text: MMRI

text: public

text: human

text: Donor 5 tumor, V3 capture design

text: Homo sapiens

text: Homo sapiens


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MMRI

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

characteristic: common name

text: Donor 6 non-tumor brain,V3 capture design

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: title


text: MMRI

text: public

text: human

text: Donor 6 tumor, V3 capture design

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 7 non-tumor brain,V3 capture design

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 7 tumor, V3 capture design

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 8 non-tumor brain,V3 capture design

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 8 tumor, V3 capture design

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 9 non-tumor brain,V3 capture design

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 9 tumor, V3 capture design

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 10 blood, V3 capture design

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 11 blood, V3 capture design

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 12 blood, V3 capture design

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 14 blood, V3 capture design

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 6 blood, V3 capture design

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 7 blood, V3 capture design

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 8 blood, V3 capture design

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 9 blood, V3 capture design

text: Homo sapiens

text: Homo sapiens


status: KILLED

text: Homo sapiens

characteristic: ArrayExpress-Species

text: SC

text: killed

characteristic: Sample Description

characteristic: Strain

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo sapiens

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: Mus musculus


text: 17 months

characteristic: ArrayExpress-Age

text: Olfactory mucosa

characteristic: ArrayExpress-OrganismPart

text: male

characteristic: ArrayExpress-Sex

text: Bos taurus

text: LIMX

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: cattle

text: Bos taurus

text: RNA from OE

characteristic: sample description

text: Bos taurus

text: LIMX

characteristic: strain


text: 25 months

text: Olfactory mucosa

text: male

text: Bos taurus

text: LIMX

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: cattle

text: Bos taurus

text: RNA from OE

text: Bos taurus

text: LIMX


text: 22 months

text: Olfactory mucosa

text: male

text: Bos taurus

characteristic: ArrayExpress-Species

text: Brit Blue

text: SC

text: public

text: cattle

characteristic: common name

text: Bos taurus

characteristic: organism

text: RNA from OE

text: Bos taurus

text: Brit Blue


text: 84 years

characteristic: ArrayExpress-Age

text: Olfactory mucosa

text: female

text: Homo sapien

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: human

text: Homo sapiens

text: RNA from OE

text: Homo sapiens


text: 65 years

text: Olfactory mucosa

characteristic: ArrayExpress-OrganismPart

text: female

characteristic: ArrayExpress-Sex

text: Homo sapien

text: SC

text: public

text: human

text: Homo sapiens

text: RNA from OE

text: Homo sapiens


text: 83 years

text: Olfactory mucosa

text: female

text: Homo sapien

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: human

text: Homo sapiens

text: RNA from OE

characteristic: sample description

text: Homo sapiens


text: 12.5 months

text: Olfactory mucosa

text: male

text: Callithrix jacchus

characteristic: External Id

text: SC

text: public

text: white-tufted-ear marmoset

text: Callithrix jacchus

text: RNA from OE

text: Callithrix jacchus


text: 122 months

text: Olfactory mucosa

text: male

text: Callithrix jacchus

text: SC

characteristic: INSDC center name

text: public

text: white-tufted-ear marmoset

text: Callithrix jacchus

text: RNA from OE

text: Callithrix jacchus


text: 28 months

text: Olfactory mucosa

text: male

text: Callithrix jacchus

text: SC

characteristic: INSDC first public

text: public

text: white-tufted-ear marmoset

text: Callithrix jacchus

text: RNA from OE

text: Callithrix jacchus


text: 77 months

text: Olfactory mucosa

text: male

text: Macaca mulatta

text: SC

characteristic: INSDC last update

text: public

text: Rhesus monkey

text: Macaca mulatta

text: RNA from OE

text: Macaca mulatta


text: 52 months

text: Olfactory mucosa

text: male

text: Macaca mulatta

text: SC

text: public

characteristic: INSDC status

text: Rhesus monkey

text: Macaca mulatta

text: RNA from OE

text: Macaca mulatta


text: 51 months

text: Olfactory mucosa

text: male

text: Macaca mulatta

text: SC

text: public

characteristic: SRA accession

text: Rhesus monkey

text: Macaca mulatta

text: RNA from OE

text: Macaca mulatta


text: IOA

text: public

characteristic: Submitter Id

text: European seabass

text: Dicentrarchus labrax

text: Dicentrarchus labrax

characteristic: title


text: male

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: Mouse_v2_library_pKLV2_gRNA5_BbsI__PGKpuroBFP_W-sc-2105709

text: house mouse

characteristic: common name

text: Mus musculus

text: Pooled PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: MouseV2_pKLV2_gRNA5_BbsI__sEF1apuroBFP_W-sc-2105710

text: house mouse

text: Mus musculus

characteristic: organism

text: Pooled PCR products

text: Mus musculus


text: male

text: Mus musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: MouseV2_pKLV2_gRNA5_BbsI__PGKpuro_W-sc-2105711

text: house mouse

text: Mus musculus

text: Pooled PCR products

text: Mus musculus


text: male

text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: MouseV2_pKLV2_gRNA5_BbsI__sEF1aBFP_W-sc-2105712

text: house mouse

text: Mus musculus

text: Pooled PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pooled PCR products

text: Mus musculus


text: Mouse

text: SC

text: public

text: house mouse

text: Mus musculus

text: mRNAseq Nextera library made from RNA extracted from haemopoetic stem and progenitor cells

text: Mus musculus


text: INRA

text: public

text: ArrayExpress

characteristic: broker name

text: horse

text: Protocols: Samples were collected on the same location in the middle of the trochlea to avoid technical bias due to sample location in the joint. Explants including epiphyseal cartilage and about 5 mm of the soft underlying bone (considered as subchondral bone) were washed in PBS and placed in DMEM culture medium for subsequent mechanical-loading experiments or flash frozen in liquid nitrogen for subsequent RNA-seq analysis. Harvested cartilage explants were placed into individual compression wells of Biopress culture plates (Flexercell International) in 1.5 ml of culture medium (DMEM, containing penicillin-streptomycin 1%, glutamine 2%, albumin 0.1% and Hepes 30 mM). All experiments were performed at 37C, under ambient atmosphere. A compressive stress was applied to individual samples by the Flexercell FX-4000C system (sinusoidal waveform at 0.5 Hz, 1MPa, 24h00) whereas the control explants stayed in unloaded conditions. Protaglandin E2 (PGE2) production was measured in the media by a high sensitivity commercially available enzyme immunoassay kit (Cayman Chemical). The mirVana miRNA Isolation Kit (Ambion, Life Technologies) was used to extract in parallel Total RNA and small RNA (smRNA) from cartilage following the manufacturers protocol. Total RNA quality was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies) loaded with a RNA 6000 Nano Kit. The concentrations of smRNA were determined using a NanoDrop ND-1000 Spectrophotometer and the size and purity were determined using the Bioanalyzer 2100 loaded with a RNA 6000 Nano Kit. SOLiD Total RNA-Seq Kit (Applied Biosystems, Life Technologies). Small RNAs were hybridized and ligated with SOLiD Adaptor Mix, a reverse transcription was performed and the cDNAs were purified using the MinElute PCR purification kit (Qiagen). The 60-80 base pair fraction of the cDNA was excised from a 10% acrylamide gel stained with SYBR Gold (Invitrogen, Life Technologies) and an amplification was realized by PCR (95C - 1min, 18 x (95C -30s, 62C, 30s, 72C, 30s), 72C, 7min) using the SOLiD 5 prime PCR primer and a 3 prime library-specific barcoded SOLiD primer. The amplified DNA was purified using the Purelink PCR micro kit (Invitrogen, Life Technologies) and the 110-130 bp region was excised from a 6% acrylamide gel stained with SYBR Gold (Invitrogen, Life Technologies). The yield and size distribution of the amplified DNA were assessed and pools of three different horses were made to decrease the effect of individual variability.

characteristic: description

text: osteochondrosis

characteristic: disease

text: CXII

characteristic: individual

text: Equus caballus

text: Equus caballus

text: median femoral trochlea from cartilage

characteristic: organism part

text: Equus caballus

text: female

characteristic: sex

type: has member


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: horse

text: Protocols: Samples were collected on the same location in the middle of the trochlea to avoid technical bias due to sample location in the joint. Explants including epiphyseal cartilage and about 5 mm of the soft underlying bone (considered as subchondral bone) were washed in PBS and placed in DMEM culture medium for subsequent mechanical-loading experiments or flash frozen in liquid nitrogen for subsequent RNA-seq analysis. Harvested cartilage explants were placed into individual compression wells of Biopress culture plates (Flexercell International) in 1.5 ml of culture medium (DMEM, containing penicillin-streptomycin 1%, glutamine 2%, albumin 0.1% and Hepes 30 mM). All experiments were performed at 37C, under ambient atmosphere. A compressive stress was applied to individual samples by the Flexercell FX-4000C system (sinusoidal waveform at 0.5 Hz, 1MPa, 24h00) whereas the control explants stayed in unloaded conditions. Protaglandin E2 (PGE2) production was measured in the media by a high sensitivity commercially available enzyme immunoassay kit (Cayman Chemical). Total RNA was purified from bone using the miRNeasy Mini kit (Qiagen) and the RNeasy MinElute Cleanup kit (Qiagen) for enrichment of small RNA (<200 nt) following the manufacturers protocol. Total RNA quality was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies) loaded with a RNA 6000 Nano Kit. The concentrations of smRNA were determined using a NanoDrop ND-1000 Spectrophotometer and the size and purity were determined using the Bioanalyzer 2100 loaded with a RNA 6000 Nano Kit. SOLiD Total RNA-Seq Kit (Applied Biosystems, Life Technologies). Small RNAs were hybridized and ligated with SOLiD Adaptor Mix, a reverse transcription was performed and the cDNAs were purified using the MinElute PCR purification kit (Qiagen). The 60-80 base pair fraction of the cDNA was excised from a 10% acrylamide gel stained with SYBR Gold (Invitrogen, Life Technologies) and an amplification was realized by PCR (95C - 1min, 18 x (95C -30s, 62C, 30s, 72C, 30s), 72C, 7min) using the SOLiD 5 prime PCR primer and a 3 prime library-specific barcoded SOLiD primer. The amplified DNA was purified using the Purelink PCR micro kit (Invitrogen, Life Technologies) and the 110-130 bp region was excised from a 6% acrylamide gel stained with SYBR Gold (Invitrogen, Life Technologies). The yield and size distribution of the amplified DNA were assessed and pools of three different horses were made to decrease the effect of individual variability.

text: osteochondrosis

text: CXIII

text: Equus caballus

text: Equus caballus

text: median femoral trochlea from bone

text: Equus caballus

text: female


text: INRA

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: horse

text: osteochondrosis

text: CV

text: Equus caballus

text: Equus caballus

text: median femoral trochlea from bone

text: Equus caballus

text: female


text: INRA

text: public

text: ArrayExpress

text: horse

characteristic: common name

text: healthy

text: CVIII

text: Equus caballus

characteristic: organism

text: Equus caballus

text: median femoral trochlea from bone

text: Equus caballus

text: male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INRA

text: public

text: ArrayExpress

characteristic: broker name

text: horse

text: healthy

text: CIX

text: Equus caballus

text: Equus caballus

text: median femoral trochlea from cartilage

text: Equus caballus

text: female


text: INRA

text: public

text: ArrayExpress

text: horse

characteristic: description

text: healthy

characteristic: disease

text: CX

characteristic: individual

text: Equus caballus

text: Equus caballus

text: median femoral trochlea from cartilage

text: Equus caballus

text: male


characteristic: ENA-LAST-UPDATE

text: INRA

text: public

text: ArrayExpress

text: horse

text: healthy

text: CVIII

text: Equus caballus

text: Equus caballus

text: median femoral trochlea from cartilage

characteristic: organism part

text: Equus caballus

text: male

characteristic: sex


characteristic: External Id

text: INRA

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: horse

text: healthy

text: CVI

text: Equus caballus

text: Equus caballus

text: median femoral trochlea from cartilage

text: Equus caballus

text: female


text: INRA

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: horse

text: healthy

text: CVII

text: Equus caballus

text: Equus caballus

text: median femoral trochlea from bone

text: Equus caballus

text: male


text: INRA

text: public

characteristic: Submitter Id

text: ArrayExpress

text: horse

characteristic: common name

text: osteochondrosis

text: CXII

text: Equus caballus

characteristic: organism

text: Equus caballus

text: median femoral trochlea from bone

text: Equus caballus

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INRA

text: public

text: ArrayExpress

text: horse

text: healthy

text: CVI

text: Equus caballus

text: Equus caballus

text: median femoral trochlea from bone

text: Equus caballus

text: female

characteristic: title


text: INRA

text: public

text: ArrayExpress

characteristic: broker name

text: horse

characteristic: description

text: healthy

characteristic: disease

text: CX

text: Equus caballus

text: Equus caballus

text: median femoral trochlea from bone

text: Equus caballus

text: male


characteristic: ENA-LAST-UPDATE

text: INRA

text: public

text: ArrayExpress

text: horse

text: osteochondrosis

text: CIV

characteristic: individual

text: Equus caballus

text: Equus caballus

text: median femoral trochlea from cartilage

characteristic: organism part

text: Equus caballus

text: male


characteristic: External Id

text: INRA

characteristic: INSDC center name

text: public

text: ArrayExpress

text: horse

text: osteochondrosis

text: CIV

text: Equus caballus

text: Equus caballus

text: median femoral trochlea from bone

text: Equus caballus

text: male

characteristic: sex


text: INRA

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: horse

text: osteochondrosis

text: CXI

text: Equus caballus

text: Equus caballus

text: median femoral trochlea from cartilage

text: Equus caballus

text: male


text: INRA

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: horse

characteristic: common name

text: osteochondrosis

text: CXIII

text: Equus caballus

text: Equus caballus

text: median femoral trochlea from cartilage

text: Equus caballus

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INRA

text: public

text: ArrayExpress

text: horse

text: osteochondrosis

text: CV

text: Equus caballus

characteristic: organism

text: Equus caballus

text: median femoral trochlea from cartilage

text: Equus caballus

text: female


text: Danio rerio

characteristic: ArrayExpress-Species

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.

characteristic: sample description

text: Danio rerio


text: Hindbrain

characteristic: ArrayExpress-CellType

text: mus musculus

characteristic: ArrayExpress-TimePoint

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Hindbrain

text: Tdg+/+

characteristic: ArrayExpress-Genotype

text: mus musculus

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Hindbrain

text: Tdg-/-

text: mus musculus

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: MMRI

characteristic: INSDC first public

text: public

text: human

text: Donor 10 blood, V3 capture design, additional MiSeq run

characteristic: description

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: MMRI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human

text: Donor 11 blood, V3 capture design, additional MiSeq run

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: MMRI

text: public

characteristic: Submitter Id

text: human

characteristic: common name

text: Donor 12 blood, V3 capture design, additional MiSeq run

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: MMRI

text: public

text: human

text: Donor 14 blood, V3 capture design, additional MiSeq run

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 6 blood, V3 capture design, additional MiSeq run

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 7 blood, V3 capture design, additional MiSeq run

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 8 blood, V3 capture design, additional MiSeq run

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

text: human

text: Donor 9 blood, V3 capture design, additional MiSeq run

text: Homo sapiens

text: Homo sapiens


text: Pharyngula:Prim 5 - ZFS:0000029

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_56_1_phenotypic_1-sc-2114663

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (ATCACGTT) 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_ph56

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ZMP_phenotype_56_1_phenotypic_2-sc-2114664

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (CGATGTTT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ZMP_phenotype_56_1_phenotypic_3-sc-2114665

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TTAGGCAT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: SRA accession

text: ZMP_phenotype_56_1_phenotypic_4-sc-2114666

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TGACCACT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_56_1_phenotypic_5-sc-2114667

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (ACAGTGGT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: ZMP_phenotype_56_1_phenotypic_6-sc-2114668

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (GCCAATGT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_56_1_phenotypic_7-sc-2114669

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (CAGATCTG) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: ZMP_phenotype_56_1_phenotypic_8-sc-2114670

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (ACTTGATG) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_56_1_phenotypic_9-sc-2114671

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (GATCAGCG) 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_ph56

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: ZMP_phenotype_56_1_phenotypic_10-sc-2114672

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TAGCTTGT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ZMP_phenotype_56_1_non_phenotypic_1-sc-2114673

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TGGTTGTT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ZMP_phenotype_56_1_non_phenotypic_2-sc-2114674

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TCTCGGTT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: SRA accession

text: ZMP_phenotype_56_1_non_phenotypic_3-sc-2114675

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TAAGCGTT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_56_1_non_phenotypic_4-sc-2114676

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TCCGTCTT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: ZMP_phenotype_56_1_non_phenotypic_5-sc-2114677

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TGTACCTT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_56_1_non_phenotypic_6-sc-2114678

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TTCTGTGT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: ZMP_phenotype_56_1_non_phenotypic_7-sc-2114679

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TCTGCTGT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_56_1_non_phenotypic_8-sc-2114680

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TTGGAGGT) 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_ph56

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: ZMP_phenotype_56_1_non_phenotypic_9-sc-2114681

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TCGAGCGT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ZMP_phenotype_56_1_non_phenotypic_10-sc-2114682

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TGATACGT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ZMP_phenotype_56_1_non_phenotypic_11-sc-2114683

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TGCATAGT) 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_ph56

text: Danio rerio

text: mixed


text: Pharyngula:Prim 5 - ZFS:0000029

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: SRA accession

text: ZMP_phenotype_56_1_non_phenotypic_12-sc-2114684

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 56 clutch 1. A 8 base indexing sequence (TTGACTCT) 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_ph56

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_77_1_phenotypic_1-sc-2114685

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 77 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_ph77

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

text: ZMP_phenotype_77_1_phenotypic_2-sc-2114686

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 77 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_ph77

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_77_1_phenotypic_3-sc-2114687

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 77 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_ph77

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_77_1_phenotypic_4-sc-2114688

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 77 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_ph77

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_77_1_phenotypic_5-sc-2114689

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 77 clutch 1. A 8 base indexing sequence (TCCTCAAT) 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_ph77

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval - Day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: ZMP_phenotype_77_1_phenotypic_6-sc-2114690

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 77 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_ph77

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

characteristic: INSDC first public

text: public

text: ZMP_phenotype_77_1_phenotypic_7-sc-2114691

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 77 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_ph77

text: Danio rerio

text: mixed


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_77_1_phenotypic_8-sc-2114692

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 77 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_ph77

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

characteristic: SRA accession

text: ZMP_phenotype_77_1_phenotypic_9-sc-2114693

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 77 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_ph77

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_77_1_phenotypic_10-sc-2114694

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 77 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_ph77

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

text: ZMP_phenotype_77_1_phenotypic_11-sc-2114695

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 77 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_ph77

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_77_1_non_phenotypic_1-sc-2114696

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 77 clutch 1. A 8 base indexing sequence (TACTTCGG) 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_ph77

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_77_1_non_phenotypic_2-sc-2114697

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 77 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_ph77

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_77_1_non_phenotypic_3-sc-2114698

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 77 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_ph77

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval - Day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: ZMP_phenotype_77_1_non_phenotypic_4-sc-2114699

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 77 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_ph77

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

characteristic: INSDC first public

text: public

text: ZMP_phenotype_77_1_non_phenotypic_5-sc-2114700

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 77 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_ph77

text: Danio rerio

text: mixed


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_77_1_non_phenotypic_6-sc-2114701

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 77 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_ph77

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

characteristic: SRA accession

text: ZMP_phenotype_77_1_non_phenotypic_7-sc-2114702

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 77 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_ph77

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_77_1_non_phenotypic_8-sc-2114703

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 77 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_ph77

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

text: ZMP_phenotype_77_1_non_phenotypic_9-sc-2114704

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 77 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_ph77

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_77_1_non_phenotypic_10-sc-2114705

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 77 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_ph77

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_77_1_non_phenotypic_11-sc-2114706

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 77 clutch 1. A 8 base indexing sequence (TACTAGTC) 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_ph77

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_77_1_non_phenotypic_12-sc-2114707

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 77 clutch 1. A 8 base indexing sequence (TTCAGCTC) 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_ph77

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


E-MTAB-2869:Ler 16 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Exeter

text: public

text: E-MTAB-2869:Ler 16 2

tag: Namespace:University of Exeter

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Protocols: Total RNA is extracted using sodium tetraborate extraction, lithium chloride precipitation and cleaned up with the RNAeasy kit (Qiagen) cDNA library is prepared using TruSeq Stranded mRNA Sample Prep Kits to 25 ul minimum at 10 nM.

characteristic: description

text: grown at 16 degree Celcius before fertilization, then 22 degree Celcius

characteristic: growth condition

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: siluge without seeds

characteristic: organism part

text: Arabidopsis thaliana

text: Ler 16 2

characteristic: title


E-MTAB-2869:ft-1 seeds 1

characteristic: ENA-CHECKLIST

text: University of Exeter

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2869:ft-1 seeds 1

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

text: grown at 22 degree Celsius

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: seed

text: Arabidopsis thaliana

text: ft-1 seeds 1


E-MTAB-2869:Ler seeds 1

characteristic: ENA-FIRST-PUBLIC

text: University of Exeter

text: public

text: E-MTAB-2869:Ler seeds 1

text: ArrayExpress

text: thale cress

characteristic: common name

text: grown at 22 degree Celsius

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: seed

text: Arabidopsis thaliana

text: Ler seeds 1


E-MTAB-2869:ft-1 22 2

characteristic: ENA-LAST-UPDATE

text: University of Exeter

text: public

text: E-MTAB-2869:ft-1 22 2

text: ArrayExpress

text: thale cress

text: grown at 22 degree Celsius

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: siluge without seeds

text: Arabidopsis thaliana

text: ft-1 22 2


E-MTAB-2869:ft-1 22 1

characteristic: External Id

text: University of Exeter

text: public

text: E-MTAB-2869:ft-1 22 1

text: ArrayExpress

text: thale cress

text: grown at 22 degree Celsius

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: siluge without seeds

text: Arabidopsis thaliana

text: ft-1 22 1


E-MTAB-2869:ft-1 seeds 2

text: University of Exeter

text: public

text: E-MTAB-2869:ft-1 seeds 2

text: ArrayExpress

characteristic: broker name

text: thale cress

text: grown at 22 degree Celsius

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: seed

text: Arabidopsis thaliana

text: ft-1 seeds 2


E-MTAB-2869:Ler 22 1

text: University of Exeter

text: public

text: E-MTAB-2869:Ler 22 1

text: ArrayExpress

text: thale cress

characteristic: description

text: grown at 22 degree Celsius

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: siluge without seeds

text: Arabidopsis thaliana

text: Ler 22 1


E-MTAB-2869:Ler seeds 2

text: University of Exeter

text: public

text: E-MTAB-2869:Ler seeds 2

text: ArrayExpress

text: thale cress

text: grown at 22 degree Celsius

characteristic: growth condition

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: seed

text: Arabidopsis thaliana

text: Ler seeds 2


E-MTAB-2869:Ler 22 2

text: University of Exeter

text: public

text: E-MTAB-2869:Ler 22 2

text: ArrayExpress

text: thale cress

text: grown at 22 degree Celsius

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: siluge without seeds

characteristic: organism part

text: Arabidopsis thaliana

text: Ler 22 2


E-MTAB-2869:Ler 16 1

text: University of Exeter

text: public

text: E-MTAB-2869:Ler 16 1

text: ArrayExpress

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: siluge without seeds

text: Arabidopsis thaliana

text: Ler 16 1

characteristic: title


E-MTAB-2869:Ler 22 3

characteristic: ENA-CHECKLIST

text: University of Exeter

text: public

text: E-MTAB-2869:Ler 22 3

text: ArrayExpress

text: thale cress

text: grown at 22 degree Celsius

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: siluge without seeds

text: Arabidopsis thaliana

text: Ler 22 3


E-MTAB-2869:Ler 16 3

text: University of Exeter

characteristic: INSDC center name

text: public

text: E-MTAB-2869:Ler 16 3

text: ArrayExpress

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: siluge without seeds

text: Arabidopsis thaliana

text: Ler 16 3


name: E-MTAB-2063:Neural Stem Cell Biological Replicate 2

characteristic: INSDC first public

text: public

tag: Namespace:EMBL GENOMICS CORE FACILITY, HEIDELBERG, GERMANY

text: ArrayExpress

characteristic: cell line

text: neural stem cell

characteristic: cell type

text: house mouse

text: Protocols: 46C mouse embryonic stem cells (derived from E14tg2a cell line; ESC) were grown at 37degreesC in a 5percent (v/v) CO2 incubator in Glasgow Modified Eagles Medium (GMEM, Invitrogen), supplemented with 10 percent (v/v) fetal bovine serum (FBS) (Sigma), 2 ng/ml of in-house synthesized LIF, 1 mM 2-mercaptoethanol, Non-Essential Amino Acids (Gibco) and Na-pyruvate (Gibco), on gelatin-coated (0.1percent (v/v)) dishes. We used Accutase (Sigma) for cell dissociation (which we inactivated with cell culture medium according to the manufacturers’ recommendations). Cells were passaged every other day at a seeding density of 3 million cells for a 10-cm petri dish. Medium was exchanged every day. The ESCs were differentiated to Neural Stem Cellss (NSC). Briefly, 46C ES cells were plated at the density of 2 million cells on gelatin-coated 10 cm petri dish in 50percent Dulbeco’s Modified Eagles Medium, 50percent F12 (DMEM/F12, Invitrogen) medium supplemented with N2 and B27 (Gibco), BSA (Gibco), Non-Essential Amino Acids (Gibco), glucose (final concentration of 0.03 M), HEPES (final concentration of 4.5 mM) and 0.1mM beta-mercaptoethanol (Differentiation medium). Medium was exchanged after 24 and 48 hours and the cultures grown for additional 72 hours. Cells were then gently dissociated using Accutase (Sigma), the GFP+ cell fraction (corresponding to c.a. 70 percent of cells) was FACSorted and seeded onto laminin (Sigma) coated 75 cm2 Nunc flask (final concentration of laminin 10 mg/cm2 of culture surface, coating time - minimum 4 hours at 37 degrees C). Subsequently, cells were grown in Differentiation medium supplemented with in-house prepared recombinant murine EGF and bFGF (both at concentration of 10 mg/ml) until loss of GFP expression and uniform up-regulation of Nestin expression. Cells where passaged when reaching 80 percent confluence, medium as exchanged every day. Buffers for the procedure, Lysis buffer: 10 mM HEPES pH=8, 10 mM NaCl, 0.2percent NP-40, Wash buffer: 50 mM Tris-HCl pH = 8, 50 mM NaCl, 1 mM EDTA, EZ-Link Iodoacetyl PEG2 Biotin resuspension buffer - EZ RB: 50 mM Tris-HCl, 5 mM EDTA, pH = 8 - 8.3, Dialysis buffer: 10 mM Tris HCl pH = 8, 1 mM EDTA, PBST: PBS, 0.01 percent of Tween, Beads wash buffer 10 mM Tris-HCl pH = 8, 50 mM NaCl, 0.4 percent Triton X-100, Klenow Wash Buffer: 50 mM Tris-HCl pH = 7.4, 0.4 percent Triton X-100, 0.1 mM EDTA, DNA extraction buffer: 50 mM Tris-HCl pH = 8, 0.2 percent SDS, 1 mM EDTA, 100 mM NaCl, DNA resuspension solution: 10 mM Tris-HCl pH = 8, Bind and Wash Buffer: 2x : 10 mM Tris-HCl pH = 7.5, 1mM EDTA, 2 M NaCl, Cell crossling protocol: Put 100 million cell pellet in 45 ml of fresh medium and add 1.25 ml of 37 percent formaldehyde, Incubate 10 min at RT, Add 2.5 ml of 2.5M glycine , Incubate 5 min at RT, Incubate 15 min on ice, Divide the cell mixture into 4 equal parts, Centrifuge at 1500 rpm for 5 min. at 4 degrees and store the pellets if needed. To start the TCC procedure, Lyse the cells in 550 ul lysis buffer completed with PIC using a homogenizer , Incubate on ice at least 15 minutes , Lyse the cells using the Dounce homogenizer by moving the pestile A up and down 10 times, Incubate on ice for 1 minutes , Apply 10 more strokes of the pestile, Transfer the sample to 2ml tube, Wash the cells twice with the wash buffer, spin conditions: 2500g for 5 minutes, V = 250 ul, Re suspend the cell pellet in 250 ul of wash buffer, Add 95 ul of 2percent SDS and incubate at 65 degreeC for 10 min, Prepare the EZ link Iodoacetyl-PEG2-Biotin For two reactions, Equilibrate the powder to RT to reduce humidification of the reagen, take 3 mg of the EZ link Iodoacetyl-PEG2-Biotin and re suspend in 220 ul of EZ RB in an amber tube, Cool the chromatin suspension to RT, Mix the suspension with 105ul of 25 mM EZlink Iodoacetyl-PEG2-Biotin (IPB), Rock at the room temperature for 1 hour, protect from light, Mix the chromatin with 1300 ul of 1x NEB Buffer 2, Incubate on ice for 5 minutes, Mix the sample with 225 ul of 10 percent triton X-100, Incubate on ice for 10 min , Incubate at 37degree C for 10 minutes, Now the sample is ready to be digested to this end, add, 100 ul of 10x NEB buffer 2, 350 ul of water, 5 ul of 1M DTT, 20 ul of HindIIII (100U/ul), dispose the sample to two tubes and incubate the digestion reaction OVN at 37 degreeC with overhead shaking.Place the mixture in a 20 kD cutoff Slide-A-Lyser Cassette, dialyse it against 1L of dialysis buffer for 3 hours, Renew the buffer and dialyze for an additional hour, Transfer the dialyzed sample (ca 2.5 ml) to a 15 ml falcon tube, During the last step, prepare the T1 beads. Take 400 ul of beads per chromatin sample, Wash the beads 3 times with PBST, Re suspend the beads in 2 ml of PBST, Divide the chromatin after dialysis into 5 equal parts, put them into 1.5 ml eppendorf tubes and add 400 ul of the above-mentioned bead suspension to these 5 aliquots of chromatin, Rock the chromatin with beads at RT for 30 minutes, During this time prepare the neutralized IPB solution - nIPB, take 0.750 mg IPB and add 52.5 ul of the resuspension buffer , add 7.75 mili-mols of bME - 9 ul of bME stock (14.3 Molar solution), Mix each aliquot of chromatin with 5 ul of nIPB, Incubate with rotation for 15 minutes at RT, Wash the beads once with 600 ul of TPBS, Wash the beads with 600 ul of Beads Wash Buffer, Re-suspend the beads in 100 ul of Beads Wash Buffer, add 69 ul of water, 1.1 ul of 1M MgCl2, 11 ul of 10x NEB buffer 2, 0.77 ul of 10 uM dATP, 0.77 ul of 10 uM dTTP, 0.77ul of 10 uM dGTPαS, 16.5 ul 0.4 mM Biotin-14-dCTP, 4.4 ul of 10 percent Triton-X100, 5 ul of 5U/ul Klenow. Fill in the overhangs by 40 minute rocking incubation at RT with 100 ul of the above-mentioned mix, After the incubation with Klenow add 5ul of 0.5 M EDTA to the suspension, Wash the beads twice with 600 ul of Klenow Wash Buffer, Re-suspend the beads in 500 ul of Klenow wash buffer and transfer them all in a new 50 ml falcon tube (V = 2.5 ml), Prepare the ligation mix (0.275 ul 10X NEB T4 Ligase buffer, 4.3 ml water, 198 ul 10percent triton X-100, 110 ul 1 M Tris-Hcl, pH=7.4, 55ul 10mg/ml BSA, 2ul Qucik Ligase NEB), Rock the mix for 4 hours at 16 degreeC , Stop the ligation by adding 200 ul of 0.5 M EDTA, Place the bead suspension on the magnet and aspirate the supernatant, Reverse the crosslinks: resuspend the beads in 400 ul of an extraction buffer, Add 20 ul of 20 mg/ml proteinase K, Incubate at 65 degreeC OVN , Add 5 ul of 20 mg/ml proteinase K, Incubate for 2 additional hours at 65 degreeC, Transfer the supernatant to a new tube and extract the DNA twice with, phenol : chloroform : isoamyl alcohol, Once with an equal volume of chloroform, Mix the resulting aqueous phase with , NaCl (final concentration: 200 mM), Glycogen (final concentration: 25 ug/ul), Add 900 ul of 98 percent ethanol, Incubate at -20 ovn or at -80 for 1 hour, Centrifuge for 20 minutes at 4 degreeC at max speed, Wash the pellet with 80 percent ethanol, Resuspend the pellet in 20 ul of DNA resuspension solution and pull the 5 samples, Mix the solution with 1 ul of RNase A and incubate for 30 minutes at 37 degreeC Isolate the DNA by phenol chloroform isolation and ethnol precipitation Resuspend the pellet in water. ExoIII treatment: take 5 ug of the purified DNA and resuspend it in a total volume of 90 ul of 1x NEB buffer 1 Add 300 U of ExoIII, Incubate for 1 hour at 37 degreeC, Stop the reaction by adding 2 ul of 0.5 M EDTA and 2 ul of 5 M NaCl, Incubate the reaction at 70 degreeC for 20 minutes, Add water to 100 ul and shear on Covaris S2 apparatus to an average size of 100-400 bp:, duty cycle: 5percent, intensity: 5, cycles/burst: 200, time: 180 seconds, Purify the DNA by Ampure bead solution, elute in 90 ul of water, End repair the sample for 30 minutes at 20 degrees: add 10 ul of 10x T4 ligase buffer supplemented with ATP and DTT, add 1.6 ul of 25 mM dNTP mix, 5 U of Klenow - 1ul, 15 U T4 polymerase - 5 ul, 50 U of PNK - 5ul, Purify the DNA by Quiaquick/Ampure beads, elute in 44 ul of water Add the A-overhangs incubate for 30 minutes at 37 degrees with :, add 5 ul of water, 5 ul of 10x NEB Buffer 2, 1 ul of 10 mM dATP solution , 3 ul of exo-Klenow, Stop the reaction by adding 1 ul of 0.5 EDTA, Wash 50 ul of MyOne Streptavidin C1 beads twice with 500 ul of 1x Wash and Bind buffer in DNA Lo-Bind tubes, Re suspend the beads in 50 ul of 2x, Wash and bind buffer, Mix the beads with the A-added DNA sample and rock the mixture for 30 min at RT, After the incubation, wash the beads once with 500 ul of supplemented bind Wash buffer., Wash the beads once in DNA resuspension solution, Now we would like to add sequencing adapters to this end re-suspend the beads in the following mix: 50 ul 2x rapid ligation mix, 3 ul of sequencing adapters (5uM), 47 ul of water, add 1 ul of rapid ligase, incubate at RT with mixing for 20 minutes, Stop the reaction by adding 6 ul of 0.5 M EDTA/100 ul of ligation mix, Wash the beads twice with 1x Bind and wash buffer, Wash the beads once with TE, Resuspend the beads in 30 ul of water Perform the PCR amplification and size excision. Prepare Phusion mix: 0.5 ul of primer, 5 ul of beads, 25 ul of Phusion MM, 19.5 ul of water. Do PCR with the following setup: 98 degrees: 30 sec and 15 cycles of 98 degrees: 10 sec,60 degrees: 60 sec, 72 degrees: 30 sec, 72 degrees: 7 minute. Gel excise fragments of 400 nt and sequence by paired-end sequencing

characteristic: individual

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

text: Neural Stem Cell Biological Replicate 2


name: E-MTAB-2063:Embryonic Stem Cell Biological Replicate 2

characteristic: ENA-FIRST-PUBLIC

text: EMBL GENOMICS CORE FACILITY, HEIDELBERG, GERMANY

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen


name: E-MTAB-2063:Embryonic Stem Cell Biological Replicate 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: fresh specimen


name: E-MTAB-2063:Neural Stem Cell Biological Replicate 1

characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

text: neural stem cell

text: house mouse

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

text: Neural Stem Cell Biological Replicate 1

characteristic: title


text: EMBL Genome Biology

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:EMBL Genome Biology

text: ArrayExpress

characteristic: cell line

text: fruit fly

text: Protocols: Cells were seeded in Nunc T-25 flasks at a concentration of 2.5 million cells in serum free Gibco Sneider 2.5 million cells were treated with 40 µg MSL1 dsRNA (approx 500bp) and harvested after 4 days of treatment. RNA was extracted with ALL prep DNA/RNA Mini Kit QIAGEN according to the manufacturer instructions. Poly-A RNA isolation, RNA fragmentation, and complementary DNA (cDNA) synthesis protocols were performed as in Yoon and Brem (2010). The cDNA was processed for DNA library preparation according to Parkhomchuk et al. (2009). In summary, the protocol includes RNA fragmentation, first-strand synthesis, and second-strand synthesis using deoxyribo- nucleotide triphosphates (dNTPs) and deoxyuridine triphosphates (dUTPs). End repair, A-tailing, and ligation were then performed as well as size selection for fragments of 300-350 bp. The second strand was cleaved by hydrolysis of uracil in the dsDNA. The resulting strand-specific cDNA was amplified before sequencing.

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: male

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

text: EMBL Genome Biology

text: public

text: ArrayExpress

text: fruit fly

text: Protocols: Cells were seeded in Nunc T-25 flasks at a concentration of 2.5 million cells in serum free Gibco Sneider 2.5 million cells were treated with 40 µg GFP dsRNA (approx 500bp) and harvested after 4 days of treatment. RNA was extracted with ALL prep DNA/RNA Mini Kit QIAGEN according to the manufacturer instructions. Poly-A RNA isolation, RNA fragmentation, and complementary DNA (cDNA) synthesis protocols were performed as in Yoon and Brem (2010). The cDNA was processed for DNA library preparation according to Parkhomchuk et al. (2009). In summary, the protocol includes RNA fragmentation, first-strand synthesis, and second-strand synthesis using deoxyribo- nucleotide triphosphates (dNTPs) and deoxyuridine triphosphates (dUTPs). End repair, A-tailing, and ligation were then performed as well as size selection for fragments of 300-350 bp. The second strand was cleaved by hydrolysis of uracil in the dsDNA. The resulting strand-specific cDNA was amplified before sequencing.

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: male


sample_ATW_4565_LR1 - levé racine

text: GSC

characteristic: INSDC last update

text: public

text: sample_ATW_4565_LR1 - levé racine

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum


text: Yale University

text: public

characteristic: INSDC status

tag: Namespace:Yale University

text: ArrayExpress

characteristic: cell type

text: house mouse

text: Protocols: We obtained Myosin VI sufficient and deficient mice from the Jackson Laboratory (Bar Harbor, ME), and bred them in accordance with Yale University Institutional Animal Care and Use Committee. CD4+T cells were isolated from the spleens, axillary, submaxillary and inguinal lymph nodes of 6-8 week-old Myosin VI sufficient and deficient mice. This was done by positive selection with MACS CD4 (L3T4) beads (Miltenyi Biotec, Inc.). Naive CD62Lhigh/CD44low/CD4+/Nk.1.1-/CD25- T cells were purified by flow cytometric cell (FACS) sorting. These cells were in vitro differentiated towards the Th1 lineage by plating 1.5x10^6 naÃ¯ve CD4 T cells with plate-bound anti-CD3 (10mg/ml) (clone 145-2C11 clone, American Type Culture Collection) and anti-CD28 (2mg/ml) mouse antibodies (Pharmingen) in complete Clicks medium in the presence of 50 U/ml rhIL-2 (Peprotech), 3.5 ng/ml murine rIL-12 (generous gift from Genetics Institute) and 10mg/ml 11B11 (anti-IL-4). After 4-5 days of in vitro differentiation, the cells were harvested, separated in a Ficoll gradient, and stimulated or not with plate-bound anti-CD3 (10mg/ml) for 1 hour. In vitro differentiated Th1 cells were stimulated or not with plate-bound anti-CD3 (10mg/ml) for 1 hour. We have followed the protocol previously published in Core, L., Waterfall, J. & Lis, J. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845-1848 (2008). Briefly, nuclei from treated cells were isolated and incubated for 5 minutes with nucleotides and bromo-UTP analog. The nascent RNA from the labeling reaction was isolated and subjected to immunoaffinity purification using Br-dUTP antibody (Santa Cruz Biotech). After first round of purification of nascent RNA, the resulting RNA was ligated with 5' small RNA adaptor RNA (Illumina) and subjected to second Br-UTP purififcation. The resulting RNA is futher ligated using 3' adaptor RNA and subjected to third round of purification. The final purified RNA was reverse transcribed and PCR amplified and size selected (150-250bp) using polyacrylamide gel electrophoresis to generate the final sequencing library. A modified small RNA library contruction protocol based on the Illumina Truseq small RNA kit was modified and incorporated with the nucleic acid extraction protocol of this expermient. Please see the nucleic acid extraction protocol for details.

text: untreated

characteristic: growth condtiion

text: Mus musculus

text: Mus musculus

text: myosin 6 sufficient

characteristic: phenotype

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Yale University

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

text: treated with anti-CD3

text: Mus musculus

text: Mus musculus

text: myosin 6 deficient

text: Mus musculus

text: fresh specimen


characteristic: ENA-CHECKLIST

text: Yale University

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: untreated

text: Mus musculus

characteristic: organism

text: Mus musculus

text: myosin 6 deficient

text: Mus musculus

text: fresh specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: Yale University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: house mouse

text: treated with anti-CD3

text: Mus musculus

text: Mus musculus

text: myosin 6 sufficient

text: Mus musculus

text: fresh specimen


characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:School of Agriculture, Policy and Development, The University of Reading, UK

text: 4 to 6 week

characteristic: age

text: ArrayExpress

text: thale cress

text: Leaf tissues collected from AtPOL2a T-DNA mutant plants (accession number: N676289) Protocols: Seeds were germinated and grown on vermiculite containing soil and maintained at 25oC in 60% Relative Humidity with a day-night cycle of 16/8 h light/dark in controlled environmental conditions. Total RNA was extracted using the RNeasy® Plant Mini Kit (Qiagen, UK) according to the manufacturer’s protocol. The cDNA libraries were constructed in accordance with the Illumina TruSeq RNA sample preparation guide v2 for Illumina paired-end multiplexed sequencing by Source Bioscience, UK.

text: floral transition

characteristic: developmental stage

characteristic: ecotype

text: insertion

characteristic: genetic modification

text: AtPOL2a mutant (T-DNA)

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: leaf

characteristic: organism part

text: Arabidopsis thaliana

text: frozen specimen


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: School of Agriculture, Policy and Development, The University of Reading, UK

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 4 to 6 week

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Leaf tissues collected from wild type plants (N7000) Protocols: Seeds were germinated and grown on vermiculite containing soil and maintained at 25oC in 60% Relative Humidity with a day-night cycle of 16/8 h light/dark in controlled environmental conditions. Total RNA was extracted using the RNeasy® Plant Mini Kit (Qiagen, UK) according to the manufacturer’s protocol. The cDNA libraries were constructed in accordance with the Illumina TruSeq RNA sample preparation guide v2 for Illumina paired-end multiplexed sequencing by Source Bioscience, UK.

text: floral transition

text: No modification

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: leaf

text: Arabidopsis thaliana

text: frozen specimen

characteristic: specimen with known storage state


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: 4 to 6 week

text: ArrayExpress

text: thale cress

characteristic: common name

text: Leaf tissues collected from AtPOL2b T-DNA mutant plants (accession number: N859809) Protocols: Seeds were germinated and grown on vermiculite containing soil and maintained at 25oC in 60% Relative Humidity with a day-night cycle of 16/8 h light/dark in controlled environmental conditions. Total RNA was extracted using the RNeasy® Plant Mini Kit (Qiagen, UK) according to the manufacturer’s protocol. The cDNA libraries were constructed in accordance with the Illumina TruSeq RNA sample preparation guide v2 for Illumina paired-end multiplexed sequencing by Source Bioscience, UK.

characteristic: description

text: floral transition

text: insertion

text: AtPOL2b mutant (T-DNA)

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: leaf

text: Arabidopsis thaliana

text: frozen specimen

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 4 to 6 week

characteristic: age

text: ArrayExpress

text: thale cress

text: Leaf tissues collected from AtPOL2b T-DNA mutant plants (accession number: N859810) Protocols: Seeds were germinated and grown on vermiculite containing soil and maintained at 25oC in 60% Relative Humidity with a day-night cycle of 16/8 h light/dark in controlled environmental conditions. Total RNA was extracted using the RNeasy® Plant Mini Kit (Qiagen, UK) according to the manufacturer’s protocol. The cDNA libraries were constructed in accordance with the Illumina TruSeq RNA sample preparation guide v2 for Illumina paired-end multiplexed sequencing by Source Bioscience, UK.

text: floral transition

characteristic: developmental stage

text: insertion

text: AtPOL2b mutant (T-DNA)

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: leaf

text: Arabidopsis thaliana

text: frozen specimen


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: 4 to 6 week

text: ArrayExpress

text: thale cress

text: Leaf tissues collected from AtPOL2b T-DNA mutant plants (accession number: N501413) Protocols: Seeds were germinated and grown on vermiculite containing soil and maintained at 25oC in 60% Relative Humidity with a day-night cycle of 16/8 h light/dark in controlled environmental conditions. Total RNA was extracted using the RNeasy® Plant Mini Kit (Qiagen, UK) according to the manufacturer’s protocol. The cDNA libraries were constructed in accordance with the Illumina TruSeq RNA sample preparation guide v2 for Illumina paired-end multiplexed sequencing by Source Bioscience, UK.

text: floral transition

characteristic: ecotype

text: insertion

characteristic: genetic modification

text: AtPOL2b mutant (T-DNA)

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: leaf

characteristic: organism part

text: Arabidopsis thaliana

text: frozen specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EPFL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: pre-adipocyte

characteristic: cell type

text: house mouse

text: Protocols: 3T3-L1 mouse fibroblast cells obtained from ATCC, were cultured in high-glucose Dulbecco's modified Eagle's medium (DMEM, Invitrogen) supplemented with 10% fetal calf serum (FCS, AMIMED), with 1X penicillin/streptomycin solution (Invitrogen) in a 5% CO2 humidified atmosphere at 37degreesC and maintained at less than 80% confluence before passaging. Differentiation of 3T3-L1 cells was induced by exposing two-day post-confluent cells (day 0) to DMEM containing 10% FCS supplemented with 1_uM dexamethasone, 0.5_mM 3-isobutyl-1-methylxanthine and 167 nM insulin (Sigma), a medium called MDI. After two days (day 2), cells were washed with Dulbecco's Phosphate-Buffered Saline 1x (PBS, Amimed) and were fed with DMEM containing 10% FCS and 167 nM insulin. Two days later (day 4), the media was changed to 10% FCS/DMEM. Full differentiation is usually achieved by day 6. ZFP277-HA overexpressing cells: For stable and selected lines, 3T3-L1 cells at a density of 5 x 104 cells were transduced with 10 ul viral particles in a 6-well plate. After 12 hours, the medium was changed and puromycin (Life Technologies, 2 _g/ml) was added after 72 hours to select stably transduced cells. If the cell confluence reached 80%, the cells were split and transferred into larger dishes. After every two days, puromycin selection media was changed and the stably transduced cells were selected for two weeks before performing actual experiments. 3T3-L1 stably selected cells were collected at days -2, 0, 2 and 4. The cells were fixed as described previously (Raghav et al., Mol Cell Biol 2012) and stored at -80�C. Ten million cells were used for each immunoprecipitation (IP). The ChIP experiment was performed as described previously in Raghav et al. (2012), under �Chromatin Immunoprecipitation of SMRT� in the Supplementary materials. A ZEB1 antibody (Santa Cruz, sc-25388, 10 _g per IP) and a rabbit isotype control IgG (Santa Cruz, SC-8994) was used for each time point. The DNA was stored at -20�C till verification of ChIP enrichment by qPCR and ChIP-seq library preparation. Multiplex libraries were prepared using barcoded adapters (see table below) for each sample following the protocol described in (Raghav and Deplancke, 2012) with slight modifications. In brief, ChIP-DNA fragments were end-repaired using an End-IT DNA end repair kit (Epicentre Technologies) followed by addition of an A-base and ligation of bar-coded adapters. After the ligation incubation, the DNA was cleaned up using AMPure XP Beads (Agencourt) and eluted in 12 ul. These purified, ligated DNA fragments were separated on a 2% agarose gel to select 200-500 bp-sized DNA fragments and DNA was subsequently isolated from gel slices using a Qiagen gel extraction kit. The gel-extracted DNA was then amplified for 17 cycles by PCR using high fidelity Phusion hot start polymerase (NEB). The concentration and quality of purified, amplified DNA were estimated using respectively a Qubit dsDNA high sensitivity kit (Invitrogen) and a high sensitivity DNA assay Bioanalyzer 2100 (Agilent).

text: ZFP277-HA overexpression

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: frozen specimen

characteristic: specimen with known storage state


text: EPFL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: pre-adipocyte

text: house mouse

characteristic: common name

characteristic: description

text: wild type

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: frozen specimen

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EPFL

text: public

text: ArrayExpress

text: adipocyte

text: house mouse

text: wild type

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: frozen specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

tag: Namespace:College of Veterinary Medicine, Shaanxi Center for Stem Cell Engineering and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China;

text: ArrayExpress

text: somatic cell

text: pig

text: pig embryo fibroblast Protocols: The piPS cells were maintained on mitotically inactive mouse embryonic fibroblasts (MEFs) feeder derived from ICR mice supplemented with 10% FBS, sodium pyruvate, nonessential amino acids, beta-mercaptoethanol, and LIF, bFGF. Total RNA was isolated from cell cultures or snap-frozen tissues, in biological triplicates or greater, using TRIzol extraction and purified with the Qiagen RNA Purification Kit. A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA.) following manufacturer’s recommendations and index odes were added to attribute sequences to each sample. Briefly, NEB 3-prime SR Adaptor was directly and specifically ligated to 3-prime end of miRNA, siRNA and piRNA. After the 3-prime ligation reaction, the SR RT Primer hybridized to the excess of 3-prime SR Adaptor (that remained free after the 3-prime ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5 prime SR Adaptor in the subsequent ligation step. 5 prime ends adapter was ligated to 5 prime ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140-160 bp (the length of small noncoding RNA plus the 3-prime and 5-prime adaptors) were recovered and dissolved in 8 uL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturers instructions

text: Sus scrofa

text: Sus scrofa

text: Sus scrofa

text: PEF


text: College of Veterinary Medicine, Shaanxi Center for Stem Cell Engineering and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China;

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: stem cell

text: pig

text: The FGF dependent piPSC lines piPS-w which is kindly provided by Franklin.D West labshowed flat and compact colony morphology which were similar to human ESCs and mouse EpiSCs Protocols: The piPS cells were maintained on mitotically inactive mouse embryonic fibroblasts (MEFs) feeder derived from ICR mice supplemented with 10% FBS, sodium pyruvate, nonessential amino acids, beta-mercaptoethanol, and LIF, bFGF. Total RNA was isolated from cell cultures or snap-frozen tissues, in biological triplicates or greater, using TRIzol extraction and purified with the Qiagen RNA Purification Kit. A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA.) following manufacturer’s recommendations and index odes were added to attribute sequences to each sample. Briefly, NEB 3-prime SR Adaptor was directly and specifically ligated to 3-prime end of miRNA, siRNA and piRNA. After the 3-prime ligation reaction, the SR RT Primer hybridized to the excess of 3-prime SR Adaptor (that remained free after the 3-prime ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5 prime SR Adaptor in the subsequent ligation step. 5 prime ends adapter was ligated to 5 prime ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140-160 bp (the length of small noncoding RNA plus the 3-prime and 5-prime adaptors) were recovered and dissolved in 8 uL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturers instructions

text: Sus scrofa

text: Sus scrofa

text: Sus scrofa

text: iPS-w


text: public

text: ArrayExpress

text: stem cell

characteristic: cell type

text: pig

text: LIF dependent pig iPS cell lines derived in their lab previously Protocols: The piPS cells were maintained on mitotically inactive mouse embryonic fibroblasts (MEFs) feeder derived from ICR mice supplemented with 10% FBS, sodium pyruvate, nonessential amino acids, beta-mercaptoethanol, and LIF, bFGF. Total RNA was isolated from cell cultures or snap-frozen tissues, in biological triplicates or greater, using TRIzol extraction and purified with the Qiagen RNA Purification Kit. A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA.) following manufacturer’s recommendations and index odes were added to attribute sequences to each sample. Briefly, NEB 3-prime SR Adaptor was directly and specifically ligated to 3-prime end of miRNA, siRNA and piRNA. After the 3-prime ligation reaction, the SR RT Primer hybridized to the excess of 3-prime SR Adaptor (that remained free after the 3-prime ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5 prime SR Adaptor in the subsequent ligation step. 5 prime ends adapter was ligated to 5 prime ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140-160 bp (the length of small noncoding RNA plus the 3-prime and 5-prime adaptors) were recovered and dissolved in 8 uL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturers instructions

text: Sus scrofa

text: Sus scrofa

text: Sus scrofa

text: iPS-j


characteristic: INSDC center name

text: public

text: ArrayExpress

text: stem cell

text: pig

text: The piPSC-g lines derived in our labwith culture media added both bFGF and LIF also showed the flattened morphology Protocols: The piPS cells were maintained on mitotically inactive mouse embryonic fibroblasts (MEFs) feeder derived from ICR mice supplemented with 10% FBS, sodium pyruvate, nonessential amino acids, beta-mercaptoethanol, and LIF, bFGF. Total RNA was isolated from cell cultures or snap-frozen tissues, in biological triplicates or greater, using TRIzol extraction and purified with the Qiagen RNA Purification Kit. A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA.) following manufacturer’s recommendations and index odes were added to attribute sequences to each sample. Briefly, NEB 3-prime SR Adaptor was directly and specifically ligated to 3-prime end of miRNA, siRNA and piRNA. After the 3-prime ligation reaction, the SR RT Primer hybridized to the excess of 3-prime SR Adaptor (that remained free after the 3-prime ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5 prime SR Adaptor in the subsequent ligation step. 5 prime ends adapter was ligated to 5 prime ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140-160 bp (the length of small noncoding RNA plus the 3-prime and 5-prime adaptors) were recovered and dissolved in 8 uL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturers instructions

text: Sus scrofa

text: Sus scrofa

text: Sus scrofa

text: iPS-g


text: GSC

characteristic: INSDC first public

text: public

text: fungi

text: Samples were pooled in this way (tag gradient site altitude(m) Tman(°C)) : TCTG France Aire sur l'Adour (40) 110 13,79 AGAG France Aroz (70) 228 10,65 CACG Spain Artikutza Embalse 534 11,47 TACA Spain Baztan 538 12,03 CTAG France Betplan (32) 310 13,54 CACA France Briaucourt (70) 252 10,14 ACGA France Buzinval (76) 195 10,20 ATGT France Cheraute (64) 400 11,91 AGAT Spain Ermita Aitziber (Urdiain-NA) 580 11,15 ATCA Sweden Fano 25 6,32 ATCT France Fraisans (39) 267 10,72 CGTA Poland Gdynia 164 6,44 CATA Sweden Hallandsasen 120 7,88 ACAG France Harlettes (62) 196 9,77 CGAG France Josbaig (64) 266 11,91 ATAT France Kerpich aux bois (57) 275 9,39 TATG France La Feuillie (76) 164 10,43 TGCG France Lasseube (64) 202 11,03 TACG France Le rheu (35) 48 11,54 TATA France Le Vaudreuil (27) 128 10,73 TCTA Poland Lebork 148 6,44 CTGA Italy Monte Soro (Sicily) 1800 12,18 AGTG Sweden Norra Gr▒nby 68 8,02 ATCG Italy Pian Cansiglio (Veneto) 1200 12,40 ACAT France Ponsan Soubiran (32) 340 12,74 ATAG France Retonval (76) 187 9,86 AGCG France Rosteig 266 9,38 TCAG France Sennevieres(37) 84 11,47 TGTG France Serenac (81) 345 12,36 TAGA Italy Serralunga (Abruzzo) 1350 11,61 ACTA Poland Szczecinek 161 8,37

text: Fungi

text: Fungi


characteristic: INSDC last update

text: public

tag: Namespace:Systems Biology Ireland, University College Dublin now: European Molecular Biology Laboratory

text: ArrayExpress

characteristic: cell line

text: human

text: Protocols: Total mRNA was extracted using TRI Reagent (Sigma-Aldrich) according to manufacturers protocol and DNA was digested with DNA-free Kit (Applied Biosystems). RNA quality was checked by RT-qPCR (as above) and on a 2100 Bioanalyser (Agilent) using a Eukaryote Total RNA Nano Chip (version 2.6). All samples had a RIN value in the range of 9.8-10. Sequencing libraries were generated from 2ug of total RNA per sample with TruSeq RNA sample preparation Kit v2 (Illumina) according to manufacturers protocol. Size and purity of the libraries were analysed on a Bioanalyser High Sensitivity DNA chip (Agilent). Libraries were clustered using TruSeq Single-End Cluster Kit v5-CS-GA (Illumina). Cells were cultured in RPMI 1640 (Gibco), supplemented with 10% fetal bovine serum (FBS) (Gibco), 2mM L-glutamine (Gibco) and 1% Penicillin-Streptomycin solution (Gibco) Azak was dissolved in DMSO in order to apply it to the cells. Therefore a vehicle control consisting of SY5Y-MYCN cells treated with 24h 1µl/ml DMSO only was used in duplicates. Doxycycline (Sigma) dissolved in water was used at a final concentration of 1μg/ml to induce MYCN expression in SY5Y-MYCN. A co-treatment study with Dox and Azak was conducted. SY5Y-MYCN cells were treated with 24h Azak, 24h Azak & 48h Dox and 48h Dox, with biological duplicates. 1 μM RA (dissolved in DMSO) and 1 μg/mL Doxycycline were given individually and in combination. SY5Y-MYCN cells were treated with 24h RA, 24h RA & 48h Dox, and 48h Dox and RNA was extracted in biological duplicates. For the 24h RA & 48h Dox co-treatment cells were treated with Dox for 24h and then with RA and fresh Dox for a further 24h. mRNA was extracted using TRI Reagent (Sigma-Aldrich) according to manufacturers protocol

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Systems Biology Ireland, University College Dublin now: European Molecular Biology Laboratory

text: public

characteristic: INSDC status

text: ArrayExpress

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


E-MTAB-2663:MCF7 CTRL

text: UNIVERSITY

text: public

text: E-MTAB-2663:MCF7 CTRL

text: ArrayExpress

text: human

text: Protocols: MCF7 cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with non-essential amino-acids (1%), penicillin and streptomycine (1%), gentamycin (0.1%), fungizone (0.1%) and 10% FCS. RNAs were purified from cultured cells using the High Pure RNA isolation kit (Roche). The integrity of RNA was checked with BioAnalyser 2100 (Agilent technologies) that indicated a RQI score >8 The libraries were prepared with Truseq mRNA Sample Prep kit (Illumina) from 1 microgram of total RNA following manufacturer's instructions. mRNAs were isolated by poly-A selection and fragmented (8 minutes at 94°). Fragmented mRNAs were used for reverse-transcription in the presence of Superscript II (Invitrogen) and random primers. After second strand synthesis, end-repair, A-tailing and purification, the double strand cDNA fragments were ligated to Truseq adapters containing the index sequences. Fifteen cycles of PCR in the presence of dedicated PCR primers and PCR master mix were applied to generate the final libraries.

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: MCF7 CTRL