characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Max Planck Institute for Infection Biology - Dept. Cellular Microbiology

characteristic: Submitter Id

unit: hour

characteristic: age

text: ArrayExpress

text: fruit fly

characteristic: common name

text: Protocols: Flies were raised and maintained on standard cornmeal food at 25°C or room temperature. For experiments on wild type OrR, adult fly collections were left to lay eggs on apple juice agar plates with yeast paste overnight at 25°C. After 24h hatched larvae were washed of the plate and further larvae were allowed to hatch for 2h. Then, larvae were picked of the plate and transferred into 36mm food tubes with yeast paste at a density of 120 larvae per tube and raised at 25°C. The resulting larval collection tubes would reach 3rd instar wandering stage around 4 days after hatching, at which stage plasmatocytes were extracted. PLASMATOCYTE ISOLATION AND CROSSLINKING FOR CHIP: For plasmatocyte extraction and chromatin fixation, 94h old 3rd instar wandering OrR larvae were collected from food tubes and washed in PBS. At the same time Schneider’s medium FCS with 10 mM N-Acetyl-L-Cysteine was prepared in a well of a 6-well tissue culture plate (Sarstedt). Larvae were dried on paper towels and transferred to the tissue culture well with medium. Then they were ripped by holding the head with forceps (Dumont) and with another forceps ripping open the cuticula along the body of the larvae without disrupting the gut. 100 larvae were bled this way for each sample. The larval carcass was then removed and the plasmatocytes were allowed to attach for 10-15 minutes. Afterwards, the plasmatocytes were washed 4 times with PBS, then all supernatant was aspirated and plasmatocytes were fixed for 10 minutes at room temperature with 1,8% Formaldehyde in PBS. Afterwards, fixation was quenched for 3 minutes using 100 µl 2M glycine. Then cells were scraped of the dish using a cell scraper and transferred to 1,5 ml tube on ice. After a 5 minute incubation on ice, plasmatocytes were centrifuged (3000g, 4°C, 5 minutes), then washed 2x with PBS-Tx (PBS + 0,1% Triton X-100 w/v), each time spinning the cells down (3000g, 4°C, 5 minutes). After the final wash, as much supernatant as possible was removed from the pellet, without losing it, then the tube was snap frozen in liquid nitrogen and stored at -80°C for the ChIP.CHIP PROTOCOL: For ChIP a number of tubes corresponding to the appropriate number of fixed larval plasmatocytes (see Table 8) was thawed on ice. All tubes were then resuspended in ice cold PBS-Tx (PBS + 0,1% Triton X-100 w/v) and pooled. If several different ChIPs were performed in one run, they derive from a common cell pool. If replicates of a ChIP were performed in one run, these samples derive from separate cell pools. Pooled fixed plasmatocytes were centrifuged down (4500g, 4°C, 10 minutes) and all supernatant was drained. Cells were then resuspended in RIPA buffer supplemented with protease inhibitor cocktail, PhosSTOP and 20 mM sodium butyrate to a final concentration of 3 larval equivalents of plasmatocytes per µl. Plasmatocytes were then dissociated using a syringe with a G26 needle by passing the cell suspension through it 10 times and afterwards incubated for 30 minutes on ice. The chromatin suspension was next split into prechilled Bioruptor microtubes at 100 µl per tube and then sonicated in a Bioruptor Pico using 30s on 30s off cycles at 4°C. Sonication was performed first for 3 cycles and then 2 times for 4 cycles with in-between vortexing of tubes. Sonicated chromatin samples were then spun down to remove unsheared debris (16000g, 4°C, 10 minutes) and the supernatant was pooled into a fresh DNA LoBind tube. Samples were then split into chilled tubes according to the required plasmatocyte counts (see Table 8) holding a small amount back as input. Volumes were adjusted to 100 µl using RIPA and antibodies were added at appropriate concentrations (see Table 1). The chromatin antibody mixture was then incubated on a rotating wheel at 4°C overnight. The next day a 1:1 mixture of protein A and protein G Dynabeads was washed 3 times using a DynaMag-2. Then the beads were resuspended in a small volume and added to the overnight samples to make a final amount corresponding to 5 µl of each protein A and G beads. Bead-antibody-chromatin samples were incubated on a rotating wheel at 4°C for 4 hours. Beads were pulled down using a DynaMag-2 in a cold, resuspended in fresh RIPA and washed for 10 minutes on a rotating wheel. This washing was repeated 4 times with RIPA500, once with LiCl buffer and 2 times with TE buffer, for which washing was limited to 5 minutes. Finally, the beads were resuspended in 100 µl RIPA and the same was done for the untreated input sample. Then 1 µl of RNase (10 mg/ml) was added to each sample and they were incubated for 1h at 37°C. Then 4 µl 10% SDS and 3 µl Proteinase K (20 mg/ml) was added to each sample and they were incubated overnight at 65°C shaking at 1200 rpm. The next day the magnetic beads were removed using the DynaMag-2, and DNA was isolated from the supernatant using the Zymo ChIP DNA clean and concentrator kit according to the manual. The DNA was finally eluted in 30 µl ultra-pure water and stored at -80°C. ChIP-seq libraries were prepared from the final ChIP samples using the NEBNext Ultra II DNA kit and the NEBNext Multiplex Oligos for Illumina sets according to the manual with one minor adjustment: Size selection of the library was performed after PCR amplification. For this, after PCR amplification 27,5 µl of AMpure XP beads was added to each sample and incubated for 5 minutes. Then, the tubes were placed on a DynaMag-2 and the supernatant was moved to fresh tubes, while the beads were discarded. To the supernatant 22,5 µl AMpure XP beads was added, they were incubated for 5 minutes at room temperature, then pulled down using the DynaMag-2 and the supernatant was discarded. The beads were washed 2 times on the magnetic rack with 80% EtOH and then resuspended in 17 µl ultra-pure water. After incubating for 2 minutes at room temperature, the magnetic beads were pulled down and the supernatant containing the final libraries was moved to fresh tubes. The libraries were then stored at -20°C.

text: third instar larval stage

text: wild type genotype

text: pool of individuals

characteristic: individual

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: plasmatocyte

text: Drosophila melanogaster

text: male and female

characteristic: sex

text: OrR

characteristic: strain


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Max Planck Institute for Infection Biology - Dept. Cellular Microbiology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: description

text: third instar larval stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: pool of individuals

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: plasmatocyte

characteristic: organism part

text: Drosophila melanogaster

text: male and female

text: OrR

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:The Francis Crick Institute

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: Two VHL-defective kidney cancer cell lines, RCC4 and 786-O, were used. Sublines of these cells with reintroduction of VHL or an empty vector control were prepared using lentiviral transduction, whereas HIF1B was inactivated using CRISPR/Cas9 mediated genome editing. Cells were grown in DMEM with 1 mM sodium pyruvate, 10% FBS and 5 µg/mL blasticidin at 37 ˚C in 5% CO2. For analysis of the effect of hypoxia, cells were cultured at 37 ˚C in 1% O2 and 5% CO2 for 24 hours. An RNeasy Plus Mini Kit (QIAGEN, 74136) was used to extract RNA according to the manufacturer’s instructions with the exception of technical replicate 2 of the samples from RCC4 cells. For these samples, cells were lysed with Buffer RLT Plus (QIAGEN, 1053393), and total RNA was extracted using an RNA clean and concentrator-25 kit (Zymo Research, R1018) according to the manufacturer’s instructions, except that 752.5 µL of preconditioned RNA binding buffer (367.5 µL of RNA binding buffer (supplied with RNA clean and concentrator-25 kit), 367.5 µL of absolute EtOH and 17.5 µL of 20% SDS) was added to 350 µL of the cell lysate before loading onto the column. 5′ end-Seq was performed on the extracted total RNA. In short, a full-length cDNA library was generated using a combined reverse transcription and template switching reaction, followed by PCR amplification. The amplified libraries were multiplexed, and then purified using ProNex beads (Promega). The 3′ end of the cDNA library (i.e. 5′ end of mRNAs) was amplified specifically using Tn5 transposase-mediated tagmentation and PCR amplification with primers annealing to the appropriate adapters added by the template switching reaction and tagmentation. The PCR primers contained i5 and i7 Illumina index sequences and the amplified libraries were multiplexed.

text: adult

text: renal cell adenocarcinoma

characteristic: disease

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10688:total_786O_noVHL_noHIF1B_N_2

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10688:total_786O_noVHL_noHIF1B_N_3

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

text: public

text: E-MTAB-10688:total_786O_noVHL_noHIF1B_N_1

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: empty vector

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

characteristic: INSDC status

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

characteristic: title


text: The Francis Crick Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

characteristic: disease

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: INSDC last update

text: public

tag: Namespace:Northumbria University / South Tees Hospitals NHS Foundation Trust / North Cumbria Integrated Care NHS Foundation Trust / North Tees and Hartlepool NHS Foundation Trust / Newcastle Hospitals NHS Foundation Trust

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

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

characteristic: receipt date

text: active surveillance in response to outbreak

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Northumbria University / South Tees Hospitals NHS Foundation Trust / North Cumbria Integrated Care NHS Foundation Trust / North Tees and Hartlepool NHS Foundation Trust / Newcastle Hospitals NHS Foundation Trust

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

text: not provided

characteristic: title

text: not provided


COG-UK/BIRM-BCFJEX

text: University of Birmingham

text: public

text: COG-UK/BIRM-BCFJEX

tag: Namespace:University of Birmingham

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: University of Birmingham

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: receipt date

text: not provided

text: COG-UK/BIRM-BCFJEX

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Birmingham

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

text: University of Birmingham

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


text: public

tag: Namespace:Virology Department, Sheffield Teaching Hospitals NHS Foundation Trust/Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

text: not provided

characteristic: title

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Virology Department, Sheffield Teaching Hospitals NHS Foundation Trust/Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: receipt date

text: not provided

text: not provided


text: public

tag: Namespace:Originating lab: Wales Specialist Virology Centre Sequencing lab: Pathogen Genomics Unit

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Wales

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


COG-UK/BIRM-BCREKQ

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Birmingham

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: COG-UK/BIRM-BCREKQ

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

text: University of Birmingham

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

text: not provided

text: COG-UK/BIRM-BCREKQ

characteristic: title

text: not provided


COG-UK/BIRM-BCREXR

text: University of Birmingham

text: public

text: COG-UK/BIRM-BCREXR

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: University of Birmingham

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: receipt date

text: not provided

text: COG-UK/BIRM-BCREXR

text: not provided


COG-UK/BIRM-BCFJUA

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Birmingham

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: COG-UK/BIRM-BCFJUA

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

text: University of Birmingham

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: COG-UK/BIRM-BCFJUA

text: not provided

characteristic: virus identifier


COG-UK/BIRM-BCREGS

text: University of Birmingham

text: public

text: COG-UK/BIRM-BCREGS

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: University of Birmingham

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

text: not provided

text: COG-UK/BIRM-BCREGS

characteristic: title

text: not provided


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: doxycycline induceable CK2alpha shRNA

characteristic: RNA interference

characteristic: SRA accession

tag: Namespace:Department of Biochemistry and Molecular Biology University of Southern Denmark

characteristic: Submitter Id

text: ArrayExpress

text: myoblast

text: Norway rat

characteristic: common name

text: Protocols: The cell line H9c-2 originated from rat heart was purchased from the American Type Culture Collection (ATCC, Rockville, MD, USA) and employed for the generation of the cell line H9c2-CK2alpha-44 employed in this study. The cell line was cultivated at 37ºC under a 5% CO2 atmosphere in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen, Taastrup, Denmark) supplemented with 10% foetal bovine serum (FBS, Biochrom AG, Berlin, Germany). Total RNA was extracted from cells using Isol-RNA lysis reagent (AH Diagnostics, Aarhus, Denmark). The RNA concentration, purity and integrity were analyzed on Nanodrop and Agilent 2100 Bioanalyzer using the RNA 6000 nano kit (Agilent Technologies, Inc., Santa Clara, CA, USA). RNA used for sample preparation had a RIN ≥8.0 and a 28 s/18 s ratio ≥1.8. Sample preparation was performed as described in the NEBNext ultra II RNA library prep kit (Illumina). The amplified libraries were validated by Agilent 2100 Bioanalyzer using a DNA 1000 kit from Agilent Technologies and quantified by qPCR using the KaPa Library Kits (KaPa Biosystems, Wilmington, MA, USA).

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: not applicable

text: Rattus norvegicus

text: Rattus norvegicus

text: heart

characteristic: organism part

text: Rattus norvegicus


characteristic: ENA-CHECKLIST

text: Department of Biochemistry and Molecular Biology University of Southern Denmark

text: public

text: doxycycline induceable CK2alpha shRNA

text: ArrayExpress

characteristic: broker name

text: myoblast

text: Norway rat

text: Protocols: The cell line H9c-2 originated from rat heart was purchased from the American Type Culture Collection (ATCC, Rockville, MD, USA) and employed for the generation of the cell line H9c2-CK2alpha-44 employed in this study. The cell line was cultivated at 37ºC under a 5% CO2 atmosphere in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen, Taastrup, Denmark) supplemented with 10% foetal bovine serum (FBS, Biochrom AG, Berlin, Germany). Cells were incubated with 3mM hydroxyurea for 24 h. Total RNA was extracted from cells using Isol-RNA lysis reagent (AH Diagnostics, Aarhus, Denmark). The RNA concentration, purity and integrity were analyzed on Nanodrop and Agilent 2100 Bioanalyzer using the RNA 6000 nano kit (Agilent Technologies, Inc., Santa Clara, CA, USA). RNA used for sample preparation had a RIN ≥8.0 and a 28 s/18 s ratio ≥1.8. Sample preparation was performed as described in the NEBNext ultra II RNA library prep kit (Illumina). The amplified libraries were validated by Agilent 2100 Bioanalyzer using a DNA 1000 kit from Agilent Technologies and quantified by qPCR using the KaPa Library Kits (KaPa Biosystems, Wilmington, MA, USA).

text: adult

text: normal

text: wild type genotype

text: not applicable

characteristic: isolate

text: Rattus norvegicus

characteristic: organism

text: Rattus norvegicus

text: heart

text: Rattus norvegicus

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: doxycycline induceable CK2alpha shRNA

text: ArrayExpress

text: myoblast

text: Norway rat

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Rattus norvegicus

text: Rattus norvegicus

text: heart

text: Rattus norvegicus


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: doxycycline induceable CK2alpha shRNA

characteristic: RNA interference

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: myoblast

text: Norway rat

text: Protocols: The cell line H9c-2 originated from rat heart was purchased from the American Type Culture Collection (ATCC, Rockville, MD, USA) and employed for the generation of the cell line H9c2-CK2alpha-44 employed in this study. The cell line was cultivated at 37ºC under a 5% CO2 atmosphere in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen, Taastrup, Denmark) supplemented with 10% foetal bovine serum (FBS, Biochrom AG, Berlin, Germany). Cells were incubated with 1 microgram/ml doxycycline for 72 h. Total RNA was extracted from cells using Isol-RNA lysis reagent (AH Diagnostics, Aarhus, Denmark). The RNA concentration, purity and integrity were analyzed on Nanodrop and Agilent 2100 Bioanalyzer using the RNA 6000 nano kit (Agilent Technologies, Inc., Santa Clara, CA, USA). RNA used for sample preparation had a RIN ≥8.0 and a 28 s/18 s ratio ≥1.8. Sample preparation was performed as described in the NEBNext ultra II RNA library prep kit (Illumina). The amplified libraries were validated by Agilent 2100 Bioanalyzer using a DNA 1000 kit from Agilent Technologies and quantified by qPCR using the KaPa Library Kits (KaPa Biosystems, Wilmington, MA, USA).

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Rattus norvegicus

text: Rattus norvegicus

text: heart

text: Rattus norvegicus


text: public

text: doxycycline induceable CK2alpha shRNA

text: ArrayExpress

text: myoblast

text: Norway rat

characteristic: common name

text: Protocols: The cell line H9c-2 originated from rat heart was purchased from the American Type Culture Collection (ATCC, Rockville, MD, USA) and employed for the generation of the cell line H9c2-CK2alpha-44 employed in this study. The cell line was cultivated at 37ºC under a 5% CO2 atmosphere in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen, Taastrup, Denmark) supplemented with 10% foetal bovine serum (FBS, Biochrom AG, Berlin, Germany). Cells were incubated with 1 microgram/ml doxycycline for 72 h. Cells were incubated with 3mM hydroxyurea for 24 h. Total RNA was extracted from cells using Isol-RNA lysis reagent (AH Diagnostics, Aarhus, Denmark). The RNA concentration, purity and integrity were analyzed on Nanodrop and Agilent 2100 Bioanalyzer using the RNA 6000 nano kit (Agilent Technologies, Inc., Santa Clara, CA, USA). RNA used for sample preparation had a RIN ≥8.0 and a 28 s/18 s ratio ≥1.8. Sample preparation was performed as described in the NEBNext ultra II RNA library prep kit (Illumina). The amplified libraries were validated by Agilent 2100 Bioanalyzer using a DNA 1000 kit from Agilent Technologies and quantified by qPCR using the KaPa Library Kits (KaPa Biosystems, Wilmington, MA, USA).

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: not applicable

text: Rattus norvegicus

text: Rattus norvegicus

text: heart

text: Rattus norvegicus


characteristic: ENA-CHECKLIST

text: public

tag: Namespace:Max Planck Institute for Infection Biology, Cellular Microbiology

characteristic: age

text: ArrayExpress

characteristic: broker name

text: embryonic/larval plasmatocyte

text: fruit fly

text: Protocols: FLY RAISING Flies were raised and maintained on standard cornmeal food at 25°C or room temperature. For experiments on wild type OrR, adult fly collections were left to lay eggs on apple juice agar plates with yeast paste overnight at 25°C. After 24h hatched larvae were washed of the plate and further larvae were allowed to hatch for 2h. Then, larvae were picked of the plate and transferred into 36mm food tubes with yeast paste at a density of 120 larvae per tube and raised at 25°C. The resulting larval collection tubes would reach 3rd instar wandering stage around 4 days after hatching, at which stage plasmatocytes were extracted. SWITCH GAL4 All stocks were raised as described above. Virgin females from stock P{GS.HmlΔ-GAL4} were collected and crossed to males from uas lines (P{w[+mC]=UAS-PGRP-LC.a}3; P{w[+mC]=UAS-hop.H}2; P{UAS-2xEGFP}) From these crosses, first instar larvae were collected 0-4h after hatching and aged at controlled density on standard food for 72h at 25°C. Then they were transferred to new vials with standard food or standard food supplemented with 10µM mifepristone (Sigma M8046, 10mg/ml stock solution in EtOH). Hemocytes harvested after incubation 48h 25°C by bleeding. PLASMATOCYTE ISOLATION FOR DIRECT RNA EXTRACTION For plasmatocyte extraction and RNA isolation, treated or untreated 3rd instar wandering larvae were collected from food tubes and washed in PBS. At the same time Schneider’s medium with FCS with 10 mM N-Acetyl-L-Cysteine was prepared in a well of a 24-well tissue culture plate (Sarstedt). Larvae were dried on paper towels and transferred to the tissue culture well with medium. Then they were ripped by holding the head with forceps (Dumont) and with another forceps ripping open the cuticula along the body of the larvae without disrupting the gut. In this ways 80 larvae were bled for each sample. The larval carcass was then removed and the plasmatocytes were allowed to attach for 10-15 minutes. Afterwards, the plasmatocytes were washed 4 times with PBS, then all supernatant was aspirated, they were lysed in 94.5 µl RNAdvance lysis buffer and processed immediately. RNA was isolated from freshly lysed plasmatocytes samples using the RNAdvance cell v2 kit following manufacturer’s instructions using a DynaMag-2 magnetic rack. DNase digestion was performed as suggested in the manual using Ambion DNase. Resulting RNA samples were eluted in 20 µl ultra-pure water and stored at -80°C. Libraries were generated by Eurofins Genomics.

text: third instar larva stage

text: eGFP

text: mixed

characteristic: individual

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: embryonic/larval hemolymph

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: w*

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Max Planck Institute for Infection Biology, Cellular Microbiology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: embryonic/larval plasmatocyte

text: fruit fly

text: third instar larva stage

text: eGFP

text: mixed

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: embryonic/larval hemolymph

text: Drosophila melanogaster

text: mixed

text: w*

characteristic: title


characteristic: ENA-CHECKLIST

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: embryonic/larval plasmatocyte

text: fruit fly

characteristic: common name

characteristic: description

text: third instar larva stage

characteristic: developmental stage

text: hop

characteristic: genotype

text: mixed

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: embryonic/larval hemolymph

text: Drosophila melanogaster

text: mixed

text: w*


text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: embryonic/larval plasmatocyte

text: fruit fly

text: third instar larva stage

text: PGRP-LC

text: mixed

characteristic: individual

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: embryonic/larval hemolymph

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: w*


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

text: ArrayExpress

text: embryonic/larval plasmatocyte

text: fruit fly

text: third instar larva stage

text: tkvQD

text: mixed

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: embryonic/larval hemolymph

text: Drosophila melanogaster

text: mixed

text: w*

characteristic: strain


characteristic: ENA-CHECKLIST

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: embryonic/larval plasmatocyte

text: fruit fly

characteristic: common name

text: Protocols: FLY RAISING Flies were raised and maintained on standard cornmeal food at 25°C or room temperature. For experiments on wild type OrR, adult fly collections were left to lay eggs on apple juice agar plates with yeast paste overnight at 25°C. After 24h hatched larvae were washed of the plate and further larvae were allowed to hatch for 2h. Then, larvae were picked of the plate and transferred into 36mm food tubes with yeast paste at a density of 120 larvae per tube and raised at 25°C. The resulting larval collection tubes would reach 3rd instar wandering stage around 4 days after hatching, at which stage plasmatocytes were extracted. SEPTIC INJURY Sharpened tungsten needles were then used to perform septic injury. The wire was mounted in a Moria pin holder. Larvae were taken from food tubes by washing out all larvae with a 20% sucrose solution. Larvae were quickly washed in PBS, then dried on paper towels and transferred to a rubber dish. Larvae were then pricked with the tungsten needle dipped into the bacterial pellet (septic injury). Larvae were then transferred back into normal food tubes with 3 drops of PBS and incubated at 25°C for the indicated time. For infection time courses plasmatocytes were always extracted around the same time of day at age 92h post hatching, and injuries were performed 6h prior. PLASMATOCYTE ISOLATION FOR DIRECT RNA EXTRACTION For plasmatocyte extraction and RNA isolation, treated or untreated 3rd instar wandering larvae were collected from food tubes and washed in PBS. At the same time Schneider’s medium with FCS with 10 mM N-Acetyl-L-Cysteine was prepared in a well of a 24-well tissue culture plate (Sarstedt). Larvae were dried on paper towels and transferred to the tissue culture well with medium. Then they were ripped by holding the head with forceps (Dumont) and with another forceps ripping open the cuticula along the body of the larvae without disrupting the gut. In this ways 80 larvae were bled for each sample. The larval carcass was then removed and the plasmatocytes were allowed to attach for 10-15 minutes. Afterwards, the plasmatocytes were washed 4 times with PBS, then all supernatant was aspirated, they were lysed in 94.5 µl RNAdvance lysis buffer and processed immediately. RNA was isolated from freshly lysed plasmatocytes samples using the RNAdvance cell v2 kit following manufacturer’s instructions using a DynaMag-2 magnetic rack. DNase digestion was performed as suggested in the manual using Ambion DNase. Resulting RNA samples were eluted in 20 µl ultra-pure water and stored at -80°C. Libraries were generated by us using the NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads, the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Multiplex Oligos for Illumina sets according to manufacturer's instruction. Adaptor concentrations were adjusted according to manual instructs.

characteristic: description

text: third instar larva stage

text: wild type genotype

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: blood

text: Drosophila melanogaster

text: mixed

text: Oregon R

characteristic: title


text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: embryonic/larval plasmatocyte

text: fruit fly

text: Protocols: FLY RAISING Flies were raised and maintained on standard cornmeal food at 25°C or room temperature. For experiments on wild type OrR, adult fly collections were left to lay eggs on apple juice agar plates with yeast paste overnight at 25°C. After 24h hatched larvae were washed of the plate and further larvae were allowed to hatch for 2h. Then, larvae were picked of the plate and transferred into 36mm food tubes with yeast paste at a density of 120 larvae per tube and raised at 25°C. The resulting larval collection tubes would reach 3rd instar wandering stage around 4 days after hatching, at which stage plasmatocytes were extracted. SEPTIC INJURY Sharpened tungsten needles were then used to perform septic injury. The wire was mounted in a Moria pin holder. Larvae were taken from food tubes by washing out all larvae with a 20% sucrose solution. Larvae were quickly washed in PBS, then dried on paper towels and transferred to a rubber dish. Larvae were then pricked with the tungsten needle dipped into the bacterial pellet (septic injury). Larvae were then transferred back into normal food tubes with 3 drops of PBS and incubated at 25°C for the indicated time. For infection time courses plasmatocytes were always extracted around the same time of day at age 92h post hatching, and injuries were performed 6h prior. PLASMATOCYTE ISOLATION AND CROSSLINKING FOR CHIP For plasmatocyte extraction and chromatin fixation, 94h old 3rd instar wandering OrR larvae (untreated or 6h septic injury) were collected from food tubes and washed in PBS. At the same time Schneider’s medium FCS with 10 mM N-Acetyl-L-Cysteine was prepared in a well of a 6-well tissue culture plate (Sarstedt). Larvae were dried on paper towels and transferred to the tissue culture well with medium. Then they were ripped by holding the head with forceps (Dumont) and with another forceps ripping open the cuticula along the body of the larvae without disrupting the gut. 100 larvae were bled this way for each sample. The larval carcass was then removed and the plasmatocytes were allowed to attach for 10-15 minutes. Afterwards, the plasmatocytes were washed 4 times with PBS, then all supernatant was aspirated and plasmatocytes were fixed for 10 minutes at room temperature with 1,8% Formaldehyde in PBS. Afterwards, fixation was quenched for 3 minutes using 100 µl 2M glycine. Then cells were scraped of the dish using a cell scraper and transferred to 1,5 ml tube on ice. After a 5 minute incubation on ice, plasmatocytes were centrifuged (3000g, 4°C, 5 minutes), then washed 2x with PBS-Tx (PBS + 0,1% Triton X-100 w/v), each time spinning the cells down (3000g, 4°C, 5 minutes). After the final wash, as much supernatant as possible was removed from the pellet, without losing it, then the tube was snap frozen in liquid nitrogen and stored at -80°C for the ChIP. PLASMATOCYTE ISOLATION AND CROSSLINKING FOR CHIPFor plasmatocyte extraction and chromatin fixation, 94h old 3rd instar wandering OrR larvae were collected from food tubes and washed in PBS. At the same time Schneider’s medium FCS with 10 mM N-Acetyl-L-Cysteine was prepared in a well of a 6-well tissue culture plate (Sarstedt). Larvae were dried on paper towels and transferred to the tissue culture well with medium. Then they were ripped by holding the head with forceps (Dumont) and with another forceps ripping open the cuticula along the body of the larvae without disrupting the gut. 100 larvae were bled this way for each sample. The larval carcass was then removed and the plasmatocytes were allowed to attach for 10-15 minutes. Afterwards, the plasmatocytes were washed 4 times with PBS, then all supernatant was aspirated and plasmatocytes were fixed for 10 minutes at room temperature with 1,8% Formaldehyde in PBS. Afterwards, fixation was quenched for 3 minutes using 100 µl 2M glycine. Then cells were scraped of the dish using a cell scraper and transferred to 1,5 ml tube on ice. After a 5 minute incubation on ice, plasmatocytes were centrifuged (3000g, 4°C, 5 minutes), then washed 2x with PBS-Tx (PBS + 0,1% Triton X-100 w/v), each time spinning the cells down (3000g, 4°C, 5 minutes). After the final wash, as much supernatant as possible was removed from the pellet, without losing it, then the tube was snap frozen in liquid nitrogen and stored at -80°C for the ChIP.CHIP PROTOCOLFor ChIP a number of tubes corresponding to the appropriate number of fixed larval plasmatocytes (see Table 8) was thawed on ice. All tubes were then resuspended in ice cold PBS-Tx (PBS + 0,1% Triton X-100 w/v) and pooled. If several different ChIPs were performed in one run, they derive from a common cell pool. If replicates of a ChIP were performed in one run, these samples derive from separate cell pools. Pooled fixed plasmatocytes were centrifuged down (4500g, 4°C, 10 minutes) and all supernatant was drained. Cells were then resuspended in RIPA buffer supplemented with protease inhibitor cocktail, PhosSTOP and 20 mM sodium butyrate to a final concentration of 3 larval equivalents of plasmatocytes per µl. Plasmatocytes were then dissociated using a syringe with a G26 needle by passing the cell suspension through it 10 times and afterwards incubated for 30 minutes on ice. The chromatin suspension was next split into prechilled Bioruptor microtubes at 100 µl per tube and then sonicated in a Bioruptor Pico using 30s on 30s off cycles at 4°C. Sonication was performed first for 3 cycles and then 2 times for 4 cycles with in-between vortexing of tubes. Sonicated chromatin samples were then spun down to remove unsheared debris (16000g, 4°C, 10 minutes) and the supernatant was pooled into a fresh DNA LoBind tube. Samples were then split into chilled tubes according to the required plasmatocyte counts (see Table 8) holding a small amount back as input. Volumes were adjusted to 100 µl using RIPA and antibodies were added at appropriate concentrations (see Table 1). The chromatin antibody mixture was then incubated on a rotating wheel at 4°C overnight. The next day a 1:1 mixture of protein A and protein G Dynabeads was washed 3 times using a DynaMag-2. Then the beads were resuspended in a small volume and added to the overnight samples to make a final amount corresponding to 5 µl of each protein A and G beads. Bead-antibody-chromatin samples were incubated on a rotating wheel at 4°C for 4 hours. Beads were pulled down using a DynaMag-2 in a cold, resuspended in fresh RIPA and washed for 10 minutes on a rotating wheel. This washing was repeated 4 times with RIPA500, once with LiCl buffer and 2 times with TE buffer, for which washing was limited to 5 minutes. Finally, the beads were resuspended in 100 µl RIPA and the same was done for the untreated input sample. Then 1 µl of RNase (10 mg/ml) was added to each sample and they were incubated for 1h at 37°C. Then 4 µl 10% SDS and 3 µl Proteinase K (20 mg/ml) was added to each sample and they were incubated overnight at 65°C shaking at 1200 rpm. The next day the magnetic beads were removed using the DynaMag-2, and DNA was isolated from the supernatant using the Zymo ChIP DNA clean and concentrator kit according to the manual. The DNA was finally eluted in 30 µl ultra-pure water and stored at -80°C. ChIP-seq libraries were prepared from the final ChIP samples using the NEBNext Ultra II DNA kit and the NEBNext Multiplex Oligos for Illumina sets according to the manual with one minor adjustment: Size selection of the library was performed after PCR amplification. For this, after PCR amplification 27,5 µl of AMpure XP beads was added to each sample and incubated for 5 minutes. Then, the tubes were placed on a DynaMag-2 and the supernatant was moved to fresh tubes, while the beads were discarded. To the supernatant 22,5 µl AMpure XP beads was added, they were incubated for 5 minutes at room temperature, then pulled down using the DynaMag-2 and the supernatant was discarded. The beads were washed 2 times on the magnetic rack with 80% EtOH and then resuspended in 17 µl ultra-pure water. After incubating for 2 minutes at room temperature, the magnetic beads were pulled down and the supernatant containing the final libraries was moved to fresh tubes. The libraries were then stored at -20°C.

text: third instar larva stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: mixed

characteristic: individual

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: blood

text: Drosophila melanogaster

text: mixed

text: Oregon R


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Quadram Institute Bioscience

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Quadram Institute Bioscience

text: COVID-19 Genomics UK Consortium

text: Quadram Institute Bioscience

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: receipt date

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

text: not provided

characteristic: title

text: not provided


characteristic: INSDC first public

text: public

characteristic: age

text: ArrayExpress

text: embryonic/larval plasmatocyte

text: Ez

characteristic: cohort

text: fruit fly

characteristic: common name

text: Protocols: FLY RAISING Flies were raised and maintained on standard cornmeal food at 25°C or room temperature. Adult fly collections were left to lay eggs on apple juice agar plates with yeast paste overnight at 25°C. After 24h hatched larvae were washed of the plate and further larvae were allowed to hatch for 2h. Then, larvae were picked of the plate and transferred into 36mm food tubes with yeast paste at a density of 120 larvae per tube and raised at 25°C. The resulting larval collection tubes would reach 3rd instar wandering stage around 4 days after hatching, at which stage plasmatocytes were extracted. CROSSES FOR MUTANT MOSAICS Crosses for the final larvae were left to lay eggs for 4h using 20 female and 10 male flies. The resulting larvae were then heat shocked twice, once in the 1st instar stadium (24h-48h after egg laying) and once in the 2nd instar stadium (48h-72h after egg laying). Then 3rd instar wandering non-tb female larvae were collected for further processing. PLASMATOCYTE ISOLATION AND FACS SORTING For FACS sorting of plasmatocytes 94h old 3rd instar wandering larvae were collected (infered genotypes: (MARCM;; Su(z)12^4,FRT2A/tubGal80,FRT2A), (MARCM;; E(z)^731,FRT2A/tubGal80,FRT2A), (hsFlp;HisC,FRT40A/ubiGFP,FRT40A;HisRescue)). These larvae were washed in PBS, dried on paper towels and transferred to Nunclon Sphera ultra-low attachment dishes filled with 0,5 ml Schneider’s medium with FCS with 10 mM N-Acetyl-L-Cysteine. Larvae were then bled by holding the head with forceps (Dumont) and with another forceps ripping open the cuticula along the body of the larvae without disrupting the gut. Carcasses were then removed and the cell suspension was cell stained using 70 µm cell FlowMi cell strainers. DAPI was added to a final concentration of 1 µg/ml to mark dead cells. Sorting of cells for RNA isolation was performed in the Flow Cytometry Core Facility (DRFZ), using the BD FACSAria ROWLF, sorting for GFP using a 488nm laser for excitation and a 530/30 filter for emission and sorting for DAPI negative cells using a 405nm laser for excitation and a 450/40 filter for emission. The resulting cells were collected, spun down (2000g, 4°C, 5 minutes) and lysed either in 500 µl TRIzol (H3 wt and H3 K27R mosaics) or 94.5 µl RNAdvance lysis buffer (Su(z)12 and E(z) mosaics). TRIzol samples were stored at -80°C, RNAdvance samples were isolated immediately. RNA ISOLATION BY TRIZOL Frozen TRIzol samples were thawed at room temperature, adjuster to 900 µl with TRIzol and moved to fresh prespun phase lock heavy tube. 250 µl chloroform was added to each sample, they were mixed thoroughly and centrifuged (12000g, room temperature, 15 minutes). The upper aqueous phase was then moved to a fresh DNA LoBind tube, making sure not to disrupt the interphase or phenol phase, and mixed with 550 µl isopropanol and 1 µl glycogen (20 mg/ml, RNAse free). Samples were mixed by inverting and incubated for 30 minutes at in the freezer at -20°C. Afterwards samples were centrifuged (16ooog, 4°C, 10 minutes) and the supernatant was removed carefully without disrupting the pellet. The pellet was resuspended in 100 µl ultra-pure water with 300 mM sodium acetate and 1 µl glycogen (20 mg/ml, RNAse free). Next, 300 µl EtOH was added and the sample was incubated for 20 minutes at -20°C, then centrifuged (16000g, 4°C, 10 minutes) and the supernatant was discarded. The pellet was washed 2 times by adding 1 ml of 70% EtOH (prepared with ultra-pure water), each time spinning down the pellet (16000g, 4°C, 3 minutes). Afterwards all supernatant was drained and the pellet was dried until no liquid was visible. The pellet was then resuspended in 15 µl of ultra-pure water and stored at -80°C. RNA ISOLATION BY RNADVANCE RNA was isolated from freshly lysed plasmatocytes samples using the RNAdvance cell v2 kit following manufacturer’s instructions using a DynaMag-2 magnetic rack. DNase digestion was performed as suggested in the manual using Ambion DNase. Resulting RNA samples were eluted in 20 µl ultra-pure water and stored at -80°C. Libraries for FACSed plasmatocytes from HisC mosaics were generated by the Max Planck Genome Centre (Cologne). RNA-seq libraries from Su(z)12/E(z) mosaics using the NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads, the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Multiplex Oligos for Illumina sets according to manufacturer's instruction. Adaptor concentrations were adjusted according to manual instructs.

characteristic: description

text: third instar larva stage

characteristic: developmental stage

characteristic: genotype

text: mixed

characteristic: individual

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: blood

characteristic: organism part

text: Drosophila melanogaster

text: female

characteristic: sex

text: w*

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: embryonic/larval plasmatocyte

text: Ez

text: fruit fly

text: third instar larva stage

text: wild type genotype

text: mixed

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: blood

text: Drosophila melanogaster

text: female

text: w*


characteristic: INSDC first public

text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: embryonic/larval plasmatocyte

characteristic: cohort

text: fruit fly

text: third instar larva stage

text: mixed

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: blood

text: Drosophila melanogaster

text: female

text: w*

characteristic: title


text: public

text: ArrayExpress

text: embryonic/larval plasmatocyte

text: fruit fly

characteristic: common name

characteristic: description

text: third instar larva stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: mixed

characteristic: individual

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: blood

characteristic: organism part

text: Drosophila melanogaster

text: female

characteristic: sex

text: w*

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: embryonic/larval plasmatocyte

text: fruit fly

text: Protocols: FLY RAISING Flies were raised and maintained on standard cornmeal food at 25°C or room temperature. For experiments on wild type OrR, adult fly collections were left to lay eggs on apple juice agar plates with yeast paste overnight at 25°C. After 24h hatched larvae were washed of the plate and further larvae were allowed to hatch for 2h. Then, larvae were picked of the plate and transferred into 36mm food tubes with yeast paste at a density of 120 larvae per tube and raised at 25°C. The resulting larval collection tubes would reach 3rd instar wandering stage around 4 days after hatching, at which stage plasmatocytes were extracted. PLASMATOCYTE ISOLATION FOR DIRECT RNA EXTRACTION For plasmatocyte extraction and RNA isolation, treated or untreated 3rd instar wandering larvae were collected from food tubes and washed in PBS. At the same time Schneider’s medium with FCS with 10 mM N-Acetyl-L-Cysteine was prepared in a well of a 24-well tissue culture plate (Sarstedt). Larvae were dried on paper towels and transferred to the tissue culture well with medium. Then they were ripped by holding the head with forceps (Dumont) and with another forceps ripping open the cuticula along the body of the larvae without disrupting the gut. In this ways 80 larvae were bled for each sample. The larval carcass was then removed and the plasmatocytes were allowed to attach for 10-15 minutes. Afterwards, the plasmatocytes were washed 4 times with PBS, then all supernatant was aspirated, they were lysed in 94.5 µl RNAdvance lysis buffer and processed immediately. RNA ISOLATION BY RNADVANCE RNA was isolated from freshly lysed plasmatocytes samples using the RNAdvance cell v2 kit following manufacturer’s instructions using a DynaMag-2 magnetic rack. DNase digestion was performed as suggested in the manual using Ambion DNase. Resulting RNA samples were eluted in 20 µl ultra-pure water and stored at -80°C. RNA was isolated from freshly lysed plasmatocytes samples using the RNAdvance cell v2 kit following manufacturer’s instructions using a DynaMag-2 magnetic rack. DNase digestion was performed as suggested in the manual using Ambion DNase. Resulting RNA samples were eluted in 20 µl ultra-pure water and stored at -80°C. Libraries were generated by the Max Planck Genome Centre (Cologne). Libraries were stranded, from polyA enriched RNA.

text: third instar larva stage

text: wild type genotype

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: blood

text: Drosophila melanogaster

text: mixed

text: Oregon R


COG-UK/BIRM-BCFZEB

text: University of Birmingham

characteristic: INSDC first public

text: public

text: COG-UK/BIRM-BCFZEB

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: University of Birmingham

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: organism

characteristic: receipt date

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: COG-UK/BIRM-BCFZEB

characteristic: title

text: not provided

characteristic: virus identifier


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

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

text: not provided

text: not provided


text: University of Birmingham

text: public

text: COVID-19 Genomics UK Consortium

text: University of Birmingham

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: organism

characteristic: receipt date

characteristic: sample capture status

text: not provided

text: not provided


COG-UK/PHWC-PYPWZJ

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Originating lab: Wales Specialist Virology Centre Sequencing lab: Pathogen Genomics Unit

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: COG-UK/PHWC-PYPWZJ

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

text: not provided

text: not provided

text: United Kingdom

text: Wales

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

text: not provided

characteristic: serotype (required for a seropositive sample)

text: COG-UK/PHWC-PYPWZJ

characteristic: title

text: not provided

characteristic: virus identifier


COG-UK/BIRM-BCFAGR

text: University of Birmingham

text: public

text: COG-UK/BIRM-BCFAGR

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: University of Birmingham

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

text: not provided

text: COG-UK/BIRM-BCFAGR

text: not provided


COG-UK/BIRM-BCFTRX

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Birmingham

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: COG-UK/BIRM-BCFTRX

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

text: University of Birmingham

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: receipt date

characteristic: sample capture status

text: not provided

text: COG-UK/BIRM-BCFTRX

text: not provided


COG-UK/BIRM-BCFIYU

text: University of Birmingham

text: public

text: COG-UK/BIRM-BCFIYU

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: University of Birmingham

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

text: not provided

characteristic: serotype (required for a seropositive sample)

text: COG-UK/BIRM-BCFIYU

characteristic: title

text: not provided

characteristic: virus identifier


COG-UK/BIRM-BCFHGY

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Birmingham

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: COG-UK/BIRM-BCFHGY

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

text: University of Birmingham

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

text: not provided

text: COG-UK/BIRM-BCFHGY

text: not provided


text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: embryonic/larval plasmatocyte

text: fruit fly

characteristic: common name

text: Protocols: FLY RAISINGFlies were raised and maintained on standard cornmeal food at 25°C or room temperature. For experiments on wild type OrR, adult fly collections were left to lay eggs on apple juice agar plates with yeast paste overnight at 25°C. After 24h hatched larvae were washed of the plate and further larvae were allowed to hatch for 2h. Then, larvae were picked of the plate and transferred into 36mm food tubes with yeast paste at a density of 120 larvae per tube and raised at 25°C. The resulting larval collection tubes would reach 3rd instar wandering stage around 4 days after hatching, at which stage plasmatocytes were extracted.RNAI CROSSESAll stocks were raised as described above. Virgin females from stock w*;;P{Hmle9-P2A-Gal4}attP2 were collected and crossed to males from TRIP RNAi lines (Set1: 33704; trr: 36916; nej: 27724; Utx: 34076; trx: 33703; luc: 31603; see table xxx) From these crosses, larvae were picked as above, and subjected to septic injury as described below.SEPTIC INJURYSharpened tungsten needles were then used to perform septic injury. The wire was mounted in a Moria pin holder. Larvae were taken from food tubes by washing out all larvae with a 20% sucrose solution. Larvae were quickly washed in PBS, then dried on paper towels and transferred to a rubber dish. Larvae were then pricked with the tungsten needle dipped into the bacterial pellet (septic injury). Larvae were then transferred back into normal food tubes with 3 drops of PBS and incubated at 25°C for the indicated time. For infection time courses plasmatocytes were always extracted around the same time of day at age 92h post hatching, and injuries were performed 6h prior.PLASMATOCYTE ISOLATION FOR DIRECT RNA EXTRACTIONFor plasmatocyte extraction and RNA isolation, treated or untreated 3rd instar wandering larvae were collected from food tubes and washed in PBS. At the same time Schneider’s medium with FCS with 10 mM N-Acetyl-L-Cysteine was prepared in a well of a 24-well tissue culture plate (Sarstedt). Larvae were dried on paper towels and transferred to the tissue culture well with medium. Then they were ripped by holding the head with forceps (Dumont) and with another forceps ripping open the cuticula along the body of the larvae without disrupting the gut. In this ways 80 larvae were bled for each sample. The larval carcass was then removed and the plasmatocytes were allowed to attach for 10-15 minutes. Afterwards, the plasmatocytes were washed 4 times with PBS, then all supernatant was aspirated, they were lysed in 94.5 µl RNAdvance lysis buffer and processed immediately. RNA was isolated from freshly lysed plasmatocytes samples using the RNAdvance cell v2 kit following manufacturer’s instructions using a DynaMag-2 magnetic rack. DNase digestion was performed as suggested in the manual using Ambion DNase. Resulting RNA samples were eluted in 20 µl ultra-pure water and stored at -80°C. Libraries were generated by the Max Planck Genome Centre (Cologne). Libraries were stranded, from polyA enriched RNA.

characteristic: description

text: third instar larva stage

characteristic: developmental stage

text: luc

characteristic: genotype

text: mixed

characteristic: individual

text: septic injury

characteristic: injury

text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: embryonic/larval hemolymph

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: w*

characteristic: strain


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

characteristic: SRA accession

text: ArrayExpress

text: embryonic/larval plasmatocyte

text: fruit fly

text: third instar larva stage

text: nej

text: mixed

text: septic injury

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: embryonic/larval hemolymph

text: Drosophila melanogaster

text: mixed

text: w*

characteristic: title


text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: embryonic/larval plasmatocyte

text: fruit fly

characteristic: common name

characteristic: description

text: third instar larva stage

characteristic: developmental stage

characteristic: genotype

text: mixed

text: septic injury

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: embryonic/larval hemolymph

text: Drosophila melanogaster

text: mixed

text: w*


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: embryonic/larval plasmatocyte

text: fruit fly

text: third instar larva stage

text: trr

text: mixed

characteristic: individual

text: septic injury

characteristic: injury

text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: embryonic/larval hemolymph

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: w*

characteristic: strain


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: ArrayExpress

text: embryonic/larval plasmatocyte

text: fruit fly

text: third instar larva stage

text: trx

text: mixed

text: septic injury

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: embryonic/larval hemolymph

text: Drosophila melanogaster

text: mixed

text: w*

characteristic: title


text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: embryonic/larval plasmatocyte

text: fruit fly

characteristic: common name

characteristic: description

text: third instar larva stage

characteristic: developmental stage

text: Utx

characteristic: genotype

text: mixed

text: septic injury

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: embryonic/larval hemolymph

text: Drosophila melanogaster

text: mixed

text: w*


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: embryonic/larval plasmatocyte

text: fruit fly

text: third instar larva stage

text: luc

text: mixed

characteristic: individual

characteristic: injury

text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: embryonic/larval hemolymph

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: w*

characteristic: strain


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: ArrayExpress

text: embryonic/larval plasmatocyte

text: fruit fly

text: third instar larva stage

text: nej

text: mixed

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: embryonic/larval hemolymph

text: Drosophila melanogaster

text: mixed

text: w*

characteristic: title


text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: embryonic/larval plasmatocyte

text: fruit fly

characteristic: common name

characteristic: description

text: third instar larva stage

characteristic: developmental stage

characteristic: genotype

text: mixed

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: embryonic/larval hemolymph

text: Drosophila melanogaster

text: mixed

text: w*


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: embryonic/larval plasmatocyte

text: fruit fly

text: third instar larva stage

text: trr

text: mixed

characteristic: individual

characteristic: injury

text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: embryonic/larval hemolymph

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: w*

characteristic: strain


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: ArrayExpress

text: embryonic/larval plasmatocyte

text: fruit fly

text: third instar larva stage

text: trx

text: mixed

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: embryonic/larval hemolymph

text: Drosophila melanogaster

text: mixed

text: w*

characteristic: title


text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: embryonic/larval plasmatocyte

text: fruit fly

characteristic: common name

characteristic: description

text: third instar larva stage

characteristic: developmental stage

text: Utx

characteristic: genotype

text: mixed

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: embryonic/larval hemolymph

text: Drosophila melanogaster

text: mixed

text: w*


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: luciferase siRNA

characteristic: RNA interference

tag: Namespace:Gehring Lab Institute for Genetics  University of Cologne

unit: year

text: ArrayExpress

text: HeLa Tet-Off

text: epithelial cell

text: human

text: Protocols: HeLa Tet-Off (Clontech) cells were maintained at 37° C, 5% CO2 and 90% humidity in Dublecco’s Modified Eagle Medium (DMEM, Thermo Fisher Scientific) supplemented with 9% fetal bovine serum (FBS) and Penicillin-Streptomycin (both Thermo Fisher Scientific). For siRNA transfection, cells were reverse transfected with 60 pmol siRNA targeting EIF4A3, RBM8A or MAGOH+MAGOHB (or Luc in the negative control) per 2-3 x 10^5 cells using 2.5 μl Lipofectamine RNAiMAX. Total RNA was extracted using peqGOLD TriFast (VWR Peqlab), followed by using the DIRECTzol Miniprep Kit (Zymo Research) according to the manufacturer's instructions. Ribosomal depletion and strand specific library preparation was carried out with TruSeq Stranded Total RNA (with Ribo-Zero Gold) according to the manufacturer's instructions.

text: adult

text: cervical adenocarcinoma

characteristic: disease

text: African American

characteristic: ethnic group

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: uterine cervix

characteristic: organism part

characteristic: replicate

text: Homo sapiens

text: female

characteristic: sex

text: SIRV-Set 1: E0

characteristic: spike in


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Gehring Lab Institute for Genetics  University of Cologne

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: luciferase siRNA

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: HeLa Tet-Off

text: epithelial cell

text: human

text: adult

text: cervical adenocarcinoma

text: African American

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: uterine cervix

text: Homo sapiens

text: female

text: SIRV-Set 1: E0

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: EIF4A3 knockdown by siRNA

characteristic: RNA interference

text: ArrayExpress

characteristic: broker name

text: HeLa Tet-Off

text: epithelial cell

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: cervical adenocarcinoma

characteristic: disease

text: African American

text: stably integrated PB-CuO-FLAG_EIF4A3

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: uterine cervix

text: Homo sapiens

text: female

text: SIRV-Set 1: E2


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: RBM8A knockdown by siRNA

text: ArrayExpress

text: HeLa Tet-Off

text: epithelial cell

text: human

text: adult

text: cervical adenocarcinoma

text: African American

characteristic: ethnic group

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: uterine cervix

characteristic: organism part

characteristic: replicate

text: Homo sapiens

text: female

characteristic: sex

text: SIRV-Set 1: E1

characteristic: spike in


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: MAGOH and MAGOHB knockdown by siRNA

characteristic: RNA interference

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: HeLa Tet-Off

text: epithelial cell

text: human

text: adult

text: cervical adenocarcinoma

text: African American

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: uterine cervix

text: Homo sapiens

text: female

text: SIRV-Set 1: E2

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: EIF4A3 knockdown by siRNA

text: ArrayExpress

text: HeLa Tet-Off

text: epithelial cell

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: cervical adenocarcinoma

characteristic: disease

text: African American

text: wild type genotype

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: uterine cervix

text: Homo sapiens

text: female

text: SIRV-Set 1: E1


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: luciferase siRNA

text: ArrayExpress

text: epithelial cell

text: human

text: Protocols: Flp-In 293 T-REx (Thermo Fisher Scientific) cells were maintained at 37° C, 5% CO2 and 90% humidity in Dublecco’s Modified Eagle Medium (DMEM, Thermo Fisher Scientific) supplemented with 9% fetal bovine serum (FBS) and Penicillin-Streptomycin (both Thermo Fisher Scientific). For siRNA transfection, cells were reverse transfected with 60 pmol siRNA targeting RNPS1 (or Luc in the negative control) per 2-3 x 10^5 cells using 2.5 μl Lipofectamine RNAiMAX. Total RNA was extracted using RNA Solv Reagent (Omega Bio-Tek), followed by using the DIRECTzol Miniprep Kit (Zymo Research) according to the manufacturer's instructions. Ribosomal depletion and strand specific library preparation was carried out with TruSeq Stranded Total RNA (with Ribo-Zero Gold) according to the manufacturer's instructions.

text: late embryonic stage

text: normal

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

characteristic: replicate

text: Homo sapiens

text: female

characteristic: sex

text: SIRV-Set 1: E0

characteristic: spike in


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: RNPS1 knockdown by siRNA

characteristic: RNA interference

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: human

text: late embryonic stage

text: normal

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

text: female

text: SIRV-Set 1: E1

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

text: public

text: RNPS1 knockdown by siRNA

text: ArrayExpress

text: epithelial cell

text: human

characteristic: common name

characteristic: description

text: late embryonic stage

characteristic: developmental stage

text: normal

characteristic: disease

text: Stably integrated PB-CuO-FLAG_emGFP_RNPS1_WT

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

text: female

text: SIRV-Set 1: E2


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: RNPS1 knockdown by siRNA

text: ArrayExpress

text: epithelial cell

text: human

text: late embryonic stage

text: normal

text: Stably integrated PB-CuO-FLAG_emGFP_RNPS1_RRM

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

characteristic: replicate

text: Homo sapiens

text: female

characteristic: sex

text: SIRV-Set 1: E2

characteristic: spike in


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Northumbria University / South Tees Hospitals NHS Foundation Trust / North Cumbria Integrated Care NHS Foundation Trust / North Tees and Hartlepool NHS Foundation Trust / Newcastle Hospitals NHS Foundation Trust

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

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

characteristic: receipt date

text: active surveillance in response to outbreak

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

characteristic: title

text: not provided

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Quadram Institute Bioscience

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: Quadram Institute Bioscience

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

text: not provided

text: not provided


text: Virology Department, Sheffield Teaching Hospitals NHS Foundation Trust/Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield

text: public

text: COVID-19 Genomics UK Consortium

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: receipt date

characteristic: sample capture status

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Birmingham

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

text: University of Birmingham

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

text: not provided

characteristic: serotype (required for a seropositive sample)

characteristic: title

text: not provided

characteristic: virus identifier


text: public

tag: Namespace:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY

text: MAC+IES genome produced by BleTIES

characteristic: description

text: Blepharisma stoltei

characteristic: organism

text: Blepharisma stoltei

characteristic: strain

text: Micronuclear genome of Blepharisma stoltei strain ATCC 30299


text: MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY

text: public

text: Nuclei from bottom (B) fraction of sucrose gradient.

text: Blepharisma stoltei

text: Blepharisma stoltei


text: public

text: Nuclei from middle lower (ML) fraction of sucrose gradient.

text: Blepharisma stoltei

text: Blepharisma stoltei


text: public

text: Nuclei from middle upper (M) fraction of sucrose gradient.

text: Blepharisma stoltei

text: Blepharisma stoltei


text: public

text: Nuclei from top (T) fraction of sucrose gradient.

text: Blepharisma stoltei

text: Blepharisma stoltei


text: CENTRE FOR GEOGENETICS

text: public

tag: Namespace:CENTRE FOR GEOGENETICS

text: University of Alberta

text: dog

characteristic: common name

text: Archaeological material

text: Russia

characteristic: geographic location (country and/or sea)

text: Canis lupus familiaris

text: Canis lupus familiaris

text: bone

text: Ancient DNA Dog sample


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Universite Toulouse III - Paul Sabatier

text: public

tag: Namespace:Universite Toulouse III - Paul Sabatier

characteristic: collection date

text: midwife toad

text: mountain habitat

characteristic: environment (biome)

text: lake

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: France

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: skin

characteristic: host body habitat

text: midwife toad

characteristic: host common name

text: host-associated

characteristic: host-associated environmental package

characteristic: investigation type

text: Alytes obstetricans

text: tadpoles skin microbiome

characteristic: project name

text: Alytes obstetricans

text: Next Generation Sequencing Illumina

characteristic: sequencing method

text: 16S rRNA gene

characteristic: target gene


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Universite Toulouse III - Paul Sabatier

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: common toad

characteristic: common name

text: mountain habitat

text: lake

text: water

text: France

text: skin

text: common toad

text: host-associated

text: Bufo bufo

characteristic: organism

text: tadpoles skin microbiome

text: Bufo bufo

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