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text: ENVO:tropical broadleaf forest biome

characteristic: env biome

text: ENVO:animalia-associated habitat

characteristic: env feature

text: ENVO:feces

text: Rainforest

text: mantled howler monkeys

text: F.f.yt

text: Illumina MiSeq

text: Alouatta palliata

characteristic: organism

text: Northwestern University

text: Northwestern University

text: True

text: Illumina

text: CCGGACTACHVGGGTWTCTAAT

text: True

text: completed

text: stool

text: Alouatta palliata

text: Leaf

text: Apalliata

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

text: public

text: FJ.M

text: False

text: CAACGCTAGAAT

text: UC Boulder

text: 12:00:00 PM

text: mantled howler monkey

text: primate metagenome

text: monkey feces, Costa Rica

text: folivore

text: Fragment

text: True

text: ENVO:tropical broadleaf forest biome

text: ENVO:animalia-associated habitat

text: ENVO:feces

characteristic: env matter

text: Rainforest

text: mantled howler monkeys

characteristic: host common name

text: FJ.M

characteristic: host subject id

characteristic: host taxid

text: Illumina MiSeq

characteristic: instrument model

characteristic: latitude

characteristic: library construction protocol

characteristic: longitude

text: Alouatta palliata

text: Northwestern University

text: Northwestern University

text: True

text: Illumina

characteristic: platform

text: CCGGACTACHVGGGTWTCTAAT

characteristic: primer

text: True

characteristic: public

text: completed

characteristic: run prefix

text: stool

characteristic: sample type

text: Alouatta palliata

text: Leaf

characteristic: season

text: Apalliata

characteristic: species


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: FJ.O

characteristic: anonymized name

text: False

text: AAGAGTCTCTAG

characteristic: barcode

text: UC Boulder

text: 12:00:00 PM

text: mantled howler monkey

characteristic: common name

text: primate metagenome

characteristic: country

text: monkey feces, Costa Rica

characteristic: description

text: folivore

characteristic: diet

text: Fragment

characteristic: disturbance

text: True

text: ENVO:tropical broadleaf forest biome

characteristic: env biome

text: ENVO:animalia-associated habitat

characteristic: env feature

text: ENVO:feces

text: Rainforest

text: mantled howler monkeys

text: FJ.O

text: Illumina MiSeq

text: Alouatta palliata

characteristic: organism

text: Northwestern University

text: Northwestern University

text: True

text: Illumina

text: CCGGACTACHVGGGTWTCTAAT

text: True

text: completed

text: stool

text: Alouatta palliata

text: Leaf

text: Apalliata

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

text: public

text: FJ.Q

text: False

text: CTATGCCGGCTA

text: UC Boulder

text: 12:00:00 PM

text: mantled howler monkey

text: primate metagenome

text: monkey feces, Costa Rica

text: folivore

text: Continuous

text: True

text: ENVO:tropical broadleaf forest biome

text: ENVO:animalia-associated habitat

text: ENVO:feces

characteristic: env matter

text: Rainforest

text: mantled howler monkeys

characteristic: host common name

text: FJ.Q

characteristic: host subject id

characteristic: host taxid

text: Illumina MiSeq

characteristic: instrument model

characteristic: latitude

characteristic: library construction protocol

characteristic: longitude

text: Alouatta palliata

text: Northwestern University

text: Northwestern University

text: True

text: Illumina

characteristic: platform

text: CCGGACTACHVGGGTWTCTAAT

characteristic: primer

text: True

characteristic: public

text: completed

characteristic: run prefix

text: stool

characteristic: sample type

text: Alouatta palliata

text: Leaf

characteristic: season

text: Apalliata

characteristic: species


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: FJ.S

characteristic: anonymized name

text: False

text: CGACACGGAGAA

characteristic: barcode

text: UC Boulder

text: 12:00:00 PM

text: mantled howler monkey

characteristic: common name

text: primate metagenome

characteristic: country

text: monkey feces, Costa Rica

characteristic: description

text: folivore

characteristic: diet

text: Continuous

characteristic: disturbance

text: True

text: ENVO:tropical broadleaf forest biome

characteristic: env biome

text: ENVO:animalia-associated habitat

characteristic: env feature

text: ENVO:feces

text: Rainforest

text: mantled howler monkeys

text: FJ.S

text: Illumina MiSeq

text: Alouatta palliata

characteristic: organism

text: Northwestern University

text: Northwestern University

text: True

text: Illumina

text: CCGGACTACHVGGGTWTCTAAT

text: True

text: completed

text: stool

text: Alouatta palliata

text: Leaf

text: Apalliata

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

text: public

text: FM

text: False

text: CACCGAAATCTG

text: UC Boulder

text: 12:00:00 PM

text: mantled howler monkey

text: primate metagenome

text: monkey feces, Costa Rica

text: folivore

text: Continuous

text: True

text: ENVO:tropical broadleaf forest biome

text: ENVO:animalia-associated habitat

text: ENVO:feces

characteristic: env matter

text: Rainforest

text: mantled howler monkeys

characteristic: host common name

text: FM

characteristic: host subject id

characteristic: host taxid

text: Illumina MiSeq

characteristic: instrument model

characteristic: latitude

characteristic: library construction protocol

characteristic: longitude

text: Alouatta palliata

text: Northwestern University

text: Northwestern University

text: True

text: Illumina

characteristic: platform

text: CCGGACTACHVGGGTWTCTAAT

characteristic: primer

text: True

characteristic: public

text: completed

characteristic: run prefix

text: stool

characteristic: sample type

text: Alouatta palliata

text: Leaf

characteristic: season

text: Apalliata

characteristic: species


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: M

characteristic: anonymized name

text: False

text: TATGGTACCCAG

characteristic: barcode

text: UC Boulder

text: 12:00:00 PM

text: mantled howler monkey

characteristic: common name

text: primate metagenome

characteristic: country

text: monkey feces, Costa Rica

characteristic: description

text: folivore

characteristic: diet

text: Continuous

characteristic: disturbance

text: True

text: ENVO:tropical broadleaf forest biome

characteristic: env biome

text: ENVO:animalia-associated habitat

characteristic: env feature

text: ENVO:feces

text: Rainforest

text: mantled howler monkeys

text: M

text: Illumina MiSeq

text: Alouatta palliata

characteristic: organism

text: Northwestern University

text: Northwestern University

text: True

text: Illumina

text: CCGGACTACHVGGGTWTCTAAT

text: True

text: completed

text: stool

text: Alouatta palliata

text: Leaf

text: Apalliata

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

text: public

text: M.B

text: False

text: ACATACTGAGCA

text: UC Boulder

text: 12:00:00 PM

text: mantled howler monkey

text: primate metagenome

text: monkey feces, Costa Rica

text: folivore

text: Fragment

text: True

text: ENVO:tropical broadleaf forest biome

text: ENVO:animalia-associated habitat

text: ENVO:feces

characteristic: env matter

text: Rainforest

text: mantled howler monkeys

characteristic: host common name

text: M.B

characteristic: host subject id

characteristic: host taxid

text: Illumina MiSeq

characteristic: instrument model

characteristic: latitude

characteristic: library construction protocol

characteristic: longitude

text: Alouatta palliata

text: Northwestern University

text: Northwestern University

text: True

text: Illumina

characteristic: platform

text: CCGGACTACHVGGGTWTCTAAT

characteristic: primer

text: True

characteristic: public

text: completed

characteristic: run prefix

text: stool

characteristic: sample type

text: Alouatta palliata

text: Leaf

characteristic: season

text: Apalliata

characteristic: species


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: M.G

characteristic: anonymized name

text: False

text: TGACGTAGAACT

characteristic: barcode

text: UC Boulder

text: 12:00:00 PM

text: mantled howler monkey

characteristic: common name

text: primate metagenome

characteristic: country

text: monkey feces, Costa Rica

characteristic: description

text: folivore

characteristic: diet

text: Fragment

characteristic: disturbance

text: True

text: ENVO:tropical broadleaf forest biome

characteristic: env biome

text: ENVO:animalia-associated habitat

characteristic: env feature

text: ENVO:feces

text: Rainforest

text: mantled howler monkeys

text: M.G

text: Illumina MiSeq

text: Alouatta palliata

characteristic: organism

text: Northwestern University

text: Northwestern University

text: True

text: Illumina

text: CCGGACTACHVGGGTWTCTAAT

text: True

text: completed

text: stool

text: Alouatta palliata

text: Leaf

text: Apalliata

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

text: public

text: MJ.L

text: False

text: GGCTAAACTATG

text: UC Boulder

text: 12:00:00 PM

text: mantled howler monkey

text: primate metagenome

text: monkey feces, Costa Rica

text: folivore

text: Fragment

text: True

text: ENVO:tropical broadleaf forest biome

text: ENVO:animalia-associated habitat

text: ENVO:feces

characteristic: env matter

text: Rainforest

text: mantled howler monkeys

characteristic: host common name

text: MJ.L

characteristic: host subject id

characteristic: host taxid

text: Illumina MiSeq

characteristic: instrument model

characteristic: latitude

characteristic: library construction protocol

characteristic: longitude

text: Alouatta palliata

text: Northwestern University

text: Northwestern University

text: True

text: Illumina

characteristic: platform

text: CCGGACTACHVGGGTWTCTAAT

characteristic: primer

text: True

characteristic: public

text: completed

characteristic: run prefix

text: stool

characteristic: sample type

text: Alouatta palliata

text: Leaf

characteristic: season

text: Apalliata

characteristic: species


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MJ.N

characteristic: anonymized name

text: False

text: CATAAGGGAGGC

characteristic: barcode

text: UC Boulder

text: 12:00:00 PM

text: mantled howler monkey

characteristic: common name

text: primate metagenome

characteristic: country

text: monkey feces, Costa Rica

characteristic: description

text: folivore

characteristic: diet

text: Continuous

characteristic: disturbance

text: True

text: ENVO:tropical broadleaf forest biome

characteristic: env biome

text: ENVO:animalia-associated habitat

characteristic: env feature

text: ENVO:feces

text: Rainforest

text: mantled howler monkeys

text: MJ.N

text: Illumina MiSeq

text: Alouatta palliata

characteristic: organism

text: Northwestern University

text: Northwestern University

text: True

text: Illumina

text: CCGGACTACHVGGGTWTCTAAT

text: True

text: completed

text: stool

text: Alouatta palliata

text: Leaf

text: Apalliata

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

text: public

text: MJ.T

text: False

text: AAGAGCAGAGCC

text: UC Boulder

text: 12:00:00 PM

text: mantled howler monkey

text: primate metagenome

text: monkey feces, Costa Rica

text: folivore

text: Continuous

text: True

text: ENVO:tropical broadleaf forest biome

text: ENVO:animalia-associated habitat

text: ENVO:feces

characteristic: env matter

text: Rainforest

text: mantled howler monkeys

characteristic: host common name

text: MJ.T

characteristic: host subject id

characteristic: host taxid

text: Illumina MiSeq

characteristic: instrument model

characteristic: latitude

characteristic: library construction protocol

characteristic: longitude

text: Alouatta palliata

text: Northwestern University

text: Northwestern University

text: True

text: Illumina

characteristic: platform

text: CCGGACTACHVGGGTWTCTAAT

characteristic: primer

text: True

characteristic: public

text: completed

characteristic: run prefix

text: stool

characteristic: sample type

text: Alouatta palliata

text: Leaf

characteristic: season

text: Apalliata

characteristic: species


E-MTAB-4008:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-4008:Sample 1

tag: Namespace:Department of Molecular Neuroscience, UCL Institute of Neurology

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

characteristic: common name

text: Protocols: HR1 cells were reverse-transfected with 5nM siRNA targeting hnRNPC mRNA (HSS179304 and HSS179305) or siRNA targeting Upf1 mRNA (HSS109172) as well as control siRNA Negative Control with medium GC content (Invitrogen). Depletion of hnRNPC was achieved 48 hours after initial siRNA transfection. For depletion of Upf1, cells were transfected a second time after 48 hours, and collected 96 hours after the first siRNA transfection. RNA was extracted using trizol as per manufacturer instructions. RNAseq libraries were produced using TruSeq stranded mRNAseq library kit (Illumina).

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: siRNA control

characteristic: rna interference

text: Homo sapiens

text: Sample 1

characteristic: title


E-MTAB-4008:Sample 10

text: Department of Molecular Neuroscience, UCL Institute of Neurology

characteristic: INSDC center name

text: public

text: E-MTAB-4008:Sample 10

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #1 + Upf1

text: Homo sapiens

text: Sample 10


E-MTAB-4008:Sample 11

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-4008:Sample 11

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: siRNA control

text: Homo sapiens

text: Sample 11


E-MTAB-4008:Sample 12

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-4008:Sample 12

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #1

text: Homo sapiens

text: Sample 12


E-MTAB-4008:Sample 13

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-4008:Sample 13

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #2

text: Homo sapiens

text: Sample 13


E-MTAB-4008:Sample 14

characteristic: External Id

text: public

text: E-MTAB-4008:Sample 14

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: siRNA Upf1

text: Homo sapiens

text: Sample 14


E-MTAB-4008:Sample 15

characteristic: INSDC first public

text: public

text: E-MTAB-4008:Sample 15

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #1 + Upf1

text: Homo sapiens

text: Sample 15


E-MTAB-4008:Sample 2

characteristic: INSDC last update

text: public

text: E-MTAB-4008:Sample 2

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #1

text: Homo sapiens

text: Sample 2


E-MTAB-4008:Sample 3

text: public

characteristic: INSDC status

text: E-MTAB-4008:Sample 3

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #2

text: Homo sapiens

text: Sample 3


E-MTAB-4008:Sample 4

text: public

characteristic: SRA accession

text: E-MTAB-4008:Sample 4

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: siRNA Upf1

text: Homo sapiens

text: Sample 4


E-MTAB-4008:Sample 5

text: public

text: E-MTAB-4008:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #1 + Upf1

text: Homo sapiens

text: Sample 5


E-MTAB-4008:Sample 6

text: public

text: E-MTAB-4008:Sample 6

text: ArrayExpress

characteristic: broker name

text: human

text: Homo sapiens

text: Homo sapiens

text: siRNA control

text: Homo sapiens

text: Sample 6


E-MTAB-4008:Sample 7

text: public

text: E-MTAB-4008:Sample 7

text: ArrayExpress

characteristic: cell line

text: human

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #1

text: Homo sapiens

text: Sample 7


E-MTAB-4008:Sample 8

text: public

text: E-MTAB-4008:Sample 8

text: ArrayExpress

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #2

text: Homo sapiens

text: Sample 8


E-MTAB-4008:Sample 9

text: public

text: E-MTAB-4008:Sample 9

text: ArrayExpress

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: siRNA Upf1

text: Homo sapiens

text: Sample 9


text: EMBL

text: public

text: ArrayExpress

text: human

text: Protocols: Cells were cultured at 37C, 95 % humidity and 5 % CO2 in 1 ?? high glucose DMEM supplemented with 10 % fetal bovine serum, 2 mM L-glutamine, 100 U/mL penicillin and 100 ??g/mL streptomycin sulfate. Induced HEK293 Flp-In TRex cell lines expressing FASTKD2-GFP (10 ng/mL tetracyclin, 16 hrs) were washed twice with PBS and irradiated with UV light at 254 nm (150 mJ/cm2) on ice. Immediately after irradiation cells were lysed in three cell pellet volumes of lysis buffer (100 mM KCI, 5 mM MgCl2, 10 mM Tris-HCI pH 7.5, 0.5 % NP-40, 4 mM DTT, 100 U/mL RNasin [Promega], 200 ??M ribonucleoside vanadyl complex [NEB], EDTA-free protease inhibitor cocktail [Roche]). Lysates were cleared by centrifugation at 16 000 x g for 20 min at 4C. Cleared lysates (typically 2 mL) were then mixed 1:4 with 5 ?? High Salt Buffer (1.25 M NaCl, 100 mM Tris-HCl pH 7.5, 0.5 % sodium dodecyl sulphate). The lysates were pre-cleared by incubation with 60 ??L of equilibrated blocked magnetic particle suspension (Chromotek) per mL of lysate (1 h, 4C, gentle rotation). GFP fusion proteins were then captured from pre-cleared lysates by incubation with 60 ??L of GFP-Trap magnetic particle suspension (GFP-Trap_M, Chromotek) per mL of lysate (2 h, 4C, gentle rotation). Beads were collected using a magnet and washed twice with high salt buffer. The beads were then washed twice with medium salt buffer (250 mM NaCl, 20 mM Tris-HCl pH 7.5, 1 mM MgCl2, 0.05 % NP-40, 100 U/mL RNasin, 200 ??M ribonucleoside vanadyl complex, EDTA-free protease inhibitor cocktail) and once with low salt buffer (150 mM NaCl, 20 mM Tris-HCl pH 7.5, 1 mM MgCl2, 0.01 % NP-40, 50 U/mL RNasin, EDTA-free protease inhibitor cocktail). Beads were resuspended in 1 mL low salt buffer without RNasin and incubated (3 min, 37C, 1 100 rpm) with 4 U of RNAse I (Life Technologies) and 4 U of Turbo DNAse (Life Technologies). Beads were washed once with high salt buffer, twice with low salt buffer, re-suspended in 20 ??L of PNK mix (70 mM Tris-HCl pH 6.5, 10 mM MgCl2, 5 mM DTT, 250 U/mL T4 polynucleotide kinase [NEB], 500 U/mL RNasin) and incubated with agitation (1 100 rpm) for 20 min at 37C. Beads were then washed twice with high salt buffer, twice with low salt buffer and incubated for 16 h (1 100 rpm, 16C) in 20 ??L ligation mix (50 mM Tris-HCl pH 7.5, 10 mM MgCl2, 10 mM DTT, 500 U/mL T4 RNA ligase 1, 500 U/mL RNasin, 1.5 ??M pre-adenylated linker L3 [5???-rApp-AGA TCG GAA GAG CGG TTC AG-ddC-3???], 20 % PEG-400 [Sigma]). The beads were washed three times with high salt buffer, twice with low salt buffer, proteins digested with proteinase K and samples processed for all subsequent steps as described previously (Nat Struct Mol Biol 17:909-915, 2010.). cDNA libraries obtained after PCR amplification with universal Solexa primers (25 cycles) were multiplexed and sequenced using an Illumina HiSeq2000 platform.

characteristic: genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


text: EMBL

text: public

text: E-MATB-4010:FASTKD2_K2_1_11_06_14_rclip10

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: EMBL

characteristic: INSDC center name

text: public

text: E-MATB-4010:FASTKD2_K2_3_11_06_14_rclip15

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: EMBL

text: public

text: E-MATB-4010:FASTKD2_K2_2_11_06_14_rclip12

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


E-MATB-4009:Sample 1

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MATB-4009:Sample 1

text: ArrayExpress

text: human

text: Protocols: HR1 cells were reverse-transfected with 5nM siRNA targeting hnRNPC mRNA (HSS179304 and HSS179305) or control siRNA Negative Control with medium GC content (Invitrogen). Depletion of hnRNPC was achieved 48 hours after one siRNA transfection. RNA was extracted using trizol as per manufacturer instructions. RNAseq libraries were produced using TruSeq unstranded RNAseq library kit (Illumina).

text: cytoplasmic RNA

characteristic: fraction

text: Homo sapiens

text: Homo sapiens

text: no siRNA transfected

characteristic: rna interference

text: Homo sapiens

unit: minute

characteristic: time

text: Sample 1


E-MATB-4009:Sample 10

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MATB-4009:Sample 10

text: ArrayExpress

text: human

text: cytoplasmic RNA

text: Homo sapiens

text: Homo sapiens

text: siRNA control

text: Homo sapiens

text: Sample 10


E-MATB-4009:Sample 11

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MATB-4009:Sample 11

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: cytoplasmic RNA

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #1

text: Homo sapiens

text: Sample 11


E-MATB-4009:Sample 12

text: public

text: E-MATB-4009:Sample 12

text: ArrayExpress

characteristic: cell line

text: human

characteristic: common name

characteristic: description

text: cytoplasmic RNA

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #2

text: Homo sapiens

text: Sample 12


E-MATB-4009:Sample 13

characteristic: INSDC center name

text: public

text: E-MATB-4009:Sample 13

text: ArrayExpress

text: human

text: nuclear RNA

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: no siRNA transfected

text: Homo sapiens

text: Sample 13

characteristic: title


E-MATB-4009:Sample 14

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MATB-4009:Sample 14

text: ArrayExpress

text: human

text: nuclear RNA

characteristic: fraction

text: Homo sapiens

text: Homo sapiens

text: siRNA control

text: Homo sapiens

text: Sample 14


E-MATB-4009:Sample 15

characteristic: ENA-LAST-UPDATE

text: public

text: E-MATB-4009:Sample 15

text: ArrayExpress

text: human

text: nuclear RNA

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #1

characteristic: rna interference

text: Homo sapiens

characteristic: time

text: Sample 15


E-MATB-4009:Sample 16

characteristic: External Id

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MATB-4009:Sample 16

text: ArrayExpress

text: human

text: nuclear RNA

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #2

text: Homo sapiens

text: Sample 16


E-MATB-4009:Sample 17

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MATB-4009:Sample 17

characteristic: Submitter Id

text: ArrayExpress

text: human

text: nuclear RNA

text: Homo sapiens

text: Homo sapiens

text: no siRNA transfected

text: Homo sapiens

text: Sample 17


E-MATB-4009:Sample 18

text: public

text: E-MATB-4009:Sample 18

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

characteristic: common name

text: nuclear RNA

text: Homo sapiens

text: Homo sapiens

text: siRNA control

text: Homo sapiens

text: Sample 18


E-MATB-4009:Sample 19

characteristic: INSDC center name

text: public

text: E-MATB-4009:Sample 19

text: ArrayExpress

text: human

characteristic: description

text: nuclear RNA

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: siRNA hnRNPC #1

text: Homo sapiens

text: Sample 19


E-MATB-4009:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MATB-4009:Sample 2

text: ArrayExpress

text: human

text: cytoplasmic RNA

text: Homo sapiens

text: Homo sapiens

text: siRNA control

text: Homo sapiens

text: Sample 2

characteristic: title


E-MATB-4009:Sample 20

characteristic: ENA-LAST-UPDATE

text: public

text: E-MATB-4009:Sample 20

text: ArrayExpress

text: human

text: nuclear RNA

characteristic: fraction

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #2

characteristic: rna interference

text: Homo sapiens

text: Sample 20


E-MATB-4009:Sample 21

characteristic: External Id

characteristic: INSDC first public

text: public

text: E-MATB-4009:Sample 21

text: ArrayExpress

text: human

text: nuclear RNA

text: Homo sapiens

text: Homo sapiens

text: no siRNA transfected

text: Homo sapiens

characteristic: time

text: Sample 21


E-MATB-4009:Sample 22

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MATB-4009:Sample 22

text: ArrayExpress

text: human

text: nuclear RNA

text: Homo sapiens

text: Homo sapiens

text: siRNA control

text: Homo sapiens

text: Sample 22


E-MATB-4009:Sample 23

text: public

text: E-MATB-4009:Sample 23

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: nuclear RNA

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #1

text: Homo sapiens

text: Sample 23


E-MATB-4009:Sample 24

characteristic: INSDC center name

text: public

text: E-MATB-4009:Sample 24

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: nuclear RNA

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #2

text: Homo sapiens

text: Sample 24


E-MATB-4009:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MATB-4009:Sample 3

text: ArrayExpress

text: human

text: cytoplasmic RNA

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: siRNA hnRNPC #1

text: Homo sapiens

text: Sample 3


E-MATB-4009:Sample 4

characteristic: ENA-LAST-UPDATE

text: public

text: E-MATB-4009:Sample 4

text: ArrayExpress

text: human

text: cytoplasmic RNA

characteristic: fraction

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #2

text: Homo sapiens

text: Sample 4

characteristic: title


E-MATB-4009:Sample 5

characteristic: External Id

characteristic: INSDC first public

text: public

text: E-MATB-4009:Sample 5

text: ArrayExpress

text: human

text: cytoplasmic RNA

text: Homo sapiens

text: Homo sapiens

text: no siRNA transfected

characteristic: rna interference

text: Homo sapiens

text: Sample 5


E-MATB-4009:Sample 6

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MATB-4009:Sample 6

text: ArrayExpress

text: human

text: cytoplasmic RNA

text: Homo sapiens

text: Homo sapiens

text: siRNA control

text: Homo sapiens

characteristic: time

text: Sample 6


E-MATB-4009:Sample 7

text: public

characteristic: SRA accession

text: E-MATB-4009:Sample 7

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: cytoplasmic RNA

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #1

text: Homo sapiens

text: Sample 7


E-MATB-4009:Sample 8

characteristic: INSDC center name

text: public

text: E-MATB-4009:Sample 8

text: ArrayExpress

characteristic: cell line

text: human

characteristic: common name

text: cytoplasmic RNA

text: Homo sapiens

text: Homo sapiens

text: siRNA hnRNPC #2

text: Homo sapiens

text: Sample 8


E-MATB-4009:Sample 9

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MATB-4009:Sample 9

text: ArrayExpress

text: human

characteristic: description

text: cytoplasmic RNA

text: Homo sapiens

text: Homo sapiens

text: no siRNA transfected

text: Homo sapiens

text: Sample 9


text: Yeast

characteristic: ArrayExpress-Phenotype

text: Saccharomyces cerevisiae

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae


text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: External Id

text: SC

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: Lin_neg_bone marrow

characteristic: sample description

text: Mus musculus


text: female

text: Mus musculus

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: Lin_neg_bone marrow

text: Mus musculus


text: Mouse

text: Mus Musculus

text: SC

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: Homo Sapien

characteristic: ENA-CHECKLIST

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CCCTATGGCCC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GACAAAGAGAA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( AACCACAGCAC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CAGGTGACGGC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GAGTCGCGACG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( AGGAACTACAC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GGGCTCCGACA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CAACGCCAAAA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( TACCTAACGCA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CATAATGGCGA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( ACGAGACACCC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( AGTACTACGCG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GCTTGAGGACC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CCAAGCAGGCC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( AAAGAATCGCC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GGCTTAAGAGA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CTCCACGCAAG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Peking University

text: public

tag: Namespace:Peking University

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Protocols: The 14-day homozygous 4EnhpEXB1-EXB1GR-13 transgenetic plants were treated with 30 IzM DEX or DMSO (mock). The tissues around leaf axils were collected. Total RNAs were prepared using TRIzol reagent (Invitrogen). The library was constructed by the Biodynamic Optical Imaging Center (BIOPIC) of Peking University following their standard procedure.

characteristic: description

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

characteristic: title


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-4000:iCLIP_EIF4A3_293Flp_RNase1:500_Hs_NNNCTGCNN_20150803_Mx1_17

tag: Namespace:Department of Molecular Neuroscience at the UCL Institute of Neurology. http://ulelab.info/

text: NNNCTGCNN

characteristic: barcode

text: ArrayExpress

text: HeLa

characteristic: cell line

text: human

text: Protocols: HEK293 cells were crosslinked with 0.15mJ/cm2 254nm UV light. 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. The 3 prime adapter sequence is AGATCGGAAG

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: External Id

text: Department of Molecular Neuroscience at the UCL Institute of Neurology. http://ulelab.info/

text: public

text: E-MTAB-4000:iCLIP_EIF4A3_293Flp_RNase1:500_Hs_NNNGAGCNN_20150803_Mx1_18

text: NNNGAGCNN

text: ArrayExpress

text: HeLa

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


characteristic: INSDC first public

text: public

tag: Namespace:Institute of Biosciences and Medical Technology

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-001 baseline


text: Institute of Biosciences and Medical Technology

characteristic: INSDC last update

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-001 progression


text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-002 baseline


text: public

characteristic: SRA accession

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-002 progression


characteristic: INSDC center name

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-005 baseline


text: public

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-005 progression


text: public

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: VC-007 baseline


characteristic: ENA-CHECKLIST

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-007 on-treatment


characteristic: ENA-FIRST-PUBLIC

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-007 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-008 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-008 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-008 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-010 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-011 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-011 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-012 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-012 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-016 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-016 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-017 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-017 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-017 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-019 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-019 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-020 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-020 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-021 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-022 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-022 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-022 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-024 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-024 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-024 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-025 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-025 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-025 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-027 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-028 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-028 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-029 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-030 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-032 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-034 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-034 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-035 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-035 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-036 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-036 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-037 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-037 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-041 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-041 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-042 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-044 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-044 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-045 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-045 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-045 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-046 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-046 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-047 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-048 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-048 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-051 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-052 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-052 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-052 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-055 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-055 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-056 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-056 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-057 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-057 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-057 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-058 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-058 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-061 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-061 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-062 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-062 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-063 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-063 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-068 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-068 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-070 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-070 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-070 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-071 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-071 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-071 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-072 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-072 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-073 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-073 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-074 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-074 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-075 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-077 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-077 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-079 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-080 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-080 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-081 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-081 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-081 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-082 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-082 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-083 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-083 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-084 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-085 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-085 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-086 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-087 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-087 on-treatment


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-088 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-089 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-090 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-092 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-093 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-094 baseline


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-095 baseline


text: MPI-TUEBINGEN

text: public

text: guppy

text: LP Oropuche

text: Poecilia reticulata

text: Poecilia reticulata

text: F

characteristic: sex


E-MTAB-4021:Sample 1

text: OXFORD

text: public

text: E-MTAB-4021:Sample 1

text: ArrayExpress

characteristic: broker name

text: bundle sheath

characteristic: cell type

text: sorghum

text: Protocols: Plants grown in greenhouse QIAGEN RNeasy Plant Minikit Illumina TruSeq

characteristic: description

text: 3 leaf fully expanded stage

characteristic: developmental stage

text: Sorghum bicolor

text: Sorghum bicolor

text: leaf

characteristic: organism part

text: Sorghum bicolor

text: Sample 1


E-MTAB-4021:Sample 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: OXFORD

text: public

text: E-MTAB-4021:Sample 2

text: ArrayExpress

text: bundle sheath

text: sorghum

text: 3 leaf fully expanded stage

text: Sorghum bicolor

text: Sorghum bicolor

text: leaf

text: Sorghum bicolor

text: Sample 2

characteristic: title


E-MTAB-4021:Sample 3

text: OXFORD

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-4021:Sample 3

text: ArrayExpress

text: bundle sheath

text: sorghum

text: 3 leaf fully expanded stage

text: Sorghum bicolor

characteristic: organism

text: Sorghum bicolor

text: leaf

text: Sorghum bicolor

text: Sample 3


E-MTAB-4021:Sample 4

text: OXFORD

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-4021:Sample 4

text: ArrayExpress

text: leaf mesophyll

text: sorghum

text: 3 leaf fully expanded stage

text: Sorghum bicolor

text: Sorghum bicolor

text: leaf

text: Sorghum bicolor

text: Sample 4


E-MTAB-4021:Sample 5

characteristic: ENA-CHECKLIST

text: OXFORD

text: public

text: E-MTAB-4021:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: leaf mesophyll

text: sorghum

characteristic: common name

text: 3 leaf fully expanded stage

text: Sorghum bicolor

text: Sorghum bicolor

text: leaf

text: Sorghum bicolor

text: Sample 5


E-MTAB-4021:Sample 6

characteristic: ENA-FIRST-PUBLIC

text: OXFORD

text: public

text: E-MTAB-4021:Sample 6

text: ArrayExpress

characteristic: broker name

text: leaf mesophyll

text: sorghum

text: 3 leaf fully expanded stage

text: Sorghum bicolor

text: Sorghum bicolor

text: leaf

text: Sorghum bicolor

text: Sample 6


E-MTAB-4014:Sample 1

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 1

tag: Namespace:Queen's University Belfast

text: ArrayExpress

text: velvet grass

text: Protocols: Plant and soil collection: H. lanatus plants and topsoil were collected from three locations: 6 plants (6 lime genotypes) were selected from a disused limestone quarry soil (pH 7.5) in County Antrim, NI, hereafter referred to as lime, 6 plants (6 acid genotypes) from an acidic peat bog (pH 3.5) in County Tyrone, NI, hereafter referred to as acid, and 6 plants (6 intermediate genotypes) from an acid mineral rough grassland (pH 5.5) (County Down, NI), hereafter refereed to as intermediate. In each case plants were carefully selected within each habitat, with all plants at least 5m apart, so that each of the 6 plants represents a clone for a unique genotype of that particular habitat. Tillers from each plant were trans-planted into John Innes no. 2 compost to nutritionally neutralize all plants. Tillers from compost grown lime and acid ecotypes (5 genotypes each) were subsequently used for set up of a full factorial soil transplant experiment. Tillers from one genotype of each the acid, lime and intermediate population were subsequently grown in hydroponics for additional root acid stress relevant transcriptome sequencing data. Full factorial reciprocal soil transplant experiment: Tillers from 5 genotypes of each the acid and lime ecotype were transplanted from compost onto acid bog soil (total 10 pots) and grown in the growth chamber for 7 weeks. Replication was at the level of ecotype by using 5 tillers from 5 different clonal plants from each ecotype (5 genotypes per ecotype) rather than using multiple tillers from one plant, to ensure that natural variation within the two H. lanatus ecotypes could be investigated. At harvest at 7 weeks, roots and shoots were washed thoroughly with deionized water, separated, frozen in liquid nitrogen and stored at -80C until RNA extraction. RNA Extraction, QA and RNAseq: RNA extraction of frozen shoot tissue: Shoot samples were homogenized in FastPrep Lysing tubes containing Lysing Matrix D (MP Biomedicals, USA) using two 20-second Precellys 24-Dual (Bertin Technologies, France) runs at 5500rpm to produce a fine powder. Inbetween runs the tubes were submerged into liquid nitrogen to prevent degradation of RNA. RNA was extracted using an RNeasy Plant Mini Kit (QIAGEN), according to protocol and with inclusion of a DNA digestion step (DNase Set, QIAGEN) with the following amendment: 450l Buffer RLT (containing 4.5l -Mercaptoethanol) was added to the Precellys lysing tube containing the ground tissue and homogenised again using the Precellys 24-Dual for 5 seconds at 5500rpm to ensure that the powdered sample was suspended as quickly as possible to prevent RNA degradation. The lysate was transferred to a QIAshredder spin column and centrifuged at 14,000rpm for 2 minutes, followed by RNA extraction according to the standard protocoll. RNA was then eluted twice using the same eluate to further concentrate the RNA and stored at -80 C. RNA was quantified using a Nanodrop 8000 spectrophotometer (Thermo Scientific) and Agilent 2200 Tapestation (Agilent Technologies) to assess quality (purity and integrity) of the RNA. 19/20 shoot samples passed the QA and were submitted for RNAseq. 1 shoots sample from the soil experiment failed the QC and could therefore not be processed for library preparation for the RNAseq study, hence there are 5 replicates for 3 treatments and 4 replicates for 1 treatment. Transcriptome sequencing (Illumina, RNAseq) was conducted at the Genome Analysis Centre (TGAC), Norwich, UK. Barcoded 125bp paired end TruSeq RNA libraries (polyA selected) were generated for each RNA sample and sequenced on the Illumina HiSeq 2500.

characteristic: description

text: acid

characteristic: ecotype

text: D

characteristic: genotype

text: acid bog soil

characteristic: growth condition

text: Holcus lanatus

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 1


E-MTAB-4014:Sample 10

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 10

text: ArrayExpress

text: velvet grass

text: lime

text: H

text: acid bog soil

text: Holcus lanatus

text: Holcus lanatus

text: shoot

characteristic: organism part

text: Holcus lanatus

text: Sample 10


E-MTAB-4014:Sample 11

text: Queen's University Belfast

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-4014:Sample 11

text: ArrayExpress

text: velvet grass

text: Protocols: Plant and soil collection: H. lanatus plants and topsoil were collected from three locations: 6 plants (6 lime genotypes) were selected from a disused limestone quarry soil (pH 7.5) in County Antrim, NI, hereafter referred to as lime, 6 plants (6 acid genotypes) from an acidic peat bog (pH 3.5) in County Tyrone, NI, hereafter referred to as acid, and 6 plants (6 intermediate genotypes) from an acid mineral rough grassland (pH 5.5) (County Down, NI), hereafter refereed to as intermediate. In each case plants were carefully selected within each habitat, with all plants at least 5m apart, so that each of the 6 plants represents a clone for a unique genotype of that particular habitat. Tillers from each plant were trans-planted into John Innes no. 2 compost to nutritionally neutralize all plants. Tillers from compost grown lime and acid ecotypes (5 genotypes each) were subsequently used for set up of a full factorial soil transplant experiment. Tillers from one genotype of each the acid, lime and intermediate population were subsequently grown in hydroponics for additional root acid stress relevant transcriptome sequencing data. Full factorial reciprocal soil transplant experiment: Tillers from 5 genotypes of each the acid and lime ecotype were transplanted from compost onto limestone quarry soil (total 10 pots) and grown in the growth chamber for 7 weeks. Replication was at the level of ecotype by using 5 tillers from 5 different clonal plants from each ecotype (5 genotypes per ecotype) rather than using multiple tillers from one plant, to ensure that natural variation within the two H. lanatus ecotypes could be investigated. At harvest at 7 weeks, roots and shoots were washed thoroughly with deionized water, separated, frozen in liquid nitrogen and stored at -80C until RNA extraction. RNA Extraction, QA and RNAseq: RNA extraction of frozen shoot tissue: Shoot samples were homogenized in FastPrep Lysing tubes containing Lysing Matrix D (MP Biomedicals, USA) using two 20-second Precellys 24-Dual (Bertin Technologies, France) runs at 5500rpm to produce a fine powder. Inbetween runs the tubes were submerged into liquid nitrogen to prevent degradation of RNA. RNA was extracted using an RNeasy Plant Mini Kit (QIAGEN), according to protocol and with inclusion of a DNA digestion step (DNase Set, QIAGEN) with the following amendment: 450l Buffer RLT (containing 4.5l -Mercaptoethanol) was added to the Precellys lysing tube containing the ground tissue and homogenised again using the Precellys 24-Dual for 5 seconds at 5500rpm to ensure that the powdered sample was suspended as quickly as possible to prevent RNA degradation. The lysate was transferred to a QIAshredder spin column and centrifuged at 14,000rpm for 2 minutes, followed by RNA extraction according to the standard protocoll. RNA was then eluted twice using the same eluate to further concentrate the RNA and stored at -80 C. RNA was quantified using a Nanodrop 8000 spectrophotometer (Thermo Scientific) and Agilent 2200 Tapestation (Agilent Technologies) to assess quality (purity and integrity) of the RNA. 19/20 shoot samples passed the QA and were submitted for RNAseq. 1 shoots sample from the soil experiment failed the QC and could therefore not be processed for library preparation for the RNAseq study, hence there are 5 replicates for 3 treatments and 4 replicates for 1 treatment. Transcriptome sequencing (Illumina, RNAseq) was conducted at the Genome Analysis Centre (TGAC), Norwich, UK. Barcoded 125bp paired end TruSeq RNA libraries (polyA selected) were generated for each RNA sample and sequenced on the Illumina HiSeq 2500.

text: acid

text: D

text: lime quarry soil

text: Holcus lanatus

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 11

characteristic: title


E-MTAB-4014:Sample 12

text: Queen's University Belfast

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: E-MTAB-4014:Sample 12

text: ArrayExpress

text: velvet grass

text: acid

text: A

text: lime quarry soil

text: Holcus lanatus

characteristic: organism

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 12


E-MTAB-4014:Sample 13

characteristic: ENA-CHECKLIST

text: Queen's University Belfast

text: public

characteristic: SRA accession

text: E-MTAB-4014:Sample 13

characteristic: Submitter Id

text: ArrayExpress

text: velvet grass

text: acid

text: F

text: lime quarry soil

text: Holcus lanatus

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 13


E-MTAB-4014:Sample 14

characteristic: ENA-FIRST-PUBLIC

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 14

text: ArrayExpress

characteristic: broker name

text: velvet grass

characteristic: common name

text: acid

text: B

text: lime quarry soil

text: Holcus lanatus

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 14


E-MTAB-4014:Sample 15

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 15

text: ArrayExpress

text: velvet grass

characteristic: description

text: acid

characteristic: ecotype

text: C

characteristic: genotype

text: lime quarry soil

text: Holcus lanatus

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 15


E-MTAB-4014:Sample 16

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 16

text: ArrayExpress

text: velvet grass

text: lime

text: R

text: lime quarry soil

characteristic: growth condition

text: Holcus lanatus

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 16


E-MTAB-4014:Sample 17

text: Queen's University Belfast

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-4014:Sample 17

text: ArrayExpress

text: velvet grass

text: lime

text: O

text: lime quarry soil

text: Holcus lanatus

text: Holcus lanatus

text: shoot

characteristic: organism part

text: Holcus lanatus

text: Sample 17


E-MTAB-4014:Sample 18

text: Queen's University Belfast

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: E-MTAB-4014:Sample 18

text: ArrayExpress

text: velvet grass

text: lime

text: I

text: lime quarry soil

text: Holcus lanatus

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 18

characteristic: title


E-MTAB-4014:Sample 19

characteristic: ENA-CHECKLIST

text: Queen's University Belfast

text: public

characteristic: SRA accession

text: E-MTAB-4014:Sample 19

text: ArrayExpress

text: velvet grass

text: lime

text: H

text: lime quarry soil

text: Holcus lanatus

characteristic: organism

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 19


E-MTAB-4014:Sample 2

characteristic: ENA-FIRST-PUBLIC

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: velvet grass

text: acid

text: A

text: acid bog soil

text: Holcus lanatus

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 2


E-MTAB-4014:Sample 20

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 20

text: ArrayExpress

text: velvet grass

characteristic: common name

text: Protocols: Plant and soil collection: H. lanatus plants and topsoil were collected from three locations: 6 plants (6 lime genotypes) were selected from a disused limestone quarry soil (pH 7.5) in County Antrim, NI, hereafter referred to as lime, 6 plants (6 acid genotypes) from an acidic peat bog (pH 3.5) in County Tyrone, NI, hereafter referred to as acid, and 6 plants (6 intermediate genotypes) from an acid mineral rough grassland (pH 5.5) (County Down, NI), hereafter refereed to as intermediate. In each case plants were carefully selected within each habitat, with all plants at least 5m apart, so that each of the 6 plants represents a clone for a unique genotype of that particular habitat. Tillers from each plant were trans-planted into John Innes no. 2 compost to nutritionally neutralize all plants. Tillers from compost grown lime and acid ecotypes (5 genotypes each) were subsequently used for set up of a full factorial soil transplant experiment. Tillers from one genotype of each the acid, lime and intermediate population were subsequently grown in hydroponics for additional root acid stress relevant transcriptome sequencing data. Full factorial reciprocal soil transplant experiment: Tillers from 5 genotypes of each the acid and lime ecotype were transplanted from compost onto acid bog soil (total 10 pots) and grown in the growth chamber for 7 weeks. Replication was at the level of ecotype by using 5 tillers from 5 different clonal plants from each ecotype (5 genotypes per ecotype) rather than using multiple tillers from one plant, to ensure that natural variation within the two H. lanatus ecotypes could be investigated. At harvest at 7 weeks, roots and shoots were washed thoroughly with deionized water, separated, frozen in liquid nitrogen and stored at -80C until RNA extraction. RNA Extraction, QA and RNAseq: RNA extraction of frozen root tissue: Root samples were partly pre-ground, whilst cooling with liquid nitrogen, by hand in 1.5ml microcentrifuge tubes with 106m acid washed glass beads (Sigma-Aldrich) using disposable pestles (Sigma Aldrich), before processing in FastPrep tubes containing Lysing Matrix A on the Precellys 24-Dual using the same conditions as for shoots. RNA was extracted using an RNeasy Plant Mini Kit (QIAGEN), according to protocol and with inclusion of a DNA digestion step (DNase Set, QIAGEN) with the following amendment: 450l Buffer RLT (containing 4.5l -Mercaptoethanol) was added to the Precellys lysing tube containing the ground tissue and homogenised again using the Precellys 24-Dual for 5 seconds at 5500rpm to ensure that the powdered sample was suspended as quickly as possible to prevent RNA degradation. The lysate was transferred to a QIAshredder spin column and centrifuged at 14,000rpm for 2 minutes, followed by RNA extraction according to the standard protocoll. RNA was then eluted twice using the same eluate to further concentrate the RNA and stored at -80 C. RNA was quantified using a Nanodrop 8000 spectrophotometer (Thermo Scientific) and Agilent 2200 Tapestation (Agilent Technologies) to assess quality (purity and integrity) of the RNA. 21/23 root samples passed the QA and were submitted for RNAseq (all three hydroponics root samples passed, but 3 roots samples from the soil experiment failed the QC and could therefore not be processed for library preparation for the RNAseq study, hence there are 4 replicates for 3 treatments and 5 replicates for 1 treatment. Transcriptome sequencing (Illumina, RNAseq) was conducted at the Genome Analysis Centre (TGAC), Norwich, UK. Barcoded 125bp paired end TruSeq RNA libraries (polyA selected) were generated for each RNA sample and sequenced on the Illumina HiSeq 2500.

characteristic: description

text: acid

characteristic: ecotype

text: D

text: acid bog soil

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 20


E-MTAB-4014:Sample 21

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 21

text: ArrayExpress

text: velvet grass

text: acid

text: A

characteristic: genotype

text: acid bog soil

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 21


E-MTAB-4014:Sample 22

text: Queen's University Belfast

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-4014:Sample 22

text: ArrayExpress

text: velvet grass

text: acid

text: B

text: acid bog soil

characteristic: growth condition

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 22


E-MTAB-4014:Sample 23

text: Queen's University Belfast

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: E-MTAB-4014:Sample 23

text: ArrayExpress

text: velvet grass

text: acid

text: C

text: acid bog soil

text: Holcus lanatus

text: Holcus lanatus

text: root

characteristic: organism part

text: Holcus lanatus

text: Sample 23


E-MTAB-4014:Sample 24

characteristic: ENA-CHECKLIST

text: Queen's University Belfast

text: public

characteristic: SRA accession

text: E-MTAB-4014:Sample 24

text: ArrayExpress

text: velvet grass

text: lime

text: K

text: acid bog soil

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 24

characteristic: title


E-MTAB-4014:Sample 25

characteristic: ENA-FIRST-PUBLIC

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 25

characteristic: Submitter Id

text: ArrayExpress

text: velvet grass

text: lime

text: O

text: acid bog soil

text: Holcus lanatus

characteristic: organism

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 25


E-MTAB-4014:Sample 26

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 26

text: ArrayExpress

characteristic: broker name

text: velvet grass

characteristic: common name

characteristic: description

text: lime

text: I

text: acid bog soil

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 26


E-MTAB-4014:Sample 27

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 27

text: ArrayExpress

text: velvet grass

text: lime

characteristic: ecotype

text: H

text: acid bog soil

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 27