E-MTAB-11914:DAOY wt empty vector

text: public

characteristic: SRA accession

text: E-MTAB-11914:DAOY wt empty vector

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Daoy

text: human

text: juvenile stage

text: desmoplastic/nodular medulloblastoma

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: posterior cranial fossa

text: Homo sapiens

text: DAOY wt empty vector

characteristic: title


E-MTAB-11914:USP13 wt empty vector

status: PUBLIC

tag: attribute

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: E-MTAB-11914:USP13 wt empty vector

tag: Namespace:European Research Institute for the Biology of Ageing University Medical Center Groningen

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: Half a million cells were plated on six well plates. After 48 hours, cells were harvested using Tryple. Pelleted cells were washed with 1xPBS before being stored as dry pellets at -80 degree Celsius. For whole transcriptome analysis, RNA was isolated using the RNeasy mini kit (Qiagen) in accordance to manufacturer's protocol and RNA quality was examined using the Agilent 2100 Bioanalyzer (Agilent Technologies). 250-500 ng of total RNA was used as input for mRNA enrichment using NEXTflex Poly(A) Beads (Bio Scientific) followed by library preparation using a NEXTflex Rapid Directional qRNA-Seq Kit (Bio Scientific).

characteristic: description

text: juvenile stage

characteristic: developmental stage

text: medulloblastoma

characteristic: disease

text: wild type genotype

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: mixed brain and cerebellum

characteristic: organism part

text: Homo sapiens

text: USP13 wt empty vector


E-MTAB-11920:Sample 1

text: public

characteristic: SRA accession

text: E-MTAB-11920:Sample 1

tag: Namespace:Department of Cell and Molecular Biology Karolinska Institutet

characteristic: Submitter Id

text: embryonic day 12.5

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Dorsal skin of mouse embryos (C57BL/6J - E12.5, E13.5, and E14.5) was dissected with the help of fine dissection tools and dissected skins were incubated in Dispase II (2mg/ml), Collagenase IA (0.2%), and DNAse I (20U/ul) in PBS for 40 minutes at 37°C in ultra-low attachment plates (Corning Costar) on an orbital shaker. The obtained cell suspension was passed through a 40 mm cell strainer. The flow-through was spun down, and subsequently resuspended in PBS + 0.04% BSA. Samples were transported to core facility in PBS + 0.04% BSA in Eppendorf tubes that had been coated with PBS + 20% BSA overnight. Viability of the cell suspension was determined using trypan blue on an EVE automatic cell counter. Nucleic acid extraction was performed using the 10X Genomics Chromium Single Cell 3’ kit v2 according to the manufacturer’s instruction. Single-cell cDNA libraries were prepared using the 10X Genomics Chromium Single Cell 3’ kit v2 according to the manufacturer’s instruction.

text: embryo

text: normal

text: wild type genotype

characteristic: id at core facility

text: E12.5 Replicate 1

characteristic: individual

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: dorsal skin

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

text: Sample 1


E-MTAB-11920:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Cell and Molecular Biology Karolinska Institutet

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11920:Sample 2

text: embryonic day 12.5

text: ArrayExpress

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: E12.5 Replicate 2

text: not applicable

text: Mus musculus

text: Mus musculus

text: dorsal skin

text: Mus musculus

text: female

text: Sample 2

characteristic: title


E-MTAB-11920:Sample 3

text: public

characteristic: SRA accession

text: E-MTAB-11920:Sample 3

characteristic: Submitter Id

text: embryonic day 14.5

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: E14.5 Replicate 1

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: dorsal skin

characteristic: organism part

text: Mus musculus

text: male

text: Sample 3


E-MTAB-11920:Sample 4

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11920:Sample 4

text: embryonic day 14.5

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: embryo

text: normal

text: wild type genotype

characteristic: id at core facility

text: E14.5 Replicate 2

characteristic: individual

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: dorsal skin

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: Sample 4


E-MTAB-11920:Sample 8

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11920:Sample 8

characteristic: Submitter Id

text: embryonic day 13.5

text: ArrayExpress

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: E13.5 Replicate 1

text: not applicable

text: Mus musculus

text: Mus musculus

text: dorsal skin

text: Mus musculus

text: male

text: Sample 8

characteristic: title


E-MTAB-11920:Sample 9

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11920:Sample 9

text: embryonic day 13.5

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: E13.5 Replicate 2

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: dorsal skin

characteristic: organism part

text: Mus musculus

text: male

text: Sample 9


E-MTAB-11920:Sample 5

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11920:Sample 5

text: embryonic day 12.5

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: embryo

text: normal

text: wild type genotype

characteristic: id at core facility

text: E12.5 Replicate 3

characteristic: individual

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: dorsal skin

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

text: Sample 5


E-MTAB-11920:Sample 6

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11920:Sample 6

characteristic: Submitter Id

text: embryonic day 12.5

text: ArrayExpress

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: E12.5 Replicate 4

text: not applicable

text: Mus musculus

text: Mus musculus

text: dorsal skin

text: Mus musculus

text: female

text: Sample 6

characteristic: title


E-MTAB-11920:Sample 7

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11920:Sample 7

text: embryonic day 12.5

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: E12.5 Replicate 5

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: dorsal skin

characteristic: organism part

text: Mus musculus

text: female

text: Sample 7


E-MTAB-11920:Sample 10

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11920:Sample 10

text: embryonic day 13.5

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: embryo

text: normal

text: wild type genotype

characteristic: id at core facility

text: E13.5 Replicate 3

characteristic: individual

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: dorsal skin

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

text: Sample 10


E-MTAB-11920:Sample 11

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11920:Sample 11

characteristic: Submitter Id

text: embryonic day 13.5

text: ArrayExpress

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: E13.5 Replicate 4

text: not applicable

text: Mus musculus

text: Mus musculus

text: dorsal skin

text: Mus musculus

text: female

text: Sample 11

characteristic: title


E-MTAB-11920:Sample 12

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11920:Sample 12

text: embryonic day 13.5

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: E13.5 Replicate 5

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: dorsal skin

characteristic: organism part

text: Mus musculus

text: male

text: Sample 12


E-MTAB-11920:Sample 13

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11920:Sample 13

text: embryonic day 14.5

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: embryo

text: normal

text: wild type genotype

characteristic: id at core facility

text: E14.5 Replicate 3

characteristic: individual

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: dorsal skin

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

text: Sample 13


E-MTAB-11920:Sample 14

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11920:Sample 14

characteristic: Submitter Id

text: embryonic day 14.5

text: ArrayExpress

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: E14.5 Replicate 4

text: not applicable

text: Mus musculus

text: Mus musculus

text: dorsal skin

text: Mus musculus

text: male

text: Sample 14

characteristic: title


E-MTAB-11920:Sample 15

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11920:Sample 15

text: embryonic day 14.5

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: E14.5 Replicate 5

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: dorsal skin

characteristic: organism part

text: Mus musculus

text: male

text: Sample 15


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MURDOCH UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-07-2022-05:46:48:335-103659

tag: Namespace:MURDOCH UNIVERSITY

characteristic: collection date

text: Ground water without treatment recovered in BHI

text: Entic Haplustolls

characteristic: environment (biome)

text: groundwater

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Colombia

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: original sample recovered in BHI (No treatment applied)

characteristic: isolation and growth condition

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: groundwater metagenome

characteristic: organism

text: Groundwater and surfacewater disinfection processes

characteristic: project name

text: groundwater metagenome

text: Illumina

characteristic: sequencing method

text: GWNT


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MURDOCH UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-08-07-2022-05:46:48:335-103660

characteristic: Submitter Id

text: Ground water with chlorination treatment recovered in BHI

characteristic: description

text: Entic Haplustolls

text: groundwater

text: water

text: Colombia

text: mimarks-survey

text: recovered in BHI after chlorination

text: groundwater metagenome

text: groundwater metagenome

text: Illumina

text: GWCl

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MURDOCH UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-07-2022-05:46:48:336-103661

characteristic: collection date

text: Ground water with photo Fenton treatment recovered in BHI

text: Entic Haplustolls

characteristic: environment (biome)

text: groundwater

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Colombia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

text: recovered in BHI after photo Fenton

text: groundwater metagenome

text: groundwater metagenome

text: Illumina

text: GWPF


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MURDOCH UNIVERSITY

characteristic: INSDC center name

text: public

text: ena-SAMPLE-TAB-08-07-2022-05:46:48:336-103662

text: Ground water with UVC treatment recovered in BHI

text: Entic Haplustolls

text: groundwater

text: water

text: Colombia

text: mimarks-survey

characteristic: investigation type

text: recovered in BHI after UVC

characteristic: isolation and growth condition

characteristic: miscellaneous environmental package

text: groundwater metagenome

characteristic: organism

characteristic: project name

text: groundwater metagenome

text: Illumina

characteristic: sequencing method

text: GWUVC


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MURDOCH UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-08-07-2022-05:46:48:336-103663

characteristic: Submitter Id

text: Ground water with ozonation treatment recovered in BHI

characteristic: description

text: Entic Haplustolls

text: groundwater

text: water

text: Colombia

text: mimarks-survey

text: recovered in BHI after ozonation

text: groundwater metagenome

text: groundwater metagenome

text: Illumina

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MURDOCH UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-07-2022-05:46:48:336-103664

characteristic: collection date

text: Surface water without treatment recovered in BHI

text: Entic Haplustolls

characteristic: environment (biome)

text: surface water

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Colombia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

text: freshwater metagenome

text: freshwater metagenome

text: Illumina

text: SWNT


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MURDOCH UNIVERSITY

characteristic: INSDC center name

text: public

text: ena-SAMPLE-TAB-08-07-2022-05:46:48:336-103665

text: Surface water with chlorination treatment recovered in BHI

text: Entic Haplustolls

text: surface water

text: water

text: Colombia

text: mimarks-survey

characteristic: investigation type

text: recovered in BHI after chlorination

characteristic: isolation and growth condition

characteristic: miscellaneous environmental package

text: freshwater metagenome

characteristic: organism

characteristic: project name

text: freshwater metagenome

text: Illumina

characteristic: sequencing method

text: SWCl


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MURDOCH UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-08-07-2022-05:46:48:336-103666

characteristic: Submitter Id

text: Surface water with UVC treatment recovered in BHI

characteristic: description

text: Entic Haplustolls

text: surface water

text: water

text: Colombia

text: mimarks-survey

text: recovered in BHI after UVC

text: freshwater metagenome

text: freshwater metagenome

text: Illumina

text: SWUVC

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MURDOCH UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-07-2022-05:46:48:336-103667

characteristic: collection date

text: Surface water with ozonation treatment recovered in BHI

text: Entic Haplustolls

characteristic: environment (biome)

text: surface water

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Colombia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

text: recovered in BHI after ozonation

text: freshwater metagenome

text: freshwater metagenome

text: Illumina


text: foot muscle

characteristic: ArrayExpress-PHENOTYPE

text: unknown

characteristic: ArrayExpress-SEX

text: Phorcus lineatus

characteristic: ArrayExpress-SPECIES

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Unknown

characteristic: GENDER

text: SC

characteristic: INSDC center name

text: public

text: foot muscle

characteristic: PHENOTYPE

text: Phorcus lineatus

characteristic: common name

text: Phorcus lineatus

characteristic: organism

text: Phorcus lineatus


text: intestinal crypts

text: unknown

text: Mus musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Unknown

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: intestinal crypts

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus

characteristic: title


text: Skeletal muscle

characteristic: ArrayExpress-PHENOTYPE

text: unknown

characteristic: ArrayExpress-SEX

text: Mus musculus

text: Unknown

text: SC

text: public

text: Skeletal muscle

text: house mouse

text: Mus musculus

text: Mus musculus


text: Liver

text: unknown

text: Mus musculus

characteristic: ArrayExpress-SPECIES

characteristic: ENA-LAST-UPDATE

text: Unknown

text: SC

text: public

text: Liver

text: house mouse

text: Mus musculus

text: Mus musculus


text: Pancreas -acini

text: unknown

text: Mus musculus

characteristic: External Id

text: Unknown

characteristic: GENDER

text: SC

text: public

text: Pancreas -acini

text: house mouse

text: Mus musculus

text: Mus musculus


text: Pancreas -islets

text: unknown

text: Mus musculus

text: Unknown

text: SC

characteristic: INSDC center name

text: public

text: Pancreas -islets

characteristic: PHENOTYPE

text: house mouse

text: Mus musculus

text: Mus musculus


text: Large intestine crypt

text: unknown

text: Mus musculus

text: Unknown

text: SC

text: public

text: Large intestine crypt

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus


text: Heart

text: unknown

text: Mus musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Unknown

text: SC

text: public

text: Heart

text: house mouse

text: Mus musculus

text: Mus musculus


text: Kidney-glomeruli

text: unknown

text: Mus musculus

text: Unknown

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Kidney-glomeruli

text: house mouse

text: Mus musculus

text: Mus musculus


text: Kidney-exterior tubules

text: unknown

text: Mus musculus

text: Unknown

text: SC

text: public

characteristic: INSDC status

text: Kidney-exterior tubules

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

tag: Namespace:Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Protocols: M. pneumoniae cell cultures were grown in Haylick rich medium as previously described (Yus et al., 2009). Briefly, M. pneumoniae strains were grown per duplicate in tissue culture flasks containing 5 ml of Hayflick medium supplemented with 20 µg/ml of chloramphenicol. After 48h of culture at 37°C under 5% CO2, the culture medium was changed with fresh one, and the cells further incubated for 6h prior RNA extraction. Cells were washed with PBSx1 and lysed immediately with 700μl Qiazol (Qiagen). RNA was isolated using the miRNeasy kit (Qiagen) following the manufacturer’s instructions, including the in-column DNase I treatment. The quality of RNA (amount and integrity) was assessed using a BioAnalyzer (Agilent). Eight to ten micrograms of Total RNA were loaded on a 15% denaturing urea polyacrylamide gel (EC6885BOX, Thermo Scientific) and RNA fragments of 60 to 100nt were selected. They were then subjected to limited alkaline hydrolysis, followed by dephosphorylation using Antarctic phosphatase (M0289, New England Biolabs) and rephosphorylation using PNK (M0201, New England Biolabs). RNA-seq libraries were prepared at the CRG ultrasequencing facility. Briefly, 3 prime and 5 prime adapters were ligated to the RNA fragments, and these were subsequently reverse transcribed and amplified by PCR, where different indexed primers were used to allow multiplexed sequencing. Final libraries were analyzed using Agilent High Sensitivity chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to amplification with Illumina's cBot.

characteristic: description

text: not applicable

characteristic: isolate

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

characteristic: replicate

text: Mycoplasma pneumoniae M129

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology

text: public

text: ArrayExpress

text: not applicable

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


characteristic: INSDC center name

text: public

text: ArrayExpress

text: Protocols: M. pneumoniae cell cultures were grown in Haylick rich medium as previously described (Yus et al., 2009) for 72h, split into biological duplicates and grown for 6h (exponential phase, standard conditions). In order to block ribosomes at the initiation stage, cells were treated with 40μg/ml of tetracycline during 1 min before lysis. Except for tetracycline-treated samples, cells were treated during 1 min with chloramphenicol at 100 μg/ml final concentration in order to stop translation. After treatment cell media was removed and cells were harvested by scraping and centrifuged at 8000g during 5 min in a 2 ml tube. Supernatant was discarded and cell pellet was resuspended in 1.5ml of lysis buffer, once pellet was resuspended lysis pressure was applied using a prechilled 4639 Cell Disruption Vessel (two passes). The cell lysate was centrifuged in a cooled desktop centrifuge at 16000g for 13 min and the supernatant was frozen into liquid nitrogen for further procedures. In order to block ribosomes at the initiation stage, cells were treated with 40μg/ml of tetracycline during 1 min before lysis. Except for tetracycline-treated samples, cells were treated during 1 min with chloramphenicol at 100 μg/ml final concentration in order to stop translation. In order to get ribosome footprints, a controlled digestion with MNase was performed as described in (Becker et al., 2013). Digestion reaction was stopped with EGTA. With the purpose of isolating ribosomes, a sucrose cushion was performed. We loaded the supernatant lysate onto 45 ml of 25% (for E. coli cells) or 15% (for Mpn cells) sucrose cushion buffer and ultracentrifuged the samples at 45000 rpm during 4h and 30 min at 4 C in a TI-45 rotor Beckman. The cushion buffer was removed carefully with a vacuum system and the pellet resuspended with 200μl of wash buffer. Finally 900μl of Trizol was added in order to perform RNA extraction (manufacture instructions). Once the RNA was purified, we isolated the footprints following the steps described in (Becker et al., 2013) in supplementary methods, page 6, sections “Size selection of the footprint fragments” and “Dephosphorylation”. The RNA-seq libraries were prepared at the CRG Genomics Unit using the TruSeq stranded mRNA Library Prep kit (96 samples ref. 20020595 or 48 samples ref. 20020594) according to the manufacturer's protocol, without the initial polyA selection, to convert total RNA into a library of template molecules of known strand origin and suitable for subsequent cluster generation and DNA sequencing. Briefly, 100 ng of total RNA were fragmented under elevated temperature and primed with random hexamers for cDNA synthesis. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and random primers. After that, second strand cDNA was synthesized, removing the RNA template and synthesizing a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA using DNA Polymerase I and RNase H. To these cDNA fragments, a single 'A' base was added to the 3’ends to prevent self-ligation during the adapter addition. A corresponding single T nucleotide on the 3’ end of the adapter provides a complementary overhang for ligating the adapter to the fragments. Subsequent ligation of the multiple indexing adapter to the ends of the ds cDNA was done. Finally, PCR selectively enriched those DNA fragments that had adapter molecules on both ends. The PCR was performed with a PCR Primer Cocktail that anneals to the ends of the adapters. Final libraries were analyzed using Bioanalyzer DNA 1000 or Fragment Analyzer Standard Sensitivity (ref: 5067-1504 or ref: DNF-473, Agilent) to estimate the quantity and validate the size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (REF. 07960204001, Roche) prior to the amplification with Illumina’s cBot.

text: total RNA

characteristic: fraction

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: Escherichia coli K-12


text: public

text: ArrayExpress

text: Protocols: M. pneumoniae cell cultures were grown in Haylick rich medium as previously described (Yus et al., 2009) for 72h, split into biological duplicates and grown for 6h (exponential phase, standard conditions). In order to block ribosomes at the initiation stage, cells were treated with 40μg/ml of tetracycline during 1 min before lysis. Except for tetracycline-treated samples, cells were treated during 1 min with chloramphenicol at 100 μg/ml final concentration in order to stop translation. After treatment cell media was removed and cells were harvested by scraping and centrifuged at 8000g during 5 min in a 2 ml tube. Supernatant was discarded and cell pellet was resuspended in 1.5ml of lysis buffer, once pellet was resuspended lysis pressure was applied using a prechilled 4639 Cell Disruption Vessel (two passes). The cell lysate was centrifuged in a cooled desktop centrifuge at 16000g for 13 min and the supernatant was frozen into liquid nitrogen for further procedures. In order to block ribosomes at the initiation stage, cells were treated with 40μg/ml of tetracycline during 1 min before lysis. Except for tetracycline-treated samples, cells were treated during 1 min with chloramphenicol at 100 μg/ml final concentration in order to stop translation. In order to get ribosome footprints, a controlled digestion with MNase was performed as described in (Becker et al., 2013). Digestion reaction was stopped with EGTA. With the purpose of isolating ribosomes, a sucrose cushion was performed. We loaded the supernatant lysate onto 45 ml of 25% (for E. coli cells) or 15% (for Mpn cells) sucrose cushion buffer and ultracentrifuged the samples at 45000 rpm during 4h and 30 min at 4 C in a TI-45 rotor Beckman. The cushion buffer was removed carefully with a vacuum system and the pellet resuspended with 200μl of wash buffer. Finally 900μl of Trizol was added in order to perform RNA extraction (manufacture instructions). Once the RNA was purified, we isolated the footprints following the steps described in (Becker et al., 2013) in supplementary methods, page 6, sections “Size selection of the footprint fragments” and “Dephosphorylation”. Libraries were prepared using the NEBNext® Small RNA Library Prep Set for Illumina® kit (ref. E7330) according to the manufacturer's protocol. Briefly, 50ng of RNA were subjected to adaptor ligation at 3´and 5´ and first strand cDNA synthesis. After that, PCR selectively enriched those DNA fragments that had adapter molecules on both ends. Library amplification was performed by PCR using NEBNext® Multiplex Oligos for Illumina (Index Primers Set 1, ref. E7335). All purification steps were performed using AgenCourt AMPure XP beads (ref. A63882, Beckman Coulter). Final libraries were analyzed using Agilent Bioanalyzer (ref. 5067-4626) to estimate the quantity and check size distribution. Libraries were quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to amplification with Illumina's cBot.

text: ribosome footprints

text: not applicable

text: Escherichia coli K-12

characteristic: organism

text: Escherichia coli K-12

text: Escherichia coli K-12


characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-11935:MPN_RP10_P2_Tet_FP_15166_GATCAG

text: ArrayExpress

text: ribosome footprints

text: not applicable

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11935:MPN_RP10_S1_Tet_15114_CTTGTA

text: ArrayExpress

text: total RNA

text: not applicable

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


characteristic: INSDC first public

text: public

text: ArrayExpress

text: total RNA

text: not applicable

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


characteristic: INSDC last update

text: public

text: ArrayExpress

text: ribosome footprints

text: not applicable

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

characteristic: INSDC status

tag: Namespace:Statens Serum Institut and the Danish Covid19 Genome Consortium (DCGC)

text: Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Sjaelland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

characteristic: host description

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

text: Severe acute respiratory syndrome coronavirus 2

text: active surveillance in response to outbreak

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Statens Serum Institut and the Danish Covid19 Genome Consortium (DCGC)

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Danish Covid-19 Genome Consortium

text: Original

characteristic: description

text: Denmark

text: Syddanmark

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Sjaelland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Hovedstaden

text: Human

characteristic: host description

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: sample capture status


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Danish Covid-19 Genome Consortium

text: Original

characteristic: description

text: Denmark

text: Midtjylland

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Nordjylland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Hovedstaden

text: Human

text: n_infections=2,last_infection_date=2021-11-29

characteristic: host description

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Danish Covid-19 Genome Consortium

text: Original

characteristic: description

text: Denmark

text: Hovedstaden

text: Human

text: n_infections=2,last_infection_date=2022-01-24

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Syddanmark

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-271599/2021

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Hovedstaden

text: Human

text: n_infections=2,last_infection_date=2021-12-06

characteristic: host description

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: sample capture status


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Danish Covid-19 Genome Consortium

text: Original

characteristic: description

text: Denmark

text: Syddanmark

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-242851/2021

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Syddanmark

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Hovedstaden

text: Human

text: n_infections=2,last_infection_date=2021-12-27

characteristic: host description

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Danish Covid-19 Genome Consortium

text: Original

characteristic: description

text: Denmark

text: Midtjylland

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Sjaelland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-83005/2021

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Sjaelland

text: Human

text: n_infections=2,last_infection_date=2022-01-10

characteristic: host description

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: sample capture status


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Danish Covid-19 Genome Consortium

text: Original

characteristic: description

text: Denmark

text: Nordjylland

text: Human

text: n_infections=2,last_infection_date=2020-12-28

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Syddanmark

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Midtjylland

text: Human

text: n_infections=2,last_infection_date=2022-01-31

characteristic: host description

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Danish Covid-19 Genome Consortium

text: Original

characteristic: description

text: Denmark

text: Sjaelland

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Syddanmark

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Midtjylland

text: Human

characteristic: host description

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: sample capture status


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Danish Covid-19 Genome Consortium

text: Original

characteristic: description

text: Denmark

text: Hovedstaden

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Hovedstaden

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_date=2022-02-14

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Hovedstaden

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-46671/2020

characteristic: host description

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Danish Covid-19 Genome Consortium

text: Original

characteristic: description

text: Denmark

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Midtjylland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-150092/2021

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Hovedstaden

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-213533/2021

characteristic: host description

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: sample capture status


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Danish Covid-19 Genome Consortium

text: Original

characteristic: description

text: Denmark

text: Midtjylland

text: Human

text: n_infections=2,last_infection_date=2022-02-07

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

text: active surveillance in response to outbreak

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Statens Serum Institut and the Danish Covid19 Genome Consortium (DCGC)

characteristic: INSDC center name

text: public

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Hovedstaden

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-187394/2021

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Hovedstaden

text: Human

characteristic: host description

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Danish Covid-19 Genome Consortium

text: Original

characteristic: description

text: Denmark

text: Hovedstaden

text: Human

text: n_infections=2,last_infection_date=2021-11-22

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Midtjylland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_date=2020-11-30

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


E-MTAB-11900:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LabMedMolGe

characteristic: INSDC center name

text: public

text: E-MTAB-11900:Sample 1

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: human

characteristic: common name

text: Protocols: Kidney cancer line (A498, ATCC) were cultured in Dulbecco modified Eagle’s medium, containing 10% fetal bovin serum in an atmosphere of 5% CO2. Human Kidney Carcinoma Cell Line (A498, and A498 over-expressing praja2 WT or praja2RM under a tetracycline-inducible promoter), were maintained in DMEM medium (Gibco) supplemented with 10% Fetal Bovine Serum, NCS (Sigma-Aldrich), 1% L-glutamine, 1% penicillin/ Sigma-Aldrich). Inducible lentiviral vectors, were generated using the In-Fusion® HD Cloning Kit technology. praja2 CDSs were amplified by PCR using Origene plasmids vectors as template, and cloned in PCW57.1 vector (Addgene #41393) digested Bam HI. A498 cells were transfected by calcium-phosphate, using a DNA mix containing plasmid for over-expression (12 µg) harboring or not praja2 CDSs and psPAX2 (Addgene #12260) (18 µg) and pMD2.G (Addgene #12259) (13 µg) as packaging vectors. Forty-eight hours post-transfection, cell supernatants were collected, filtered through a 0.45 µM filter, and 10 µg/mL of polybrene (Merk) was added. A498 cell media was then replaced with infective media, and cells were incubated for 6 h. Later, the infective cell medium was replaced with normal medium and, after an additional 24 h, 1 µg/mL of puromycin was added to start selection. The day after the transfection, cells were induced (using 1 µg/ml of doxycycline for 72h) or not, then cells were collected and lysed for Western blotting analysis. RNA purity and integrity were assessed with a Nanodrop 2000c spectrophotometer (ThermoFisher Scientific, Waltham, MA, USA) and a 4200 TapeStation instrument (Agilent Technologies, Santa Clara, CA, USA), respectively. For RNA purity, an A260/280 ratio of 2.0 and an A260/230 ratio of 2.0-2.2 were considered acceptable; for RNA integrity, an RNA Integrity Number (RIN) of 9.0-10.0 has been obtained for all samples, indicating the absence of degradation and high integrity of RNA samples. For a precise estimation of the RNA concentration, a Qubit 2.0 fluorometer assay (Thermo Fisher Scientific, Waltham, MA, USA) has been employed. For RNA sequencing, 1mg of high-quality total RNA was used for library preparation with a TruSeq Stranded Total RNA Sample Prep Kit (Illumina, San Diego, CA, USA)

text: adult

characteristic: developmental stage

text: carcinoma

characteristic: disease

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: praja2 overexpression

characteristic: phenotype

text: Homo sapiens

text: female

characteristic: sex

text: Sample 1


E-MTAB-11900:Sample 2

characteristic: ENA-FIRST-PUBLIC

text: LabMedMolGe

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11900:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: epithelial cell

text: human

characteristic: description

text: adult

text: carcinoma

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: praja2 overexpression

text: Homo sapiens

text: female

text: Sample 2

characteristic: title


E-MTAB-11900:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LabMedMolGe

characteristic: INSDC center name

text: public

text: E-MTAB-11900:Sample 3

characteristic: age

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: human

characteristic: common name

text: adult

text: carcinoma

text: overexpressing praja2 WT

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: praja2 overexpression

text: Homo sapiens

text: female

text: Sample 3


E-MTAB-11900:Sample 4

characteristic: ENA-FIRST-PUBLIC

text: LabMedMolGe

text: public

text: E-MTAB-11900:Sample 4

text: ArrayExpress

text: epithelial cell

text: human

text: adult

characteristic: developmental stage

text: carcinoma

characteristic: disease

text: overexpressing praja2 WT

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: praja2 overexpression

characteristic: phenotype

text: Homo sapiens

text: female

characteristic: sex

text: Sample 4


E-MTAB-11900:Sample 5

text: LabMedMolGe

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11900:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: epithelial cell

text: human

characteristic: description

text: adult

text: carcinoma

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: kidney

text: praja2 overexpression

text: Homo sapiens

text: female

text: Sample 5


E-MTAB-11900:Sample 6

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LabMedMolGe

characteristic: INSDC center name

text: public

text: E-MTAB-11900:Sample 6

characteristic: age

text: ArrayExpress

text: epithelial cell

text: human

text: adult

text: carcinoma

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: praja2 overexpression

text: Homo sapiens

text: female

text: Sample 6

characteristic: title


E-MTAB-11900:Sample 7

characteristic: ENA-FIRST-PUBLIC

text: LabMedMolGe

text: public

text: E-MTAB-11900:Sample 7

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: carcinoma

characteristic: disease

text: overexpressing praja2 WT

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: praja2 overexpression

text: Homo sapiens

text: female

text: Sample 7


E-MTAB-11900:Sample 8

text: LabMedMolGe

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11900:Sample 8

characteristic: Submitter Id

text: ArrayExpress

text: epithelial cell

text: human

text: adult

text: carcinoma

text: overexpressing praja2 WT

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: praja2 overexpression

characteristic: phenotype

text: Homo sapiens

text: female

characteristic: sex

text: Sample 8


text: human metagenome

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: human metagenome

text: human metagenome

text: human metagenome


text: Escherichia coli

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Escherichia coli

characteristic: common name

text: Escherichia coli

characteristic: organism

text: Escherichia coli

characteristic: title


text: mixed

characteristic: ArrayExpress-SEX

text: Panagrolaimus superbus

text: Mixed

characteristic: GENDER

text: SC

text: public

text: Panagrolaimus superbus

text: Panagrolaimus superbus

text: Panagrolaimus superbus


text: mixed

text: Panagrolaimus detritophagus

text: Mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Panagrolaimus detritophagus

text: Panagrolaimus detritophagus

text: Panagrolaimus detritophagus


text: Academisch Medical Center

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Academisch Medical Center

text: Soil sample from Nigeria

characteristic: description

text: Nigeria

characteristic: geographic location (country and/or sea)

text: Burkholderia thailandensis

text: Burkholderia thailandensis

text: B. thailendensis BthF1


text: Academisch Medical Center

text: public

characteristic: Submitter Id

text: Soil sample from Nigeria

text: Nigeria

text: Burkholderia pseudomallei

text: Burkholderia pseudomallei

text: B. pseudomallei BpsH3


characteristic: ENA-CHECKLIST

text: Academisch Medical Center

text: public

text: Soil sample from Nigeria

text: Nigeria

text: Burkholderia pseudomallei

text: Burkholderia pseudomallei

text: B. pseudomallei BpsF1


characteristic: ENA-LAST-UPDATE

text: Academisch Medical Center

text: public

text: Soil sample from Nigeria

text: Nigeria

text: Burkholderia thailandensis

text: Burkholderia thailandensis

text: B. thailandensis BthE1


characteristic: External Id

text: Academisch Medical Center

text: public

text: Soil sample from Nigeria

text: Nigeria

text: Burkholderia pseudomallei

text: Burkholderia pseudomallei

text: B. pseudomallei BpsH1


text: Academisch Medical Center

characteristic: INSDC center name

text: public

text: Soil sample from Nigeria

text: Nigeria

text: Burkholderia pseudomallei

text: Burkholderia pseudomallei

text: B. pseudomallei BpsC1


characteristic: ENA-FIRST-PUBLIC

text: Academisch Medical Center

text: public

text: Soil sample from Nigeria

text: Nigeria

text: Burkholderia pseudomallei

text: Burkholderia pseudomallei

text: B. pseudomallei BpsG1


text: Academisch Medical Center

text: public

text: Soil sample from Nigeria

text: Nigeria

text: Burkholderia pseudomallei

text: Burkholderia pseudomallei

text: B. pseudomallei BpsF2


text: Academisch Medical Center

text: public

text: Soil sample from Nigeria

text: Nigeria

text: Burkholderia pseudomallei

text: Burkholderia pseudomallei

text: B. pseudomallei BpsH2


text: Academisch Medical Center

text: public

text: Soil sample from Nigeria

text: Nigeria

text: Burkholderia pseudomallei

text: Burkholderia pseudomallei

text: B. pseudomallei BpsC2


text: Academisch Medical Center

text: public

text: Soil sample from Nigeria

text: Nigeria

text: Burkholderia thailandensis

text: Burkholderia thailandensis

text: B. thailandensis BthD1


text: Academisch Medical Center

text: public

text: Soil sample from Nigeria

text: Nigeria

text: Burkholderia pseudomallei

text: Burkholderia pseudomallei

text: B. pseudomallei BpsF3


text: EMBL

text: public

text: 2 to 3

unit: hour

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: Protocols: Adult flies from specific genotypes were placed in medium-sized cages. After three 1 h pre-lays, a 1 h embryo laying was allowed on apple juice agar plates with yeast paste. 2 hours later, embryos were immediately dechorionated using 50% bleach transferred to a 1.5ml tube containing ice-cold PBTr (PBS + 0.1 % TritonX-100). Embryos at NC14 were then manually selected under a stereoscope based on morphological features. 100 embryos per replicate were selected and transferred to a new 1.5ml tube. The PBTr was removed by pipetting, and the embryos were snap-frozen in liquid nitrogen. Fly embryos were homogenised in TRI Reagent (Sigma-Aldrich) using pestles and a cordless motor for pellet mixing and total RNA extraction was performed according to the manufacturer's instructions. Remaining DNA was digested using RNase-free DNase I (Roche), followed by a clean up using the Agencourt RNAClean XP kit (Beckman Coulter) according to the manufacturer's protocol. Poly(A) mRNA isolation and fragmentation were performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer's instruction manual E7420, Chapter 1. 1 �g total RNA was used as starting material and the protocol optimised for 200 bp RNA inserts was followed. RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina according to the manufacturer's instruction manual E7420, Chapter 1. For library enrichment, 12 PCR cycles were used. Indexed RNA-seq libraries were pooled in an equimolar ratio and paired-end sequenced with a read length of 75 bp on an Illumina NextSeq 500 High Output Flow Cell.

characteristic: developmental stage

text: transgenic

characteristic: genetic modification

text: Mat-Tub-gal4 Beaf-32 RNAi

characteristic: genotype

text: egg laying

characteristic: initial time point

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole embryo

characteristic: organism part

text: Drosophila melanogaster

text: mixed sex

characteristic: sex


text: EMBL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 2 to 3

text: ArrayExpress

text: fruit fly

characteristic: description

text: transgenic

text: MTD-gal4 CP190 RNAi

text: egg laying

text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole embryo

text: Drosophila melanogaster

text: mixed sex

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: 2 to 3

characteristic: age

text: ArrayExpress

text: fruit fly

text: gene knock out

text: CTCF m-z-

text: egg laying

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole embryo

text: Drosophila melanogaster

text: mixed sex


name: E-MTAB-11978:yw_NC14_rep1 (BEAF RNAi batch)

text: EMBL

text: public

text: 2 to 3

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

characteristic: developmental stage

characteristic: genetic modification

text: wild type genotype

characteristic: genotype

text: egg laying

characteristic: initial time point

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole embryo

text: Drosophila melanogaster

text: mixed sex

text: yw_NC14_rep1 (BEAF RNAi batch)


name: E-MTAB-11978:yw_NC14_rep1 (CP190 RNAi batch)

text: EMBL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 2 to 3

text: ArrayExpress

text: fruit fly

characteristic: description

text: wild type genotype

text: egg laying

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole embryo

characteristic: organism part

text: Drosophila melanogaster

text: mixed sex

characteristic: sex

text: yw_NC14_rep1 (CP190 RNAi batch)


name: E-MTAB-11978:yw_NC14_rep1 (CTCF KO batch)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC center name

text: public

text: 2 to 3

text: ArrayExpress

text: fruit fly

text: wild type genotype

text: egg laying

text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole embryo

text: Drosophila melanogaster

text: mixed sex

text: yw_NC14_rep1 (CTCF KO batch)

characteristic: title


name: E-MTAB-11978:yw_NC14_rep2 (BEAF RNAi batch)

text: EMBL

text: public

characteristic: Submitter Id

text: 2 to 3

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

characteristic: developmental stage

characteristic: genetic modification

text: wild type genotype

characteristic: genotype

text: egg laying

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole embryo

text: Drosophila melanogaster

text: mixed sex

text: yw_NC14_rep2 (BEAF RNAi batch)


name: E-MTAB-11978:yw_NC14_rep2 (CP190 RNAi batch)

text: EMBL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 2 to 3

text: ArrayExpress

text: fruit fly

characteristic: description

text: wild type genotype

text: egg laying

characteristic: initial time point

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole embryo

text: Drosophila melanogaster

text: mixed sex

text: yw_NC14_rep2 (CP190 RNAi batch)


name: E-MTAB-11978:yw_NC14_rep2 (CTCF KO batch)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC center name

text: public

text: 2 to 3

text: ArrayExpress

text: fruit fly

text: wild type genotype

text: egg laying

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole embryo

characteristic: organism part

text: Drosophila melanogaster

text: mixed sex

characteristic: sex

text: yw_NC14_rep2 (CTCF KO batch)


name: E-MTAB-11978:yw_NC14_rep3 (BEAF RNAi batch)

text: EMBL

text: public

characteristic: Submitter Id

text: 2 to 3

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

characteristic: developmental stage

text: wild type genotype

text: egg laying

text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole embryo

text: Drosophila melanogaster

text: mixed sex

text: yw_NC14_rep3 (BEAF RNAi batch)

characteristic: title


name: E-MTAB-11978:yw_NC14_rep3 (CP190 RNAi batch)

text: EMBL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 2 to 3

text: ArrayExpress

text: fruit fly

characteristic: description

characteristic: genetic modification

text: wild type genotype

characteristic: genotype

text: egg laying

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole embryo

text: Drosophila melanogaster

text: mixed sex

text: yw_NC14_rep3 (CP190 RNAi batch)


name: E-MTAB-11978:yw_NC14_rep3 (CTCF KO batch)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC center name

text: public

text: 2 to 3

text: ArrayExpress

text: fruit fly

text: wild type genotype

text: egg laying

characteristic: initial time point

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole embryo

text: Drosophila melanogaster

text: mixed sex

text: yw_NC14_rep3 (CTCF KO batch)


text: BAH-GU

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: ER- BC patients with ductal carcinoma who underwent curative tumour resection surgery in Glasgow Royal Infirmary, Western Infirmary, or Stobhill Hospitals (Glasgow, UK) between 1995 and 1998 were included in the study. Resected tumour tissue was formalin-fixed and paraffin-embedded. FFPE tissue was deparaffinised prior to tissue digestion. The tissue lysate was combined with detector oligos which were annealed in immediate juxtaposition to each other on the targeted RNA template and ligated. Amplification of ligated oligos was performed using a unique primer set for each sample, introducing a sample-specific barcode and Illumina adaptors.

text: estrogen-receptor negative breast cancer

characteristic: disease

text: cancer

text: lymph node status negative

characteristic: disease staging

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: CAIX expression low

characteristic: phenotype

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: female

characteristic: sex


text: BAH-GU

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

characteristic: description

text: cancer

text: lymph node status negative

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: CAIX expression high

text: neoplasm

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BAH-GU

characteristic: INSDC center name

text: public

text: ArrayExpress

text: human

text: cancer

text: lymph node status positive

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: breast

text: CAIX expression low

text: neoplasm

text: Homo sapiens

text: female


text: BAH-GU

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: disease

text: cancer

text: lymph node status positive

characteristic: disease staging

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: CAIX expression high

text: neoplasm

text: Homo sapiens

text: female


text: Escherichia coli

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli


text: not applicable

characteristic: ArrayExpress-PHENOTYPE

text: not applicable

characteristic: ArrayExpress-SEX

text: Mus musculus

text: Not Applicable

characteristic: GENDER

text: SC

text: public

text: not applicable

characteristic: PHENOTYPE

characteristic: SRA accession

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF WATERLOO

characteristic: INSDC center name

text: public

tag: Namespace:UNIVERSITY OF WATERLOO

characteristic: Submitter Id

text: oxidized mill tailings

characteristic: description

text: mill tailings

characteristic: environmental medium

text: Canada

characteristic: geographic location (country and/or sea)

text: mine tailings metagenome

text: mine tailings metagenome

text: Illumina MiSeq

characteristic: sequencing method


text: UNIVERSITY OF WATERLOO

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: unoxidized mill tailings

text: mill tailings

text: Canada

text: mine tailings metagenome

text: mine tailings metagenome

text: Illumina MiSeq


text: UNIVERSITY OF WATERLOO

text: public

text: peat

text: mill tailings

text: Canada

text: mine tailings metagenome

text: mine tailings metagenome

text: Illumina MiSeq


text: UNIVERSITY OF WATERLOO

text: public

text: native soil

text: mill tailings

text: Canada

text: mine tailings metagenome

text: mine tailings metagenome

text: Illumina MiSeq


text: public

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

text: Syddanmark

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Danish Covid-19 Genome Consortium

text: Original

characteristic: description

text: Denmark

text: Hovedstaden

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Midtjylland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Nordjylland

text: Human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Danish Covid-19 Genome Consortium

text: Original

characteristic: description

text: Denmark

text: Sjaelland

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

tag: Namespace:CNRS, University Paris I Pantheon-Sorbonne & Gustave Roussy

unit: month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Lin- lymphocyte

text: house mouse

characteristic: common name

text: Protocols: Bone marrow megakaryocytes were sorted from recipient mice 8-12 weeks after tamoxifen feeding. Lin- cells were enriched by immunomagnetic negative selection (IMag; BD Biosciences) using Ter119, CD3, B220, Cd11b and Gr1 antibodies before being labeled with PE-conjugated anti-CD41 (clone MCReg30, BD) and APC-conjugated anti-CD42d (clone 1C2, Biolegend) antibodies. CD41+ CD42d+ cells were sorted using Influx 5 laser BD cell sorter in Trizol LS and stored at -80°C RNA isolation was performed using RNA isolation protocol with chloroform and GenElute LPA (Sigma) protocol cDNA Libraries were generated using the SMART-Seq® v4 Ultra® Low Input RNA and final libraries where generated with TruSeq Sample Preparation v.2 Guide (Illumina).

text: adult

characteristic: developmental stage

characteristic: genotype

text: lineage negative

characteristic: immunophenotype

characteristic: individual

text: not applicable

text: Mus musculus

text: Mus musculus

text: blood

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CNRS, University Paris I Pantheon-Sorbonne & Gustave Roussy

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Lin- lymphocyte

text: house mouse

text: adult

text: lineage negative

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: blood

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Lin- lymphocyte

text: house mouse

characteristic: description

text: adult

text: Srsf2-P95H Jak2-V617F

text: lineage negative

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: blood

text: Mus musculus

text: female

characteristic: title


text: public

text: ArrayExpress

text: Lin- lymphocyte

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

text: Scl

characteristic: genotype

text: lineage negative

characteristic: immunophenotype

characteristic: individual

text: not applicable

text: Mus musculus

text: Mus musculus

text: blood

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: megakaryocyte

text: house mouse

text: adult

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: blood

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

characteristic: age

text: ArrayExpress

characteristic: broker name

text: megakaryocyte

text: house mouse

characteristic: description

text: adult

text: Srsf2-P95H Jak2-V617F

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: blood

text: Mus musculus

text: female

characteristic: title


text: public

text: ArrayExpress

text: megakaryocyte

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

text: Scl

characteristic: genotype

characteristic: immunophenotype

characteristic: individual

text: not applicable

text: Mus musculus

text: Mus musculus

text: blood

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


text: Bladder cell line

characteristic: ArrayExpress-PHENOTYPE

text: female

characteristic: ArrayExpress-SEX

text: Homo sapiens

characteristic: ArrayExpress-SPECIES

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Female

characteristic: GENDER

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Bladder cell line

characteristic: PHENOTYPE

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Homo sapiens


text: Escherichia coli

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: INSDC status

text: Escherichia coli

characteristic: common name

text: Escherichia coli

characteristic: organism

text: Escherichia coli

characteristic: title


characteristic: DO %

characteristic: DO mg/L

text: Stockholm University

text: public

characteristic: SPC

tag: Namespace:Stockholm University

characteristic: Temperature °C

text: freshwater lake

characteristic: broad-scale environmental context

characteristic: collection date

unit: m

characteristic: depth

text: Lake M�laren (Brostugan)

characteristic: description

text: water

characteristic: environmental medium

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: surface lake water

characteristic: local environmental context

text: uncultured prokaryote

text: Swedish Lakes Metagenomes

characteristic: project name

text: uncultured prokaryote

characteristic: scientific name

text: Illumina NovaSeq

characteristic: sequencing method

type: derived-from


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stockholm University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: freshwater lake

text: Lake M�laren (Drottingholm)

text: water

text: Sweden

text: surface lake water

text: uncultured prokaryote

characteristic: organism

text: Swedish Lakes Metagenomes

text: uncultured prokaryote

text: Illumina NovaSeq

characteristic: title


characteristic: DO %

characteristic: DO mg/L

text: Stockholm University

text: public

characteristic: SPC

characteristic: Temperature °C

text: freshwater lake

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: depth

text: Lake M�laren (Brostugan)

characteristic: description

text: water

characteristic: environmental medium

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: surface lake water

text: uncultured prokaryote

text: Swedish Lakes Metagenomes

text: uncultured prokaryote

text: Illumina NovaSeq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stockholm University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: freshwater lake

text: Lake Malaren (Brostugan)

text: water

text: Sweden

text: surface lake water

characteristic: local environmental context

text: uncultured prokaryote

text: Swedish Lakes Metagenomes

characteristic: project name

text: uncultured prokaryote

characteristic: scientific name

text: Illumina NovaSeq

characteristic: sequencing method


characteristic: DO %

characteristic: DO mg/L

text: Stockholm University

text: public

characteristic: SPC

characteristic: SRA accession

characteristic: Submitter Id

characteristic: Temperature °C

text: freshwater lake

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: depth

text: Lake Malaren (Drottingholm)

characteristic: description

text: water

text: Sweden

text: surface lake water

text: uncultured prokaryote

characteristic: organism

text: Swedish Lakes Metagenomes

text: uncultured prokaryote

text: Illumina NovaSeq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stockholm University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: freshwater lake

text: Lake Malaren (Brostugan)

text: water

characteristic: environmental medium

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: surface lake water

text: uncultured prokaryote

text: Swedish Lakes Metagenomes

text: uncultured prokaryote

text: Illumina NovaSeq


characteristic: DO %

characteristic: DO mg/L

text: Stockholm University

text: public

characteristic: SPC

characteristic: SRA accession

characteristic: Submitter Id

characteristic: Temperature °C

text: freshwater lake

characteristic: broad-scale environmental context

characteristic: collection date

text: Lake Malaren (Drottingholm)

text: water

text: Sweden

text: surface lake water

characteristic: local environmental context

text: uncultured prokaryote

text: Swedish Lakes Metagenomes

characteristic: project name

text: uncultured prokaryote

characteristic: scientific name

text: Illumina NovaSeq

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

tag: Namespace:EUROPEAN RESEARCH INSTITUTE FOR THE BIOLOGY OF AGEING, UNIVERSITY OF GRONINGEN, UNIVERSITY MEDICAL CENTER GRONINGEN

text: human

characteristic: common name

text: Primary human medulloblastoma biopsy specimen MB-1/2/3; treatment-naive

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: title


text: EUROPEAN RESEARCH INSTITUTE FOR THE BIOLOGY OF AGEING, UNIVERSITY OF GRONINGEN, UNIVERSITY MEDICAL CENTER GRONINGEN

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Homo sapiens


text: public

text: house mouse

text: Primary, uncultured cerebellar granule neuron progenitors from postnatal day 8 (P8) old mouse cerebellum; FACS purified

text: Mus musculus

text: Mus musculus


text: public

text: house mouse

text: Primary, uncultured cerebellar granule neuron progenitors from postnatal day 13 (P13) old mouse cerebellum; FACS purified

text: Mus musculus

text: Mus musculus


text: mixed

characteristic: ArrayExpress-SEX

text: Auanema sp. 5

characteristic: ArrayExpress-SPECIES

text: Mixed

characteristic: GENDER

text: SC

text: public

text: Auanema sp. 5

text: Auanema sp. APS23

text: Auanema sp. APS23


text: mixed

text: Oscheius sp. E

characteristic: ENA-CHECKLIST

text: Mixed

text: SC

text: public

text: Oscheius sp. E

text: Oscheius sp. DF5083

text: Oscheius sp. DF5083


text: Salmonella enterica

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Salmonella enterica

text: Salmonella enterica

text: Salmonella enterica


E-MTAB-12000:HCC1806 siControl.2_H2Bub1

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-12000:HCC1806 siControl.2_H2Bub1

tag: Namespace:University Medical Center Gottingen Department of Gynecology and Obstetrics Molecular Gynecology

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: HCC1806 cells were grown in RPMI GlutaMax medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin and 100 μg/ml streptomycin at 37 C and 5% CO2 siRNA transfections were performed using Lipofectamine RNAiMAX(Invitrogen) according to the manufacturer's instructions Chromatin immunoprecipitation was performed 48 hrs after transfection using antibodies against H2Bub1 (Cat. No. 5546 S, Cell Signaling Technology), H3K79me3 (Cat. No. C15410068, Diagenode), H3K27ac (Cat. No. C15410196, Diagenode). Next-generation sequencing library was prepared using the KAPA Hyper Prep Kit (KR0961–v6.17) according to the manufacturer’s instructions and samples were sequenced (single-end 50 bp).

text: adult

characteristic: developmental stage

text: triple-negative breast cancer

characteristic: disease

text: wild type genotype

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: mammary gland

characteristic: organism part

characteristic: replicate

text: Homo sapiens

text: HCC1806 siControl.2_H2Bub1


E-MTAB-12000:HCC1806 siRNF40.2_H2Bub1

characteristic: External Id

text: University Medical Center Gottingen Department of Gynecology and Obstetrics Molecular Gynecology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12000:HCC1806 siRNF40.2_H2Bub1

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: adult

text: triple-negative breast cancer

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: mammary gland

text: Homo sapiens

text: HCC1806 siRNF40.2_H2Bub1


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-12000:HCC1806 siControl.2_H3K27ac

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: triple-negative breast cancer

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: Homo sapiens

text: HCC1806 siControl.2_H3K27ac

characteristic: title


E-MTAB-12000:HCC1806 siRNF40.2_H3K27ac

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-12000:HCC1806 siRNF40.2_H3K27ac

text: ArrayExpress

characteristic: broker name

text: human

text: adult

characteristic: developmental stage

text: triple-negative breast cancer

characteristic: disease

text: wild type genotype

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: Homo sapiens

text: HCC1806 siRNF40.2_H3K27ac


characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-12000:HCC1806 siControl.2_H3K79me3

text: ArrayExpress

text: human

text: adult

text: triple-negative breast cancer

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: mammary gland

characteristic: organism part

characteristic: replicate

text: Homo sapiens

text: HCC1806 siControl.2_H3K79me3


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12000:HCC1806 siControl.3_H3K79me3

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: adult

text: triple-negative breast cancer

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: Homo sapiens

text: HCC1806 siControl.3_H3K79me3


E-MTAB-12000:HCC1806 siRNF40.2_H3K79me3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-12000:HCC1806 siRNF40.2_H3K79me3

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: triple-negative breast cancer

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: mammary gland

text: Homo sapiens

text: HCC1806 siRNF40.2_H3K79me3


E-MTAB-12000:HCC1806 siRNF40.3_H3K79me3

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-12000:HCC1806 siRNF40.3_H3K79me3

text: ArrayExpress

characteristic: broker name

text: human

text: adult

characteristic: developmental stage

text: triple-negative breast cancer

characteristic: disease

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: Homo sapiens

text: HCC1806 siRNF40.3_H3K79me3

characteristic: title


E-MTAB-12000:HCC1806 siControl.2_input

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-12000:HCC1806 siControl.2_input

text: ArrayExpress

text: human

text: adult

text: triple-negative breast cancer

text: wild type genotype

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: mammary gland

characteristic: organism part

text: Homo sapiens

text: HCC1806 siControl.2_input


E-MTAB-12000:HCC1806 siRNF40.2_input

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12000:HCC1806 siRNF40.2_input

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: triple-negative breast cancer

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mammary gland

characteristic: replicate

text: Homo sapiens

text: HCC1806 siRNF40.2_input


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: SRA accession

tag: Namespace:UNIVERSITY OF MANCHESTER

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: four-striped grass mouse

text: Protocols: Animals were sedated with isoflurane and immediately culled by cervical dislocation at ZT2 or ZT14. Retina, lung and liver tissues was dissected and snap frozen immediately. For SCN samples, punches were collected from 1 mm thick brain slices containing a sample corer. All samples were stored at -80°C until RNA extraction. For retina, lung and liver samples total RNA was extracted from < 5 mg frozen tissue using the Qiagen RNeasy Mini kit (Qiagen 74104). For SCN, total RNA was extracted from snap-frozen brain punches using the Qiagen RNeasy Micro kit (Qiagen 74004). All samples were quantified using a 4200 TapeStation (Agilent Technologies). For retina, lung and liver samples, cDNA libraries were generated using the Illumina Stranded mRNA Prep Ligation kit (Illumina, Inc. 20040532). For SCN samples, cDNA libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit V3 - Pico Input Mammalian (Takara Bio 634485).

characteristic: description

text: adult

text: normal

text: wild type genotype

text: 12 hour light-dark cycle

characteristic: growth condition

characteristic: individual

text: not applicable

text: Rhabdomys pumilio

text: Rhabdomys pumilio

text: retina

text: Rhabdomys pumilio

text: female

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: four-striped grass mouse

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: 12 hour light-dark cycle

text: not applicable

text: Rhabdomys pumilio

characteristic: organism

text: Rhabdomys pumilio

text: retina

text: Rhabdomys pumilio

text: male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: four-striped grass mouse

characteristic: common name

text: adult

text: normal

text: wild type genotype

text: 12 hour light-dark cycle

text: not applicable

characteristic: isolate

text: Rhabdomys pumilio

text: Rhabdomys pumilio

text: lung

characteristic: organism part

text: Rhabdomys pumilio

text: female