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text: soil metagenome

text: pyrosequencing

characteristic: sequencing method

text: soil

text: Luvisol

text: LSU rRNA

text: plowing

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Cambridge

text: public

tag: Namespace:University of Cambridge

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: Protocols: Cells from culture samples were harvested rapidly by centrifugation (1 min, 4000g) and the cell pellets flash frozen in liquid nitrogen and stored at −80 °C until required. For the glucose grown chemostats, precultures of each strain were prepared by inoculating YNB minimal medium (0.67% w/v Yeast Nitrogen Base (SIGMA) and 0.5% w/v ammonium sulphate) containing 2% glucose with a single colony picked from an agar plate and incubating at 30°C 200 rpm for 24 h. Fermentors (2 L) containing F1 medium (1000 ml) with 0.25% glucose were inoculated with aliquots of the precultures to produce a starting OD600nm absorbance of 0.05, and grown in batch for 24 h (30 °C, 750 rpm stirrer speed, aeration with 1 L min−1 air). Cultures were then switched to continuous mode, maintaining the pH at 4.5 and the dilution rate at 0.11-0.12 h-1. Initial steady-state culture conditions (designated SS1) were deemed to have been established after more than five vessel volume changes and with cultures exhibiting a constant biomass, at which point culture samples were taken for analysis. For induction, DOX was added to the steady-state cultures to produce a final concentration of 5 g/ml. Culture samples were harvested for analysis at 3 (designated T1) , 6 (designated T2) and 9 h (designated T3) after induction, and a final sample taken after the cultures had reached a new steady state (SS2), as determined by the passage of six vessel volume changes and with cultures exhibiting a constant biomass. A similar protocol was followed for the acetate grown chemostat experiments except the initial preculture was performed for 42 h in YNB minimal medium containing 0.5% sodium acetate and 1% glucose. This was used to inoculate batch growth in fermentors containing YNB minimal medium with 0.5% sodium acetate and 0.05% glucose, then switched to continuous mode using only 0.5% sodium acetate as the carbon source and controlling the pH at 5.0 and the dilution rate at 0.07-0.08 h-1. After taking the induced steady state samples, designated SS2, an additional experiment was performed to analyse the response to adding glucose to the respiring, induced cultures. Glucose (40%) was added to each fermentor (and to the feed for each fermentor) to produce a final concentration of 1.6%, and culture samples taken at 15 min (designated G1), 30 min (designated G2) and 60 min (designated G3) after glucose addition. For RNA purification, frozen cells were resuspended in trizol™(Invitrogen) and lysed mechanically at 4 °C by bead beating using a FastPrep™ homogeniser (MP Biomedicals; 5×1 min cycles of shaking at 6 m/s). DNA and protein were removed from the lysed samples by extraction with chloroform (×2) and total RNA purified using RNeasy columns (Qiagen). Illumina TruSeq Stranded Total RNA Library Prep Kit

characteristic: description

text: TetO7pr:: TDH3pr::SFV3559

characteristic: genotype

text: acetate

characteristic: growth condition

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: control for DOX-inducible expression of GTP-cycling pathway

characteristic: phenotype

text: Saccharomyces cerevisiae

characteristic: strain


characteristic: External Id

text: University of Cambridge

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: baker's yeast

text: TetO7pr:: TDH3pr::SFV3559

text: glucose

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: ENA-CHECKLIST

text: University of Cambridge

text: public

text: ArrayExpress

text: baker's yeast

text: TetO7pr::dgcA TDH3pr::SFV3559

text: acetate

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: DOX-inducible expression of GTP-cycling pathway

text: Saccharomyces cerevisiae

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Cambridge

text: public

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: TetO7pr::dgcA TDH3pr::SFV3559

text: glucose

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: University of Cambridge

text: public

text: ArrayExpress

text: baker's yeast

characteristic: common name

characteristic: description

text: TetO7pr:: TDH3pr::yybT

characteristic: genotype

text: acetate

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: control for DOX-inducible expression of ATP-cycling pathway

text: Saccharomyces cerevisiae


text: University of Cambridge

text: public

text: ArrayExpress

text: baker's yeast

text: TetO7pr:: TDH3pr::yybT

text: glucose

characteristic: growth condition

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: phenotype

text: Saccharomyces cerevisiae

characteristic: strain


characteristic: External Id

text: University of Cambridge

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: baker's yeast

text: TetO7pr::ybbP TDH3pr::yybT

text: acetate

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: DOX-inducible expression of ATP-cycling pathway

text: Saccharomyces cerevisiae


text: University of Cambridge

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: baker's yeast

text: TetO7pr::ybbP TDH3pr::yybT

text: glucose

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


E-MTAB-51711477313668:Blood DNA-seq

characteristic: ENA-CHECKLIST

text: CRUK-CI University of Cambridge

text: public

text: E-MTAB-51711477313668:Blood DNA-seq

tag: Namespace:CRUK-CI University of Cambridge

characteristic: Submitter Id

unit: year

characteristic: age

text: ArrayExpress

text: human

text: Protocols: Brain tumour biopsies were fixed in 10% formalin and embedded in paraffin wax from which 4-µm-thick sections were cut and stained with haematoxylin and eosin. The diagnosis of glioblastoma multiforme (WHO grade IV) was made by light microscopical examination of H&E-stained sections. Supra-total resection of a right frontal intrinsic tumour with maximum diameter of the enhancing component of 19mm, surrounded by only minimal oedema. Surgical samples were taken from the enhancing tumour mass and corresponding non-enhancing margin using advanced surgical techniques. Each tumour and margin sample was frozen to -80°C immediately on collection. The frozen samples were then defrosted and a 50 mg portion taken for DNA/RNA extraction. The samples were homogenised and then divided for DNA and RNA extraction. DNA extraction of both tissues and blood was performed using the QIAGEN DNeasy Blood and Tissue Kit, RNA extraction was performed using the QIAGEN RNeasy Mini Kit. Quantification was performed using the Qubit quantification assay. The tumour/normal pair used in this study was the sample judged most pure by comparison with blood DNA using whole genome sequencing. PCR-free ReBuilT libraries for bisulfite sequencing were generated following our previously published method (pubmed id: 27031619). For the generation of PCR-free libraries for oxBS, libraries were oxidised (TrueMethyl Kit from CEGX) prior to bisulfite treatment. In brief, 350 and 175 ng of sonicated DNA from tumour and margin respectively were end repaired and dA-tailed before ligation of customized adapter pair. After (oxidative)-bisulfite treatment, degraded fragments were recovered through primer extension before dA-tailing and second adapter ligation. The high-resolution aim of this project led to divide each sample in 3 parts in order to be able to perform sequencing. Parts were subsequently immobilized on streptavidin coated magnetic beads, washed with binding buffer, eluted with 50 mM NaOH at 60°C for 15 minutes.

text: normal

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

text: Blood DNA-seq


E-MTAB-51711477313668:Margin DNA-seq

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CRUK-CI University of Cambridge

text: public

text: E-MTAB-51711477313668:Margin DNA-seq

text: ArrayExpress

characteristic: broker name

text: Surgical sample taken from the non-enhancing margin

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: normal

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: female

text: Margin DNA-seq

characteristic: title


E-MTAB-51711477313668:Margin RNA-seq

characteristic: External Id

text: CRUK-CI University of Cambridge

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-51711477313668:Margin RNA-seq

text: ArrayExpress

text: human

text: Protocols: Brain tumour biopsies were fixed in 10% formalin and embedded in paraffin wax from which 4-µm-thick sections were cut and stained with haematoxylin and eosin. The diagnosis of glioblastoma multiforme (WHO grade IV) was made by light microscopical examination of H&E-stained sections. Supra-total resection of a right frontal intrinsic tumour with maximum diameter of the enhancing component of 19mm, surrounded by only minimal oedema. Surgical samples were taken from the enhancing tumour mass and corresponding non-enhancing margin using advanced surgical techniques. Libraries for each part of the tumour and margin samples were prepared using TruSeq RNA Access kit (Illumina), using an input of 40 and 20ng respectively. Each tumour and margin sample was frozen to -80°C immediately on collection. The frozen samples were then defrosted and a 50 mg portion taken for DNA/RNA extraction. The samples were homogenised and then divided for DNA and RNA extraction. DNA extraction of both tissues and blood was performed using the QIAGEN DNeasy Blood and Tissue Kit, RNA extraction was performed using the QIAGEN RNeasy Mini Kit. Quantification was performed using the Qubit quantification assay. The tumour/normal pair used in this study was the sample judged most pure by comparison with blood DNA using whole genome sequencing. PCR-free ReBuilT libraries for bisulfite sequencing were generated following our previously published method (pubmed id: 27031619). For the generation of PCR-free libraries for oxBS, libraries were oxidised (TrueMethyl Kit from CEGX) prior to bisulfite treatment. In brief, 350 and 175 ng of sonicated DNA from tumour and margin respectively were end repaired and dA-tailed before ligation of customized adapter pair. After (oxidative)-bisulfite treatment, degraded fragments were recovered through primer extension before dA-tailing and second adapter ligation. The high-resolution aim of this project led to divide each sample in 3 parts in order to be able to perform sequencing. Parts were subsequently immobilized on streptavidin coated magnetic beads, washed with binding buffer, eluted with 50 mM NaOH at 60°C for 15 minutes.

text: normal

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: female

text: Margin RNA-seq


E-MTAB-51711477313668:Tumour DNA-seq

characteristic: ENA-CHECKLIST

text: CRUK-CI University of Cambridge

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-51711477313668:Tumour DNA-seq

characteristic: Submitter Id

text: ArrayExpress

text: Surgical sample taken from the enhancing tumour mass

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: female

text: Tumour DNA-seq

text: WHO grade IV

characteristic: tumor grading


text: Mus musculus

characteristic: ArrayExpress-Species

text: C57 Bl/6

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: spleen from a mouse infected with SEP-1 KO Pcc AS (6 days post-infection), biological replicate 2

characteristic: sample description

text: Mus musculus

text: C57 Bl/6

characteristic: strain


text: Mus musculus

text: C57 Bl/6

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: spleen from a mouse infected with SEP-1 KO Pcc AS (9 days post-infection), biological replicate 1

text: Mus musculus

text: C57 Bl/6


text: Mus musculus

text: C57 Bl/6

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

text: spleen from a na?ve mouse, biological replicate 1

text: Mus musculus

text: C57 Bl/6

characteristic: title


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: WT Pcc BS, 6 dBys post infection in C57 Bl/6 mice, biological replicate 3

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Mus musculus

text: C57 Bl/6

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

text: house mouse

text: Mus musculus

text: spleen from a mouse infected with WT Pcc AS (6 days post-infection) biological replicate 3

text: Mus musculus

text: C57 Bl/6


text: Mus musculus

text: C57 Bl/6

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: spleen from a mouse infected with WT Pcc AS (12 days post-infection), biological replicate 2

text: Mus musculus

text: C57 Bl/6


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

text: SC

text: public

characteristic: Submitter Id

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: SEP-1 KO Pcc AS, 6 days post infection in C57 Bl/6 mice, biological replicate 3

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Mus musculus

characteristic: ArrayExpress-Species

text: C57 Bl/6

text: SC

text: public

text: house mouse

text: Mus musculus

text: spleen from a mouse infected with SEP 1 KO Pcc AS (12 days post-infection), biological replicate 4

text: Mus musculus

text: C57 Bl/6


text: Mus musculus

text: C57 Bl/6

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: house mouse

text: Mus musculus

text: spleen from B mouse infected with WT Pcc BS (9 dBys post-infection), biological replicate 2

text: Mus musculus

text: C57 Bl/6


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

text: SC

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

characteristic: organism

text: WT Pcc AS, 12 days post infection in C57 Bl/6 mice, biological replicate 1

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Mus musculus

text: C57 Bl/6

text: SC

text: public

text: house mouse

text: Mus musculus

text: spleen from a na?ve mouse, biological replicate 3

characteristic: sample description

text: Mus musculus

text: C57 Bl/6


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

text: SC

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: WT Pcc AS, 9 days post infection in C57 Bl/6 mice, biological replicate 3

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

characteristic: strain


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: SEP 1 KO Pcc AS, 12 days post infection in C57 Bl/6 mice, biological replicate 4

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Mus musculus

text: C57 Bl/6

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Mus musculus

text: spleen from a mouse infected with WT Pcc AS (9 days post-infection), biological replicate 3

text: Mus musculus

text: C57 Bl/6


text: Mus musculus

text: C57 Bl/6

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: spleen from a mouse infected with WT Pcc AS (6 days post-infection) biological replicate 1

text: Mus musculus

text: C57 Bl/6


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

characteristic: External Id

text: SC

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: SEP-1 KO Pcc AS, 9 days post infection in C57 Bl/6 mice, biological replicate 1

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Mus musculus

text: C57 Bl/6

text: SC

text: public

text: house mouse

text: Mus musculus

text: spleen from a mouse infected with SEP 1 KO Pcc AS (12 days post-infection), biological replicate 1

text: Mus musculus

text: C57 Bl/6

characteristic: title


text: Mus musculus

text: C57 Bl/6

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Mus musculus

text: spleen from a mouse infected with SEP 1 KO Pcc AS (12 days post-infection), biological replicate 2

text: Mus musculus

text: C57 Bl/6


text: Mus musculus

text: C57 Bl/6

text: SC

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: spleen from a mouse infected with WT Pcc AS (6 days post-infection) biological replicate 2

text: Mus musculus

text: C57 Bl/6


text: Mus musculus

text: C57 Bl/6

characteristic: ENA-CHECKLIST

text: SC

text: public

text: house mouse

text: Mus musculus

text: spleen from a mouse infected with SEP-1 KO Pcc AS (9 days post-infection), biological replicate 3

text: Mus musculus

text: C57 Bl/6


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

text: SC

characteristic: INSDC last update

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: WT Pcc BS, 6 dBys post infection in C57 Bl/6 mice, biological replicate 1

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

text: SC

text: public

characteristic: INSDC status

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: WT Pcc AS, 9 days post infection in C57 Bl/6 mice, biological replicate 2

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

text: SC

text: public

characteristic: SRA accession

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: SEP 1 KO Pcc AS, 12 days post infection in C57 Bl/6 mice, biological replicate 1

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Mus musculus

text: C57 Bl/6

text: SC

text: public

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: spleen from a mouse infected with SEP-1 KO Pcc AS (6 days post-infection), biological replicate 3

text: Mus musculus

text: C57 Bl/6


text: Mus musculus

characteristic: ArrayExpress-Species

text: C57 Bl/6

text: SC

text: public

text: house mouse

text: Mus musculus

text: spleen from a mouse infected with SEP-1 KO Pcc AS (9 days post-infection), biological replicate 2

text: Mus musculus

text: C57 Bl/6


text: Mus musculus

text: C57 Bl/6

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: house mouse

text: Mus musculus

text: spleen from a mouse infected with WT Pcc AS (12 days post-infection), biological replicate 4

text: Mus musculus

text: C57 Bl/6


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

text: SC

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

characteristic: organism

text: WT Pcc AS, 12 days post infection in C57 Bl/6 mice, biological replicate 2

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

text: SC

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: SEP-1 KO Pcc BS, 6 dBys post infection in C57 Bl/6 mice, biological replicate 2

characteristic: sample description

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Mus musculus

text: C57 Bl/6

text: SC

text: public

text: house mouse

text: Mus musculus

text: spleen from a mouse infected with WT Pcc AS (12 days post-infection), biological replicate 1

text: Mus musculus

text: C57 Bl/6

characteristic: strain


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: WT Pcc AS, 12 days post infection in C57 Bl/6 mice, biological replicate 3

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Mus musculus

text: C57 Bl/6

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Mus musculus

text: spleen from B mouse infected with WT Pcc BS (9 dBys post-infection), biological replicate 1

text: Mus musculus

text: C57 Bl/6


text: Mus musculus

text: C57 Bl/6

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: spleen from a mouse infected with WT Pcc AS (12 days post-infection), biological replicate 3

text: Mus musculus

text: C57 Bl/6


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

characteristic: External Id

text: SC

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: SEP 1 KO Pcc AS, 12 days post infection in C57 Bl/6 mice, biological replicate 3

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Mus musculus

text: C57 Bl/6

text: SC

text: public

text: house mouse

text: Mus musculus

text: spleen from a mouse infected with SEP-1 KO Pcc AS (6 days post-infection), biological replicate 1

text: Mus musculus

text: C57 Bl/6

characteristic: title


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

text: SC

characteristic: INSDC center name

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: SEP 1 KO Pcc AS, 12 days post infection in C57 Bl/6 mice, biological replicate 2

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

text: SC

characteristic: INSDC first public

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: SEP-1 KO Pcc AS, 9 days post infection in C57 Bl/6 mice, biological replicate 2

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: WT Pcc BS, 6 dBys post infection in C57 Bl/6 mice, biological replicate 2

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

text: SC

characteristic: INSDC last update

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: WT Pcc AS, 9 days post infection in C57 Bl/6 mice, biological replicate 1

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

text: SC

text: public

characteristic: INSDC status

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: WT Pcc AS, 12 days post infection in C57 Bl/6 mice, biological replicate 4

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Mus musculus

text: C57 Bl/6

text: SC

text: public

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: spleen from a na?ve mouse, biological replicate 2

text: Mus musculus

text: C57 Bl/6


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

text: SC

text: public

characteristic: Submitter Id

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: SEP-1 KO Pcc AS, 9 days post infection in C57 Bl/6 mice, biological replicate 3

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: Mus musculus

characteristic: ArrayExpress-Species

text: C57 Bl/6

text: SC

text: public

text: house mouse

text: Mus musculus

text: spleen from a mouse infected with SEP 1 KO Pcc AS (12 days post-infection), biological replicate 3

text: Mus musculus

text: C57 Bl/6


text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Plasmodium chabaudi

text: Plasmodium chabaudi

text: SEP-1 KO Pcc AS, 6 days post infection in C57 Bl/6 mice, biological replicate 1

text: Plasmodium chabaudi

text: Plasmodium chabaudi chabaudi AS


text: CRG

text: public

text: Jurkat T-cell

characteristic: cell type

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: T-ALL

characteristic: tissue type


characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:The Center of Translational Medicine, Taipei Medical University (TMU), Taipei, Taiwan

unit: month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: The wild-type male mice were purchased from National Laboratory Animal Center and maintained in a specific pathogen-free facility. Skeletal muscle tissues were obtained from the wild-type mice at 3 months and 24 months of age. The animal protocol was approved by the Institutional Animal Care and Use Committee of National Yang-Ming University. Total RNA was isolated from mouse skeletal muscle using TRIzol Reagent (Life Technology). Total RNA was extracted twice with phenol-chloroform and precipitated with isopropanol. Subsequently, in order to remove the chemicals, total RNA was precipitated with ethanol twice and dissolved in autoclaved water. The sequencing library for mRNA-seq was prepared using TruSeq RNA Sample Preparation Kit v2 (Illumina) according to manufacturer's instruction. Briefly, 4 mg of total high quality RNA (RNA integrity number > 8) was subjected to poly-A mRNA isolation using poly-T oligonucleotides. The poly-A mRNA was fragmented and the first-strand cDNA was synthesized using random hexamers followed by second-strand cDNA synthesis, end repair, addition of a single A base and adapter ligation. The adapter-ligated double-stranded cDNA library was enriched with 7-9 cycles of PCR using KAPA HiFi DNA polymerase (Kapa Biosystems).

characteristic: description

text: Mus musculus

text: Mus musculus

text: skeletal muscle organ

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Center of Translational Medicine, Taipei Medical University (TMU), Taipei, Taiwan

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: skeletal muscle organ

text: Mus musculus

text: male

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text: public

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characteristic: SRA accession

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text: Protocols: Wild-type male and female mice at 3 months of age were purchased from National Laboratory Animal Center and maintained in pathogen-free facility. Mice were sacrificed with five brain sub-regions (cortex, hippocampus, thalamus, hypothalamus, and cerebellum) and liver being harvested. The animal protocol was approved by the Institutional Animal Care and Use Committee of the Taipei Medical University. Purified genomic DNA was sonicated into short fragments with a size range of 100-500 bp by a Bioruptor (Diagenode, Sparta, NJ). The sheared DNA was then subjected to enrich 5-hmC-containing DNA using the Hydorxymethyl Collector kit (Active Motif, Carlsbad, CA) according to manufacturer's instruction. The resulting enriched 5-hmC DNA was then subjected to sequencing library construction. Tissues were lysed in the NTES buffer [1 M NaCl, 0.5% SDS, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA] with proteinase K (200 μg/ml). Total DNA was extracted twice with phenol-chloroform, precipitated with ethanol, and finally dissolved in autoclaved water. 10 nanogram of enriched 5-hmC DNA and sheared genomic DNA without 5-hmC enrichment were end-repaired, A-tailed, and ligated to adaptors using Illumina TruSeq ChIP Sample Preparation kit (Illumina). The adapter-ligated 5-hmC library was amplified by PCR for 10 cycles using KAPA HiFi DNA polymerase (Kapa Biosystems).

text: Mus musculus

text: Mus musculus

text: cerebellum

text: Mus musculus

text: female

text: Female-Cerebellum-N

type: has member


characteristic: ENA-FIRST-PUBLIC

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text: Mus musculus

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text: Female-Cerebellum-S


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characteristic: ENA-FIRST-PUBLIC

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characteristic: organism

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text: human gut metagenome

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Premio

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text: Premio

tag: Namespace:INRA CLERMONT-FERRAND - THEIX

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text: Whole genome resequencing of 4 European wheat elite lines

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Renan

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text: public

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Robigus

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text: Reich Lab

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text: Bacteroides sp. Marseille-P3108

text: Bacteroides sp. Marseille-P3108

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text: Max Planck Institute for Chemistry

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text: ESE

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text: Microbotryum silenes-acaulis

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text: University of the Azores

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text: rRNA amplicon sequencing from hydrothermal sediment

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