-MTAB-3104:Sample 2

text: Instituto Gulbenkian de Ciencia

text: public

text: E-MTAB-3104:Sample 2

tag: Namespace:Instituto Gulbenkian de Ciencia

text: ArrayExpress

characteristic: cell line

text: neural progenitor cell

characteristic: cell type

text: house mouse

text: Protocols: NS5 cells were cultured as previously described (Conti et al. 2005), using laminin as a media supplement (20ug/mL), and plated at a density of 28,000/cm2 NS5 cells were infected with pBABE-Ascl1-ERT2-IRES-GFP-puro (NS5_Ascl1), followed by selection in complete medium containing 1ug/mL puromycin (Calbiochem), and collected 24 hours after induction with 4-Hydroxytamoxifen at a final concentration of 50nM NS cells were fixed sequentially with di(N-succimidyl) glutarate and 1% formaldehyde in phosphate buffered saline and then lysed, sonicated and immunoprecipitated, as previously described (Castro et al., 2011), with antibodies anti-H3K27Ac and anti-H3K4me1 (ab4729 and ab8895 from Abcam). DNA libraries were prepared from 10ng of immunoprecipitated DNA according to the standard Illumina ChIP-seq protocol.

characteristic: description

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Ascl1-ERT2 expressed and Tamoxifen-activated

characteristic: phenotype

text: Mus musculus

text: Sample 2

characteristic: title


E-MTAB-3104:Sample 4

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Instituto Gulbenkian de Ciencia

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3104:Sample 4

text: ArrayExpress

text: neural progenitor cell

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Sample 4


E-MTAB-3104:Sample 1

characteristic: External Id

text: Instituto Gulbenkian de Ciencia

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3104:Sample 1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: neural progenitor cell

text: house mouse

text: Protocols: NS5 cells were cultured as previously described (Conti et al. 2005), using laminin as a media supplement (20ug/mL), and plated at a density of 28,000/cm2 NS5 cells were infected with pBABE-Ascl1-ERT2-IRES-GFP-puro (NS5_Ascl1), followed by selection in complete medium containing 1ug/mL puromycin (Calbiochem), and then collected for chromatin extraction NS cells were fixed sequentially with di(N-succimidyl) glutarate and 1% formaldehyde in phosphate buffered saline and then lysed, sonicated and immunoprecipitated, as previously described (Castro et al., 2011), with antibodies anti-H3K27Ac and anti-H3K4me1 (ab4729 and ab8895 from Abcam). DNA libraries were prepared from 10ng of immunoprecipitated DNA according to the standard Illumina ChIP-seq protocol.

text: Mus musculus

text: Mus musculus

text: Ascl1-ERT2 expressed, but inactive

text: Mus musculus

text: Sample 1


E-MTAB-3104:Sample 3

text: Instituto Gulbenkian de Ciencia

text: public

text: E-MTAB-3104:Sample 3

text: ArrayExpress

characteristic: cell line

text: neural progenitor cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: Ascl1-ERT2 expressed, but inactive

text: Mus musculus

text: Sample 3


text: Stowers Institute for Medical Research

text: public

tag: Namespace:Stowers Institute for Medical Research

text: 4 to 6 week

characteristic: age

text: ArrayExpress

text: long term hematopoietic stem cell

text: house mouse

text: Protocols: All the mice in this study were kept in C57BL/6J background. All mice used in this study were between 4-6 weeks of age and were housed in the animal facility at the Stowers Institute for Medical Research (SIMR) and handled according to SIMR and National Institute of Health (NIH) guidelines. All procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of SIMR. RNA was extracted by convention using chloroform-isopropanol trizol method. The RNA-sequencing library was prepared from approximately 20 ng of total RNA for each sample using illumina TruSeq Small RNA Sample Preparation Kit [catalog number: RS-200-0012]). The fragment size in the generated library ranged from 140 to 300 bps. This is higher than called for by the stock Illumina sRNA protocol, because we also wanted to sequence larger species like tRNAs and snoRNAs in addition to the typical miRNAs and piRNAs.

characteristic: description

text: Lin-, Sca1+, c-Kit+, CD34-, Flk2-, CD49b low

characteristic: gating

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: strain

text: LT-HSC


E-MTAB-3080:Maternal WT

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Stowers Institute for Medical Research

text: public

text: E-MTAB-3080:Maternal WT

text: ArrayExpress

text: fetal liver hematopoietic progenitor cell

text: house mouse

text: embryonic day 15

characteristic: developmental stage

text: Lin-, Sca1+, c-Kit+

text: wild type

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Maternal WT

characteristic: title


E-MTAB-3080:Maternal dIG-DMR

characteristic: External Id

text: Stowers Institute for Medical Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3080:Maternal dIG-DMR

text: ArrayExpress

text: house mouse

text: embryonic day 15

text: Lin-, Sca1+, c-Kit+

text: delta IG-DMR

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Maternal dIG-DMR


text: Stowers Institute for Medical Research

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 4 to 6 week

text: ArrayExpress

characteristic: broker name

text: hematopoietic multipotent progenitor cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Lin-, Sca1+, c-Kit+, CD34+, Flk2+

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: MPP


characteristic: ENA-CHECKLIST

text: Stowers Institute for Medical Research

text: public

text: 4 to 6 week

characteristic: age

text: ArrayExpress

text: short term hematopoietic stem cell

text: house mouse

characteristic: description

text: Lin-, Sca1+, c-Kit+, CD34+, Flk2-

characteristic: gating

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: strain

text: ST-HSC


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Stowers Institute for Medical Research

text: public

text: 4 to 6 week

text: ArrayExpress

text: long term hematopoietic stem cell

text: house mouse

text: Lin-, Sca1+, c-Kit+, CD34-, Flk2-, CD49b high

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: IT-HSC

characteristic: title


characteristic: External Id

text: Stowers Institute for Medical Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 4 to 6 week

text: ArrayExpress

text: nucleate erythrocyte

text: house mouse

text: Protocols: All the mice in this study were kept in C57BL/6J background. All mice used in this study were between 4-6 weeks of age and were housed in the animal facility at the Stowers Institute for Medical Research (SIMR) and handled according to SIMR and National Institute of Health (NIH) guidelines. All procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of SIMR. RNA was extracted by convention using chloroform-isopropanol trizol method. The RNA-sequencing library was prepared from approximately 20 ng of total RNA for each sample using illumina TruSeq Small RNA Sample Preparation Kit [catalog number: RS-200-0012]). The fragment size in the generated library ranged from 140 to 300 bps.

text: Ter119+, CD71+, CD3-, CD4-, CD8-, B220-, IgM-, Gr1-, Mac1-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Nuc.Erythro


E-MTAB-3079:Maternal WT

text: Stowers Institute for Medical Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3079:Maternal WT

text: ArrayExpress

text: house mouse

text: embryonic day 15

characteristic: developmental stage

text: Lin-, Sca1+, c-Kit+

text: wild type

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Maternal WT


E-MTAB-3079:T Cell

text: Stowers Institute for Medical Research

text: public

characteristic: SRA accession

text: E-MTAB-3079:T Cell

characteristic: Submitter Id

text: 4 to 6 week

text: ArrayExpress

characteristic: broker name

text: T cell

characteristic: cell type

text: house mouse

characteristic: common name

text: CD3+, CD4+, CD8+, B220-, IgM-, Ter119-, Gr1-, Mac1-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: T Cell


E-MTAB-3079:NK Cell

characteristic: ENA-CHECKLIST

text: Stowers Institute for Medical Research

text: public

text: E-MTAB-3079:NK Cell

text: 4 to 6 week

characteristic: age

text: ArrayExpress

text: natural killer cell

text: house mouse

characteristic: description

text: NK1.1+, B220-, IgM-, Gr1-, Mac1-, Ter119-

characteristic: gating

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: strain

text: NK Cell


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stowers Institute for Medical Research

characteristic: INSDC center name

text: public

text: 4 to 6 week

text: ArrayExpress

text: dendritic cell

text: house mouse

text: CD11c+, CD83+, CD3-, CD4-, CD8-, IgM-, Ter119-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Dendritic

characteristic: title


E-MTAB-3079:Maternal dIG-DMR

text: Stowers Institute for Medical Research

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3079:Maternal dIG-DMR

text: ArrayExpress

text: house mouse

text: embryonic day 15

characteristic: developmental stage

text: Lin-, Sca1+, c-Kit+

text: delta IG-DMR

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Maternal dIG-DMR


text: Stowers Institute for Medical Research

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 4 to 6 week

text: ArrayExpress

characteristic: broker name

text: granulocyte monocyte progenitor cell

characteristic: cell type

text: house mouse

text: Lin-, CD127-, Sca1-, c-Kit+, CD16/32 high, CD34+

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: GMP


E-MTAB-3079:Adult LSK

characteristic: ENA-CHECKLIST

text: Stowers Institute for Medical Research

text: public

text: E-MTAB-3079:Adult LSK

text: 4 to 6 week

characteristic: age

text: ArrayExpress

text: Kit and Sca1-positive hematopoietic stem cell

text: house mouse

characteristic: common name

characteristic: description

text: Lin- Sca1+ cKit+ Flk2-

characteristic: gating

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Adult LSK


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stowers Institute for Medical Research

characteristic: INSDC center name

text: public

text: 4 to 6 week

text: ArrayExpress

text: megakaryocyte-erythroid progenitor cell

text: house mouse

text: Lin-, CD127-, Sca1-, c-Kit+, CD16/32-, CD34-

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: strain

text: MEP


text: Stowers Institute for Medical Research

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 4 to 6 week

text: ArrayExpress

text: monocyte

text: house mouse

text: Gr1 medium, Mac1+, CFMS+, CD3-, CD4-, CD8-, IgM-, Ter119-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Mono

characteristic: title


text: Stowers Institute for Medical Research

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 4 to 6 week

text: ArrayExpress

characteristic: broker name

text: common lymphoid progenitor

text: house mouse

text: Lin-, CD127+, Sca1 medium, c-Kit+

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: CLP


characteristic: ENA-CHECKLIST

text: Stowers Institute for Medical Research

text: public

text: 4 to 6 week

text: ArrayExpress

text: granulocyte

characteristic: cell type

text: house mouse

text: Gr1+, Mac1+, CD3-, CD4-, CD8-, IgM-, Ter119-

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Granulo


text: Stowers Institute for Medical Research

text: public

text: 4 to 6 week

characteristic: age

text: ArrayExpress

text: common myeloid progenitor

text: house mouse

characteristic: common name

characteristic: description

text: Lin-, CD127-, Sca1-, c-Kit+, CD16/32 low, CD34+

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: CMP


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Stowers Institute for Medical Research

text: public

text: 4 to 6 week

text: ArrayExpress

text: megakaryocyte

text: house mouse

text: Pf4 Cre+; tdTomato+

characteristic: gating

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Megakaryo


E-MTAB-3079:B Cell

characteristic: External Id

text: Stowers Institute for Medical Research

characteristic: INSDC center name

text: public

text: E-MTAB-3079:B Cell

text: 4 to 6 week

text: ArrayExpress

text: lymphocyte of B lineage

text: house mouse

text: B220+, IgM+, CD3-, CD4-, CD8-, Ter119-, Gr1-, Mac1-

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: strain

text: B Cell


text: 11.1 weeks

characteristic: ArrayExpress-Age

text: Lin- bone marrow cells

characteristic: ArrayExpress-CellType

text: WT

characteristic: ArrayExpress-Genotype

text: wild type

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: Lin- bone marrow cells

characteristic: sample description

text: Mus musculus


text: 11.1 weeks

text: Lin- bone marrow cells

text: double HET

text: wild type

text: male

text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Lin- bone marrow cells

text: Mus musculus


text: 9.5 weeks

text: Lin- bone marrow cells

text: WT

text: wild type

text: male

text: Mus Musculus

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Mus musculus

text: Lin- bone marrow cells

text: Mus musculus


text: 9.5 weeks

characteristic: ArrayExpress-Age

text: Lin- bone marrow cells

characteristic: ArrayExpress-CellType

text: HEMI

characteristic: ArrayExpress-Genotype

text: wild type

text: male

text: Mus Musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Lin- bone marrow cells

text: Mus musculus


text: public

tag: Namespace:Department of Biochemistry University of Cambridge

text: ArrayExpress

characteristic: broker name

text: HeLa

characteristic: cell line

text: human

text: Protocols: Following the iCLIP protocol the retrieval of protein-bound RNAs and construction of Illumina compatible libraries was done as described in Huppertz et al, 2014

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: Department of Biochemistry University of Cambridge

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: HeLa

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Homo Sapien

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Homo sapiens

characteristic: sample description

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MMRI

text: public

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: C.elegans

characteristic: ArrayExpress-Phenotype

text: Homo Sapien

text: SC

characteristic: INSDC center name

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: ESC

characteristic: ArrayExpress-CellType

text: undifferentiated

characteristic: ArrayExpress-DevelopmentalStage

text: primed

characteristic: ArrayExpress-GrowthCondition

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: ESC

text: Mus musculus


text: ES cells

text: WT

characteristic: ArrayExpress-Genotype

text: mus musculus

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: bisulfite treated genomic DNA from mouse wt ES cells replicate1

text: Mus musculus


text: ES cells

text: WT

text: mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: bisulfite treated genomic DNA from mouse wt ES cells replicate2

text: Mus musculus


text: ES cells

text: WT

text: mus musculus

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

text: bisulfite treated genomic DNA from mouse wt ES cells replicate3

characteristic: sample description

text: Mus musculus


text: ES cells

text: Sall4 KO

text: mus musculus

text: SC

characteristic: INSDC center name

text: public

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: bisulfite treated genomic DNA from mouse Sall4KO ES cells replicate1

text: Mus musculus


text: ES cells

characteristic: ArrayExpress-CellType

text: Sall4 KO

text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: bisulfite treated genomic DNA from mouse Sall4KO ES cells replicate2

text: Mus musculus


text: ES cells

text: Sall4 KO

text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: bisulfite treated genomic DNA from mouse Sall4KO ES cells replicate3

text: Mus musculus


text: ES cells

text: MBD3 KO

text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: bisulfite treated genomic DNA from mouse Mbd3KO ES cells replicate1

text: Mus musculus


text: ES cells

text: MBD3 KO

text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: bisulfite treated genomic DNA from mouse Mbd3KO ES cells replicate2

text: Mus musculus


text: ES cells

text: MBD3 KO

text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: bisulfite treated genomic DNA from mouse Mbd3KO ES cells replicate3

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: BS treated DNA; PBAT library

text: Mus musculus


E-MTAB-3109:Ring1a/b dKO CHiC

text: London Research Institute CRUK

text: public

text: E-MTAB-3109:Ring1a/b dKO CHiC

tag: Namespace:London Research Institute CRUK

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

characteristic: cell type

text: house mouse

text: Protocols: Ring1A−/−;Ring1Bfl/fl;Rosa26::CreERT2 mESCs (Ring1A-KO) were cultured as described previously in Endoh et al. 2012 Conditional deletion of Ring1B in Ring1A-KO cells was carried out by addition of 800 nM tamoxifen for 48 h as previously described in Endoh et al. 2012 Hi-C was performed following (Lieberman-Aiden et al., Science, 2009, DOI: 10.1126/science.1181369 ) with modifications detailed in Schoenfelder et al.

characteristic: description

text: Ring1a/b double knock out

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Ring1a/b dKO CHiC

characteristic: title


E-MTAB-3109:Ring1a KO CHiC

text: London Research Institute CRUK

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3109:Ring1a KO CHiC

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Protocols: Ring1A−/−;Ring1Bfl/fl;Rosa26::CreERT2 mESCs (Ring1A-KO) were cultured as described previously in Endoh et al. 2012 Hi-C was performed following (Lieberman-Aiden et al., Science, 2009, DOI: 10.1126/science.1181369 ) with modifications detailed in Schoenfelder et al.

text: Ring1a knock out

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Ring1a KO CHiC


characteristic: ENA-CHECKLIST

text: Rothamsted Research

text: public

characteristic: SRA accession

tag: Namespace:Rothamsted Research

characteristic: Submitter Id

text: ArrayExpress

text: bread wheat

text: Holdfast

characteristic: cultivar

text: Protocols: Immature grain at 12 days post-anthesis were collected from floret positions 1 & 2 of spikelets in the central 3/4 of the ears. Three tissue layers were isolated by manual dissection: the 'outer pericarp', which included the cuticle, outer epidermis, hypodermis and parenchyma cells; the 'inner pericarp' which comprised the cross cells, inner epidermis, integuments and aleurone; and the endosperm. Tissues were frozen in liquid nitrogen and stored at -80oC Plants growth in 15cm pots of a peat and loam-based compost in a glasshouse: 16 hr day (), 8 hr night (). Plant were tagged at anthesis. RNA was extracted according to Wan et al. (2009) Plant Biotechnol J 7, 401-410. Libraries were prepared using the Illumina TruSeq mRNA sample kit using 4ug of total RNA as described in the Illumina TruSeq RNA sample preparation guide, Part 15008136 Rev A, Nov 2010.

text: 12 days post anthesis

characteristic: developmental stage

text: Triticum aestivum

text: Triticum aestivum

text: outer pericarp

characteristic: organism part

text: Triticum aestivum


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Rothamsted Research

characteristic: INSDC center name

text: public

text: ArrayExpress

text: bread wheat

characteristic: common name

text: Holdfast

text: 12 days post anthesis

text: Triticum aestivum

text: Triticum aestivum

text: inner pericarp

text: Triticum aestivum


text: Rothamsted Research

text: public

text: ArrayExpress

characteristic: broker name

text: bread wheat

text: Holdfast

characteristic: description

text: 12 days post anthesis

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

text: endosperm

text: Triticum aestivum


text: Medical University of Gdansk

characteristic: INSDC first public

text: public

tag: Namespace:Medical University of Gdansk

text: ArrayExpress

text: human

text: Protocols: A custom SureSelect target enrichment library (design ID 0488011) was designed using the SureDesign online tool (Agilent Technologies, https://earray.chem.agilent.com/suredesign/). The library consisted of 42155 probes (2.6 Mbp) which encompassed 301 targets comprising 3059 genomic regions at 97.5% average coverage. The library targeted exonic as well as noncoding elements that were previously identified as predisposition loci, or were affected by somatic driver mutations in breast cancer.

text: breast carcinoma

characteristic: disease

text: Copy Number Alterations: 1

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

characteristic: sex

characteristic: title


characteristic: ENA-CHECKLIST

text: Medical University of Gdansk

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

text: breast carcinoma

text: Copy Number Alterations: 223

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Medical University of Gdansk

text: public

text: ArrayExpress

text: human

text: breast carcinoma

text: Copy Number Alterations: 67

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: female


characteristic: External Id

text: Medical University of Gdansk

characteristic: INSDC center name

text: public

text: ArrayExpress

text: human

characteristic: common name

text: breast carcinoma

text: Copy Number Alterations: 56

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female


text: Medical University of Gdansk

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: breast carcinoma

text: Copy Number Alterations: 8

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: female


text: Medical University of Gdansk

characteristic: INSDC first public

text: public

text: ArrayExpress

text: human

text: breast carcinoma

characteristic: disease

text: Copy Number Alterations: 359

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

text: EBI

text: public

text: ENA

text: fission yeast

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

characteristic: strain

text: BioSample entry for genome collection GCA_000002945

characteristic: title


text: EBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ENA

text: Sumatran orangutan

characteristic: isolate

text: mitochondrion

characteristic: organelle

text: Pongo abelii

text: Pongo abelii

text: BioSample entry for genome collection GCA_000003175


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EBI

text: public

characteristic: Submitter Id

text: ENA

text: pig

text: mitochondrion

text: Sus scrofa

text: Sus scrofa

text: BioSample entry for genome collection GCA_000008965


text: EBI

characteristic: INSDC center name

text: public

text: ENA

characteristic: broker name

text: western lowland gorilla

characteristic: common name

text: mitochondrion

text: Gorilla gorilla gorilla

text: Gorilla gorilla gorilla

text: gorilla

characteristic: sub species

text: BioSample entry for genome collection GCA_000027365


text: EBI

characteristic: INSDC first public

text: public

text: ENA

text: baker's yeast

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: BioSample entry for genome collection GCA_000091065


characteristic: ENA-CHECKLIST

text: EBI

text: public

text: ENA

text: torafugu

text: Japan:Shizuoka

characteristic: geographic location (country and/or sea)

text: Takifugu rubripes

text: Takifugu rubripes

text: male

characteristic: sex

text: testis

characteristic: tissue type

text: BioSample entry for genome collection GCA_000180615


text: EBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ENA

text: spotted green pufferfish

text: Tetraodon nigroviridis

text: Tetraodon nigroviridis

text: BioSample entry for genome collection GCA_000180735

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EBI

text: public

text: ENA

text: house mouse

text: Mus musculus

text: Mus musculus

text: BioSample entry for genome collection GCA_000181195


characteristic: External Id

text: EBI

text: public

characteristic: Submitter Id

text: ENA

text: Atlantic cod

text: Gadus morhua

text: Gadus morhua

text: BioSample entry for genome collection GCA_000231765


text: EBI

characteristic: INSDC center name

text: public

text: ENA

characteristic: broker name

text: common canary

text: Serinus canaria

text: Serinus canaria

text: BioSample entry for genome collection GCA_000534875


text: EBI

text: public

text: ENA

text: European ash

characteristic: common name

text: Fraxinus excelsior

text: Fraxinus excelsior

text: BioSample entry for genome collection GCA_000576895


text: EBI

characteristic: INSDC first public

text: public

text: ENA

text: Bactrian camel

text: Camelus bactrianus

text: Camelus bactrianus

text: BioSample entry for genome collection GCA_000604445


text: EBI

text: public

text: ENA

text: gray rockcress

text: Arabis alpina

characteristic: organism

text: Arabis alpina

text: BioSample entry for genome collection GCA_000612745


characteristic: ENA-CHECKLIST

text: EBI

text: public

text: ENA

text: brown bear

text: Ursus arctos

text: Ursus arctos

text: BioSample entry for genome collection GCA_000612945


text: EBI

text: public

text: ENA

text: human whipworm

text: Trichuris trichiura

text: Trichuris trichiura

text: BioSample entry for genome collection GCA_000613005


text: EBI

text: public

text: ENA

text: rape

text: Brassica napus

text: Brassica napus

text: BioSample entry for genome collection GCA_000751015


text: Larval:Day 5 - ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zmp_phenotype_48_1_phenotypic_1-sc-2177877

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TGCGATCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: zmp_phenotype_48_1_phenotypic_2-sc-2177878

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TTCCTGCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zmp_phenotype_48_1_phenotypic_3-sc-2177879

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TAGTGACT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

text: public

text: zmp_phenotype_48_1_phenotypic_4-sc-2177880

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TACAGGAT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

text: public

text: zmp_phenotype_48_1_phenotypic_6-sc-2177881

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TGTGGTTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

text: zmp_phenotype_48_1_phenotypic_7-sc-2177882

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TAGTCTTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zmp_phenotype_48_1_phenotypic_8-sc-2177883

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TTCCATTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zmp_phenotype_48_1_phenotypic_10-sc-2177884

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TAACGCTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zmp_phenotype_48_1_phenotypic_11-sc-2177885

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TTGGTATG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zmp_phenotype_48_1_phenotypic_12-sc-2177886

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TGAACTGG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: SRA accession

text: zmp_phenotype_48_1_non_phenotypic_2-sc-2177887

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TCTCACGG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zmp_phenotype_48_1_non_phenotypic_3-sc-2177888

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TCAGGAGG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

text: public

text: zmp_phenotype_48_1_non_phenotypic_4-sc-2177889

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TAAGTTCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

text: public

text: zmp_phenotype_48_1_non_phenotypic_5-sc-2177890

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TCCAGTCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

text: zmp_phenotype_48_1_non_phenotypic_6-sc-2177891

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TGTATGCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zmp_phenotype_48_1_non_phenotypic_7-sc-2177892

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TCATTGAG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zmp_phenotype_48_1_non_phenotypic_8-sc-2177893

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TGGCTCAG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zmp_phenotype_48_1_non_phenotypic_9-sc-2177894

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TATGCCAG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zmp_phenotype_48_1_non_phenotypic_10-sc-2177895

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 48 clutch 1. A 8 base indexing sequence (TCAGATTC) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph48

text: Danio rerio

text: mixed