text: CHRISTIAN MEDICAL COLLEGE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: IPD isolates from INDIA

characteristic: description

text: India

text: diseased

text: Homo sapiens

text: Human, Fluid

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Genetic evolution of pneumococci


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CHRISTIAN MEDICAL COLLEGE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

tag: Namespace:CHRISTIAN MEDICAL COLLEGE

characteristic: Submitter Id

characteristic: collection date

text: IPD isolates from INDIA

text: India

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human, Blood

characteristic: isolation source

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae

text: Genetic evolution of pneumococci

characteristic: title


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

text: Plasmodium falciparum

characteristic: subject id


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

tag: Namespace:Latvian Biomedical Research and Study Centre

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: fibroblast

characteristic: cell type

text: human

text: Protocols: Cells were seeded in DMEM-F12 complete medium at a density of 1x105 cells per well in 12-well plates and 1x104 EVs per cell (total 1x109 EVs / well) were added to the cells and they were grown as a monolayer for 48 hours. Untreated control cells were grown in parallel. After that, the cells were washed with PBS and lysed with 1ml TRI-Reagent® (Sigma Aldrich, USA) and RNA was extracted according to manufacturer’s protocol. The cells were washed with PBS and lysed with 1ml TRI-Reagent® (Sigma Aldrich, USA) and RNA was extracted according to manufacturer’s protocol. Briefly, 200 μl of chloroform was added, the samples were centrifuged at 12 000g for 15 min at +4˚C, the aqueous phase was transferred to a new tube and isopropanol was used to precipitate the RNA by centrifuging at 12 000g for 10 min at +4˚C. After that, the RNA was washed with 70% Ethanol-DEPC and the DNA was removed with DNA-free™ (Thermo Fisher Scientific, USA) DNA removal kit according to manufacturer's protocol. The RNA concentration was measured with NanoDrop 1000 (Thermo Ficher Scientific, USA) and the integrity of the RNA was measured with Agilent Bioanalyzer using RNA Pico chip (Agilent Technologies, USA). For transcriptome sequencing, the rRNA was removed from 200 ng of total RNA using MGIEasy rRNA depletion kit (MGI, China). The transcriptome libraries were built using MGIEasy RNA Directional Library Prep Kit (MGI, China) according to manufacturer’s protocol. Briefly, the RNA was fragmented into 250 bp pieces, and it was reverse transcribed, and the second strand was synthesized. Adapters were ligated according to the manufacturer’s recommendations and the product was amplified with PCR.

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: foreskin

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: extracellular vesicles from urine of healthy male

characteristic: stimulus


text: Latvian Biomedical Research and Study Centre

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: fibroblast

text: human

text: adult

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: foreskin

text: Homo sapiens

text: male

text: extracellular vesicles from hypoxic prostate cancer line

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: fibroblast

text: human

characteristic: common name

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: foreskin

text: Homo sapiens

text: male

text: extracellular vesicles from normoxic prostate cancer line


text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: fibroblast

characteristic: cell type

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: foreskin

text: Homo sapiens

text: male

text: extracellular vesicles from urine of prostate cancer patient


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: fibroblast

text: human

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: foreskin

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

characteristic: stimulus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: fibroblast

text: human

text: adult

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: foreskin

text: Homo sapiens

text: male

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: fibroblast

text: human

characteristic: common name

text: adult

text: prostate cancer

text: Homo sapiens

text: Homo sapiens

text: prostate

text: Homo sapiens

text: male


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: fibroblast

characteristic: cell type

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: prostate cancer

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: prostate

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

text: ArrayExpress

text: fibroblast

text: human

text: adult

text: prostate cancer

text: Homo sapiens

text: Homo sapiens

text: prostate

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

characteristic: stimulus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: fibroblast

text: human

text: adult

text: prostate cancer

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: prostate

text: Homo sapiens

text: male

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: fibroblast

text: human

characteristic: common name

text: adult

text: prostate cancer

text: Homo sapiens

text: Homo sapiens

text: prostate

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: osteosarcoma cell line

text: osteoblast

characteristic: cell type

text: human

text: Protocols: Cultivated cytoplasmic hybrid cells were collected and washed with PBS. All experimental workflow was performed in two biological replicates. Total RNA isolation with RNeasy Mini Kit (QIAGEN Science, MD, USA), according to the manufacturer's instructions. The integrity of the extracted RNA was evaluated by the RNA integrity number (RIN) within the Agilent 2100 Bioanalyzer system (Agilent, USA). Ribosomal RNA depletion was done with Low Input RiboMinus Eukaryote System v2 (Thermo Fisher Scientific, USA), by processing 500ng of total RNA from each sample. For cDNA library preparation we used the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific, USA).

characteristic: description

text: adult

characteristic: developmental stage

text: Leigh syndrome

characteristic: disease

text: m.13513G>A 50%

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: bone

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: osteosarcoma cell line

text: osteoblast

text: human

text: adult

text: Leigh syndrome

text: m.13513G>A 70%

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Homo sapiens


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

text: osteosarcoma cell line

text: osteoblast

text: human

text: adult

text: Leigh syndrome

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

text: osteosarcoma cell line

characteristic: cell line

text: osteoblast

text: human

characteristic: common name

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: bone

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: osteosarcoma cell line

text: osteoblast

characteristic: cell type

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: bone

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: osteosarcoma cell line

text: osteoblast

text: human

text: adult

text: normal

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: bone

text: Homo sapiens

text: WT-U


text: Streptococcus agalactiae

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: Streptococcus agalactiae

text: Streptococcus agalactiae

characteristic: organism

text: Streptococcus agalactiae

characteristic: subject id


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

tag: Namespace:UNIVERSITY OF MANCHESTER

text: ArrayExpress

characteristic: broker name

text: bone marrow macrophage

characteristic: cell line

text: macrophage

text: house mouse

characteristic: common name

text: Protocols: After treatment, cells were harvested by scraping and stored in RNAlater (Invitrogen AM7020) for stable storage. Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) high glucose with sodium pyruvate and sodium bicarbonate (Sigma-Aldrich D6429) supplemented with 10% heat inactivated foetal bovine serum (FBS; Gibco 10500064). All incubations were done at 37oC 5% CO2 and all cell handling under laminar air flow unless otherwise stated. Fluorescence activated cell sorting (FACS) was used to sort single iBMDMs into prewarmed DMEM+FBS in 96 well TC treated plates and incubated to generate clonal populations. To reduce clumping during growth from single cells, cells were dispersed by gently reverse pipetting on days 5 and 8. When cells were 60-80% confluent (day 12-14) clonal populations were transferred to 6 well TC treated plates for an additional 24h growth. Mixed populations were seeded directly into TC treated 6 well plates at a similar density to clonal populations. Lipid A diphosphoryl from Salmonella enterica serotype Minnesota Re595 (Sigma-Aldrich L0774) stock was prepared at 500mg ml-1 in 50% DMSO and stored at -20oC until use. Clonal or mixed populations in 6 well plates at approximately 50% confluence were stimulated with Lipid A at a final concentration of 500ng ml-1 for 3h. Unstimulated controls were treated with an equivalent volume of 50% DMSO for 3h. Cells were pelleted by centrifugation and RNAlater removed prior to RNA extraction with the RNeasy Plus mini kit (Qiagen 74136) according to the manufacturer’s instructions. RNA was stored at -80oC. RNA concentration, purity and integrity was assessed by Quant-it Qubit RNA BR assay (Invitrogen 10266793), nanodrop and RNA ScreenTape Tapestation analysis (Agilent 5067-5577 and 5067-5576) respectively. Quality and integrity of the RNA samples were assessed using a 4200 TapeStation (Agilent Technologies) and then libraries generated using the Illumina® Stranded mRNA Prep. Ligation kit (Illumina, Inc.) according to the manufacturer’s protocol.

text: adult

text: wild type genotype

text: clonal

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: Mus musculus

characteristic: strain

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: bone marrow macrophage

text: macrophage

characteristic: cell type

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

text: mixed

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus


E-MTAB-11040:Sample 1

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11040:Sample 1

characteristic: Submitter Id

unit: day

characteristic: age

text: ArrayExpress

text: chondrocyte

text: house mouse

text: Protocols: Primary chondrocytes from 5 day old mice were isolated as follows. 5 day old C57bl/6 PER2::Luc mice were sacrificed by decapitation. Knee, hip and shoulder joints were dissected, and any soft tissue removed. Joint cartilage was subjected to pre-digestion with collagenase D (3 mg/mL) in DMEM two times for 30 min at 37°C with intermittent vortex to remove soft tissue leftovers. Subsequently, cartilage was diced using a scalpel and digested overnight at 37°C. Cells were dispersed by pipetting and passed through 70 μM cell strainer. Cell suspension was then centrifuged and the pellet was re-suspended in DMEM/F12 with 10% FBS and plated in T75 flasks. Cells were passaged only once before experiments. Mouse primary chondrocytes were passaged into 6-well plates. Upon reaching confluency, media were changed to fresh and ~30 hr later osmolarity was increased by +200 mOsm using sorbitol. T0 sample was collected just before the addition of sorbitol. Then samples were collected every 4 hr for 48 hr. The experiment was repeated three times for replicates A,B and C. mRNA was extracted using RNeasy micro kit (Qiagen) according to the manufacturer’s protocol. Quality and integrity of the RNA samples were assessed using a 2200 TapeStation (Agilent Technologies). Libraries were generated by the Genomic Technologies Core Facility using the TruSeq® Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s protocol.

characteristic: genotype

text: media

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cartilage

text: A

characteristic: replicate

text: Mus musculus

text: Sample 1


E-MTAB-11040:Sample 2

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

text: E-MTAB-11040:Sample 2

text: ArrayExpress

characteristic: broker name

text: chondrocyte

text: house mouse

characteristic: common name

text: media

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: cartilage

characteristic: organism part

text: B

text: Mus musculus

characteristic: strain

text: Sample 2

characteristic: title


E-MTAB-11040:Sample 3

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11040:Sample 3

text: ArrayExpress

text: chondrocyte

characteristic: cell type

text: house mouse

characteristic: description

text: media

text: Mus musculus

text: Mus musculus

text: cartilage

text: C

text: Mus musculus

text: Sample 3


E-MTAB-11040:Sample 4

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11040:Sample 4

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: chondrocyte

text: house mouse

characteristic: genotype

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

text: A

text: Mus musculus

text: osmotic stress treatment

characteristic: stimulus

text: Sample 4


E-MTAB-11040:Sample 5

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

text: E-MTAB-11040:Sample 5

text: ArrayExpress

characteristic: broker name

text: chondrocyte

text: house mouse

characteristic: common name

text: 200 mOsm sorbitol

characteristic: growth condition

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cartilage

characteristic: organism part

text: B

characteristic: replicate

text: Mus musculus

text: osmotic stress treatment

text: Sample 5


E-MTAB-11040:Sample 6

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11040:Sample 6

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

text: C

text: Mus musculus

text: osmotic stress treatment

characteristic: strain

text: Sample 6

characteristic: title


E-MTAB-11040:Sample 7

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11040:Sample 7

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: chondrocyte

characteristic: cell type

text: house mouse

characteristic: description

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

text: A

text: Mus musculus

text: osmotic stress treatment

text: Sample 7


E-MTAB-11040:Sample 8

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

text: E-MTAB-11040:Sample 8

text: ArrayExpress

characteristic: broker name

text: chondrocyte

text: house mouse

characteristic: common name

characteristic: genotype

text: 200 mOsm sorbitol

characteristic: growth condition

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cartilage

text: B

text: Mus musculus

text: osmotic stress treatment

characteristic: stimulus

text: Sample 8


E-MTAB-11040:Sample 9

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11040:Sample 9

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

characteristic: organism part

text: C

characteristic: replicate

text: Mus musculus

text: osmotic stress treatment

text: Sample 9


E-MTAB-11040:Sample 10

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11040:Sample 10

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

text: A

text: Mus musculus

text: osmotic stress treatment

characteristic: strain

text: Sample 10

characteristic: title


E-MTAB-11040:Sample 11

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

text: E-MTAB-11040:Sample 11

text: ArrayExpress

characteristic: broker name

text: chondrocyte

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

characteristic: genotype

text: 200 mOsm sorbitol

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: cartilage

text: B

text: Mus musculus

text: osmotic stress treatment

text: Sample 11


E-MTAB-11040:Sample 12

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11040:Sample 12

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cartilage

text: C

text: Mus musculus

text: osmotic stress treatment

characteristic: stimulus

text: Sample 12


E-MTAB-11040:Sample 13

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11040:Sample 13

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

characteristic: organism part

text: A

characteristic: replicate

text: Mus musculus

text: osmotic stress treatment

text: Sample 13


E-MTAB-11040:Sample 14

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

text: E-MTAB-11040:Sample 14

text: ArrayExpress

characteristic: broker name

text: chondrocyte

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

text: B

text: Mus musculus

text: osmotic stress treatment

characteristic: strain

text: Sample 14

characteristic: title


E-MTAB-11040:Sample 15

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11040:Sample 15

text: ArrayExpress

text: chondrocyte

text: house mouse

characteristic: genotype

text: 200 mOsm sorbitol

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: cartilage

text: C

text: Mus musculus

text: osmotic stress treatment

text: Sample 15


E-MTAB-11040:Sample 16

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11040:Sample 16

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cartilage

text: A

text: Mus musculus

text: osmotic stress treatment

characteristic: stimulus

text: Sample 16


E-MTAB-11040:Sample 17

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

text: E-MTAB-11040:Sample 17

text: ArrayExpress

characteristic: broker name

text: chondrocyte

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

characteristic: organism part

text: B

characteristic: replicate

text: Mus musculus

text: osmotic stress treatment

text: Sample 17


E-MTAB-11040:Sample 18

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11040:Sample 18

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

text: C

text: Mus musculus

text: osmotic stress treatment

characteristic: strain

text: Sample 18

characteristic: title


E-MTAB-11040:Sample 19

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11040:Sample 19

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: chondrocyte

text: house mouse

characteristic: genotype

text: 200 mOsm sorbitol

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: cartilage

text: A

text: Mus musculus

text: osmotic stress treatment

text: Sample 19


E-MTAB-11040:Sample 20

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

text: E-MTAB-11040:Sample 20

text: ArrayExpress

characteristic: broker name

text: chondrocyte

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: 200 mOsm sorbitol

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cartilage

text: B

text: Mus musculus

text: osmotic stress treatment

characteristic: stimulus

text: Sample 20


E-MTAB-11040:Sample 21

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11040:Sample 21

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

characteristic: organism part

text: C

characteristic: replicate

text: Mus musculus

text: osmotic stress treatment

text: Sample 21


E-MTAB-11040:Sample 22

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11040:Sample 22

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

text: A

text: Mus musculus

text: osmotic stress treatment

characteristic: strain

text: Sample 22

characteristic: title


E-MTAB-11040:Sample 23

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

text: E-MTAB-11040:Sample 23

text: ArrayExpress

characteristic: broker name

text: chondrocyte

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

characteristic: genotype

text: 200 mOsm sorbitol

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: cartilage

text: B

text: Mus musculus

text: osmotic stress treatment

text: Sample 23


E-MTAB-11040:Sample 24

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11040:Sample 24

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cartilage

text: C

text: Mus musculus

text: osmotic stress treatment

characteristic: stimulus

text: Sample 24


E-MTAB-11040:Sample 25

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11040:Sample 25

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

characteristic: organism part

text: A

characteristic: replicate

text: Mus musculus

text: osmotic stress treatment

text: Sample 25


E-MTAB-11040:Sample 26

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

text: E-MTAB-11040:Sample 26

text: ArrayExpress

characteristic: broker name

text: chondrocyte

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

text: B

text: Mus musculus

text: osmotic stress treatment

characteristic: strain

text: Sample 26

characteristic: title


E-MTAB-11040:Sample 27

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11040:Sample 27

text: ArrayExpress

text: chondrocyte

text: house mouse

characteristic: genotype

text: 200 mOsm sorbitol

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: cartilage

text: C

text: Mus musculus

text: osmotic stress treatment

text: Sample 27


E-MTAB-11040:Sample 28

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11040:Sample 28

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cartilage

text: A

text: Mus musculus

text: osmotic stress treatment

characteristic: stimulus

text: Sample 28


E-MTAB-11040:Sample 29

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

text: E-MTAB-11040:Sample 29

text: ArrayExpress

characteristic: broker name

text: chondrocyte

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

characteristic: organism part

text: B

characteristic: replicate

text: Mus musculus

text: osmotic stress treatment

text: Sample 29


E-MTAB-11040:Sample 30

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11040:Sample 30

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

text: C

text: Mus musculus

text: osmotic stress treatment

characteristic: strain

text: Sample 30

characteristic: title


E-MTAB-11040:Sample 31

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11040:Sample 31

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: chondrocyte

text: house mouse

characteristic: genotype

text: 200 mOsm sorbitol

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: cartilage

text: A

text: Mus musculus

text: osmotic stress treatment

text: Sample 31


E-MTAB-11040:Sample 32

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

text: E-MTAB-11040:Sample 32

text: ArrayExpress

characteristic: broker name

text: chondrocyte

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: 200 mOsm sorbitol

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cartilage

text: B

text: Mus musculus

text: osmotic stress treatment

characteristic: stimulus

text: Sample 32


E-MTAB-11040:Sample 33

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11040:Sample 33

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

characteristic: organism part

text: C

characteristic: replicate

text: Mus musculus

text: osmotic stress treatment

text: Sample 33


E-MTAB-11040:Sample 34

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11040:Sample 34

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

text: A

text: Mus musculus

text: osmotic stress treatment

characteristic: strain

text: Sample 34

characteristic: title


E-MTAB-11040:Sample 35

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

text: E-MTAB-11040:Sample 35

text: ArrayExpress

characteristic: broker name

text: chondrocyte

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

characteristic: genotype

text: 200 mOsm sorbitol

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: cartilage

text: B

text: Mus musculus

text: osmotic stress treatment

text: Sample 35


E-MTAB-11040:Sample 36

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11040:Sample 36

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cartilage

text: C

text: Mus musculus

text: osmotic stress treatment

characteristic: stimulus

text: Sample 36


E-MTAB-11040:Sample 37

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11040:Sample 37

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: chondrocyte

text: house mouse

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

characteristic: organism part

text: A

characteristic: replicate

text: Mus musculus

text: osmotic stress treatment

text: Sample 37


E-MTAB-11040:Sample 38

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

text: E-MTAB-11040:Sample 38

text: ArrayExpress

characteristic: broker name

text: chondrocyte

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: 200 mOsm sorbitol

text: Mus musculus

text: Mus musculus

text: cartilage

text: B

text: Mus musculus

text: osmotic stress treatment

characteristic: strain

text: Sample 38

characteristic: title


E-MTAB-11040:Sample 39

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11040:Sample 39

text: ArrayExpress

text: chondrocyte

text: house mouse

characteristic: genotype

text: 200 mOsm sorbitol

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: cartilage

text: C

text: Mus musculus

text: osmotic stress treatment

text: Sample 39


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Department of Biochemistry University of Cambridge

characteristic: Submitter Id

text: ArrayExpress

text: Protocols: 5X10^7 exponentially growing (5.5hrs post-inoculation) and early post-diauxic shift (13hrs post-inoculation for WT and hda1Δ, 14.5hrs post-inoculation for gcn5Δ and gcn5Δhda1Δ) cells were harvested be centrifugation at 16,100xg for 1 min at 4°C. Total RNA was isolated using an RNeasy Mini kit (Qiagen, 74104). After the QC procedures of total RNA, mRNA is enriched using oligo(dT) beads. Enriched mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is first synthesized by using random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

text: early post-diauxic shift phase

characteristic: developmental stage

text: gcn5 deletion

text: glucose starved

text: Saccharomyces cerevisiae S288C

characteristic: organism

text: Saccharomyces cerevisiae S288C

text: whole organism

text: Saccharomyces cerevisiae S288C


text: Department of Biochemistry University of Cambridge

characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

text: early post-diauxic shift phase

text: gcn5 deletion

text: glucose starved

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: whole organism

characteristic: organism part

text: Saccharomyces cerevisiae S288C


text: public

text: ArrayExpress

characteristic: description

text: early post-diauxic shift phase

text: gcn5 and hda1 deletion

text: glucose starved

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: whole organism

text: Saccharomyces cerevisiae S288C

characteristic: strain

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: early post-diauxic shift phase

text: hda1 deletion

text: glucose starved

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: whole organism

text: Saccharomyces cerevisiae S288C


text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: early post-diauxic shift phase

text: wild type genotype

characteristic: genotype

text: glucose starved

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: whole organism

text: Saccharomyces cerevisiae S288C


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

text: ArrayExpress

text: exponential phase

text: gcn5 deletion

text: glucose replete

characteristic: growth condition

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: whole organism

text: Saccharomyces cerevisiae S288C


characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

text: exponential phase

characteristic: developmental stage

text: gcn5 and hda1 deletion

text: glucose replete

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: whole organism

text: Saccharomyces cerevisiae S288C


characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

text: exponential phase

text: hda1 deletion

text: glucose replete

text: Saccharomyces cerevisiae S288C

characteristic: organism

text: Saccharomyces cerevisiae S288C

text: whole organism

text: Saccharomyces cerevisiae S288C


text: public

text: ArrayExpress

characteristic: description

text: exponential phase

text: wild type genotype

text: glucose replete

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: whole organism

characteristic: organism part

text: Saccharomyces cerevisiae S288C

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Institut fur Biomedizinische Alternsforschung, Leopold-Franzens-Universitat Innsbruck

characteristic: age

text: ArrayExpress

text: Protocols: To obtain synchronized populations, gravid adults were treated with hypochlorite and eggs were allowed to hatch in M9 overnight. ~ 1,600 L1 larvae per strain were plated on two 10 cm NG agar plates seeded with concentrated E. coli OP50 and cultured at 20 °C. At the L4-stage, 1,500 worms per strain were manually transferred to two E. coli OP50-seeded 10 cm NG agar plates supplemented with 20 µM FUDR to inhibit germ cell proliferation and progeny production. At day 1 of adulthood, worms were harvested by washing them off their plates with M9. After additional washing with M9 and RNAse-free water, worms were suspended in 1 ml Trizol, snap-frozen in liquid nitrogen and stored at -80 °C until RNA-extraction. RNA was extracted using Trizol and cleaned up with the Monarch® Total RNA Miniprep Kit or RNA Cleanup Kit (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions. Equal amounts of RNA extracted from three biological replicates were pooled for RNA-sequencing to mitigate batch effects. RNA library preparation was performed by Eurofins Genomics (Konstanz, Germany) using proprietary protocols and NEBNext Ultra II Directional RNA library preparation kit for Illumina.

text: adult

text: wild type genotype

text: 20 °C, 20 µM FUDR from L4 onwards

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite

characteristic: sex

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Institut fur Biomedizinische Alternsforschung, Leopold-Franzens-Universitat Innsbruck

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: adult

text: egl-8(md1971) V

characteristic: genotype

text: 20 °C, 20 µM FUDR from L4 onwards

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

text: adult

characteristic: developmental stage

text: unc-43(n498n1186) IV

text: 20 °C, 20 µM FUDR from L4 onwards

characteristic: growth condition

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite


characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

characteristic: description

text: adult

text: unc-43(n498) IV

text: 20 °C, 20 µM FUDR from L4 onwards

text: Caenorhabditis elegans

characteristic: organism

text: Caenorhabditis elegans

text: whole organism

characteristic: organism part

text: Caenorhabditis elegans

text: hermaphrodite


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: age

text: ArrayExpress

text: adult

text: daf-2(e1370) III

text: 20 °C, 20 µM FUDR from L4 onwards

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: adult

text: daf-2(e1370) III; egl-8(md1971) V

text: 20 °C, 20 µM FUDR from L4 onwards

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

text: adult

characteristic: developmental stage

text: daf-2(e1370) III; unc-43(n498n1186) IV

characteristic: genotype

text: 20 °C, 20 µM FUDR from L4 onwards

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite


characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

characteristic: description

text: adult

text: daf-2(e1370) III; unc-43(n498) IV

text: 20 °C, 20 µM FUDR from L4 onwards

characteristic: growth condition

text: Caenorhabditis elegans

characteristic: organism

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Max Planck Institute for Biology of Ageing

unit: month

characteristic: age

characteristic: batch

text: ArrayExpress

text: house mouse

characteristic: common name

text: Protocols: Organoid cultures of different passages (4-13) were transferred into medium supplemented with 10% matrigel and maintained in a 37°C incubator, 5% CO2, 20% O2 shaking at 80-90 rpm. The organoids were passaged every 4 days with mechanical dissociation of the matrigel. For the differentiation assays, the medium was exchanged with differentiation medium (Broutier et al., 2016) (Advanced DMEM F12, 10mM Hepes, 1%GlutaMAX, 1:50 B27 supplement (without vitamin A), 1 mM N-acetylcysteine, 10 nM recombinant human [Leu15]-gastrin I, 50 ng/ml recombinant mouse EGF, 100 ng/ml recombinant human FGF10, 50 nM A83-01 and 10 μM DAPT) after 3 days of culture and was re-newed every 2 days. The 13th-15th day of differentiation, the medium was changed daily with the supplementation of 3uM of dexamethasone. Assessment of differentiation was performed on day 16th. Total RNA from young and old organoids at passages 10-13 was extracted in two batches (batch1: n=4 and batch2: n=3 per age) with the Zymoresearch Direct-zol RNA Miniprep (R2051) kit. 50ng RNA per sample were used for cDNA synthesis with Maxima H Minus reverse transcriptase (Thermo Fisher Scientific). During reverse transcription, unique barcodes including unique molecular identifiers (UMI) were attached to each sample. After cDNA synthesis, all samples were pooled and processed in one single tube. DNA was purified using AmpureXP beads (Beckman Coulter) and the eluted cDNA was subjected to Exonuclease I treatment (New England Biolabs). cDNA was PCR-amplified for 12 cycles and subsequently purified. After purification, cDNA was tagmented in 10 technical replicates of 1 ng cDNA each using the Nextera XT Kit (Illumina), according to the manufacturer's instructions. The final library was purified and concentration and size were validated by Qubit and High Sensitivity TapeStation D1000 analyses.

text: organoid culture

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

characteristic: replicate

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Max Planck Institute for Biology of Ageing

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: house mouse

text: organoid culture

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

characteristic: title


text: OREGON STATE UNIVERS

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5689:Seedling-shoot-2-days-light-replicate-1

tag: Namespace:OREGON STATE UNIVERS

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Nipponbare

characteristic: cultivar

text: Protocols: The chamber was set to cycle between 20C for 12 hours and 18C for the next 12 hours, and the soil was kept moist by gently spraying with water every 72 hours. Sampling was done at about 10 am under light. Continuous light: Samples harvested after growing the seedlings in continuous dark for 8 days after germination followed by 48hrs (48LL) of continuous exposure to light (120µmol/m2/sec at soil surface). Total RNA from frozen seedling shoot samples was extracted as per manufacturer's protocol for RNA Plant reagent (Invitrogen Inc., USA), RNeasy kits (Qiagen Inc., USA), and RNase-free DNase (Life Technologies Inc., USA). True-Seq kit (Illumina Inc.) was used to prepare RNA-seq libraries, according to the manufacturer’s protocol.

text: LP.02 two leaves visible stage

characteristic: developmental stage

text: continuous dark (no light) regimen

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: shoot

text: Oryza sativa Japonica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5689:Seedling-shoot-2-days-light-replicate-2

characteristic: age

text: ArrayExpress

text: Japanese rice

text: Nipponbare

characteristic: description

text: LP.02 two leaves visible stage

text: continuous dark (no light) regimen

characteristic: growth condition

text: Oryza sativa Japonica Group

characteristic: organism

text: Oryza sativa Japonica Group

text: shoot

text: Oryza sativa Japonica Group


characteristic: ENA-CHECKLIST

characteristic: External Id

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5689:Seedling-shoot-2-days-light-replicate-3

text: ArrayExpress

text: Japanese rice

characteristic: common name

text: Nipponbare

text: LP.02 two leaves visible stage

text: continuous dark (no light) regimen

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: shoot

characteristic: organism part

text: Oryza sativa Japonica Group


text: OREGON STATE UNIVERS

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5689:Seedling-shoot-8-days-dark-replicate-1

text: ArrayExpress

text: Japanese rice

text: Nipponbare

text: Protocols: The chamber was set to cycle between 20C for 12 hours and 18C for the next 12 hours, and the soil was kept moist by gently spraying with water every 72 hours. Sampling was done at about 7.30 pm under green lights. Continuous dark: Samples harvested after growing the seedlings in continuous dark for 8 days (8DD) after germination. Total RNA from frozen seedling shoot samples was extracted as per manufacturer's protocol for RNA Plant reagent (Invitrogen Inc., USA), RNeasy kits (Qiagen Inc., USA), and RNase-free DNase (Life Technologies Inc., USA). True-Seq kit (Illumina Inc.) was used to prepare RNA-seq libraries, according to the manufacturer’s protocol.

text: LP.02 two leaves visible stage

text: continuous dark (no light) regimen

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: shoot

text: Oryza sativa Japonica Group

characteristic: title


text: OREGON STATE UNIVERS

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5689:Seedling-shoot-8-days-dark-replicate-2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Nipponbare

text: LP.02 two leaves visible stage

text: continuous dark (no light) regimen

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: shoot

text: Oryza sativa Japonica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5689:Seedling-shoot-8-days-dark-replicate-3

text: ArrayExpress

text: Japanese rice

text: Nipponbare

characteristic: cultivar

text: LP.02 two leaves visible stage

characteristic: developmental stage

text: continuous dark (no light) regimen

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: shoot

text: Oryza sativa Japonica Group


text: public

tag: Namespace:Charles University, Faculty of Science Department of Cell Biology

text: ArrayExpress

text: fission yeast

text: Protocols: S. pombe cells were cultivated to exponential growth phase in complex YES medium. At OD 0.5, 400 ml yeast culture was fixed by adding formaldehyde to final concentration of 1%. After 30 min incubation, remaining formaldehyde was quenched by 125 mM glycine for 10 min. Cells were washed with PBS and broken with glass beads in Lysis Buffer (50 mM Hepes pH 7.6, 1 mM EDTA pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, FY protease inhibitors [Serva], 1 mM PMSF) using the FastPrep24 machine (MP Biomedicals). Extracted chromatin was sheared with the Bioruptor sonicator (Diagenode) using 15 (biol. rep. 1-3) or 30 cycles (biol. rep. 4) of 30s on, 30s off on high power settings. For each immunoprecipitation (IP) within a biological replicate we used the same amount of chromatin extract (in mg of total protein, range 2.5 - 3.7 mg between replicates), for input DNA control 1/10 of chromatin extract amount was kept. For each IP 5 ug antibody (H3: Ab1791, H3K9ac: Ab4441, H3K9me2: Ab1220, all Abcam) were incubated with chromatin extract for 1 hour at 4°C. Then, 50 ul BSA-blocked Protein A-coated magnetic beads (ThermoFisherScientific, 10002D) were added to chromatin extract-antibody suspension and incubated for further 4 hours at 4°C. Crosslinks were reversed in both the precipitated material and input chromatin extract, and samples were treated with RNase A and proteinase K. DNA was purified using phenol-chloroform extraction and sodium acetate/ethanol precipitation. Concentration of DNA was measured by Quantus and size distribution was checked on Agilent Bioanalyzer using the High Sensitivity DNA Assay. In biological replicate #4, purification on Agencourt AMPure XP beads (Beckman Coulter, AC63880) was performed following the phenol-chloroform extraction to remove low-molecular fragments/RNA. Library construction was performed by BGI Tech Solutions (Hong Kong), according to the company's standard BGISEQ-500 ChIP-seq procedure.

characteristic: description

text: targeted mutation

characteristic: genetic modification

text: Pcut6 mutant

characteristic: genotype

text: Schizosaccharomyces pombe

characteristic: organism

text: Schizosaccharomyces pombe

characteristic: replicate

text: Schizosaccharomyces pombe


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Charles University, Faculty of Science Department of Cell Biology

characteristic: INSDC center name

text: public

text: ArrayExpress

text: fission yeast

characteristic: common name

text: targeted mutation

text: Pcut6 mutant

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe


text: mixed

characteristic: ArrayExpress-SEX

text: Panagrolaimus superbus

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Panagrolaimus superbus

text: Mixed

characteristic: gender

text: Panagrolaimus superbus

text: Panagrolaimus superbus

characteristic: subject id

characteristic: title


text: mixed

text: Heligmosomoides polygyrus bakeri

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: Heligmosomoides polygyrus bakeri

text: Mixed

text: Heligmosomoides polygyrus bakeri

text: Heligmosomoides polygyrus bakeri


text: UNIVERSITY OF MELBOURNE

text: public

tag: Namespace:UNIVERSITY OF MELBOURNE

characteristic: collection date

text: Australia

characteristic: geographic location (country and/or sea)

text: Human

characteristic: host

characteristic: isolate

text: Blood Culture

characteristic: isolation source

text: Staphylococcus aureus

characteristic: organism

text: Staphylococcus aureus


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UNIVERSITY OF MELBOURNE

characteristic: INSDC center name

text: public

text: Australia

text: Human

text: Aspirate

text: Staphylococcus aureus

text: Staphylococcus aureus


text: UCSDMI

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: anonymized name

text: human feces

characteristic: description

text: TRUE

characteristic: elevation

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: human-gut

characteristic: env package

text: feces

characteristic: experimental group

text: Israel:Ramat Gan

characteristic: geo loc name

characteristic: host age

text: UBERON:feces

characteristic: host body habitat

text: not provided

characteristic: host body mass index

text: UBERON:feces

characteristic: host body product

text: human

characteristic: host common name

text: adult

characteristic: host life stage

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: years

characteristic: latitude

characteristic: longitude

text: human gut metagenome

text: Bar-Ilan University

text: FALSE

text: feces

characteristic: sample type

text: human gut metagenome

text: F

characteristic: sex

text: acute GVHD patients treated with fecal microbiota transplantation


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: anonymized name

text: not provided

text: human feces

characteristic: description

text: TRUE

characteristic: elevation

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: human-gut

text: feces

text: Donor

text: Israel:Ramat Gan

text: not provided

text: UBERON:feces

text: not provided

text: UBERON:feces

text: human

text: adult

text: Homo sapiens

text: years

text: human gut metagenome

characteristic: organism

text: Bar-Ilan University

text: FALSE

text: feces

text: human gut metagenome

text: not provided

characteristic: title


characteristic: ENA-CHECKLIST

text: UCSDMI

text: public

text: not provided

text: human feces

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: human-associated habitat

text: human-gut

characteristic: env package

text: feces

text: Donor

characteristic: experimental group

text: Israel:Ramat Gan

characteristic: geo loc name

text: not provided

characteristic: host age

text: UBERON:feces

characteristic: host body habitat

text: not provided

characteristic: host body mass index

text: UBERON:feces

characteristic: host body product

text: human

characteristic: host common name

text: adult

characteristic: host life stage

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: years

characteristic: latitude

characteristic: longitude

text: human gut metagenome

text: Bar-Ilan University

text: FALSE

text: feces

characteristic: sample type

text: human gut metagenome

text: not provided

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: anonymized name

text: human feces

characteristic: description

text: TRUE

characteristic: elevation

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: human-gut

text: feces

text: Israel:Ramat Gan

text: UBERON:feces

text: not provided

text: UBERON:feces

text: human

text: adult

text: Homo sapiens

text: years

text: human gut metagenome

characteristic: organism

text: Bar-Ilan University

text: FALSE

text: feces

text: human gut metagenome

text: F

characteristic: title


characteristic: ENA-CHECKLIST

text: UCSDMI

text: public

text: human feces

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: human-associated habitat

text: human-gut

characteristic: env package

text: feces

characteristic: experimental group

text: Israel:Ramat Gan

characteristic: geo loc name

characteristic: host age

text: UBERON:feces

characteristic: host body habitat

text: not provided

characteristic: host body mass index

text: UBERON:feces

characteristic: host body product

text: human

characteristic: host common name

text: adult

characteristic: host life stage

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: years

characteristic: latitude

characteristic: longitude

text: human gut metagenome

text: Bar-Ilan University

text: FALSE

text: feces

characteristic: sample type

text: human gut metagenome

text: M

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: anonymized name

text: human feces

characteristic: description

text: TRUE

characteristic: elevation

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: human-gut

text: feces

text: Israel:Ramat Gan

text: UBERON:feces

text: not provided

text: UBERON:feces

text: human

text: adult

text: Homo sapiens

text: years

text: human gut metagenome

characteristic: organism

text: Bar-Ilan University

text: FALSE

text: feces

text: human gut metagenome

text: M

characteristic: title


characteristic: ENA-CHECKLIST

text: UCSDMI

text: public

text: not provided

text: human feces

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: human-associated habitat

text: human-gut

characteristic: env package

text: feces

characteristic: experimental group

text: Israel:Ramat Gan

characteristic: geo loc name

characteristic: host age

text: UBERON:feces

characteristic: host body habitat

text: not provided

characteristic: host body mass index

text: UBERON:feces

characteristic: host body product

text: human

characteristic: host common name

text: adult

characteristic: host life stage

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: years

characteristic: latitude

characteristic: longitude

text: human gut metagenome

text: Bar-Ilan University

text: FALSE

text: feces

characteristic: sample type

text: human gut metagenome

text: M

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: JIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: thale cress

characteristic: common name

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: Time course transcriptomics study of Arabidopsis thaliana response to elicitors

characteristic: title


text: Technische Universitat Munchen - WZW

text: public

tag: Namespace:Technische Universitat Munchen - WZW

text: Cephalotrichum gorgonifer was isolated from arable soil in Lower Austria (Austria) (Ref: Klaubauf et al., Fungal Diversity 44:65-75, 2010). The genome was sequenced using 454.

characteristic: description

text: Cephalotrichum gorgonifer

text: Cephalotrichum gorgonifer

text: Sequencing and annotation of Cephalotrichum gorgonifer


text: public

text: ArrayExpress

characteristic: broker name

text: liver organoid cells

characteristic: cell type

text: house mouse

text: Protocols: For nuclei extraction, organoids were pooled from three different wells of mixed organoid dome cultures (young n>2, old n>3). After breaking the domes with mechanical dissociation, organoids were dounce homogenised in 1 ml EZ-buffer (SIGMA) (20 strokes with loose and a tight pestle, respectively) and spun 5 min at 300 g. The organoids were incubated on ice for 10 min in EZ-buffer supplemented with DNAseI NEB M0303S (4 units/ml) and 1X DNAseI buffer. Equal volume of EZ-buffer was added, the organoids were spun 5 min at 500 g and incubated again 10 min on ice in EZ-buffer supplemented with DNAseI NEB M0303S (8 units/ml) and 1X DNAseI buffer. Equal volume of EZ-buffer was added, the organoids were spun 5 min at 500 g, resuspended in NSB (1087.5 µl 1XPBS, 5.5 µl 2% BSA, 1.5 µl RNase Inhibitor) and filtered through a 0.22 µm strainer and resuspended again to reach 300,000 nuclei/ml for DroNc-seq. For the DroNc-seq libraries 155,000 Macosko V+ beads (86) were resuspended in 250 µl of cold Lysis buffer (6% w/v Ficoll PM-400, 0.2% Sarkosyl, 20mM EDTA, 200mM Tris pH 7.5, 50 mM DTT). Beads, emulsion oil and 75,000 nuclei in NSB (1087.5 µl 1X PBS, 5.5 µl 2% BSA, 1.5 µl RNase Inhibitor) were loaded on a Nadia Dolomite Bio instrument and run according to the manufacturer’s instructions. After emulsion breakage with 6X SSC/PFO (perfluorooctanol), the beads were washed with 6X SSC, reverse transcribed with TSO- Macosko primer and treated with ExoI. 2000 BEADS in 20 replicates were used for PCR with SMART PCR primer for 12 cycles. cDNA was purified with Ampure XP beads and run on a 5000 Bioanalyser High Sensitivity Chip. 600 pg of DNA in 6 replicates was tagmented with the Nextera XT kit and amplified by PCR using a 10 µM New-P5-SMART PCT hybrid oligo and a 10 µM Nextera N70 indexed oligo for 12 cycles. The DNA was purified with AMPpure XP beads and run on a 1000 Bioanalyser High Sensitivity chip.

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: organoid culture

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: male

characteristic: strain

text: 18 months

characteristic: time


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: liver organoid cells

text: house mouse

text: adult

text: wild type genotype

text: organoid culture

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

characteristic: sex

text: 3 months


text: CHONNAM NATIONAL UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:CHONNAM NATIONAL UNIVERSITY

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: title


E-MTAB-11089:PBS HIO-1

text: UNIVERSITY OF MICHIGAN

text: public

text: E-MTAB-11089:PBS HIO-1

tag: Namespace:UNIVERSITY OF MICHIGAN

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: intestinal cell

characteristic: cell type

text: monoculture

characteristic: coculture

text: human

text: Protocols: 5 organoids were collected per replicate with 4 replicate for each condition at each time point. HIOs were generated by the In Vivo Animal and Human StudiesCore at the University of Michigan Center for Gastrointestinal Research. Human ES cell line WA09 (H9) was obtained from Wicell International Stem Cell Bank and cultured on Matrigel (BD Biosciences)-coated 6-well plates in mTeSR1 medium (Stem Cell Technologies) at 37°C in 5% CO2. Cells were seeded onto Matrigel-coated 24-well plates in fresh mTeSR1 medium and grown until 85 to 90% confluence. Definitive endoderm differentiation was induced by washing the cells with PBS and culturing in endoderm differentiation medium (RPMI 1640, 2% fetal bovine serum [FBS], 2 mM L-glutamine, 100 ng/ml activin A, and 100 U/ml penicillin/streptomycin) for 3 days, and media were exchanged each day. Cells were then washed with endoderm differentiation medium without activin A and cultured in mid/hindgut differentiation medium (RPMI 1640, 2% FBS, 2 mM L-glutamine, 500 ng/ml FGF4, 500 ng/ml WNT3A, and 100 U/ml penicillin-streptomycin) for 4 days until spheroids were present. Spheroids were collected, mixed with ice-cold Matrigel (50ml of Matrigel plus 25ml of media plus 50 spheroids), placed in the center of each well of a 24-well plate, and incubated at 37°C for 10 min to allow Matrigel to solidify. Matrigel embedded spheroids were grown in ENR medium (Dulbecco’s modified Eagle medium [DMEM]-F12, 1 B27 supplement, 2 mM L-glutamine, 100 ng/ml epidermal growth factor [EGF], 100 ng/ml Noggin, 500 ng/ml Rspondin1, and 15 mM HEPES) for 14 days, and medium was replaced every 4 days. Spheroids growing into organoids (HIOs) were dissociated from Matrigel by pipetting using a cut wide-tip pipette (2 to 3 mm). HIOs were mixed with Matrigel (6 HIOs plus 25ml of media plus 50ml of Matrigel) and placed in the center of each well of 24-well plates and incubated at 37°C for 10 min. HIOs were further grown for 14 days in ENR medium with medium exchanged every 4 days. Before use in experiments, HIOs were carved out of Matrigel, washed with DMEM-F12, and replated with 5 HIO/well in 50ml of Matrigel in ENR medium with medium exchanged every 2 to 3 days for 7 days prior to microinjection. Organoids were microinjected with 10^5 CFU/HIO of each Salmonella strain and samples were harvested at 8h post injection. Transcript reads were pseudoaligned to the human genome (GRCh38.p12) using kallisto software RNA was isolated using the mirVana miRNA isolation kit cDNA libraries were prepared by the University of Michigan DNA Sequencing Core using the TruSeq Stranded mRNA Kit (Illumina)

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: organoid culture

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: PBS HIO-1


E-MTAB-11089:PBS HIO-2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MICHIGAN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11089:PBS HIO-2

text: ArrayExpress

text: intestinal cell

text: monoculture

text: human

text: embryo

text: normal

text: organoid culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: PBS HIO-2


E-MTAB-11089:PBS HIO-3

text: UNIVERSITY OF MICHIGAN

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11089:PBS HIO-3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: intestinal cell

text: monoculture

text: human

characteristic: common name

text: embryo

text: normal

text: organoid culture

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: PBS HIO-3

characteristic: title


E-MTAB-11089:PBS HIO-4

text: UNIVERSITY OF MICHIGAN

text: public

text: E-MTAB-11089:PBS HIO-4

text: ArrayExpress

characteristic: cell line

text: intestinal cell

characteristic: cell type

text: monoculture

characteristic: coculture

text: human

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: organoid culture

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: PBS HIO-4


E-MTAB-11089:SE HIO-1

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-11089:SE HIO-1

text: ArrayExpress

text: intestinal cell

text: monoculture

text: human

text: embryo

text: normal

text: organoid culture

text: mixed Salmonella enterica subsp. enterica serovar Typhimurium and Salmonella enterica subsp. enterica serovar Enteritidis

characteristic: infect

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: SE HIO-1


E-MTAB-11089:SE HIO-2

text: UNIVERSITY OF MICHIGAN

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11089:SE HIO-2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: intestinal cell

text: monoculture

text: human

characteristic: common name

text: embryo

text: normal

text: organoid culture

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: SE HIO-2


E-MTAB-11089:SE HIO-3

text: UNIVERSITY OF MICHIGAN

text: public

text: E-MTAB-11089:SE HIO-3

text: ArrayExpress

characteristic: cell line

text: intestinal cell

characteristic: cell type

text: monoculture

characteristic: coculture

text: human

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: organoid culture

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: SE HIO-3

characteristic: title


E-MTAB-11089:SE HIO-4

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-11089:SE HIO-4

text: ArrayExpress

text: intestinal cell

text: monoculture

text: human

text: embryo

text: normal

text: organoid culture

characteristic: infect

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: SE HIO-4


E-MTAB-11089:STM HIO-1

text: UNIVERSITY OF MICHIGAN

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11089:STM HIO-1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: intestinal cell

text: monoculture

text: human

characteristic: common name

text: embryo

text: normal

text: organoid culture

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: STM HIO-1


E-MTAB-11089:STM HIO-2

text: UNIVERSITY OF MICHIGAN

text: public

text: E-MTAB-11089:STM HIO-2

text: ArrayExpress

characteristic: cell line

text: intestinal cell

characteristic: cell type

text: monoculture

characteristic: coculture

text: human

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: organoid culture

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: STM HIO-2

characteristic: title


E-MTAB-11089:STM HIO-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-11089:STM HIO-3

text: ArrayExpress

text: intestinal cell

text: monoculture

text: human

text: embryo

text: normal

text: organoid culture

characteristic: infect

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: STM HIO-3


E-MTAB-11089:STM HIO-4

text: UNIVERSITY OF MICHIGAN

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11089:STM HIO-4

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: intestinal cell

text: monoculture

text: human

characteristic: common name

text: embryo

text: normal

text: organoid culture

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: STM HIO-4


E-MTAB-11089:PMNs only-1

text: UNIVERSITY OF MICHIGAN

text: public

text: E-MTAB-11089:PMNs only-1

text: ArrayExpress

characteristic: cell line

text: intestinal cell

characteristic: cell type

text: coculture with mature neutrophil

characteristic: coculture

text: human

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: 2D adherent culture

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: PMNs only-1

characteristic: title


E-MTAB-11089:PMNs only-2

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-11089:PMNs only-2

text: ArrayExpress

text: intestinal cell

text: coculture with mature neutrophil

text: human

text: embryo

text: normal

text: 3D adherent culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: PMNs only-2


E-MTAB-11089:PMNs only-3

text: UNIVERSITY OF MICHIGAN

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11089:PMNs only-3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: intestinal cell

text: coculture with mature neutrophil

text: human

characteristic: common name

text: embryo

text: normal

text: 4D adherent culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: PMNs only-3


E-MTAB-11089:PMNs only-4

text: UNIVERSITY OF MICHIGAN

text: public

text: E-MTAB-11089:PMNs only-4

text: ArrayExpress

characteristic: cell line

text: intestinal cell

characteristic: cell type

text: coculture with mature neutrophil

characteristic: coculture

text: human

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: 5D adherent culture

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: PMNs only-4


E-MTAB-11089:PBS PMN-HIO-1

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-11089:PBS PMN-HIO-1

text: ArrayExpress

text: intestinal cell

text: coculture with mature neutrophil

text: human

text: embryo

text: normal

text: organoid culture

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: PBS PMN-HIO-1

characteristic: title


E-MTAB-11089:PBS PMN-HIO-2

text: UNIVERSITY OF MICHIGAN

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11089:PBS PMN-HIO-2

characteristic: Submitter Id

text: ArrayExpress

text: intestinal cell

text: coculture with mature neutrophil

text: human

text: embryo

text: normal

text: organoid culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: PBS PMN-HIO-2


E-MTAB-11089:PBS PMN-HIO-3

text: UNIVERSITY OF MICHIGAN

text: public

text: E-MTAB-11089:PBS PMN-HIO-3

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: intestinal cell

characteristic: cell type

text: coculture with mature neutrophil

characteristic: coculture

text: human

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

text: organoid culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: PBS PMN-HIO-3


E-MTAB-11089:PBS PMN-HIO-4

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-11089:PBS PMN-HIO-4

text: ArrayExpress

text: intestinal cell

text: coculture with mature neutrophil

text: human

text: embryo

text: normal

characteristic: disease

text: organoid culture

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: PBS PMN-HIO-4


text: UNIVERSITY OF MICHIGAN

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: intestinal cell

text: coculture with mature neutrophil

text: human

text: embryo

text: normal

text: organoid culture

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

characteristic: title


E-MTAB-11089:SE PMN-HIO-1

text: UNIVERSITY OF MICHIGAN

text: public

text: E-MTAB-11089:SE PMN-HIO-1

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: intestinal cell

characteristic: cell type

text: coculture with mature neutrophil

characteristic: coculture

text: human

characteristic: common name

text: embryo

text: normal

text: organoid culture

characteristic: infect

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: SE PMN-HIO-1


E-MTAB-11089:SE PMN-HIO-2

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-11089:SE PMN-HIO-2

text: ArrayExpress

text: intestinal cell

text: coculture with mature neutrophil

text: human

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: organoid culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: SE PMN-HIO-2


E-MTAB-11089:SE PMN-HIO-3

text: UNIVERSITY OF MICHIGAN

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11089:SE PMN-HIO-3

characteristic: Submitter Id

text: ArrayExpress

text: intestinal cell

text: coculture with mature neutrophil

text: human

text: embryo

text: normal

text: organoid culture

characteristic: growth condition

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: SE PMN-HIO-3

characteristic: title


E-MTAB-11089:SE PMN-HIO-4

text: UNIVERSITY OF MICHIGAN

text: public

text: E-MTAB-11089:SE PMN-HIO-4

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: intestinal cell

characteristic: cell type

text: coculture with mature neutrophil

characteristic: coculture

text: human

characteristic: common name

text: embryo

text: normal

text: organoid culture

characteristic: infect

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: SE PMN-HIO-4


E-MTAB-11089:STM PMN-HIO-1

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-11089:STM PMN-HIO-1

text: ArrayExpress

text: intestinal cell

text: coculture with mature neutrophil

text: human

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: organoid culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: STM PMN-HIO-1


E-MTAB-11089:STM PMN-HIO-2

text: UNIVERSITY OF MICHIGAN

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11089:STM PMN-HIO-2

characteristic: Submitter Id

text: ArrayExpress

text: intestinal cell

text: coculture with mature neutrophil

text: human

text: embryo

text: normal

text: organoid culture

characteristic: growth condition

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: STM PMN-HIO-2

characteristic: title


E-MTAB-11089:STM PMN-HIO-3

text: UNIVERSITY OF MICHIGAN

text: public

text: E-MTAB-11089:STM PMN-HIO-3

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: intestinal cell

characteristic: cell type

text: coculture with mature neutrophil

characteristic: coculture

text: human

characteristic: common name

text: embryo

text: normal

text: organoid culture

characteristic: infect

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: STM PMN-HIO-3


E-MTAB-11089:STM PMN-HIO-4

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-11089:STM PMN-HIO-4

text: ArrayExpress

text: intestinal cell

text: coculture with mature neutrophil

text: human

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: organoid culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: STM PMN-HIO-4


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-upload-cli

characteristic: Submitter Id

text: human metagenome

characteristic: organism

text: human metagenome

characteristic: title


text: mixed

characteristic: ArrayExpress-SEX

text: Panagrolaimus superbus

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Panagrolaimus superbus

characteristic: common name

text: Mixed

characteristic: gender

text: Panagrolaimus superbus

text: Panagrolaimus superbus

characteristic: subject id


text: mixed

text: Diploscapter coronatus

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: Diploscapter coronatus

text: Mixed

text: Diploscapter coronatus

text: Diploscapter coronatus


text: mixed

text: Caenorhabditis macrosperma

text: SC

characteristic: INSDC center name

text: public

text: Caenorhabditis macrosperma

text: Mixed

text: Caenorhabditis macrosperma

text: Caenorhabditis macrosperma


text: mixed

text: Caenorhabditis virilis

text: SC

characteristic: INSDC first public

text: public

text: Caenorhabditis virilis

text: Mixed

text: Caenorhabditis virilis

text: Caenorhabditis virilis


text: unidentified

text: SC

characteristic: INSDC last update

text: public

text: unidentified

text: unidentified

text: unidentified


text: public

characteristic: INSDC status

tag: Namespace:Klinikum rechts der Isar, II. Medizinische Klinik

text: human

text: HeLa cells treated with DMSO for 1h (replicate 1) (Barcode AAAACT)

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: RNASample


text: Klinikum rechts der Isar, II. Medizinische Klinik

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: HeLa cells treated with DMSO for 1h (replicate 2) (Barcode ATATAG)

text: Homo sapiens

text: Homo sapiens

text: RNASample


text: public

text: human

text: HeLa cells treated with GTPP for 1h (replicate 3) (Barcode CCCACG)

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: RNASample

characteristic: title


text: public

text: human

text: HeLa cells treated with GTPP for 2h (replicate 2) (Barcode CCCCGT)

text: Homo sapiens

text: Homo sapiens

text: RNASample


text: public

text: human

text: HeLa cells treated with GTPP for 3h (replicate 1) (Barcode CCCTGG)

text: Homo sapiens

text: Homo sapiens

text: RNASample


text: public

text: human

text: HeLa cells treated with GTPP for 2h (replicate 3) (Barcode CGTGGG)

text: Homo sapiens

text: Homo sapiens

text: RNASample


text: public

text: human

text: HeLa cells treated with GTPP for 3h (replicate 2) (Barcode CTGCGG)

text: Homo sapiens

text: Homo sapiens

text: RNASample


text: public

text: human

text: HeLa cells treated with GTPP for 1h (replicate 2) (Barcode GCTAGA)

text: Homo sapiens

text: Homo sapiens

text: RNASample


text: public

text: human

text: HeLa cells treated with GTPP for 3h (replicate 3) (Barcode GGCCAC)

text: Homo sapiens

text: Homo sapiens

text: RNASample


text: public

text: human

text: HeLa cells treated with GTPP for 2h (replicate 1) (Barcode GGGATT)

text: Homo sapiens

text: Homo sapiens

text: RNASample


text: public

text: human

text: HeLa cells treated with DMSO for 1h (replicate 3) (Barcode GTTTAT)

text: Homo sapiens

text: Homo sapiens

text: RNASample


text: public

text: human

text: HeLa cells treated with GTPP for 1h (replicate 1) (Barcode TGTTTA)

text: Homo sapiens

text: Homo sapiens

text: RNASample


text: public

text: human

text: Sequence reads not matching to any Barcode

text: Homo sapiens

text: Homo sapiens

text: RNASample


text: public

characteristic: collection date

text: gut

characteristic: environment (biome)

text: gut

characteristic: environment (feature)

text: facel

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

characteristic: investigation type

text: metagenome

characteristic: project name

text: metagenome

text: pyrosequencing

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: gut

text: gut

text: facel

text: China

text: host-associated

text: metagenome

text: metagenome

text: metagenome

text: pyrosequencing


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum

characteristic: subject id

characteristic: title


text: public

tag: Namespace:Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Italy

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Protocols: Three leaves from each of 3 plants grown in the following experimental conditions were sampled and analyzed for F0 and F1 generation: 2.5 µM Cr (T1 (1 week) and T2 (3 weeks)); 5 µM Cr (T1 and T2), control (T1 and T2). Seeds of A. thaliana cv Col-0 were sown on peat Jyffy discs and kept in the dark at room temperature for three days. When plants reached 2 cm of total length, they were transferred in soil for 15 days and then in hydroponic culture (one plant per 500-mL pot containing Hoagland solution, (Hoagland & Arnon, 1950)) in a growth chamber (25°C for 16 hours of light at 120 µmol m-2s-1 and 22°C for 8 hours of dark, 60% of relative humidity). Plants were maintained one week in acclimation before the application of the stress. Chromium treatments (Cr(VI) supplied as K2Cr2O7) were the following: 1) 2.5 µM Cr (VI) until harvest after nine weeks of growth (chronic stress) and 5 µM Cr (VI) for three weeks and then recovering in Cr-free Hoagland solution until harvest. Five plants (biological replicates) were used for each of these stress conditions in addition to five control plants (grown in Hoagland in absence of Cr stress). Leaves were immediately frozen in liquid nitrogen and stored at -80 °C. RNA extraction was performed using 100 mg of leaves grounded with mortar and pestle in liquid nitrogen. The protocol of RNeasy Plant Mini kit (Qiagen) was followed and final elutions were performed using 50 µl of RNase-free water. Eighteen sequencing libraries were obtained following the procedure of Truseq Stranded mRNA Library Prep (Illumina) and using Truseq RNA Single Indexes.

characteristic: description

text: rosette growth stage

characteristic: developmental stage

characteristic: ecotype

characteristic: generation

text: wild type genotype

characteristic: genotype

text: pool of 3 leaves from 3 plants

characteristic: individual

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: leaf

characteristic: organism part

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Italy

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: thale cress

text: rosette growth stage

text: wild type genotype

text: pool of 3 leaves from 3 plants

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: leaf

text: Arabidopsis thaliana


E-MTAB-11119:Dengue virus mutant

text: Duke-NUS Medical School

text: public

characteristic: SRA accession

text: E-MTAB-11119:Dengue virus mutant

tag: Namespace:Duke-NUS Medical School

characteristic: Submitter Id

text: ArrayExpress

characteristic: cell line

text: hepatocyte

characteristic: cell type

text: human

characteristic: common name

text: Protocols: A pool of CRISPR mutagenized cells resisting a dengue virus mutant cytolytic infection was harvested from a live-dead genetic screen. 2 million resistant cells were harvested from each sub-library, and subjected to total genomic DNA extraction using DNA mini kit (Qiagen) according to the manufacturerвЂ™s instructions The sgRNA were amplified from gDNA in two-step PCR using Herculase II Fusion DNA Polymerase (Agilent). For first PCR, 20 ug of gDNA for each library was amplified for 16 cycles. For 2nd PCR, 1 reaction containing 5ul PCR product for each sub-library was amplified for 27 cycles, using Illumina indexed primers. PCR products were gel purified (Qiagen gel purification kit) and sequenced on Illumina MiSeq platform.

text: adult

text: hepatocellular carcinoma

characteristic: disease

text: genome-wide CRISPR KO library under phenotypic selection

characteristic: genetic modification

text: wild type genotype

text: Dengue virus mutant

characteristic: infect

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: Homo sapiens

text: male

characteristic: sex

text: Dengue virus mutant

characteristic: title


text: Laxus oneistus

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Laxus oneistus

text: Laxus oneistus

text: Laxus oneistus

characteristic: subject id


text: male

characteristic: ArrayExpress-SEX

text: Heligmosomoides bakeri

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Heligmosomoides bakeri

text: Male

characteristic: gender

text: Heligmosomoides polygyrus bakeri

text: Heligmosomoides polygyrus bakeri


text: male

text: Heligmosomoides polygyrus

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Heligmosomoides polygyrus

characteristic: common name

text: Male

text: Heligmosomoides polygyrus polygyrus

text: Heligmosomoides polygyrus polygyrus