E-MTAB-11686:Sample 21

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-11686:Sample 21

text: ArrayExpress

text: mononuclear cell

text: Down syndrome patient

characteristic: clinical information

text: human

characteristic: common name

text: child

characteristic: developmental stage

characteristic: disease

text: 78 DX

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: diagnosis

text: Homo sapiens

text: female

text: Sample 21


E-MTAB-11686:Sample 22

status: PUBLIC

tag: attribute

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-11686:Sample 22

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

characteristic: Submitter Id

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

text: Down syndrome patient

text: human

text: Protocols: Mononuclear cell by ficoll density purification of Bone Marrow aspirates RNA was isolated using guanidinium thiocyanate-phenol-chloroform extraction protocol For library preparation we used the Ovation Target Enrichment System (Nugen, Tecan Genomics, CA, USA) or Trusight Pancancer kit (Illumina, CA, USA), which provide a complete custom target enrichment and multiplex library preparation solution for targeted resequencing of 95 and 1385 genes, respectively. We started from 100-200ng of total RNA of mononucleate cells from bone marrow of tumor 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 analyzed the final library by Qubit 4.0 fluorimeter and Agilent Bioanalyzer.

characteristic: description

text: child

text: precursor B-cell acute lymphoblastic leukemia

text: 79 DX

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: diagnosis

characteristic: sampling time point

text: Homo sapiens

text: female

characteristic: sex

text: Sample 22

characteristic: title


E-MTAB-11686:Sample 23

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

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-11686:Sample 23

text: ArrayExpress

text: mononuclear cell

text: Down syndrome patient

characteristic: clinical information

text: human

characteristic: common name

text: child

characteristic: developmental stage

characteristic: disease

text: 80 DX

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: diagnosis

text: Homo sapiens

text: female

text: Sample 23


E-MTAB-11686:Sample 24

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-11686:Sample 24

characteristic: Submitter Id

text: ArrayExpress

text: mononuclear cell

text: Down syndrome patient

text: human

text: child

text: 81 DX

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: diagnosis

text: Homo sapiens

text: male

text: Sample 24


E-MTAB-11686:Sample 25

text: public

text: E-MTAB-11686:Sample 25

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

text: Down syndrome patient

text: human

characteristic: description

text: child

text: 82 DX

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: diagnosis

characteristic: sampling time point

text: Homo sapiens

text: female

text: Sample 25


E-MTAB-11686:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-11686:Sample 3

text: ArrayExpress

text: mononuclear cell

text: Down syndrome patient

characteristic: clinical information

text: human

characteristic: common name

text: child

text: 41 DX

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: diagnosis

text: Homo sapiens

text: female

characteristic: sex

text: Sample 3

characteristic: title


E-MTAB-11686:Sample 4

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11686:Sample 4

text: ArrayExpress

text: mononuclear cell

text: Down syndrome patient

text: human

text: child

characteristic: developmental stage

characteristic: disease

text: 35 DX

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: diagnosis

text: Homo sapiens

text: female

text: Sample 4


E-MTAB-11686:Sample 5

text: public

characteristic: SRA accession

text: E-MTAB-11686:Sample 5

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

text: Down syndrome patient

text: human

characteristic: description

text: child

text: 42 DX

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: diagnosis

text: Homo sapiens

text: male

text: Sample 5


E-MTAB-11686:Sample 6

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-11686:Sample 6

text: ArrayExpress

text: mononuclear cell

text: Down syndrome patient

characteristic: clinical information

text: human

characteristic: common name

text: child

text: 34 DX

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: diagnosis

characteristic: sampling time point

text: Homo sapiens

text: male

text: Sample 6


E-MTAB-11686:Sample 7

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11686:Sample 7

text: ArrayExpress

text: mononuclear cell

text: Down syndrome patient

text: human

text: child

text: 37 DX

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: diagnosis

text: Homo sapiens

text: male

characteristic: sex

text: Sample 7

characteristic: title


E-MTAB-11686:Sample 8

text: public

characteristic: SRA accession

text: E-MTAB-11686:Sample 8

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

text: Down syndrome patient

text: human

characteristic: description

text: child

characteristic: developmental stage

characteristic: disease

text: 38 DX

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: diagnosis

text: Homo sapiens

text: male

text: Sample 8


E-MTAB-11686:Sample 9

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-11686:Sample 9

text: ArrayExpress

text: mononuclear cell

text: Down syndrome patient

characteristic: clinical information

text: human

characteristic: common name

text: child

text: 40 DX

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: diagnosis

text: Homo sapiens

text: male

text: Sample 9


E-MTAB-11678:Sample 11

characteristic: External Id

text: LabMedMolGe

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11678:Sample 11

text: ArrayExpress

text: human

text: Protocols: A549 cell lines were incubated in triplicate with high glucose (20 mM) and low glucose (1 mM) a total of about 15 ×106 cells were fixed, lysed to isolate nuclei, sonicated, and diluted as described by Nassa et al44. An aliquot of nuclear extract was taken as input to be used used as control for sequencing and data analysis. For H3K27me3 and H3K4me3 pull-down, 50 µl of equilibrated Dynabeads M-280 Sheep Anti-Rabbit IgG (Thermo Fisher Scientific) were incubated overnight at 4°C with 10 µg of the antibodies chosen for immunoprecipitations (for H3K27me3: ab195477, Abcam; for H3K4me3: ab8580, Abcam). Bead washing, elution, reverse crosslinking and DNA extraction were then performed as described in Tarallo et al (Tarallo et al, Genome Biology Genome Biol 18, 189; 2017). Size distribution of each ChIP DNA sample was assessed by running a 1 µl aliquot on an Agilent High Sensitivity DNA chip using an Agilent Technologies TapeStation (Agilent Technologies). The concentration of each DNA sample was determined by using a Quant-IT DNA Assay Kit-High Sensitivity and a Qubit Fluorometer (Life Technologies). Purified ChIP and input DNAs (6 ng each) were used as the starting material for sequencing library preparation by using the TruSeq ChIP Sample Prep Kit (Illumina Inc.)

text: adult

text: lung cancer

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: lung

characteristic: organism part

text: Homo sapiens

text: Sample 11


E-MTAB-11678:Sample 12

text: LabMedMolGe

text: public

characteristic: SRA accession

text: E-MTAB-11678:Sample 12

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

text: lung cancer

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: Sample 12

characteristic: title


E-MTAB-11678:Sample 13

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LabMedMolGe

text: public

text: E-MTAB-11678:Sample 13

text: ArrayExpress

text: human

text: adult

characteristic: developmental stage

text: lung cancer

characteristic: disease

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: Sample 13


E-MTAB-11678:Sample 5

characteristic: External Id

text: LabMedMolGe

text: public

text: E-MTAB-11678:Sample 5

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: lung cancer

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

text: Homo sapiens

text: Sample 5


E-MTAB-11678:Sample 6

text: LabMedMolGe

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11678:Sample 6

text: ArrayExpress

text: human

text: adult

text: lung cancer

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: Sample 6


E-MTAB-11678:Sample 7

text: LabMedMolGe

text: public

characteristic: INSDC status

text: E-MTAB-11678:Sample 7

text: ArrayExpress

text: human

text: adult

text: lung cancer

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: lung

characteristic: organism part

text: Homo sapiens

text: Sample 7


E-MTAB-11678:Sample 8

text: LabMedMolGe

text: public

characteristic: SRA accession

text: E-MTAB-11678:Sample 8

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: lung cancer

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: Sample 8


E-MTAB-11678:Sample 9

characteristic: ENA-CHECKLIST

text: LabMedMolGe

text: public

text: E-MTAB-11678:Sample 9

text: ArrayExpress

text: human

characteristic: description

text: adult

text: lung cancer

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: Sample 9

characteristic: title


E-MTAB-11678:Sample 10

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LabMedMolGe

text: public

text: E-MTAB-11678:Sample 10

text: ArrayExpress

text: human

text: adult

characteristic: developmental stage

text: lung cancer

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: Sample 10


E-MTAB-11678:Sample 2

characteristic: External Id

text: LabMedMolGe

text: public

text: E-MTAB-11678:Sample 2

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: lung cancer

characteristic: disease

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: Sample 2


E-MTAB-11678:Sample 3

text: LabMedMolGe

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11678:Sample 3

text: ArrayExpress

text: human

text: adult

text: lung cancer

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

text: Homo sapiens

text: Sample 3


E-MTAB-11678:Sample 4

text: LabMedMolGe

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11678:Sample 4

text: ArrayExpress

text: human

text: adult

text: lung cancer

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: Sample 4


E-MTAB-11678:Sample 1

text: LabMedMolGe

text: public

characteristic: SRA accession

text: E-MTAB-11678:Sample 1

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: lung cancer

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: lung

characteristic: organism part

text: Homo sapiens

text: Sample 1


characteristic: ENA-CHECKLIST

text: public

tag: Namespace:Max Planck Insitute for Marine Microbiolgy

characteristic: collection date

text: Marine gutless oligochaete Olavius algarvensis and associated bacteria, sample 4410.B. PacBio CLR reads extracted from a single worm. The worm was collected in Sant�Andrea (Elba, Italy) in September 2019 and kept in aquarium until November 2019 when it was processed. Large (> 10 kb) gDNA library were prepared and 1 SMRT cell was sequenced.

characteristic: description

text: marine neritic benthic zone biome

characteristic: environment (biome)

text: bay

characteristic: environment (feature)

text: shallow marine sediment

characteristic: environment (material)

text: 1.7 Gb

characteristic: estimated size

text: Italy

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: Olavius algarvensis

characteristic: project name

text: Sediments in which gutless annelids occur were collected by scuba diving.

characteristic: sample collection device or method

text: The worms were extracted manually from the sediment and kept in aquarium.

characteristic: sample material processing

text: Olavius algarvensis

text: PacBio Sequel

characteristic: sequencing method

text: Olavius algarvensis, O.algarvensis_4


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Max Planck Insitute for Marine Microbiolgy

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Marine gutless oligochaete Olavius ilvae and associated bacteria, sample 4410.A. PacBio CLR reads extracted from a single worm. The worm was collected in Sant�Andrea (Elba, Italy) in September 2019 and kept in aquarium until November 2019 when it was processed. Large (> 10 kb) gDNA library were prepared and 1 SMRT cell was sequenced.

text: marine neritic benthic zone biome

text: bay

text: shallow marine sediment

text: 1.7 Gb

text: Italy

text: host-associated

text: metagenome

text: Olavius ilvae

characteristic: organism

text: Olavius ilvae

text: PacBio Sequel

text: Oalvius ilvae, O.ilvae_3

characteristic: title


text: Norway

characteristic: GEOGRAPHIC LOCATION

text: NORWEGIAN VETERINARY INSTITUTE

text: public

characteristic: TITLE

text: bootswab

characteristic: description

text: poultry

text: Escherichia coli

text: Escherichia coli


text: Sweden

text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: poultry

text: Escherichia coli

text: Escherichia coli


text: Norway

text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: poultry

text: Escherichia coli

text: Escherichia coli


characteristic: ENA first public

text: public

tag: Namespace:Department of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic

text: ArrayExpress

characteristic: broker name

text: Protocols: 150 ml exponential phase and 50 ml stationary phase cells were pelleted and washed in lysis buffer (20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, 1 mM dithiothreitol (DTT) and frozen in -70°C. Bacillus subtilis 168 trp+ BaSysBio cells (LK2711) were inoculated into 200 ml of LB medium at OD600 0.03 and grown at 37°C. Bacteria were harvested in exponential (OD600 ∼0.25) or stationary phase (OD600 ∼3–4, 7-8 hrs of cultivation). Cells resuspended in lysis buffer (20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, 1 mM dithiothreitol (DTT), 0.5 mM phenylmethylsulfonyl fluoride (PMSF), supplemented with Calbiochem Protease Inhibitor Cocktail Set III protease inhibitors), sonicated 15 × 10 s with 1 minute pauses on ice and centrifuged. 1.5 mg (protein) of lysates were incubated for 16-18 hours at 4°C with 20 μl of Protein G plus agarose beads (Santa Cruz) coated with 5 μg mouse monoclonal anti-beta subunit of RNAP antibody [clone 8RB13] (Biolegend), 2.5 μg of anti-Sigma70 antibody [clone 2G10] (Biolegend), or 5 μg of mouse nonspecific IgG (Sigma-Aldrich) used as a negative control, respectively. The captured complexes were washed four times using 20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, finally resuspended in 200 μl 1% SDS, 150 mM KCl, 20 mM Tris–HCl pH 7.9, 1 mM MgCl2 and incubated on a rotating platform with 200 μl acidic phenol (pH∼3):chloroform (1:1) for 15 minutes. Eluted RNA was precipitated with ethanol, dissolved in water and DNase treated (TURBO DNA-free Kit, Ambion). Inputs are total RNA samples isolated from the bacterial lysates. 10% of lysate that was used for one immunoprecipitation was diluted in 1% SDS, 20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2 to final volume 200 μl and RNA was isolated with the same protocol as the immunoprecipitated RNA. 20 ul of RNA sample was used for library construction according to the NEXTFLEX® Rapid Directional RNA-Seq Kit. DNA concentrations of IgG control libraries were not measurable, therefore these libraries were not sequenced.

text: exponential phase

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bacillus subtilis subsp. subtilis str. 168

characteristic: replicate


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Department of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic

text: public

text: ArrayExpress

text: exponential phase

text: not applicable


characteristic: INSDC center name

text: public

text: ArrayExpress

text: stationary phase

text: not applicable


characteristic: INSDC last update

text: public

text: ArrayExpress

text: Protocols: 50 ml of bacterial culture from 42 hrs of growth and 50 ml of bacterial culture from 66 hrs of growth were pelleted and washed in lysis buffer (20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, 1 mM dithiothreitol (DTT) and frozen in -70°C. Streptomyces coelicolor A3(2) strain expressing HA-tagged HrdB and its growth was described previously (Šmídová et al., Nucleic Acids Research, 2019). Briefly, spore stock was thawed and inoculated to 2YT medium. Germination was carried out at 30°C for 5 hours. The germinated spores were harvested by centrifugation (3200 × g, 25°C, 5 minutes), inoculated into Na-glutamate medium supplemented with trace element solution and TMS, cultivated at 30°C and harvested by centrifugation (3200 x g, 4°C, 5 minutes) at two different time points after germination (42 and 66 hrs). Cells resuspended in lysis buffer (20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, 1 mM dithiothreitol (DTT), 0.5 mM phenylmethylsulfonyl fluoride (PMSF), supplemented with Calbiochem Protease Inhibitor Cocktail Set III protease inhibitors), sonicated 15 × 10 s with 1 minute pauses on ice and centrifuged. 0.5 mg (protein) of lysates were incubated for 16-18 hours at 4°C with 20 μl of Protein G plus agarose beads (Santa Cruz) coated with 5 μg mouse monoclonal anti-beta subunit of RNAP antibody [clone 8RB13] (Biolegend), 2.5 μg of anti-Sigma70 antibody [clone 2G10] (Biolegend), or 5 μg of mouse nonspecific IgG (Sigma-Aldrich) used as a negative control, respectively. The captured complexes were washed four times using 20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, finally resuspended in 200 μl 1% SDS, 150 mM KCl, 20 mM Tris–HCl pH 7.9, 1 mM MgCl2 and incubated on a rotating platform with 200 μl acidic phenol (pH∼3):chloroform (1:1) for 15 minutes. Eluted RNA was precipitated with ethanol, dissolved in water and DNase treated (TURBO DNA-free Kit, Ambion). Inputs are total RNA samples isolated from the bacterial lysates. 10% of lysate that was used for one immunoprecipitation was diluted in 1% SDS, 20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2 to final volume 200 μl and RNA was isolated with the same protocol as the immunoprecipitated RNA. 20 ul of RNA sample was used for library construction according to the NEXTFLEX® Rapid Directional RNA-Seq Kit. DNA concentrations of IgG control libraries were not measurable, therefore these libraries were not sequenced.

text: not applicable

text: Streptomyces coelicolor A3(2)

text: Streptomyces coelicolor A3(2)

text: 42 hours after germination

characteristic: sampling time point

text: Streptomyces coelicolor A3(2)


text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: not applicable

text: Streptomyces coelicolor A3(2)

text: Streptomyces coelicolor A3(2)

text: 66 hours after germination

text: Streptomyces coelicolor A3(2)


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Iceland

text: NORWEGIAN VETERINARY INSTITUTE

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: poultry

text: Escherichia coli

characteristic: organism

text: Escherichia coli


text: Iceland

characteristic: GEOGRAPHIC LOCATION

text: NORWEGIAN VETERINARY INSTITUTE

text: public

characteristic: TITLE

text: meat

characteristic: description

text: poultry

text: Escherichia coli

text: Escherichia coli

characteristic: title


text: public

tag: Namespace:Department of Molecular Microbiology John Innes Centre

text: ArrayExpress

characteristic: broker name

text: Protocols: The cultures were mixed with 1/5 of stop solution (5% Phenol saturated with 0.1 M citrate pH 4.3, 95% ethanol) and then rapidly chilled on ice for 20 minutes. A. vinelandii was grown at 30°C and 250 rpm in NIL medium (containing 0.2 g/L MgCl2, 90 mg/L CaCl2, 0.8 g/L KH2PO4, 0.2 g/L K2HPO4, 14 mg/L Na2SO4, 120 mg/L Fe2(SO4)3 and 2.4 mg/L Na2MoO4) supplemented with 2% sucrose. To examine regulation of alternative nitrogenases in the absence of molybdenum, trace Mo (up to 8 ppb) was selectively removed by filtering NIL media through activated charcoal. A. vinelandii strains were grown under conditions of nitrogen access (NIL medium with ammonium acetate 25 mM) and subsequently subjected to nitrogen step down by centrifugation and resuspension to an O.D600 of 0.5 in NIL medium, supplemented with either Mo (1μM ), V (1μM) or no added metal (Fe-only conditions) and subsequently incubated for 6 hours prior to RNA extraction. Reads originating from processed RNAs (postfix PSS) were separated from those originating from primary transcripts (postfix TSS) on basis of different ligated tags by the sequencing contractor. RNA was purified using the TRI Reagent (Sigma #T9424) following manufacturer instructions. Genomic DNA was removed by three treatments with the TURBO DNA-free DNAse (Ambion #AM1907) according to the manufacturer instructions. cDNA synthesis was performed with SuperScript II Reverse Transcriptase (Invitrogen #18064014) using 0.1-1 μg of total RNA as recommended by the manufacturer. The concentration and integrity of the RNAs were verified with a Bioanalyer (Agilent) with the RNA 6000 nano kit (Agilent #5067-1511) following the manufacturer’s instructions. Library preparation and sequencing were performed by the external contractor Vertis Biotechnologie AG as follows. 5' triphosphorylated RNA was capped with 3'- desthiobiotin-TEG-guanosine 5' triphosphate (DTBGTP) (NEB) using the vaccinia capping enzyme (VCE) (NEB) for reversible binding of biotinylated RNA species to streptavidin. Then biotinylated RNA species were captured on streptavidin beads and eluted to obtain the 5' fragment of the primary transcripts. The Cappable-seq enriched RNAs were first poly(A)-tailed using poly(A) polymerase. Then, the 5' Illumina TruSeq sequencing adapters, which carry sequence tags ATTACTCG and TCCGGAGA (in a proportion of 50% of each adapter), were ligated to the 5' mono-phosphate groups (5'P) of processsed transcripts. The sample was then treated with CapClip Acid Pyrophosphatase (Cellscript) in order to convert 5' triphosphate (5'PPP) structures into 5' monophosphate ends. To the newly formed 5'P groups were ligated the 5' Illumina TruSeq sequencing adapters, which carry sequence tag CGCTCATT and GAGATTCC (50% each). First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR- amplified to about 10-20 ng/µl using a high fidelity DNA polymerase.

text: optical density at 600 nm of 0.5

characteristic: developmental stage

text: NIL medium; 25 mM ammonium acetate

characteristic: growth condition

text: Azotobacter vinelandii DJ

text: Azotobacter vinelandii DJ

text: whole organism

characteristic: organism part

text: processed RNAs (postfix PSS)

characteristic: protocol

text: Azotobacter vinelandii DJ

unit: hour

characteristic: time


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Department of Molecular Microbiology John Innes Centre

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: optical density at 600 nm of 0.5

text: NIL medium; 25 mM ammonium acetate

text: Azotobacter vinelandii DJ

text: Azotobacter vinelandii DJ

text: whole organism

text: primary transcripts (postfix TSS)

text: Azotobacter vinelandii DJ


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: optical density at 600 nm of 0.5

text: NIL medium; 25 mM ammonium acetate

text: Azotobacter vinelandii DJ

text: Azotobacter vinelandii DJ

text: whole organism

text: processed RNAs (postfix PSS)

text: Azotobacter vinelandii DJ

text: molybdenum; 1 micromolar

characteristic: stimulus


text: public

text: ArrayExpress

characteristic: broker name

characteristic: description

text: optical density at 600 nm of 0.5

text: NIL medium; 25 mM ammonium acetate

text: Azotobacter vinelandii DJ

characteristic: organism

text: Azotobacter vinelandii DJ

text: whole organism

text: primary transcripts (postfix TSS)

text: Azotobacter vinelandii DJ

text: molybdenum; 1 micromolar

characteristic: title


text: public

text: ArrayExpress

text: optical density at 600 nm of 0.5

characteristic: developmental stage

text: NIL medium; 25 mM ammonium acetate

characteristic: growth condition

text: Azotobacter vinelandii DJ

text: Azotobacter vinelandii DJ

text: whole organism

characteristic: organism part

text: processed RNAs (postfix PSS)

characteristic: protocol

text: Azotobacter vinelandii DJ

text: vanadium; 1 micromolar


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: optical density at 600 nm of 0.5

text: NIL medium; 25 mM ammonium acetate

text: Azotobacter vinelandii DJ

text: Azotobacter vinelandii DJ

text: whole organism

text: primary transcripts (postfix TSS)

text: Azotobacter vinelandii DJ

text: vanadium; 1 micromolar

characteristic: time


E-MTAB-11663_2:Sample 1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Lunenfeld-Tanenbaum Research Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11663_2:Sample 1

text: 10 to 12

unit: week

characteristic: age

text: ArrayExpress

text: endothelial cell

text: house mouse

characteristic: common name

text: Protocols: Before euthanizing the mice, tumor dissociation solution was prepared by adding 4mL of 10X collagenase A in 26 mL of DMEM F12, 10mL of BSA fraction V and 0.5mg/mL DNase and was kept on ice. Primary tumor was harvested and washed with cold 1XPBS. Tumor section (~3 cm3 ) was placed in a 10cm dish containing 5mL of dissociation solution. Tumor tissue was minced with a scalpel into small pieces (~1mm3 ) and transferred to 10mL tubes. Another 5mL of dissociation solution was added and the tubes were placed in 370C incubator for 20 mins rotating slowly in a Mini Tube Rotator (Fisher Scientific). The tissue suspension was passed through 70μm cell strainer for 53 twice. The left-over unfiltered tissue was grinded with a 3ml syringe plunger. Cell pellet was collected by spinning at 300g for 5mins at 40C, resuspended and incubated in 1mL RBC solution for 10min at room temperature. After centrifugation, cell pellet was resuspended in 2mL of PBS-based washing buffer containing 0.5% BSA. Cell suspension was incubated with 7.5μg/mL E-cadherin (CD34, eBioscience) antibody for 10 min to deplete tumor cells by using Dynabeads® Sheep Anti-Rat antibody (ThermoFisher Scientific). The remaining cells were used to enrich CD31-positive endothelial cells by using 7.5μg/mL anti-CD31 antibody (eBioscience) and the EasySep™ PE Positive Selection Kit II (Stemcell Technologies). The obtained cells were resuspended in 1mL PBS + 0.04% BSA and were used for single cell sequencing by 10X genomics (CA, USA). Libraries for single-cell RNA sequencing were prepared according to 10X Genomics procedures (Pleasanton, CA). Briefly, Samples with >95% viability were selected and resuspended with the appropriate volume of 1X PBS + 0.1% BSA to reach a concentration of 1,000 cells/mL. The cell suspension was then used to generate the gel bead-in emulsions, reverse transcription, cDNA amplification, library preparation, and sample indexing following the latest available manufacturer’s protocol, using the 10X Chromium Controller (PN-1000202), the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3 (PN-1000075), the Chromium Next GEM Chip B Single Cell Kit (PN-1000073) and the Single Index Chromium i7 Multiplex Kit, (PN-120262).

text: adult

text: wild type genotype

characteristic: genotype

text: LLC1 tumor grown in mice

text: CD31 positive

characteristic: immunophenotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: LLC1 primary tumor

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

text: Sample 1


E-MTAB-11663_2:Sample 2

text: Lunenfeld-Tanenbaum Research Institute

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11663_2:Sample 2

characteristic: Submitter Id

text: 10 to 12

text: ArrayExpress

characteristic: broker name

text: endothelial cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

text: APLN knockout

text: LLC1 tumor grown in mice

characteristic: growth condition

text: CD31 positive

text: Mus musculus

characteristic: organism

text: Mus musculus

text: LLC1 primary tumor

characteristic: organism part

text: Mus musculus

text: male

text: Sample 2

characteristic: title


E-MTAB-11663_2:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Lunenfeld-Tanenbaum Research Institute

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11663_2:Sample 3

text: 10 to 12

characteristic: age

text: ArrayExpress

text: endothelial cell

text: house mouse

text: adult

text: wild type genotype

text: LLC1 tumor grown in mice

text: CD31 positive

text: Mus musculus

text: Mus musculus

text: LLC1 primary tumor

text: Mus musculus

text: male

text: Sample 3


E-MTAB-11663_2:Sample 4

text: Lunenfeld-Tanenbaum Research Institute

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11663_2:Sample 4

text: 10 to 12

text: ArrayExpress

text: endothelial cell

text: house mouse

characteristic: common name

text: adult

text: APLN knockout

characteristic: genotype

text: LLC1 tumor grown in mice

text: CD31 positive

characteristic: immunophenotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: LLC1 primary tumor

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

text: Sample 4


E-MTAB-11710:Sample 8

text: public

text: E-MTAB-11710:Sample 8

tag: Namespace:Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: stromal cell

text: human

text: Protocols: After surgical excision torn tissues were collected sterile phosphate buffered saline on ice and processed within one hour of resection. For enzymatic dissociation of human lymph nodes, torn tissues were collected in RPMI 1640 medium containing 2% FCS, 20 mM HEPES pH 7.2 (Lonza), 2.4 mg/ml Dispase (Roche), 0.375 mg/ml Collagenase P (Roche) and 25 mg/ml DNaseI (Applichem). To enrich for stromal cells, hematopoietic cells and erythrocytes were depleted by incubating the cell suspension with MACS anti-CD45 and anti-CD235a microbeads (Miltenyi Biotec) and passing it through a MACS LS column (Miltenyi Biotec). The unbound single cell suspension was stained for further cell sorting. For isolation of hematopoietic cells, tissues were gently smashed across a 26-gauge wire mesh and washed with medium (RMPI-1640 containing 2% FCS (Sigma), 1% Penicillin-Streptomycin (Corning) and 20mM HEPES (Sigma)) until further staining for cell sorting. Hematopoietic cells were stained with fluorochrome-conjugated antibodies against human CD45, CD3, CD19 and CD14 and stromal cells with fluorochrome-conjugated antibodies against human CD45 and CD235a. Live/dead cell discrimination was performed by adding 7-amino-actinomycin D (7AAD; Calbiochem) prior to acquisition. CD45- CD235a- stromal cells, CD45+ CD3+ T cells and CD45+ CD19+ B cells were sorted with a BD FACS Melody cell sorter (BD Biosciences) and run on the 10x Chromium analyzer (10X Genomics). cDNA library generation was performed following the established commercial protocol for Chromium Single Cell 3’ Reagent Kit (v3 Chemistry).

characteristic: description

text: adult

characteristic: developmental stage

text: cervical cyst

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lymph node

characteristic: organism part

text: Homo sapiens

text: male

text: Sample 8

characteristic: title


E-MTAB-11710:Sample 5

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11710:Sample 5

characteristic: age

text: ArrayExpress

text: T cell

text: human

text: adult

text: chronic hyperplastic tonsilitis

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: male

text: Sample 5


E-MTAB-11710:Sample 6

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11710:Sample 6

text: ArrayExpress

text: B cell

text: human

characteristic: common name

text: adult

text: chronic hyperplastic tonsilitis

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: male

characteristic: sex

text: Sample 6


E-MTAB-11710:Sample 7

text: public

text: E-MTAB-11710:Sample 7

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: B cell

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: chronic hyperplastic tonsilitis

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: male

text: Sample 7


E-MTAB-11710:Sample 1

text: public

text: E-MTAB-11710:Sample 1

text: ArrayExpress

text: stromal cell

text: human

text: adult

text: chronic hyperplastic tonsilitis

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lymph node

characteristic: organism part

text: Homo sapiens

text: male

text: Sample 1

characteristic: title


E-MTAB-11710:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11710:Sample 2

text: ArrayExpress

text: stromal cell

text: human

text: adult

text: chronic hyperplastic tonsilitis

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: male

text: Sample 2


E-MTAB-11710:Sample 3

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11710:Sample 3

characteristic: age

text: ArrayExpress

text: stromal cell

text: human

text: adult

text: chronic hyperplastic tonsilitis

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: male

text: Sample 3


E-MTAB-11710:Sample 9

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11710:Sample 9

text: ArrayExpress

text: stromal cell

text: human

characteristic: common name

text: adult

text: cervical cyst

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: male

characteristic: sex

text: Sample 9


E-MTAB-11710:Sample 4

text: public

text: E-MTAB-11710:Sample 4

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: stromal cell

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: chronic hyperplastic tonsilitis

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: male

text: Sample 4


E-MTAB-11710:Sample 10

text: public

text: E-MTAB-11710:Sample 10

text: ArrayExpress

text: stromal cell

text: human

text: adult

text: pleomorphic adenoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lymph node

characteristic: organism part

text: Homo sapiens

text: female

text: Sample 10

characteristic: title


E-MTAB-11710:Sample 11

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11710:Sample 11

text: ArrayExpress

text: T cell

text: human

text: adult

text: pleomorphic adenoma

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: female

text: Sample 11


E-MTAB-11710:Sample 12

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11710:Sample 12

characteristic: age

text: ArrayExpress

text: B cell

text: human

text: adult

text: pleomorphic adenoma

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: female

text: Sample 12


E-MTAB-11710:Sample 13

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11710:Sample 13

text: ArrayExpress

text: myeloid cell

text: human

characteristic: common name

text: adult

text: pleomorphic adenoma

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: female

characteristic: sex

text: Sample 13


E-MTAB-11710:Sample 14

text: public

text: E-MTAB-11710:Sample 14

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: stromal cell

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: basal cell adenoma

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: female

text: Sample 14


E-MTAB-11710:Sample 15

text: public

text: E-MTAB-11710:Sample 15

text: ArrayExpress

text: T cell

text: human

text: adult

text: basal cell adenoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lymph node

characteristic: organism part

text: Homo sapiens

text: female

text: Sample 15

characteristic: title


E-MTAB-11710:Sample 16

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11710:Sample 16

text: ArrayExpress

text: B cell

text: human

text: adult

text: basal cell adenoma

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: female

text: Sample 16


E-MTAB-11710:Sample 17

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11710:Sample 17

characteristic: age

text: ArrayExpress

text: myeloid cell

text: human

text: adult

text: basal cell adenoma

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: female

text: Sample 17


E-MTAB-11741_2:Sample 1

text: UNIVERSITY OF MICHIGAN

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11741_2:Sample 1

tag: Namespace:UNIVERSITY OF MICHIGAN

text: ArrayExpress

text: house mouse

characteristic: common name

text: Protocols: Samples were collected from mice at 7, 14, or 21 days after inoculation with 4T1 murine triple negative Tissues were broken down into a single cell suspension using a combination of enzymatic and mechanical means. Nucleic acids were extracted using Drop-Seq Library preparation was conducted using Drop-Seq

text: normal

text: mouse inoculated with 4T1 murine triple negative breast cancer cells

characteristic: growth condition

text: mouse 1

characteristic: individual

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: female

characteristic: sex

text: Balb/c

characteristic: strain

text: Sample 1


E-MTAB-11741_2:Sample 2

text: UNIVERSITY OF MICHIGAN

text: public

text: E-MTAB-11741_2:Sample 2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: description

text: triple-negative breast cancer

characteristic: disease

text: mouse 2

text: Mus musculus

characteristic: organism

text: Mus musculus

text: tumor

characteristic: sampling site

text: Mus musculus

text: female

text: Balb/c

text: Sample 2


E-MTAB-11741_2:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MICHIGAN

characteristic: INSDC center name

text: public

text: E-MTAB-11741_2:Sample 3

text: ArrayExpress

text: house mouse

text: normal

text: mouse 3

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: female

text: Balb/c

text: Sample 3

characteristic: title


E-MTAB-11741_2:Sample 4

text: UNIVERSITY OF MICHIGAN

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11741_2:Sample 4

text: ArrayExpress

text: house mouse

characteristic: common name

text: triple-negative breast cancer

text: mouse 4

text: Mus musculus

text: Mus musculus

text: tumor

text: Mus musculus

text: female

text: Balb/c

text: Sample 4


E-MTAB-11741_2:Sample 5

text: UNIVERSITY OF MICHIGAN

text: public

text: E-MTAB-11741_2:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: normal

characteristic: growth condition

text: mouse 5

characteristic: individual

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: female

characteristic: sex

text: Balb/c

characteristic: strain

text: Sample 5


E-MTAB-11741_2:Sample 6

text: UNIVERSITY OF MICHIGAN

text: public

text: E-MTAB-11741_2:Sample 6

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: description

text: triple-negative breast cancer

characteristic: disease

text: mouse 6

text: Mus musculus

characteristic: organism

text: Mus musculus

text: tumor

characteristic: sampling site

text: Mus musculus

text: female

text: Balb/c

text: Sample 6


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Norway

characteristic: GEOGRAPHIC LOCATION

text: NORWEGIAN VETERINARY INSTITUTE

characteristic: INSDC center name

text: public

characteristic: TITLE

text: not provided

text: human carrier

text: human

text: Escherichia coli

text: Escherichia coli


text: Norway

text: NORWEGIAN VETERINARY INSTITUTE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human carrier

text: human

text: Escherichia coli

text: Escherichia coli

characteristic: title


E-MTAB-11724:Sample 1

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-11724:Sample 1

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

text: Down syndrome

characteristic: clinical information

text: human

characteristic: common name

text: Protocols: Mononuclear cell by ficoll density purification of Bone Marrow aspirates DNA was extracted from cell pellets using the Promega kit Wizard® SV Genomic DNA Purification Systems. For library preparation we used the Illumina Nextera Flex for Enrichment protocol.

characteristic: description

text: juvenile stage

characteristic: developmental stage

text: B-cell precursor acute lymphoblastic leukaemia

text: diagnosis

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


E-MTAB-11724:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-11724:Sample 2

text: ArrayExpress

text: mononuclear cell

text: Down syndrome

text: human

text: juvenile stage

characteristic: disease

text: remission

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: male

text: Sample 2


E-MTAB-11724:Sample 3

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11724:Sample 3

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: mononuclear cell

text: Down syndrome

text: human

text: juvenile stage

text: diagnosis

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: male

text: Sample 3

characteristic: title


E-MTAB-11724:Sample 4

text: public

text: E-MTAB-11724:Sample 4

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

text: Down syndrome

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: juvenile stage

characteristic: developmental stage

text: remission

characteristic: disease staging

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: male

text: Sample 4


E-MTAB-11724:Sample 5

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-11724:Sample 5

text: ArrayExpress

text: mononuclear cell

text: Down syndrome

text: human

text: juvenile stage

text: diagnosis

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

text: Sample 5


E-MTAB-11724:Sample 6

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11724:Sample 6

characteristic: Submitter Id

text: ArrayExpress

text: mononuclear cell

text: Down syndrome

text: human

text: juvenile stage

characteristic: disease

text: remission

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: female

text: Sample 6


E-MTAB-11724:Sample 7

text: public

text: E-MTAB-11724:Sample 7

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

text: Down syndrome

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: juvenile stage

characteristic: developmental stage

text: diagnosis

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: male

text: Sample 7

characteristic: title


E-MTAB-11724:Sample 8

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-11724:Sample 8

text: ArrayExpress

text: mononuclear cell

text: Down syndrome

text: human

text: juvenile stage

text: remission

characteristic: disease staging

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: male

text: Sample 8


E-MTAB-11724:Sample 10

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11724:Sample 10

characteristic: Submitter Id

text: ArrayExpress

text: mononuclear cell

text: Down syndrome

text: human

text: juvenile stage

text: remission

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: Sample 10


E-MTAB-11724:Sample 9

text: public

text: E-MTAB-11724:Sample 9

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

text: Down syndrome

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: juvenile stage

characteristic: disease

text: diagnosis

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: male

text: Sample 9


E-MTAB-11724:Sample 11

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-11724:Sample 11

text: ArrayExpress

text: mononuclear cell

text: Down syndrome

text: human

text: juvenile stage

characteristic: developmental stage

text: diagnosis

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: male

text: Sample 11

characteristic: title


E-MTAB-11724:Sample 12

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11724:Sample 12

characteristic: Submitter Id

text: ArrayExpress

text: mononuclear cell

text: Down syndrome

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E-MTAB-11724:Sample 13

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E-MTAB-11724:Sample 14

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