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characteristic: geographic location (depth)

characteristic: geographic location (elevation)

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text: Bacterial biofouling community on acrylic panels deployed for 5 months (sampled in December 2017) at the marina in Salmiya (Kuwait)

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text: Bacterial biofouling community on acrylic panels deployed for 3 months (sampled in October 2017) at the marina in Salmiya (Kuwait)

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 34634:1930e2b6-9c4c-4874-adb7-91f9497ac2b8

characteristic: Submitter Id

text: GFBIO

characteristic: broker name

characteristic: collection date

text: Bacterial biofouling community on acrylic panels deployed for 3 months (sampled in October 2017) at the marina in Fintas (Kuwait)

characteristic: description

text: biofilm [ENVO:00002034]

characteristic: environment (biome)

text: coastal water body [ENVO:02000049]

characteristic: environment (feature)

text: biofilm material [ENVO:01000156]

characteristic: environment (material)

text: microbial mat/biofilm

characteristic: environmental package

text: Kuwait

text: Fintas

text: mimarks-survey

text: microbial mat/biofilm

text: biofilm metagenome

characteristic: organism

text: biofilm metagenome

text: Illumina MiSeq

text: true

text: 16S rRNA

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Leibniz Centre for Tropical Marine Research

text: public

text: 34633:1930e2b6-9c4c-4874-adb7-91f9497ac2b8

text: GFBIO

text: biofilm [ENVO:00002034]

text: coastal water body [ENVO:02000049]

text: biofilm material [ENVO:01000156]

text: microbial mat/biofilm

text: Kuwait

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Fintas

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: investigation type

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: biofilm metagenome

text: FWD: CCTACGGGNGGCWGCAG; REV: GACTACNVGGGTATCTAATCC

characteristic: pcr primers

characteristic: project name

characteristic: sample description

text: biofilm metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: true

characteristic: submitted to INSDC

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

characteristic: total depth of water column


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 34632:1930e2b6-9c4c-4874-adb7-91f9497ac2b8

characteristic: Submitter Id

text: GFBIO

characteristic: broker name

characteristic: collection date

characteristic: description

text: biofilm [ENVO:00002034]

characteristic: environment (biome)

text: coastal water body [ENVO:02000049]

characteristic: environment (feature)

text: biofilm material [ENVO:01000156]

characteristic: environment (material)

text: microbial mat/biofilm

characteristic: environmental package

text: Kuwait

text: Fintas

text: mimarks-survey

text: microbial mat/biofilm

text: biofilm metagenome

characteristic: organism

text: Biotechnological Applications of Marine Biofilms developing on solid surfaces in the Arabian Gulf

text: biofilm metagenome

text: Illumina MiSeq

text: true

text: 16S rRNA

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: 34631:1930e2b6-9c4c-4874-adb7-91f9497ac2b8

text: GFBIO

text: Bacterial biofouling community on acrylic panels deployed for 2 months (sampled in September 2017) at the marina in Fintas (Kuwait)

text: biofilm [ENVO:00002034]

text: coastal water body [ENVO:02000049]

text: biofilm material [ENVO:01000156]

text: microbial mat/biofilm

text: Kuwait

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Fintas

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: investigation type

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: biofilm metagenome

characteristic: pcr primers

characteristic: project name

characteristic: sample description

text: biofilm metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: true

characteristic: submitted to INSDC

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

characteristic: total depth of water column


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 34630:1930e2b6-9c4c-4874-adb7-91f9497ac2b8

characteristic: Submitter Id

text: GFBIO

characteristic: broker name

characteristic: collection date

characteristic: description

text: biofilm [ENVO:00002034]

characteristic: environment (biome)

text: coastal water body [ENVO:02000049]

characteristic: environment (feature)

text: biofilm material [ENVO:01000156]

characteristic: environment (material)

text: microbial mat/biofilm

characteristic: environmental package

text: Kuwait

text: Fintas

text: mimarks-survey

text: microbial mat/biofilm

text: biofilm metagenome

characteristic: organism

text: biofilm metagenome

text: Illumina MiSeq

text: true

text: 16S rRNA

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: 34629:1930e2b6-9c4c-4874-adb7-91f9497ac2b8

text: GFBIO

text: biofilm [ENVO:00002034]

text: coastal water body [ENVO:02000049]

text: biofilm material [ENVO:01000156]

text: microbial mat/biofilm

text: Kuwait

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Fintas

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: investigation type

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: biofilm metagenome

characteristic: pcr primers

characteristic: project name

characteristic: sample description

text: biofilm metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: true

characteristic: submitted to INSDC

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

characteristic: total depth of water column


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 34628:1930e2b6-9c4c-4874-adb7-91f9497ac2b8

characteristic: Submitter Id

text: GFBIO

characteristic: broker name

characteristic: collection date

text: Bacterial biofouling community on acrylic panels deployed for 1 month (sampled in August 2017) at the marina in Fintas (Kuwait)

characteristic: description

text: biofilm [ENVO:00002034]

characteristic: environment (biome)

text: coastal water body [ENVO:02000049]

characteristic: environment (feature)

text: biofilm material [ENVO:01000156]

characteristic: environment (material)

text: microbial mat/biofilm

characteristic: environmental package

text: Kuwait

text: Fintas

text: mimarks-survey

text: microbial mat/biofilm

text: biofilm metagenome

characteristic: organism

text: biofilm metagenome

text: Illumina MiSeq

text: true

text: 16S rRNA

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: 34627:1930e2b6-9c4c-4874-adb7-91f9497ac2b8

text: GFBIO

text: biofilm [ENVO:00002034]

text: coastal water body [ENVO:02000049]

text: biofilm material [ENVO:01000156]

text: microbial mat/biofilm

text: Kuwait

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Fintas

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: investigation type

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: biofilm metagenome

characteristic: pcr primers

characteristic: project name

characteristic: sample description

text: biofilm metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: true

characteristic: submitted to INSDC

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

characteristic: total depth of water column


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 34626:1930e2b6-9c4c-4874-adb7-91f9497ac2b8

characteristic: Submitter Id

text: GFBIO

characteristic: broker name

characteristic: collection date

characteristic: description

text: biofilm [ENVO:00002034]

characteristic: environment (biome)

text: coastal water body [ENVO:02000049]

characteristic: environment (feature)

text: biofilm material [ENVO:01000156]

characteristic: environment (material)

text: microbial mat/biofilm

characteristic: environmental package

text: Kuwait

text: Fintas

text: mimarks-survey

text: microbial mat/biofilm

text: biofilm metagenome

characteristic: organism

text: biofilm metagenome

text: Illumina MiSeq

text: true

text: 16S rRNA

characteristic: title


dArtagnan

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: INRA

text: public

text: dArtagnan

text: dArtagnan

characteristic: common name

text: Enterococcus faecium

characteristic: host

text: Enterococcus phage dArtagnan

text: Enterococcus phage dArtagnan

text: Complete genome of Enterococcus phage dArtagnan


Aramis

characteristic: External Id

text: INRA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Aramis

text: Aramis

text: Enterococcus faecium

characteristic: host scientific name

text: Enterococcus phage Aramis

text: Enterococcus phage Aramis

text: Complete genome of Enterococcus phage Aramis


Athos

text: INRA

text: public

characteristic: SRA accession

text: Athos

characteristic: Submitter Id

text: Athos

text: Enterococcus faecium

text: Enterococcus phage Athos

text: Enterococcus phage Athos

text: Complete genome of Enterococcus phage Athos


Porthos

text: INRA

text: public

text: Porthos

text: Porthos

text: Enterococcus faecium

text: Enterococcus phage Porthos

text: Enterococcus phage Porthos

text: Complete genome of Enterococcus phage Porthos


E-MTAB-9907:Sample 1

text: Weizmann Institue of Science

text: public

text: E-MTAB-9907:Sample 1

tag: Namespace:Weizmann Institue of Science

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: house mouse

text: Protocols: Cells were lysed using Trizol. Cells were grown in 37deg c, 5% CO2. Cells were transfected with either siAGO2 or siNT (Dharmacon), using Lipofectamine RNAiMAX transfection reagent according to manufacturer's orderes RNA extraction was performed using DirectZole RNA Purification Kit (Zymo Research), according to kit protocol. Library was prepared using the Lexogene Quantseq 3’ mRNA-seq Library Prep kit for Illumina (REV) with Costume Sequencing Primer (016), according to kit protocol.

characteristic: description

text: embryo

characteristic: developmental stage

text: neuroblastoma

characteristic: disease

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: Sample 1


E-MTAB-9907:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Weizmann Institue of Science

text: public

text: E-MTAB-9907:Sample 2

text: ArrayExpress

text: house mouse

text: embryo

text: neuroblastoma

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: Sample 2

characteristic: title


E-MTAB-9907:Sample 3

characteristic: External Id

text: Weizmann Institue of Science

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9907:Sample 3

text: ArrayExpress

text: house mouse

characteristic: common name

text: embryo

text: neuroblastoma

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: Sample 3


E-MTAB-9907:Sample 4

text: Weizmann Institue of Science

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9907:Sample 4

text: ArrayExpress

text: house mouse

text: embryo

text: neuroblastoma

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: Sample 4


E-MTAB-9907:Sample 5

text: Weizmann Institue of Science

text: public

text: E-MTAB-9907:Sample 5

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: house mouse

text: embryo

text: neuroblastoma

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: Sample 5


E-MTAB-9907:Sample 6

text: Weizmann Institue of Science

text: public

text: E-MTAB-9907:Sample 6

text: ArrayExpress

text: house mouse

characteristic: description

text: embryo

characteristic: developmental stage

text: neuroblastoma

characteristic: disease

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: Sample 6


E-MTAB-9925:Sample 1-pt85

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9925:Sample 1-pt85

tag: Namespace:Centro Ricerca M. Tettamanti Clinica Pediatrica, Ospedale S.Gerardo Dipartimento di Medicina e Chirurgia Universita degli Studi Milano-Bicocca

unit: month

characteristic: age

text: ArrayExpress

text: precursor B cell

characteristic: cell type

text: human

text: Protocols: Mononuclear cells purification by ficoll density gradient of Bone Marrow Aspirates guanidinium thiocyanate-phenol-chloroform extraction protocol Whole transcriptome RNA-seq analyses of diagnosis BM samples have been performed by Next Generation Sequencing (NGS), using the Universal RNAseq kit (Nugen, Tecan). The Universal RNA-Seq is an end-to-end solution for strand-specific RNA-Seq library construction used 100ng nanogram amounts of total RNA obtained from BM cells. The workflow consists of double-stranded cDNA generation using a mixture of random and poly(T) priming, optional fragmentation of double-stranded cDNA, end repair, adaptor ligation, strand selection, targeted transcript depletion with AnyDeplete for globin genes, and PCR amplification to produce the final library. The yields of final libraries were assessed by Qubit 4.0 fluorimeter and their sizing by Agilent Bioanalyzer.

text: infant

text: acute lymphoblastic leukemia

text: onset

characteristic: disease staging

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: Sample 1-pt85


E-MTAB-9925:Sample 2-pt165

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Centro Ricerca M. Tettamanti Clinica Pediatrica, Ospedale S.Gerardo Dipartimento di Medicina e Chirurgia Universita degli Studi Milano-Bicocca

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9925:Sample 2-pt165

text: ArrayExpress

text: precursor B cell

text: human

characteristic: common name

text: infant

text: acute lymphoblastic leukemia

text: onset

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: male

text: Sample 2-pt165

characteristic: title


E-MTAB-9925:Sample 3-pt810

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9925:Sample 3-pt810

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: precursor B cell

text: human

characteristic: description

text: infant

characteristic: developmental stage

text: acute lymphoblastic leukemia

characteristic: disease

text: onset

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: male

text: Sample 3-pt810


E-MTAB-9925:Sample 4-pt530

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9925:Sample 4-pt530

characteristic: age

text: ArrayExpress

text: precursor B cell

characteristic: cell type

text: human

text: infant

text: acute lymphoblastic leukemia

text: onset

characteristic: disease staging

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: female

text: Sample 4-pt530


E-MTAB-9925:Sample 5-pt604

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9925:Sample 5-pt604

text: ArrayExpress

text: precursor B cell

text: human

characteristic: common name

text: infant

text: acute lymphoblastic leukemia

text: onset

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: female

characteristic: sex

text: Sample 5-pt604


E-MTAB-9925:Sample 6-pt790

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9925:Sample 6-pt790

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: precursor B cell

text: human

characteristic: description

text: infant

text: acute lymphoblastic leukemia

text: onset

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: female

text: Sample 6-pt790

characteristic: title


E-MTAB-9925:Sample 7-pt811

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9925:Sample 7-pt811

characteristic: age

text: ArrayExpress

text: precursor B cell

characteristic: cell type

text: human

text: infant

characteristic: developmental stage

text: acute lymphoblastic leukemia

characteristic: disease

text: onset

characteristic: disease staging

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: female

text: Sample 7-pt811


E-MTAB-9925:Sample 8-pt809

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9925:Sample 8-pt809

text: ArrayExpress

text: precursor B cell

text: human

text: infant

text: acute lymphoblastic leukemia

text: onset

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: male

text: Sample 8-pt809


E-MTAB-7451:Control 1

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7451:Control 1

tag: Namespace:University of Sussex Brighton and Sussex Medical School

characteristic: Submitter Id

unit: hour

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: Protocols: Dissection of 120hr L3 wing imaginal discs in Ringers solution on ice. Larvae aged using a 3 hour egg lay. RNA was rRNA depleted by oligo hybridisation RNA extracted from 60 wing discs per sample using the miRNeasy Micro Kit Illumina TruSeq Stranded

characteristic: description

text: L3 larva

text: wild type genotype

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: wing disc

text: Drosophila melanogaster

text: dis3L2 wt

characteristic: strain

text: Control 1


E-MTAB-7451:Control 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Sussex Brighton and Sussex Medical School

text: public

text: E-MTAB-7451:Control 2

characteristic: age

text: ArrayExpress

text: fruit fly

text: L3 larva

characteristic: developmental stage

text: wild type genotype

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: wing disc

text: Drosophila melanogaster

text: dis3L2 wt

text: Control 2

characteristic: title


E-MTAB-7451:Control 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-7451:Control 3

text: ArrayExpress

text: fruit fly

text: L3 larva

text: wild type genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: wing disc

text: Drosophila melanogaster

text: dis3L2 wt

text: Control 3


E-MTAB-7451:Dis3L2 null 1

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7451:Dis3L2 null 1

characteristic: Submitter Id

text: ArrayExpress

text: fruit fly

text: L3 larva

text: Dis3L2 mutant

text: Drosophila melanogaster

text: Drosophila melanogaster

text: wing disc

characteristic: organism part

text: Drosophila melanogaster

text: dis3L2 12

text: Dis3L2 null 1


E-MTAB-7451:Dis3L2 null 2

text: public

text: E-MTAB-7451:Dis3L2 null 2

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

characteristic: description

text: L3 larva

text: Dis3L2 mutant

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: wing disc

text: Drosophila melanogaster

text: dis3L2 12

text: Dis3L2 null 2


E-MTAB-7451:Dis3L2 null 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-7451:Dis3L2 null 3

characteristic: age

text: ArrayExpress

text: fruit fly

text: L3 larva

text: Dis3L2 mutant

text: Drosophila melanogaster

text: Drosophila melanogaster

text: wing disc

text: Drosophila melanogaster

text: dis3L2 12

characteristic: strain

text: Dis3L2 null 3


characteristic: ENA-LAST-UPDATE

text: IOR - Institue of Oncology Research

text: public

tag: Namespace:IOR - Institue of Oncology Research

text: ArrayExpress

text: human

text: Protocols: PDX tumor tissue was cut into small pieces (1–0.5 mm) with a scalpel blade and then digested in CollagenaseType I media solution (200U/ml Cat#SCR103, Millipore) at 37 °C for 45-60 min. RNA was extracted using the Rnasy Mini Kit (Qiagen) and sample quality was assessed using Agilent Bioanalyzer. RNA libraries were prepared for sequencing using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®

text: prostate carcinoma

characteristic: disease

text: wild type genotype

characteristic: growth condition

text: not applicable

characteristic: isolate

text: lymph node

characteristic: metastatic site

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: prostate gland

text: Homo sapiens

characteristic: title


characteristic: External Id

text: IOR - Institue of Oncology Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: LNCaP

text: human

text: prostate carcinoma

text: wild type genotype

text: not applicable

text: left supraclavicular lymph node

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IOR - Institue of Oncology Research

text: public

text: ArrayExpress

characteristic: broker name

text: LNCaP

text: human

characteristic: common name

text: Protocols: PC3, DU-145, 22rV1, LAPC-4 and LNCaP cell lines were cultured in RPMI 1640 (21875-034 Life Technologies)supplemented with 10% Fetal Bovine Serum (FBS-11A Capricorn Scientific) and 1% Penicillin/Streptomycin(15140-122 Life Technologies) with 5% CO2 at 37°C. LAPC4 were in addition supplemented with 1 nM DHT.The LNCaP-abl cell line was cultured in Phenol-Red Free RPMI 1640 (11835063 Life Technologies) containing10% charcoal-stripped serum (CSS Fetal Bovine Serum, Charcoal Stripped A3382101 Life Technologies) and1% Penicillin/Streptomycin with 5% CO2 at 37°C.VCaP cell lines were cultured in DMEM(61965059 Life Technologies) supplemented with 10%FBS and 1% μg/ml Penicillin/Streptomycin with 5% CO2 at 37°C.MDA-PCa-2b cell line was cultured in ATCC-formulated F-12K medium (30-2004) supplemented with 20% FBS,25 ng/ml Cholera Toxin (C8252 Sigma), 10 ng/ml Epidermal Growth Factor (AF-100-15 Peprotech), 0.005 mMPhosphoethanolamine (P1348 Sigma), 100 pg/ml Hydrocortisone (H0135 Sigma), 45 nM Selenium Acid (211176Sigma), 0.005 mg/ml Human Recombinant Insulin (I1884 Sigma) and 1% Penicillin/Streptomycin with 5% CO2 at37°C. RNA was extracted using the Rnasy Mini Kit (Qiagen) and sample quality was assessed using Agilent Bioanalyzer. RNA libraries were prepared for sequencing using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®

characteristic: description

text: prostate carcinoma

text: wild type genotype

characteristic: genotype

text: xenograft

text: not applicable

text: left supraclavicular lymph node

text: Homo sapiens

text: Homo sapiens

text: prostate gland

characteristic: organism part

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

text: IOR - Institue of Oncology Research

text: public

text: ArrayExpress

text: LNCaP-ABL

text: human

text: prostate carcinoma

characteristic: disease

text: wild type genotype

text: xenograft

characteristic: growth condition

text: not applicable

characteristic: isolate

characteristic: metastatic site

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: Homo sapiens


characteristic: External Id

text: IOR - Institue of Oncology Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: LNCAP-ABL

text: human

text: prostate carcinoma

text: wild type genotype

text: xenograft

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: prostate gland

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: IOR - Institue of Oncology Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

text: prostate carcinoma

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: IOR - Institue of Oncology Research

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: prostate carcinoma

text: wild type genotype

characteristic: genotype

text: xenograft

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

text: IOR - Institue of Oncology Research

text: public

text: ArrayExpress

text: LuCaP 23.1

text: human

text: prostate carcinoma

characteristic: disease

text: wild type genotype

characteristic: growth condition

text: not applicable

characteristic: isolate

text: lymph node

text: Homo sapiens

text: Homo sapiens

text: prostate gland

characteristic: organism part

text: Homo sapiens


characteristic: External Id

text: IOR - Institue of Oncology Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: LuCaP 23.1

text: human

text: prostate carcinoma

text: wild type genotype

text: xenograft

text: not applicable

text: lymph node

characteristic: metastatic site

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: prostate gland

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: IOR - Institue of Oncology Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: LuCaP 35

text: human

text: prostate carcinoma

text: wild type genotype

text: xenograft

text: not applicable

text: lymph node

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: Homo sapiens

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: IOR - Institue of Oncology Research

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: LuCaP 78

text: human

characteristic: common name

characteristic: description

text: prostate carcinoma

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

text: IOR - Institue of Oncology Research

text: public

text: ArrayExpress

text: LuCaP 78

text: human

text: prostate carcinoma

characteristic: disease

text: wild type genotype

characteristic: genotype

text: xenograft

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: Homo sapiens


characteristic: External Id

text: IOR - Institue of Oncology Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: PNPCa

text: human

text: prostate carcinoma

text: wild type genotype

text: not applicable

characteristic: metastatic site

text: Homo sapiens

text: Homo sapiens

text: prostate gland

characteristic: organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: IOR - Institue of Oncology Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: PNPCa

text: human

text: prostate carcinoma

text: wild type genotype

text: xenograft

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: prostate gland

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: IOR - Institue of Oncology Research

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: VCaP

text: human

characteristic: common name

text: prostate carcinoma

text: wild type genotype

text: not applicable

text: vertebrae

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: Homo sapiens

characteristic: title


characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Institut national de recherche en agriculture, alimentation et environnement (INRAE)

unit: day

characteristic: age

text: ArrayExpress

text: barrel medic

text: Jemalong A17

characteristic: cultivar

text: Protocols: We initiated N-treatments and inoculated plants at different time before harvest. We collected all roots samples simultaneously in SN or LN compartments of the split-root systems. Each biological replicate is a pool of the half root systems of two plants. RNAseq analysis included 3 biological replicates per condition. We collected three replicate samples, for each time point, and each replicate was a pool of roots of two plants. Medicago truncatula Jemalong A17 seeds were scarified, germinated as described in Lambert et al. (Lambert, I. et al. J Exp Bot 2020 - http://dx.doi.org/10.1093/jxb/eraa221). Individual plantlets were transferred into hydroponic culture tanks containing a vigorously aerated HY basal nutrient solution adjusted to 5.8 with KOH and supplemented with 1 mM KNO3. We cut the primary root tips of plantlets to promote branching of the root system. The culture chambers conditions were a light intensity of 250 μmol s−1 m−2 photosynthetically active radiation, a relative humidity of 70%, a light/dark cycle of 16h/8h and an ambient temperature of 22°C/20°C. We separated the root systems of 4-week-old plants in two parts. Split-root compartments contained HY nutrient solution supplemented with KNO3 0.5mM as sole mineral nitrogen source and the pH was adjusted to 7. For the nitrogen treatments, one split root side was supplied with nutrient solution with mineral N at 0.5 mM for N-limited (LN) plants, whereas the non-N treated part was kept in nutrient solution without mineral N. Roots of all compartments were inoculated 48h after the N treatment initiation with Sinorhizobium medicae md4 (107 exponentially growing bacteria per ml). We renewed the nutrient solutions were every 4 days. We initiated N treatments at different times before harvest in order to compare plants of the same age (6 weeks old plants) differing by the duration post-inoculation. At first grinding with mortar and pestle is carried out in liquid nitrogen to allow to homogenise the sample. We took an aliquot of 200mg for the extraction of RNAs using miRNeasy® Mini Kit (Qiagen, Venlo, Netherlands) according to the supplier's recommendations. RNAs concentration were measured using the NANODROP 1000 spectrometer (Thermo-Fisher Scientific, Waltham, Massachusetts, USA) and samples kept at -20°C. RNA integrity quality control was assessed using the BioAnalyser (BioRad Laboratories Inc., Hercules, California, USA). For each RNA extraction polyadenylated plant mRNA libraries were generated and sequenced. Library preparation and sequencing were performed at the MGX-Montpellier GenomiX Facilities (Montpellier, France). Libraries for sequencing were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, USA). Library quality was checked using the Standard Sensitivity NGS Kit on the Advanced Analytical Fragment Analyzer (Agilent Technologies, Inc., Santa Clara, California, USA), and concentration optimised performing a qPCR (Light Cycler 480, Roche, Basel, Switzerland).

characteristic: description

text: wild type genotype

characteristic: genotype

text: half of roots grown in nitrogen limitation

characteristic: growth condition

text: Medicago truncatula

text: Medicago truncatula

text: root

text: Medicago truncatula


characteristic: External Id

text: Institut national de recherche en agriculture, alimentation et environnement (INRAE)

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: barrel medic

text: Jemalong A17

text: wild type genotype

text: Medicago truncatula

text: Medicago truncatula

text: root

characteristic: organism part

text: Medicago truncatula


characteristic: ENA-CHECKLIST

text: IST Austria

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:IST Austria

text: ArrayExpress

characteristic: cell line

text: neuron

characteristic: cell type

text: human

text: Protocols: Pools of three organoids at day 10 after Matrigel droplet embedding were dissociated in 700 µl Trizol (Invitrogen) by passing them 20-30 times through a 20G needle. RNA extraction was performed by adding 140 µl chloroform (Sigma), followed by centrifugation for 15 min at 12000 g at 4 °C. The aqueous upper phase was transferred to a new tube and mixed with 1.5 volumes of 100% EtOH. RNA was extracted using Zymo-Spin™ IC columns (Zymo Research). In short, the aqueous phase/ethanol mixture was loaded onto the column, washed with 400 µl 70% EtOH before being treated with RQ1 DNAseI (Promega, 5 µl + 5 µl reaction buffer + 40 µl 70% EtOH) for 15 minutes at RT. After two washes with 70% EtOH the sample was eluted from the column with DEPC-treated H2O. RNA concentration was measured using the NanoDrop spectrophotometer (Thermo Scientific) and quality was assessed with the Bioanalyzer 2100 employing the RNA 6000 Nano kit (Agilent). 1 µg of RNA was used for cDNA library preparation using the QuantSeq 3’ mRNA-Seq FWD Library Prep Kit (Lexogen) according to the manual. Library quality and size distribution were assessed with the High Sensitivity DNA Analysis Kit for the Bioanalyzer 2100 (Agilent). Concentration was measured on a Qubit® 2.0 fluorometer using the Qubit® dsDNA HS Assay Kit and libraries were pooled in equimolar amounts.

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

text: cerebral organoid day 10 after matrigel embedding

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens


E-MTAB-9933:42089_CHD8 +/-_rep1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: IST Austria

text: public

text: E-MTAB-9933:42089_CHD8 +/-_rep1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: neuron

text: human

characteristic: common name

text: embryo

text: normal

text: deletion of part of exon 19, whole exon 20 and part of exon 21

characteristic: genetic modification

text: CHD8 +/-

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: 42089_CHD8 +/-_rep1

characteristic: title


E-MTAB-9933:42090_CHD8 +/-_rep2

characteristic: ENA-CHECKLIST

characteristic: External Id

text: IST Austria

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9933:42090_CHD8 +/-_rep2

text: ArrayExpress

text: neuron

text: human

characteristic: description

text: embryo

text: normal

text: CHD8 +/-

characteristic: genotype

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

text: Homo sapiens

text: 42090_CHD8 +/-_rep2


E-MTAB-9933:42091_CHD8 +/-_rep3

text: IST Austria

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9933:42091_CHD8 +/-_rep3

text: ArrayExpress

characteristic: cell line

text: neuron

characteristic: cell type

text: human

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: CHD8 +/-

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: 42091_CHD8 +/-_rep3


E-MTAB-9933:42092_CHD8 +/-_rep4

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: IST Austria

text: public

text: E-MTAB-9933:42092_CHD8 +/-_rep4

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: neuron

text: human

characteristic: common name

text: embryo

text: normal

characteristic: genetic modification

text: CHD8 +/-

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: 42092_CHD8 +/-_rep4

characteristic: title


E-MTAB-9933:42093_CHD8 +/-_rep5

characteristic: ENA-CHECKLIST

characteristic: External Id

text: IST Austria

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9933:42093_CHD8 +/-_rep5

text: ArrayExpress

text: neuron

text: human

characteristic: description

text: embryo

text: normal

text: CHD8 +/-

characteristic: genotype

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

text: Homo sapiens

text: 42093_CHD8 +/-_rep5


E-MTAB-9933:42094_CHD8 +/-_rep6

text: IST Austria

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9933:42094_CHD8 +/-_rep6

text: ArrayExpress

characteristic: cell line

text: neuron

characteristic: cell type

text: human

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: CHD8 +/-

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: 42094_CHD8 +/-_rep6


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany  Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

characteristic: cas

text: zebrafish

characteristic: common name

text: MidExposure

characteristic: condition

text: Protocols: For each sample, 10 4-day old zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples, they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without injuring the larvae before adding 350µl of RP1 buffer (NucleoSpin RNA Protein kit; Macherey-Nagel 740933.250) for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild-type zebrafish (Danio rerio, Strain AB) broodstocks were maintained under flow-through conditions in 150 L tanks at 26 +/- 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® (Tetra Werke, Melle, Germany) main feed ad libitum and nauplii of Artemia salina. The day before test start, glass spawning-trays with artificial substrate (green glass beads stringed on stainless steel wire) were placed at the bottom of each tank. After mating and spawning in the morning hours eggs were rinsed with clear Cu-reduced water and placed into glass dishes for pre-picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes (diameter 6 cm) filled with 8 ml of the respective testing solution (Control, Low exposure, High exposure). Embryos were incubated at 27 +/- 1°C on a 14:10 h light/dark cycle. At 24 hours post fertilization (hpf), eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf, overall survival, hatching rates, morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh, aerated test solutions. At 96 hpf again, overall survival, hatching rates, morphological malformations and physiological changes were recorded before RNA and protein extraction. Methoxychlor (CAS 72-43-5, PESTANAL®) was purchased from Merck KGgA (Darmstadt, Germany). For the test solution preparation, first a high concentrated stock solution was prepared in Acetone (99.9% MS grade). From this stock, respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. At last, 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre-saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample, about 40 - 50 fertilized fish eggs were pre-picked in glass petri dishes (10 cm diameter) filled with 30 ml of the testing solution. Using an optical binokular microscope, 15 embryos of the same early blastula stage were transferred from the pre-picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw-cap eppendorf filled with 0.3 g of Lysing Matrix D (MP Biomedicals, 6913050) ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep-24© (MP Biomedicals, 6004500) at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit (Macherey-Nagel, 740933.250) according to the manufacturer’s protocol. RNA concentration (>100 ng/µl) was measured using a Nanodrop 2000 spectrophotometer (Thermo Scientific). The sample’s overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system (Agilent, G2939BA) using the Agilent RNA 6000 Nano Kit© (Agilent, 5067-1511) according to the manufacturer’s protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at -80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS-Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow, cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 (Illumina). Libraries were validated using a Fragment Analyzer system (Agilent, Santa Clara, USA) before sequencing.

text: larval day 4

characteristic: extraction date

text: wild type genotype

unit: gram per liter

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole larvae

unit: count unit

characteristic: rin

text: Danio rerio

text: male & female (pooled)

characteristic: sex

text: AB

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: zebrafish

text: MidExposure

characteristic: description

text: larval day 4

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Danio rerio

text: Danio rerio

text: whole larvae

characteristic: organism part

text: Danio rerio

text: male & female (pooled)

text: AB


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: COLD SPRING HARBOR LAB

text: public

tag: Namespace:COLD SPRING HARBOR LAB

characteristic: Submitter Id

characteristic: collection date

text: sorghum

characteristic: common name

text: 700 Mb

characteristic: estimated size

text: USA

characteristic: geographic location (country and/or sea)

text: 40° 52' 20.0568'' N

characteristic: geographic location (latitude)

text: 73° 27' 15.5088'' W

characteristic: geographic location (longitude)

text: growth chamber

characteristic: isolation and growth condition

characteristic: number of replicons

text: Sorghum bicolor

text: 18 DAG seedling

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: root, shoot

characteristic: plant structure

text: diploid

characteristic: ploidy

text: healthy

characteristic: sample health state

text: Sorghum bicolor


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9958:Evi1_LS_24-7_del_ctcf_Myc_SE_gfp_neg

tag: Namespace:Department of Hematology, Erasmus University Medical Center

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: myeloblast

characteristic: cell type

text: human

text: Protocols: For all K562 clones the NEON buffer T and same settings (1350V, 10ms, 4 pulses) were used. After a minimum of 72 hrs post nucleofection DNA or RNA was extracted (DNA Quick extract, Epicenter or Qiagen Allprep DNA/RNA mini, #80204) or cells were harvested for further analysis by respectively PCR, qPCR or flow cytometry analysis/FACS sorting. K562 cells were cultured in RPMI 1640 + L-glutamine (Hyclone SH30027.LS), 10% fetal calf serum (FCS, Gibco) and 50 U/mL penicillin and 50 μg/mL streptomycin (Gibco 15140-163). Cells were incubated at 37°C and 5% CO2 and passaged every 3-4 days to 100.000 cells/ml. CRISPR-Cas9 technology was used to make mutations or deletions in the regions described in the results section 10 million cells were crosslinked with 2% formaldehyde for 10 minutes at room temperature. Glycine (0.125 M) was added to quench the crosslinking reaction and cells were centrifuged and suspended in lysis buffer to disrupt membranes and isolate chromatin. The DNA was fragmented with DpnII as a primary restriction enzyme, Csp6I as a secondary 4 bp-cutter. To identify and quantify fragments that were ligated to the genomic region of interest, a two-step PCR was performed as previously described (Krijger et al., 2020). The first PCR step was an inverse PCR with viewpoint-specific primers that are listed in Table S1. In the second PCR step, universal primers were used that contain the Illumina adapters.

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

characteristic: genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

characteristic: title

text: CRISPR deletion MYC SE CTCF2 GFP- sorted

characteristic: treatment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Hematology, Erasmus University Medical Center

text: public

characteristic: Submitter Id

text: ArrayExpress

text: myeloblast

text: human

characteristic: common name

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: CRISPR EVI1 PR CTCF sgRNA#1 GFP- sorted


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: myeloblast

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: CRISPR EVI1 PR CTCF sgRNA#1 GFP+ sorted


text: public

text: E-MTAB-9958:Evi1_LS_24_7del_ctcf_Mecom_gfp_neg

text: ArrayExpress

characteristic: cell line

text: myeloblast

characteristic: cell type

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: CRISPR deletion EVI1 PR CTCF GFP- sorted


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9958:Evi1_LS_24_7del_ctcf_Mecom_gfp_pos

text: ArrayExpress

text: myeloblast

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

characteristic: title

text: CRISPR deletion EVI1 PR CTCF GFP+ sorted

characteristic: treatment


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9958:Evi1_LS_8_4del_ctcf_Mecom_gfp_neg

characteristic: Submitter Id

text: ArrayExpress

text: myeloblast

text: human

characteristic: common name

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9958:Evi1_LS_8_4del_ctcf_Mecom_gfp_pos

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: myeloblast

characteristic: cell type

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: CRISPR deletion EVI1 PR CTCF GFP+sorted


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9958:Evi1_LS_8_4del_ctcf_MycSE_gfp_neg

text: ArrayExpress

text: myeloblast

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-9958:Evi1_LS_8_4del_ctcf_MycSE_gfp_pos

text: ArrayExpress

text: myeloblast

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

characteristic: title

text: CRISPR deletion MYC SE CTCF2 GFP+ sorted

characteristic: treatment


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: myeloblast

text: human

characteristic: common name

text: adult

text: acute myeloid leukemia

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: myeloblast

characteristic: cell type

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-9958:Evi1_LS_del_ctcf_Myc_SE_gfp_pos

text: ArrayExpress

text: myeloblast

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: myeloblast

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

characteristic: title

text: CRISPR deletion MYC SE module D

characteristic: treatment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-9958:Evi1_SG_24-7_del_E3_Myc_SE_gfp_neg

characteristic: Submitter Id

text: ArrayExpress

text: myeloblast

text: human

characteristic: common name

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: CRISPR deletion MYC SE module C GFP- sorted


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-9958:Evi1_SG_24-7_del_E3_Myc_SE_gfp_pos

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: myeloblast

characteristic: cell type

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: CRISPR deletion MYC SE module C GFP+ sorted


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: myeloblast

text: human

text: Protocols: For all K562 clones the NEON buffer T and same settings (1350V, 10ms, 4 pulses) were used. After a minimum of 72 hrs post nucleofection DNA or RNA was extracted (DNA Quick extract, Epicenter or Qiagen Allprep DNA/RNA mini, #80204) or cells were harvested for further analysis by respectively PCR, qPCR or flow cytometry analysis/FACS sorting. K562 cells were cultured in RPMI 1640 + L-glutamine (Hyclone SH30027.LS), 10% fetal calf serum (FCS, Gibco) and 50 U/mL penicillin and 50 μg/mL streptomycin (Gibco 15140-163). Cells were incubated at 37°C and 5% CO2 and passaged every 3-4 days to 100.000 cells/ml. CRISPR-Cas9 technology was used to make mutations or deletions in the regions described in the results section 10 million cells were crosslinked with 2% formaldehyde for 10 minutes at room temperature. Glycine (0.125 M) was added to quench the crosslinking reaction and cells were centrifuged and suspended in lysis buffer to disrupt membranes and isolate chromatin. The DNA was fragmented with DpnII as a primary restriction enzyme, Csp6I as a secondary 4 bp-cutter. To identify and quantify fragments that were ligated to the genomic region of interest, a two-step PCR was performed as previously described (Krijger et al., 2020). The first PCR step was an inverse PCR with viewpoint-specific primers that are listed in Table S1. In the second PCR step, universal primers were used that contain the Illumina adapters.

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: CRISPR deletion MYC SE module I


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: myeloblast

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

characteristic: title

text: control

characteristic: treatment


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-9958:K562_24-12_t3-8_Evi1gfp_EviVP

characteristic: Submitter Id

text: ArrayExpress

text: myeloblast

text: human

characteristic: common name

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens


text: Department of Hematology, Erasmus University Medical Center

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-9958:K562_24-12_t3-8_Evi1gfp_MycVP

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: myeloblast

characteristic: cell type

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9958:Myc_LS_24-7_del_ctcf_Myc_SE_gfp_neg

text: ArrayExpress

text: myeloblast

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: CRISPR deletion MYC SE CTCF2 GFP- sorted


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: myeloblast

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

characteristic: title

text: CRISPR EVI1 PR CTCF sgRNA#1 GFP- sorted

characteristic: treatment


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: myeloblast

text: human

characteristic: common name

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: CRISPR EVI1 PR CTCF sgRNA#1 GFP+ sorted


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-9958:Myc_LS_24_7del_ctcf_Mecom_gfp_neg

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: myeloblast

characteristic: cell type

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: CRISPR deletion EVI1 PR CTCF GFP- sorted


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-9958:Myc_LS_24_7del_ctcf_Mecom_gfp_pos

text: ArrayExpress

text: myeloblast

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: CRISPR deletion EVI1 PR CTCF GFP+ sorted


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9958:Myc_LS_8_4del_ctcf_Mecom_gfp_neg

text: ArrayExpress

text: myeloblast

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

characteristic: title

characteristic: treatment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-9958:Myc_LS_8_4del_ctcf_Mecom_gfp_pos

characteristic: Submitter Id

text: ArrayExpress

text: myeloblast

text: human

characteristic: common name

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-9958:Myc_LS_8_4del_ctcf_MycSE_gfp_neg

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: myeloblast

characteristic: cell type

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9958:Myc_LS_8_4del_ctcf_MycSE_gfp_pos

text: ArrayExpress

text: myeloblast

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: CRISPR deletion MYC SE CTCF2 GFP+ sorted


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9958:Myc_LS_del_ctcf_Myc_SE_gfp_pos

text: ArrayExpress

text: myeloblast

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

characteristic: title

characteristic: treatment


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: myeloblast

text: human

characteristic: common name

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: CRISPR deletion MYC SE module D


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-9958:Myc_VP1_24-7_del_E3_Myc_SE_gfp_neg

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: myeloblast

characteristic: cell type

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: CRISPR deletion MYC SE module C GFP+ sorted


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-9958:Myc_VP1_24-7_del_E3_Myc_SE_gfp_pos

text: ArrayExpress

text: myeloblast

text: human

text: Protocols: For all K562 clones the NEON buffer T and same settings (1350V, 10ms, 4 pulses) were used. After a minimum of 72 hrs post nucleofection DNA or RNA was extracted (DNA Quick extract, Epicenter or Qiagen Allprep DNA/RNA mini, #80204) or cells were harvested for further analysis by respectively PCR, qPCR or flow cytometry analysis/FACS sorting. K562 cells were cultured in RPMI 1640 + L-glutamine (Hyclone SH30027.LS), 10% fetal calf serum (FCS, Gibco) and 50 U/mL penicillin and 50 μg/mL streptomycin (Gibco 15140-163). Cells were incubated at 37°C and 5% CO2 and passaged every 3-4 days to 100.000 cells/ml. CRISPR-Cas9 technology was used to make mutations or deletions in the regions described in the results section 10 million cells were crosslinked with 2% formaldehyde for 10 minutes at room temperature. Glycine (0.125 M) was added to quench the crosslinking reaction and cells were centrifuged and suspended in lysis buffer to disrupt membranes and isolate chromatin. The DNA was fragmented with DpnII as a primary restriction enzyme, Csp6I as a secondary 4 bp-cutter. To identify and quantify fragments that were ligated to the genomic region of interest, a two-step PCR was performed as previously described (Krijger et al., 2020). The first PCR step was an inverse PCR with viewpoint-specific primers that are listed in Table S1. In the second PCR step, universal primers were used that contain the Illumina adapters.

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Hematology, Erasmus University Medical Center

text: public

text: ArrayExpress

text: myeloblast

text: human

text: adult

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

characteristic: title

text: CRISPR deletion MYC SE module I

characteristic: treatment


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: myeloblast

text: human

characteristic: common name

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: control


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: myeloblast

characteristic: cell type

text: human

text: adult

text: acute myeloid leukemia

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens


E-MTAB-9971:Sample 1-pt387

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Centro Ricerca M. Tettamanti Clinica Pediatrica, Ospedale S.Gerardo Dipartimento di Medicina e Chirurgia Universita degli Studi Milano-Bicocca

text: public

text: E-MTAB-9971:Sample 1-pt387

characteristic: age

text: ArrayExpress

text: mononuclear cell

text: human

text: Protocols: Mononuclear cell by ficoll density purification of Bone Marrow aspirates guanidinium thiocyanate-phenol-chloroform extraction protocol For library preparation we used the Ovation Target Enrichment System (Nugen, Tecan Genomics, CA, USA), which provides a complete custom target enrichment and multiplex library preparation solution for targeted resequencing. Powered by Single Primer Enrichment Technology (SPET), we implemented a fully customizable probe design enabling the interrogation of 95 genes of custom content defined by the user. We started from 100-200ng of total RNA of mononucleate cells from bone marrow of tumour diagnosis. The protocol started processing samples as single-tube workflow to obtain double-stranded cDNA, end repaired and individually ligated with barcoded adaptors single sample by using single-index barcoding. We performed an optional normalization step to balance the input into the enrichment step and we proceeded to sample multiplexing (8-plex). Following a bead purification step, samples are combined for multiplex target enrichment during which time the targeting probes are annealed and extended, creating amplifiable library molecules. Following a second bead purification, an optional qPCR step determined the optimal number of PCR cycles to use in the final library amplification step. After library amplification, a final bead purification prepares the multiplexed, target enriched library for sequencing. We analysed the final library by Qubit 4.0 fluorimeter and Agilent Bioanalyzer.

characteristic: description

text: infant

characteristic: developmental stage

text: acute lymphoblastic leukemia

characteristic: disease

text: diagnosis

characteristic: disease staging

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: B-cell precursor

characteristic: phenotype

text: Homo sapiens

text: female

characteristic: sex

text: Sample 1-pt387


E-MTAB-9971:Sample 10-pt593

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-9971:Sample 10-pt593

characteristic: Submitter Id

text: ArrayExpress

text: mononuclear cell

text: human

characteristic: common name

text: infant

text: acute lymphoblastic leukemia

text: diagnosis

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: B-cell precursor

text: Homo sapiens

text: male

text: Sample 10-pt593

characteristic: title


E-MTAB-9971:Sample 11-pt604

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-9971:Sample 11-pt604

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

characteristic: cell type

text: human

text: infant

text: acute lymphoblastic leukemia

text: diagnosis

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: B-cell precursor

text: Homo sapiens

text: female

text: Sample 11-pt604