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characteristic: TITLE

text: urine

text: human

text: Escherichia coli

text: Escherichia coli

characteristic: title


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: IRB Barcelona / BIST

text: public

tag: Namespace:IRB Barcelona / BIST

unit: month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: AKP (Apc KO, KrasG12D and P53 KO) WT and KO organoids (Mouse Tumoral Organoids) were treated for 2d or 5d in FOLFIRI media. Folfiri was removed after 3 days, followed by addition of fresh fully-supplemented control media for two extra days (5d after FOLFIRI timepoint). Cells were sorted based on the expression of DAPI (Dapi negative to sort live cells). Only one KO (KO2) could be recovered in the 5d timepoint Organoids were culture as described in Tauriello et al. Nature 2018. AKP organoids were treated with FOLFIRI (combination of 5FU (50μg/μl) and SN38 (100nM, MedChem HY-13704)). After 3 days of treatment, drugs were removed, followed by addition of fresh fully-supplemented control media. Non multiplexed samples (Parental_folfiri_5days, WT1_folfiri_5days, KO2_folfiri_5days) Cell concentration and viability were verified by counting with a TC20™ Automated Cell Counter (Bio-Rad Laboratories, S.A) after staining cells with Trypan blue.  Cells were partitioned into Gel Bead In Emulsions with a Target Cell Recovery of 6,000 total cells per sample. cDNA sequencing libraries were prepared using the Chromium Next GEM Single Cell 3ʹ v3.1 kit (10X Genomics) following manufacturer's instructions. Briefly, after GEM-RT clean up, cDNA was amplified during 13 cycles and cDNA QC and quantification were performed on a Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies). 100 ug of cDNA were used for library preparation. Multiplexed samples (all other) Sample multiplexing was performed following the Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocol (10x Genomics). Briefly, cells were centrifuged at 500x g at room temperature with a swinging-bucket rotor, resuspended in 100 ul of Cell Multiplexing Oligo (3’ CellPlex Kit, 10x Genomics) and incubated at RT for 5 mins. Cells were washed 3 times with cold 1X PBS (Thermo Fisher Scientific) supplemented with 1% BSA (MACS Miltenyi), all centrifugations being performed at 500x g at 4C. Cells were finally resuspended in an appropriate volume of 1X PBS-0.05% BSA in order to obtain a final cell concentration of approximatively 1000 cells/ul and counted using a TC20™ Automated Cell Counter (Bio-Rad Laboratories, S.A). Samples were mixed with a 50:50 ratio and filtered with a 40 µm strainer to remove eventual clumps and the resulting pools were checked for final cell number and viability before loading onto the Chromium. Cellplex samples were partitioned into 3’ Gel Bead Emulsions with a Target Cell Recovery between 6.000 and 20.000 cells (corresponding to 3.000-5.000 cells per sample within each plex). Non multiplexed samples (Parental_folfiri_5days, WT1_folfiri_5days, KO2_folfiri_5days) Libraries were indexed by PCR using the PN-1000215 Dual Index Kit TT Set A. Size distribution and concentration of 3' cDNA libraries were verified on an Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies). Multiplexed samples (all other) Libraries were prepared following 10x Genomics Single Cell 3’ mRNA kit protocol with Feature Barcode technology for Cell Multiplexing. Briefly, after GEM-RT clean up, cDNA from poly-adenylated mRNA and barcoded DNA from the CMO Feature Barcode were amplified via PCR according to the Target Recovery cell number. A SPRI selection clean-up was done in order to separate the amplified cDNA molecules for 3' Gene Expression and the CMO-derived cDNA. 100 ng of mRNA-derived cDNA were used for GEX library construction while 5 µl of CMO-derived cDNA were used to amplify the corresponding Cellplex library. Size distribution and library concentration were determined using a Bioanalyzer High Sensitivity chip (Agilent Technologies).

text: adult

characteristic: developmental stage

text: colorectal carcinoma

characteristic: disease

text: CRISPR Cas9 mediated Mex3a KO

characteristic: genetic modification

text: ApcLoxP; Lgr5-EGFP-IRES-creERT2; LSL-K-rasG12D; p53LoxP; Tgfbr2LoxP

characteristic: genotype

text: tumour organoid

characteristic: growth condition

text: KO clone 1

characteristic: individual

text: Mus musculus

text: Mus musculus

text: colorectum

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IRB Barcelona / BIST

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: description

text: adult

text: colorectal carcinoma

text: CRISPR Cas9 mediated Mex3a KO

text: tumour organoid

text: KO clone 2

text: Mus musculus

characteristic: organism

text: Mus musculus

text: colorectum

text: Mus musculus

text: male

characteristic: title


text: IRB Barcelona / BIST

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

text: colorectal carcinoma

characteristic: disease

text: tumour organoid

text: parental clone 1

text: Mus musculus

text: Mus musculus

text: colorectum

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IRB Barcelona / BIST

text: public

text: ArrayExpress

text: house mouse

text: adult

text: colorectal carcinoma

characteristic: genotype

text: tumour organoid

characteristic: growth condition

text: parental clone 2

characteristic: individual

text: Mus musculus

text: Mus musculus

text: colorectum

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Centre for Palaeogenetics

characteristic: INSDC center name

text: public

characteristic: SRA accession

tag: Namespace:Centre for Palaeogenetics

characteristic: Submitter Id

text: woolly mammoth

text: woolly mammoth

characteristic: description

text: Mammuthus primigenius

characteristic: organism

text: Mammuthus primigenius

text: woolly mammoth

characteristic: title


Yakinf

text: Centre for Palaeogenetics

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Yakinf

text: woolly mammoth

characteristic: common name

text: woolly mammoth

text: Mammuthus primigenius

text: Mammuthus primigenius

text: woolly mammoth


E-MTAB-11750:M13_MPI_ac220_24h 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11750:M13_MPI_ac220_24h 1

tag: Namespace:Barts Cancer Institute, Queen Mary University of London

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: Cells were grown in culture and treated with AC220 (1nM) and mannose (100µM) for 24 or 72 hours as indicated RNA extracted with RNAeasy kit (Qiagen, 74106) Library preparation was performed with the dUTP directional kit NEBNext® Ultra8482 II Directional RNA Library Prep Kit for Illumina®

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: MPI knockout

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_MPI_ac220_24h 1


E-MTAB-11750:M13_MPI_ac220_24h 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Barts Cancer Institute, Queen Mary University of London

text: public

text: E-MTAB-11750:M13_MPI_ac220_24h 2

text: ArrayExpress

text: human

text: adult

text: acute myeloid leukemia

text: MPI knockout

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: M13_MPI_ac220_24h 2


E-MTAB-11750:M13_MPI_ac220_72h 1

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-11750:M13_MPI_ac220_72h 1

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: acute myeloid leukemia

text: MPI knockout

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_MPI_ac220_72h 1


E-MTAB-11750:M13_MPI_ac220_72h 2

text: public

text: E-MTAB-11750:M13_MPI_ac220_72h 2

text: ArrayExpress

text: human

characteristic: description

text: adult

text: acute myeloid leukemia

text: MPI knockout

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_MPI_ac220_72h 2

characteristic: title


E-MTAB-11750:M13_NT_ac220_24h 1

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11750:M13_NT_ac220_24h 1

text: ArrayExpress

text: human

text: adult

text: acute myeloid leukemia

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_NT_ac220_24h 1


E-MTAB-11750:M13_NT_ac220_24h 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11750:M13_NT_ac220_24h 2

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: acute myeloid leukemia

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_NT_ac220_24h 2


E-MTAB-11750:M13_NT_ac220_72h 1

text: public

text: E-MTAB-11750:M13_NT_ac220_72h 1

text: ArrayExpress

characteristic: broker name

text: human

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_NT_ac220_72h 1


E-MTAB-11750:M13_NT_ac220_72h 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11750:M13_NT_ac220_72h 2

text: ArrayExpress

text: human

text: adult

text: acute myeloid leukemia

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_NT_ac220_72h 2


E-MTAB-11750:M13_MPI_ac220_man_24h 1

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-11750:M13_MPI_ac220_man_24h 1

text: ArrayExpress

text: human

text: adult

text: acute myeloid leukemia

text: MPI knockout

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: M13_MPI_ac220_man_24h 1


E-MTAB-11750:M13_MPI_ac220_man_24h 2

text: public

text: E-MTAB-11750:M13_MPI_ac220_man_24h 2

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: description

text: adult

text: acute myeloid leukemia

text: MPI knockout

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_MPI_ac220_man_24h 2


E-MTAB-11750:M13_MPI_ac220_man_72h 1

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11750:M13_MPI_ac220_man_72h 1

text: ArrayExpress

text: human

text: adult

text: acute myeloid leukemia

text: MPI knockout

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_MPI_ac220_man_72h 1

characteristic: title


E-MTAB-11750:M13_MPI_ac220_man_72h 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

text: E-MTAB-11750:M13_MPI_ac220_man_72h 2

text: ArrayExpress

text: human

text: adult

text: acute myeloid leukemia

text: MPI knockout

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_MPI_ac220_man_72h 2


E-MTAB-11750:M13_NT_ac220_man_24h 1

text: public

text: E-MTAB-11750:M13_NT_ac220_man_24h 1

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_NT_ac220_man_24h 1


E-MTAB-11750:M13_NT_ac220_man_24h 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11750:M13_NT_ac220_man_24h 2

text: ArrayExpress

text: human

text: adult

text: acute myeloid leukemia

characteristic: disease

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_NT_ac220_man_24h 2


E-MTAB-11750:M13_NT_ac220_man_72h 1

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-11750:M13_NT_ac220_man_72h 1

text: ArrayExpress

text: human

text: adult

text: acute myeloid leukemia

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_NT_ac220_man_72h 1


E-MTAB-11750:M13_NT_ac220_man_72h 2

text: public

text: E-MTAB-11750:M13_NT_ac220_man_72h 2

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: description

text: adult

text: acute myeloid leukemia

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: M13_NT_ac220_man_72h 2


E-MTAB-11750:M13_MPI_24h 1

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11750:M13_MPI_24h 1

text: ArrayExpress

text: human

text: adult

text: acute myeloid leukemia

text: MPI knockout

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_MPI_24h 1


E-MTAB-11750:M13_MPI_24h 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11750:M13_MPI_24h 2

text: ArrayExpress

text: human

text: adult

text: acute myeloid leukemia

text: MPI knockout

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_MPI_24h 2

characteristic: title


E-MTAB-11750:M13_MPI_72h 1

text: public

characteristic: INSDC status

text: E-MTAB-11750:M13_MPI_72h 1

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: adult

text: acute myeloid leukemia

text: MPI knockout

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_MPI_72h 1


E-MTAB-11750:M13_MPI_72h 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11750:M13_MPI_72h 2

text: ArrayExpress

text: human

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

text: MPI knockout

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_MPI_72h 2


E-MTAB-11750:M13_NT_24h 1

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-11750:M13_NT_24h 1

text: ArrayExpress

text: human

text: adult

text: acute myeloid leukemia

characteristic: disease

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_NT_24h 1


E-MTAB-11750:M13_NT_24h 2

text: public

text: E-MTAB-11750:M13_NT_24h 2

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: description

text: adult

text: acute myeloid leukemia

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_NT_24h 2


E-MTAB-11750:M13_NT_72h 1

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11750:M13_NT_72h 1

text: ArrayExpress

text: human

text: adult

text: acute myeloid leukemia

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: M13_NT_72h 1


E-MTAB-11750:M13_NT_72h 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11750:M13_NT_72h 2

text: ArrayExpress

text: human

text: adult

text: acute myeloid leukemia

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: M13_NT_72h 2


text: UNIVERSITY OF COPENHAGEN

text: public

characteristic: INSDC status

tag: Namespace:UNIVERSITY OF COPENHAGEN

text: AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA;AAGTCGGATCGTAGCCATGTCGTTC

characteristic: adapters

characteristic: collection date

text: NTM caecum content

text: main associated run/experiment: ERR9742243/ERX9290963, merged from ERR4968601/ERX4787798 and ERR6785293/ERX6409073 (linked to this sample as well); Chicken meta genome data from Caecum content; animal CC08.13 from cage CC08 with treatment CC

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: El Morell; Tarragona

characteristic: geographic location (region and locality)

text: Caecum content

characteristic: host body site

text: Ross

characteristic: host breed

text: Chicken

characteristic: host common name

text: Control

characteristic: host diet treatment

text: Campylobacter:+;Salmonella:-;Clostridium:-

characteristic: host disease status

text: Gallus gallus

characteristic: host scientific name

text: male

characteristic: host sex

unit: °C

characteristic: host storage container temperature

characteristic: host subject id

characteristic: host taxid

unit: g

characteristic: host total mass

text: BEMT

characteristic: library name

text: PCR

characteristic: library selection

text: D-rex protocol

characteristic: nucleic acid extraction

text: chicken gut metagenome

text: HoloFood

characteristic: project

text: HoloFood Chicken - None targeted metabolomic

characteristic: project name

characteristic: reference host genome for decontamination

text: Shield

characteristic: sample storage buffer

text: E-matrix 2ml

characteristic: sample storage container

text: UCPH

characteristic: sample storage location

characteristic: sample storage temperature

unit: mL

characteristic: sample volume or weight for DNA extraction

text: chicken gut metagenome

characteristic: sequencing method

characteristic: title

unit: day

characteristic: trial length

characteristic: trial timepoint

type: EXTERNAL LINKS

type: BIOGENIC AMINES

type: SAMPLE

value: Index PCR cycles

value: UCPH

value: Organism

value: Chicken

value: Body site

value: caecum content

value: ng used for library build

value: Lab Process ID

value: Raw sequence name

value: Sample code