characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: bone marrow macrophage

text: house mouse

text: adult

text: normal

text: MEF2A knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: A

characteristic: replicate

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:San Raffaele Telethon Institute for Gene Therapy.

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: bone marrow macrophage

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: Bone marrow cells were collected from femurs and tibias in 50 mL PBS, filtered through a 70 µm cell strainer and centrifuged 450 x g for 5 minutes. Red blood cells were lysed using 0.2% NaCl solution, followed by 1.6% NaCl solution. Cells were filtered through a 70 µm cell strainer and centrifuged 450 x g for 5 minutes. 5 x 10^4 - 5 x 10^6 bone marrow cells were plated and cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% Fetal Bovine Serum (FBS), 20% L929-conditioned medium containing M-CSF, antibiotics (penicillin G 100 U/ml and streptomycin sulfate 100 U/ml), 2 mM L-glutamine and 5 µM 2-mercaptoethanol. After six days of culture, adherent cells were >99% Cd11b+ F4/80+, as assessed by flow cytometry BMDMs or iMACs were stimulated for four hours with the indicated stimuli Total RNA was extracted using ReliaPrep RNA Cell Miniprep System and quantified using NanoDrop 8000. RNA-Seq libraries were generated using the Smart-seq2 method (Picelli et al., 2014). Five ng of RNA were retrotranscribed, cDNA was PCR-amplified (15 cycles) and purified with AMPure XP beads. After purification, the concentration was determined using Qubit 3.0 and size distribution was assessed using Agilent 4200 TapeStation system. Then, the tagmentation reaction was performed starting from 0.5 ng of cDNA for 30 minutes at 55°C and the enrichment PCR was carried out using 12 cycles. Libraries were then purified with AMPure XP beads, quantified using Qubit 3.0 and sequenced.

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: MEF2A knockout

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: A

text: Mus musculus

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: San Raffaele Telethon Institute for Gene Therapy.

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: bone marrow macrophage

text: house mouse

text: adult

text: normal

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: A

characteristic: replicate

text: Mus musculus

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 6 to 10

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: primary cell line

text: bone marrow macrophage

text: house mouse

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

text: A

text: Mus musculus

text: male

characteristic: strain


characteristic: ENA-LAST-UPDATE

text: public

text: 6 to 10

text: ArrayExpress

text: primary cell line

characteristic: cell line

text: bone marrow macrophage

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: B

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: anonymized name

text: True

characteristic: elevation

text: Host-asssociated

text: Animal-associated

text: Animal secretion

text: urban biome

characteristic: env biome

text: human-associated habit

characteristic: env feature

text: human-oral

characteristic: env package

text: saliva

text: Australia:SA:Adelaide

characteristic: geo loc name

characteristic: host age

text: UBERON:oral cavity

characteristic: host body habitat

text: restricted access

characteristic: host body mass index

text: UBERON:saliva

characteristic: host body product

text: UBERON:mouth

characteristic: host body site

text: human

characteristic: host common name

text: restricted access

characteristic: host height

text: child

characteristic: host life stage

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: restricted access

characteristic: host weight

text: years

text: restricted access

text: restricted access

characteristic: latitude

characteristic: longitude

text: human oral metagenome

text: UofAdelaide

text: False

characteristic: sample type

text: human oral metagenome

text: Female

characteristic: sex

text: Buccal and gingival microbiota of children with type 1 diabetes


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: anonymized name

characteristic: description

text: True

characteristic: elevation

text: Host-asssociated

text: Animal-associated

text: Animal secretion

text: urban biome

characteristic: env biome

text: human-associated habit

characteristic: env feature

text: human-oral

characteristic: env package

text: saliva

text: Australia:SA:Adelaide

characteristic: geo loc name

text: UBERON:oral cavity

text: restricted access

text: UBERON:saliva

text: UBERON:mouth

text: human

text: restricted access

text: child

text: Homo sapiens

text: restricted access

text: years

text: restricted access

text: restricted access

text: human oral metagenome

characteristic: organism

text: UofAdelaide

text: False

text: human oral metagenome

text: Male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UCSDMI

text: public

text: True

text: Host-asssociated

text: Animal-associated

text: Animal secretion

text: urban biome

text: human-associated habit

text: human-oral

text: saliva

text: Australia:SA:Adelaide

characteristic: host age

text: UBERON:oral cavity

characteristic: host body habitat

text: restricted access

characteristic: host body mass index

text: UBERON:saliva

characteristic: host body product

text: UBERON:mouth

characteristic: host body site

text: human

characteristic: host common name

text: restricted access

characteristic: host height

text: child

characteristic: host life stage

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: restricted access

characteristic: host weight

text: years

text: restricted access

text: restricted access

characteristic: latitude

characteristic: longitude

text: human oral metagenome

text: UofAdelaide

text: False

characteristic: sample type

text: human oral metagenome

text: Female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: anonymized name

characteristic: description

text: True

characteristic: elevation

text: Host-asssociated

text: Animal-associated

text: Animal secretion

text: urban biome

characteristic: env biome

text: human-associated habit

characteristic: env feature

text: human-oral

characteristic: env package

text: saliva

text: Australia:SA:Adelaide

characteristic: geo loc name

text: UBERON:oral cavity

text: restricted access

text: UBERON:saliva

text: UBERON:mouth

text: human

text: restricted access

text: child

text: Homo sapiens

text: restricted access

text: years

text: restricted access

text: restricted access

text: human oral metagenome

characteristic: organism

text: UofAdelaide

text: False

text: human oral metagenome

text: Male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UCSDMI

text: public

text: True

text: Control

text: Negative

text: Sterile water blank

text: urban biome

text: research facility

text: misc environment

text: sterile water

text: Australia:SA:Adelaide

characteristic: latitude

characteristic: longitude

text: metagenome

text: UofAdelaide

text: False

characteristic: sample type

text: metagenome


characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: True

text: Control

text: Negative

text: Sterile water blank

text: urban biome

text: research facility

text: misc environment

text: sterile water

text: Australia:SA:Adelaide

text: metagenome

text: UofAdelaide

text: False

text: metagenome


text: UCSDMI

text: public

characteristic: Submitter Id

text: PCRneg

characteristic: description

text: True

characteristic: elevation

text: Control

text: Negative

text: Sterile water blank

text: urban biome

characteristic: env biome

text: research facility

characteristic: env feature

text: misc environment

text: sterile water

text: Australia:SA:Adelaide

text: metagenome

text: UofAdelaide

text: False

text: PCRneg

text: metagenome


characteristic: ENA-CHECKLIST

text: UCSDMI

text: public

text: PCRneg

text: True

text: Control

text: Negative

text: Sterile water blank

text: urban biome

text: research facility

text: misc environment

characteristic: env package

text: sterile water

text: Australia:SA:Adelaide

characteristic: geo loc name

text: metagenome

characteristic: organism

text: UofAdelaide

text: False

text: PCRneg

text: metagenome

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UCSDMI

text: public

text: BlankSwab

text: True

text: Control

text: Negative

text: Sterile water blank

text: urban biome

text: research facility

text: misc environment

text: sterile water

text: Australia:SA:Adelaide

characteristic: latitude

characteristic: longitude

text: metagenome

text: UofAdelaide

text: False

text: BlankSwab

characteristic: sample type

text: metagenome


characteristic: External Id

text: COLD SPRING HARBOR LAB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:COLD SPRING HARBOR LAB

characteristic: collection date

text: sorghum

characteristic: common name

text: USA

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: growth chamber

characteristic: isolation and growth condition

text: Sorghum bicolor

text: seedling

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: leaf

characteristic: plant structure

text: Sorghum bicolor


E-MTAB-9287:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

text: E-MTAB-9287:Sample 1

tag: Namespace:UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: The blood samples of two sporadic non-obstructive azoospermia (NOA) patients were collected in this study. Total genomic DNA (gDNA) isolated from peripheral blood of non-obstructive azoospermia (NOA) patients using the QIAamp DNA Blood Mini Kit (QIAGEN) according to the manufacturer’s instructions. An Agilent SureSelect Human All Exon v5 Kit was used to capture the known exons and exon-intron boundary sequences. DNA libraries were prepared according to the provided manufacturer’s protocol.

characteristic: description

text: adult

characteristic: developmental stage

text: azoospermia

characteristic: disease

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: Sample 1

characteristic: title


E-MTAB-9287:Sample 2

characteristic: External Id

text: UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-9287:Sample 2

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: azoospermia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: male

text: Sample 2


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

tag: Namespace:Laboratory of Angiogenesis and Vascular Metabolism VIB-KU Leuven Center for Cancer Biology (CCB)

text: ArrayExpress

text: endothelial cell

characteristic: cell type

text: house mouse

text: Protocols: RENCA cells were injected into the tail vein of the mice using a 29G needle (2 × 105 cells in 0.1 mL phosphate buffered saline (PBS)). The animals were sacrificed on day 10, day 21 or day 36 of the experiment and lungs were immediately processed for metastatic cell or EC isolation. Mice were treated with Sunitinib (LC laboratories) (40 mg/kg i.p., every day), or with a control vehicle (0.5% carboxymethylcellulose sodium, 1.8% w/v NaCl, 0.4% w/v Tween 80, 0.9% w/v benzyl alcohol dissolved in reverse osmosis deionized water adjusted to pH 6) by daily gavage of 0.2 mL. Mice were randomly allocated to the treatment condition, balanced for body weight; treatment was started from day 10 after injection of RENCA cells and continued until day 20 (Bridgeman et al., 2017) or day 35. For metastatic cells and TECs, 5 mice per treatment group were anesthetized and killed via cervical dislocation, lungs were dissected and placed under a dissection microscope. Per mouse, at least 60 metastases were micro-dissected. For NECs, control (non-tumor bearing) mice were anesthetized, lungs were perfused with 5 mL PBS at 120 mL/h and both lungs were dissected. The dissected tissue was placed into a GentleMACS C Tube (Miltenyi Biotec) containing 5 mL of digestion buffer on ice (0.1% collagenase II (Thermo Fisher Scientific), 0.25% collagenase IV (Worthington Biochemical) and DNase I (15 M) in DMEM supplemented with 1x sodium pyruvate, 1x MEM NEAAs, ECGF/Heparin, antibiotic/antimycotic (2x) and 1% penicillin/streptomycin (Thermo Fisher Scientific)). The dissected tissues were dissociated using the gentleMACSTM Dissociator (Miltenyi Biotec; on m_lung_01 protocol) and incubated in a water bath at 37°C for 30 min with manual shaking every 5 min. At the end of the tissue digestion process, the samples were again placed in the gentleMACSTM Dissociator (Miltenyi Biotec; on m_lung_02 protocol) and the reaction was stopped by adding 10 mL of an isolation buffer containing PBS, 0.5% BSA and 40 mM EDTA. Subsequently, the cell suspension was filtered through a 40 μm cell strainer (Sigma-Aldrich) and cells were rinsed with isolation buffer. Next, for TECs and NECs, ECs were enriched by magnetic bead sorting using the MACS system (Miltenyi Biotec) at room temperature. First, immune cells and epithelial cells were depleted using selection with CD45 and CD326 MicroBeads (Miltenyi Biotec), followed by positive selection of ECs with CD31 MicroBeads (Miltenyi Biotec), using LS and MS columns (Miltenyi Biotec), according to the manufacturer’s instructions. For further processing for scRNA-seq, the samples were resuspended in PBS containing 0.4% UltraPure BSA (50 mg/mL; Thermo Fisher Scientific) and filtered over 40 μm cell strainers on ice. Overall, it took between 3 to 4 h from obtaining metastases collection to obtaining single cell EC suspensions. For metastatic cells, no selection procedure was applied and it took between 1 to 2 h from collecting metastases to generating single cell metastatic cell suspensions. Nucleic acid extraction was done in single cells using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit and Chip Kit (v2, 10x Genomics) according to manufacturer’s instructions. The single cell suspensions of freshly isolated metastatic cells and ECs (MACS-bead enriched as described above) were resuspended in PBS with 0.04% ultra-pure BSA and converted to barcoded scRNA-seq libraries using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics), aiming for 6,000 cells per library. Samples were processed using kits pertaining to V2 barcoding chemistry of 10x Genomics. Single samples were always processed in a single well of a PCR plate, allowing all cells from a sample to be treated with the same master mix and in the same reaction vessel.

text: adult

text: wild type genotype

characteristic: genotype

text: control

characteristic: growth condition

text: unique pool of 5 mice

text: Mus musculus

text: Mus musculus

text: lung

text: Mus musculus


text: Laboratory of Angiogenesis and Vascular Metabolism VIB-KU Leuven Center for Cancer Biology (CCB)

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: endothelial cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

text: injected with Renca renal carcinoma cells

text: unique pool of 5 mice

characteristic: individual

text: Mus musculus

characteristic: organism

text: Mus musculus

text: lung

text: Mus musculus


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: metastatic cell

text: house mouse

text: adult

text: wild type genotype

text: unique pool of 5 mice

text: Mus musculus

text: Mus musculus

text: lung

characteristic: organism part

text: Mus musculus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: COLD SPRING HARBOR LAB

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collection date

text: sorghum

characteristic: common name

text: USA

characteristic: geographic location (country and/or sea)

text: N 36° 6.377'

characteristic: geographic location (latitude)

text: W 97° 5.3975'

characteristic: geographic location (longitude)

text: field

characteristic: isolation and growth condition

text: Sorghum bicolor

text: adult stage

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: leaf

characteristic: plant structure

text: Sorghum bicolor


Sensitive

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: COLD SPRING HARBOR LAB

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: Sensitive

characteristic: Submitter Id

text: sorghum

text: A pool of SCA sensitive RIL

characteristic: description

text: USA

text: N 36° 6.377'

text: W 97° 5.3975'

text: field

text: Sorghum bicolor

characteristic: organism

text: adult stage

text: soil

text: leaf

text: Sorghum bicolor

text: Sensitive


Resistance

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: COLD SPRING HARBOR LAB

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Resistance

text: sorghum

text: A pool of SCA Resistance RIL

text: USA

text: N 36° 6.377'

text: W 97° 5.3975'

text: field

text: Sorghum bicolor

text: adult stage

text: soil

text: leaf

text: Sorghum bicolor

text: Resistance

characteristic: title


text: EMBL

text: public

text: 6 to 8

unit: hour

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: Protocols: Wildtype flies were held in population cages at 25°C. After three one-hour pre-lays, embryos were collected at the indicated time (please see ???age???) after egg laying. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 1.8 % formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at room temperature for 15 minutes. The reaction was terminated with ice-cold 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. 0.5-1 g of frozen embryos were dounce-homogenized, 20 times with a loose pestle and 10 times with a tight pestle, in 10 ml of chilled HB buffer (15 mM Tris-HCl (pH 7.4), 0.34 M sucrose, 15 mM NaCl, 60 mM KCl, 0.2 mM EDTA and 0.2 mM EGTA) on ice. The lysate was filtered through 2 layers of Miracloth and spun at 3,500g for 10 min to pellet the nuclei. The nuclei were then washed in 10 ml of chilled HB buffer, spun at 3,500g for 10 min and resuspended in 3 ml of PBTB buffer (5% (wt/vol) BSA, 0.1% (vol/vol) Triton X-100 in PBS). The nuclei were dissociated by passing them ten times through a 20-G needle and then ten times through a 22-G needle using a 5-ml syringe, and filtered through a 20-??m Sefar Nitex membrane. The total number of nuclei was determined using a flow cytometer or cell counter. Sorting of nuclei was performed similar to what has been described in Bonn et al., 2012. Four aliquots of 25 million nuclei were used for preparation of the 3C library for each sample. 3C samples and Capture-C libraries were prepared as previously described (Davies et al. 2016, Ghavi-Helm et al., 2019), using DpnII as restriction enzyme and performing the ligation stepin nucleus. The template was then processed with the Roche Nimblegen SeqCap EZ Library SR system and a double capture strategy.

text: majority stage 10-11 embryos

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

text: non-mesoderm, non-nervous system

characteristic: organism part

text: Elav negative and Mef2 negative

characteristic: phenotype

text: Drosophila melanogaster

text: mixed

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-9310:TS_Capture_CRM_10-12h_DN_Rep2

characteristic: Submitter Id

text: 10 to 12

text: ArrayExpress

text: fruit fly

characteristic: description

text: majority stage 13-14 embryos

text: wild type genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: non-mesoderm, non-nervous system

text: Elav negative and Mef2 negative

text: Drosophila melanogaster

text: mixed


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-9310:TS_Capture_CRM_10-12h_DN_Rep3

text: 10 to 12

text: ArrayExpress

text: fruit fly

text: majority stage 13-14 embryos

text: wild type genotype

text: egg laying

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: non-mesoderm, non-nervous system

text: Elav negative and Mef2 negative

text: Drosophila melanogaster

text: mixed


text: EMBL

text: public

text: E-MTAB-9310:TS_Capture_TSS_10-12h_DN_Rep2

text: 10 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: majority stage 13-14 embryos

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: non-mesoderm, non-nervous system

text: Elav negative and Mef2 negative

text: Drosophila melanogaster

text: mixed

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

text: E-MTAB-9310:TS_Capture_CRM_10-12h_DN_Rep1

text: 10 to 12

text: ArrayExpress

text: fruit fly

text: majority stage 13-14 embryos

text: wild type genotype

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

text: non-mesoderm, non-nervous system

characteristic: organism part

text: Elav negative and Mef2 negative

characteristic: phenotype

text: Drosophila melanogaster

text: mixed

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-9310:TS_Capture_TSS_10-12h_DN_Rep1

characteristic: Submitter Id

text: 10 to 12

text: ArrayExpress

text: fruit fly

characteristic: description

text: majority stage 13-14 embryos

text: wild type genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: non-mesoderm, non-nervous system

text: Elav negative and Mef2 negative

text: Drosophila melanogaster

text: mixed


text: EMBL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-9310:TS_Capture_TSS_10-12h_DN_Rep3

text: 10 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: majority stage 13-14 embryos

text: wild type genotype

text: egg laying

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: non-mesoderm, non-nervous system

text: Elav negative and Mef2 negative

text: Drosophila melanogaster

text: mixed


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

text: E-MTAB-9310:TS_Capture_CRM_10-12h_DN_Rep4

text: 10 to 12

text: ArrayExpress

text: fruit fly

characteristic: common name

text: majority stage 13-14 embryos

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: non-mesoderm, non-nervous system

text: Elav negative and Mef2 negative

text: Drosophila melanogaster

text: mixed

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL

text: public

text: E-MTAB-9310:TS_Capture_TSS_10-12h_DN_Rep4

text: 10 to 12

text: ArrayExpress

text: fruit fly

text: majority stage 13-14 embryos

text: wild type genotype

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

text: non-mesoderm, non-nervous system

characteristic: organism part

text: Elav negative and Mef2 negative

characteristic: phenotype

text: Drosophila melanogaster

text: mixed

characteristic: sex


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-9310:TS_Capture_CRM_10-12h_elav_Rep1

characteristic: Submitter Id

text: 10 to 12

text: ArrayExpress

text: fruit fly

characteristic: description

text: majority stage 13-14 embryos

text: wild type genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: nervous system

text: Elav positive nuclei

text: Drosophila melanogaster

text: mixed


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

characteristic: INSDC status

text: E-MTAB-9310:TS_Capture_CRM_10-12h_elav_Rep2

text: 10 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: majority stage 13-14 embryos

text: wild type genotype

text: egg laying

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: nervous system

text: Elav positive nuclei

text: Drosophila melanogaster

text: mixed


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL

text: public

text: E-MTAB-9310:TS_Capture_TSS_10-12h_elav_Rep2

text: 10 to 12

text: ArrayExpress

text: fruit fly

characteristic: common name

text: majority stage 13-14 embryos

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: nervous system

text: Elav positive nuclei

text: Drosophila melanogaster

text: mixed

characteristic: title


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9310:TS_Capture_TSS_6-8h_elav_Rep1

text: 6 to 8

text: ArrayExpress

text: fruit fly

text: majority stage 10-11 embryos

text: wild type genotype

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

text: nervous system

characteristic: organism part

text: Elav positive nuclei

characteristic: phenotype

text: Drosophila melanogaster

text: mixed

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-9310:TS_Capture_TSS_10-12h_elav_Rep1

characteristic: Submitter Id

text: 10 to 12

text: ArrayExpress

text: fruit fly

characteristic: description

text: majority stage 13-14 embryos

text: wild type genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: nervous system

text: Elav positive nuclei

text: Drosophila melanogaster

text: mixed


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL

text: public

characteristic: INSDC status

text: E-MTAB-9310:TS_Capture_TSS_6-8h_elav_Rep2

text: 6 to 8

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: majority stage 10-11 embryos

text: wild type genotype

text: egg laying

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: nervous system

text: Elav positive nuclei

text: Drosophila melanogaster

text: mixed


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9310:TS_Capture_CRM_6-8h_elav_Rep2

text: 6 to 8

text: ArrayExpress

text: fruit fly

characteristic: common name

text: majority stage 10-11 embryos

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: nervous system

text: Elav positive nuclei

text: Drosophila melanogaster

text: mixed

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

text: E-MTAB-9310:TS_Capture_CRM_6-8h_elav_Rep1

text: 6 to 8

text: ArrayExpress

text: fruit fly

text: majority stage 10-11 embryos

text: wild type genotype

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

text: nervous system

characteristic: organism part

text: Elav positive nuclei

characteristic: phenotype

text: Drosophila melanogaster

text: mixed

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-9310:TS_Capture_CRM_6-8h_Mef2_Rep1

characteristic: Submitter Id

text: 6 to 8

text: ArrayExpress

text: fruit fly

text: Protocols: Wildtype flies were held in population cages at 25°C. After three one-hour pre-lays, embryos were collected at the indicated time (please see ???age???) after egg laying. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 1.8 % formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at room temperature for 15 minutes. The reaction was terminated with ice-cold 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. 0.5-1 g of frozen embryos were dounce-homogenized, 20 times with a loose pestle and 10 times with a tight pestle, in 10 ml of chilled HB buffer (15 mM Tris-HCl (pH 7.4), 0.34 M sucrose, 15 mM NaCl, 60 mM KCl, 0.2 mM EDTA and 0.2 mM EGTA) on ice. The lysate was filtered through 2 layers of Miracloth and spun at 3,500g for 10 min to pellet the nuclei. The nuclei were then washed in 10 ml of chilled HB buffer, spun at 3,500g for 10 min and resuspended in 3 ml of PBTB buffer (5% (wt/vol) BSA, 0.1% (vol/vol) Triton X-100 in PBS). The nuclei were dissociated by passing them ten times through a 20-G needle and then ten times through a 22-G needle using a 5-ml syringe, and filtered through a 20-??m Sefar Nitex membrane. The total number of nuclei was determined using a flow cytometer or cell counter. Sorting of nuclei was performed similar to what has been described in Bonn et al., 2012. Four aliquots of 25 million nuclei were used for preparation of the 3C library for each sample. 3C samples and Capture-C libraries were prepared as previously described (Davies et al. 2016, Ghavi-Helm et al., 2019), using DpnII as restriction enzyme and performing the ligation stepin nucleus. The template was then processed with the Roche Nimblegen SeqCap EZ Library SR system and a double capture strategy.

characteristic: description

text: majority stage 10-11 embryos

text: wild type genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mesoderm

text: Mef2 positive cells

text: Drosophila melanogaster

text: mixed


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-9310:TS_Capture_TSS_10-12h_Mef2_Rep1

text: 10 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: majority stage 13-14 embryos

text: wild type genotype

text: egg laying

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: mesoderm

text: Mef2 positive cells

text: Drosophila melanogaster

text: mixed


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

text: E-MTAB-9310:TS_Capture_TSS_6-8h_Mef2_Rep2

text: 6 to 8

text: ArrayExpress

text: fruit fly

characteristic: common name

text: majority stage 10-11 embryos

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mesoderm

text: Mef2 positive cells

text: Drosophila melanogaster

text: mixed

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL

text: public

text: E-MTAB-9310:TS_Capture_TSS_10-12h_Mef2_Rep2

text: 10 to 12

text: ArrayExpress

text: fruit fly

text: majority stage 13-14 embryos

text: wild type genotype

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mesoderm

characteristic: organism part

text: Mef2 positive cells

characteristic: phenotype

text: Drosophila melanogaster

text: mixed

characteristic: sex


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-9310:TS_Capture_TSS_6-8h_Mef2_Rep1

characteristic: Submitter Id

text: 6 to 8

text: ArrayExpress

text: fruit fly

characteristic: description

text: majority stage 10-11 embryos

text: wild type genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mesoderm

text: Mef2 positive cells

text: Drosophila melanogaster

text: mixed


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

characteristic: INSDC status

text: E-MTAB-9310:TS_Capture_CRM_10-12h_Mef2_Rep2

text: 10 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: majority stage 13-14 embryos

text: wild type genotype

text: egg laying

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: mesoderm

text: Mef2 positive cells

text: Drosophila melanogaster

text: mixed


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL

text: public

text: E-MTAB-9310:TS_Capture_CRM_10-12h_Mef2_Rep1

text: 10 to 12

text: ArrayExpress

text: fruit fly

characteristic: common name

text: majority stage 13-14 embryos

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mesoderm

text: Mef2 positive cells

text: Drosophila melanogaster

text: mixed

characteristic: title


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9310:TS_Capture_CRM_6-8h_Mef2_Rep2

text: 6 to 8

text: ArrayExpress

text: fruit fly

text: majority stage 10-11 embryos

text: wild type genotype

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mesoderm

characteristic: organism part

text: Mef2 positive cells

characteristic: phenotype

text: Drosophila melanogaster

text: mixed

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 2 to 3

text: ArrayExpress

text: fruit fly

characteristic: description

text: majority stage 5 embryos

text: wild type genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: whole embryo

text: Drosophila melanogaster

text: mixed


E-MTAB-9296:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

text: E-MTAB-9296:Sample 1

tag: Namespace:Department of Immunology, Genetics and Pathology, Uppsala University, Sweden

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: glial brain cell

characteristic: cell type

text: human

text: Protocols: Four days before the time series start point, 8*10^5 passage 6 U3065MG cells were infected with the BFP expressing Perturbseq lentivirus at a MOI of < 0.1. Cells were incubated with the lentivirus as a single cell suspension in 20 µl of media for 4 hours at 37°C and seeded onto a laminin coated 60 mm dish. The next day, virus containing media was replaced with fresh media. At experimental day 0, 2500 BFP positive U3065 cells (CVCL_IR87) were sorted into one well on a 96 well plate coated with laminin. Cells were allowed to grow under stem cell conditions, and culture media was changed at day 3, 10 and 17. At experimental day 7 and 14, all cells were detached and 80% of the cells frozen down in media with 10% DMSO in -150°C, while the remaining 20% were seeded into a new well. After 21 days at the experimental endpoint, all cells were frozen down. Cells were washed in 0.1% BSA in PBS before library preparation with the Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 according to the manufacturer’s instructions. Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3.

text: adult

text: glioblastoma multiforme

characteristic: disease

text: U6:sgRNA-EIFa-BFP vector

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: brain

text: Homo sapiens

text: Sample 1


E-MTAB-9296:Sample 2

text: Department of Immunology, Genetics and Pathology, Uppsala University, Sweden

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9296:Sample 2

text: ArrayExpress

text: glial brain cell

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: glioblastoma multiforme

text: U6:sgRNA-EIFa-BFP vector

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: brain

characteristic: organism part

text: Homo sapiens

text: Sample 2

characteristic: title


E-MTAB-9296:Sample 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-9296:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: glial brain cell

text: human

text: adult

text: glioblastoma multiforme

text: U6:sgRNA-EIFa-BFP vector

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: Sample 3


E-MTAB-9296:Sample 4

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

text: E-MTAB-9296:Sample 4

text: ArrayExpress

characteristic: broker name

text: glial brain cell

text: human

characteristic: description

text: adult

text: glioblastoma multiforme

text: U6:sgRNA-EIFa-BFP vector

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: Sample 4


text: Ugent

characteristic: INSDC center name

text: public

text: ArrayExpress

text: CLB-Ga

characteristic: cell line

text: neuroblast (sensu Vertebrata)

characteristic: cell type

text: human

text: Protocols: cell lines were harvested, centrifuged and stored at -80°C. Cells were grown in RPMI1640 medium supplemented with 10% fetal bovine serum, 2 mM L-Glutamine and 100 IU/ml penicillin/streptavidin at 37°C in a 5% CO2 humid atmosphere Cells were treated with Celastrol or DMSO and 48h later, cells were harvested. Total RNA was extracted using miRNEASY kit (Qiagen) according to manufacturer's instructions, including on-column DNase treatment. After RNA extraction, the concentration and quality of the total extracted RNA were checked by using the 'Quant-it ribogreen RNA assay' (Life Technologies, Grand Island, NY, USA) and the RNA 6000 Nano chip (Agilent Technologies, Santa Clara, CA, USA) 200 ng of RNA was used to perform an Illumina sequencing library preparation using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Vienna, Austria) according to the manufacturer's protocol. During the library preparation, 15 PCR cycles were used. Libraries were quantified by qPCR, according to Illumina's protocol 'Sequencing Library qPCR Quantification protocol guide', version February 2011. A High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US) was used to control the library's size distribution and quality.

text: neuroblastoma

characteristic: disease

text: wild type genotype

text: bone marrow

characteristic: metastatic site

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: nervous system

text: Homo sapiens


text: COLD SPRING HARBOR LAB

characteristic: INSDC first public

text: public

characteristic: collection date

text: sorghum

characteristic: common name

text: This is 10x data generated for genome assembly

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: growth chamber

characteristic: isolation and growth condition

text: Sorghum bicolor

text: seedling

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: fresh tissue

characteristic: plant structure

text: Sorghum bicolor

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Hopital Henri Mondor APHP

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Hopital Henri Mondor APHP

characteristic: Submitter Id

text: E. coli

text: Strain from feces of healthy volunteer

characteristic: description

text: France

text: Paris

characteristic: geographic location (region and locality)

text: Homo sapiens sapiens

characteristic: host scientific name

text: feces

characteristic: isolation source

text: Escherichia coli

text: Escherichia coli


text: UoH

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: epithelial cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: GP5d cells were trypsinized and washed with PBS. GP5d human colon adenocarcinoma cells (ECACC cat no. 95090715) were cultured in DMEM supplemented with antibiotics and 10% FBS under standard cell culture conditions. Reverse transfections were performed with 50 μl of HiPerfect (Qiagen, Cat. No. 142349463) in 750 μl of Opti-MEM (Invitrogen), according to manufacturer’s general instructions using 40 nM final concentration for siRNA (non-targeting siCtrl, ThermoFisher, Cat. No. D-001206-13-20; siCTNNB1, Dharmacon, Cat. No. M-003482-00-0005; siMAX, Santa Cruz, Cat. No. sc-38079, and siMXD1, Ambion, Cat. No. s8390) in 100 mm dishes. Cells (25 ×10^5 of cells), added on top of the transfection complex, were cultured for 72 hr before harvesting. RNA was extracted with RNeasy Mini Kit (Qiagen, Cat No. 74104). RNA was extracted with RNeasy Mini Kit (Qiagen, Cat No. 74104) For RNA-sequencing, NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, NEB #E7420S) was used for library preparation. However, due to technical problems, the libraries are not strand-specific.

text: adult

characteristic: developmental stage

text: colon carcinoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: colon

characteristic: organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UoH

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ArrayExpress

text: epithelial cell

text: human

text: adult

text: colon carcinoma

text: Homo sapiens

text: Homo sapiens

text: colon

text: Homo sapiens

text: siCtrl

characteristic: title


text: UoH

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: epithelial cell

text: human

characteristic: description

text: adult

text: colon carcinoma

text: Homo sapiens

text: Homo sapiens

text: colon

text: Homo sapiens

text: siMAX


text: CBMSO

characteristic: INSDC first public

text: public

text: GENGS-CBMSO

characteristic: broker name

text: Genome and transcriptome annotation for the Friedlin strain of Leishmania major.

text: Leishmania major strain Friedlin

text: Leishmania major strain Friedlin


text: UoH

text: public

text: 104 to 112

characteristic: age

text: ArrayExpress

text: fruit fly

characteristic: common name

text: Protocols: For each replicate about 60 wing discs were dissected from wandering larvae and immediately transferred to the lysis buffer (Buffer RLT, Qiagen) supplemented with β-mercaptoethanol (1:100) and stored at -80°C until further processing. Eggs were collected in bottles for 10h at 18°C, and then incubated for 4 days at 18°C (permissive temperature for Gal80TS), and finally transferred for 2 days to 29°C (restrictive temperature for Gal80TS) to induce expression of the UAS transgenes. Conditional expression of UAS constructs in the wing pouch was achieved by using the nub-Gal4 and the TARGET system. Total RNA from each sample was isolated using the RNasey mini kit (Qiagen) according to manufacturer's instruction and subsequently quantified with the Qubit 3.0 Fluorometer and the Qubit RNA BR Assay Kit (Thermo Fisher). RNA-seq libraries were generated with the Ovation Drosophila RNA-Seq System (NuGEN) which requires 10 and 100 ng of input RNA.

text: larval stage

characteristic: developmental stage

text: w; nub-Gal4/UAS-dMyc-RNAi106066KK; tub-Gal80TS, UAS-GFP/+

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: wing disc

text: Drosophila melanogaster

text: mixed

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UoH

text: public

text: 104 to 112

text: ArrayExpress

text: fruit fly

text: larval stage

text: w; nub-Gal4/+; tub-Gal80TS, UAS-GFP/+

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: wing disc

characteristic: organism part

text: Drosophila melanogaster

text: mixed


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UoH

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: 104 to 112

text: ArrayExpress

text: fruit fly

text: larval stage

text: w; nub-Gal4/+; tub-Gal80TS, UAS-GFP/UAS-dMyc42(III)

text: Drosophila melanogaster

text: Drosophila melanogaster

text: wing disc

text: Drosophila melanogaster

text: mixed


text: UoH

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 104 to 112

text: ArrayExpress

text: fruit fly

text: larval stage

text: w; nub-Gal4/UAS-EMPTY-RNAi60100TK; tub-Gal80TS, UAS-GFP/+

text: Drosophila melanogaster

text: Drosophila melanogaster

text: wing disc

text: Drosophila melanogaster

text: mixed

characteristic: title


text: Hopital Henri Mondor APHP

characteristic: INSDC first public

text: public

text: E. coli

text: E. coli pneumonia isolate from mechanically ventilated patient

characteristic: description

text: France

characteristic: geographic location (country and/or sea)

text: Angers

characteristic: geographic location (region and locality)

text: Homo sapiens sapiens

characteristic: host scientific name

text: lung

characteristic: isolation source

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Hopital Henri Mondor APHP

text: public

text: E. coli

characteristic: common name

text: France

text: Paris

text: Homo sapiens sapiens

text: lung

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-LAST-UPDATE

text: Hopital Henri Mondor APHP

text: public

text: E. coli

text: France

text: Bordeaux

text: Homo sapiens sapiens

text: lung

text: Escherichia coli

characteristic: organism

text: Escherichia coli


characteristic: External Id

text: Hopital Henri Mondor APHP

characteristic: INSDC center name

text: public

text: E. coli

text: France

text: Dijon

text: Homo sapiens sapiens

text: lung

text: Escherichia coli

text: Escherichia coli


text: Hopital Henri Mondor APHP

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E. coli

text: France

text: Créteil

text: Homo sapiens sapiens

text: lung

text: Escherichia coli

text: Escherichia coli


text: Hopital Henri Mondor APHP

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: E. coli

text: France

text: Lille

text: Homo sapiens sapiens

text: lung

text: Escherichia coli

text: Escherichia coli


text: Hopital Henri Mondor APHP

characteristic: INSDC first public

text: public

text: E. coli

text: France

text: Colombes

text: Homo sapiens sapiens

text: lung

text: Escherichia coli

text: Escherichia coli

characteristic: title


text: Hopital Henri Mondor APHP

text: public

text: E. coli

characteristic: description

text: France

characteristic: geographic location (country and/or sea)

text: Nantes

text: Homo sapiens sapiens

text: lung

text: Escherichia coli

text: Escherichia coli


text: Hopital Henri Mondor APHP

text: public

text: E. coli

text: France

text: Nice

characteristic: geographic location (region and locality)

text: Homo sapiens sapiens

characteristic: host scientific name

text: lung

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-CHECKLIST

text: Hopital Henri Mondor APHP

text: public

text: E. coli

text: France

text: Poitiers

text: Homo sapiens sapiens

text: lung

characteristic: isolation source

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-FIRST-PUBLIC

text: Hopital Henri Mondor APHP

text: public

text: E. coli

characteristic: common name

text: France

text: La Roche-sur-Yon

text: Homo sapiens sapiens

text: lung

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-LAST-UPDATE

text: THE ROSLIN INSTITUTE

text: public

tag: Namespace:THE ROSLIN INSTITUTE

text: chicken

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: Ethiopian indigenous chicken


characteristic: External Id

text: UNIVERSITY OF MELBOURNE

characteristic: INSDC center name

text: public

tag: Namespace:UNIVERSITY OF MELBOURNE

text: Ostreobium quekettii study

text: Germany

text: Ostreobium quekettii

text: Ostreobium quekettii

text: Ostreobium quekettii SAG6.99


text: Tromsoe Ecosystem Genomics

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Tromsoe Ecosystem Genomics

text: Viridiplantae environmental sample

text: Viridiplantae environmental sample


text: Maria Curie-Sklodowska University

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: sediment metagenome

text: sediment metagenome

text: layer 15-1


text: Maria Curie-Sklodowska University

characteristic: INSDC first public

text: public

text: sediment metagenome

text: sediment metagenome

text: layer 15-2

characteristic: title


text: Maria Curie-Sklodowska University

text: public

text: sediment metagenome

text: sediment metagenome

text: layer 35-2


text: Maria Curie-Sklodowska University

text: public

text: sediment metagenome

text: sediment metagenome

text: layer 35-1


text: Maria Curie-Sklodowska University

text: public

text: sediment metagenome

text: sediment metagenome

text: layer 63-1


text: Maria Curie-Sklodowska University

text: public

text: sediment metagenome

text: sediment metagenome

text: layer 63-2


text: Maria Curie-Sklodowska University

text: public

text: sediment metagenome

text: sediment metagenome

text: layer 67-1


text: Maria Curie-Sklodowska University

text: public

text: sediment metagenome

text: sediment metagenome

text: layer 67-2


text: Maria Curie-Sklodowska University

text: public

text: sediment metagenome

text: sediment metagenome

text: layer 85-1


text: Maria Curie-Sklodowska University

text: public

text: sediment metagenome

text: sediment metagenome

text: layer 85-2


text: Maria Curie-Sklodowska University

text: public

text: sediment metagenome

text: sediment metagenome

text: layer 93-1


text: Maria Curie-Sklodowska University

text: public

text: sediment metagenome

text: sediment metagenome

text: layer 93-2


text: UNIVERSITY OF TORONTO

text: public

tag: Namespace:UNIVERSITY OF TORONTO

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens


text: public

tag: Namespace:Neurosurgical Research, Department of Neurosurgery, University Hospital, LMU Munich, Germany

text: adult

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: Glioblastoma cell cultures were derived from human glioblastoma biopsies and were maintained under stem cell cultivation conditions in either NeuroCult Basal Medium (Cat. 05700) with Proliferation Supplement (Cat. 05701 both, STEMCELL Technologies) or DMEM-F12 (Cat. 11320-074) with 1× B27 (Cat. 17504-044), supplemented with 5% penicillin-streptomycin (Cat. 151140-122; all ThermoFisher Scientific, Waltham, MA, USA), 10 ng/ml epidermal growth factor (EGF; Cat. 236-EG; Biotechne; Minneapolis, MN, USA) and 10 ng/ml fibroblast growth factor (FGF; Cat. 100-18B PeproTech, Hamburg, Germany). All cells were maintained at 37°C in a humidified atmosphere of 95% O2 and 5% CO2. Genomic DNA (gDNA) and total RNA were isolated in parallel from the same sample using the AllPrep DNA/RNA Mini Kit (Qiagen) following the manufacturer’s instructions. The final volume of the eluate was 100 μl for gDNA. An aliquot of each gDNA sample was used to determine purity and approximate DNA concentration on the NanoDrop ND-1000 spectral photometer (Peqlab). Additionally, specific quantification of the double-stranded DNA was performed. Therefore, the gDNA samples were quantified using the highly sensitive fluorescent dye-based Qubit® dsDNA HS Assay Kit (Invitrogen). To evaluate integrity gDNA samples were analyzed using a 1.0 % agarose gel (midori green stained). Library preparation was performed with the TruSeq Custom Amplicon Low Input Library Kit according to the manufacturer´s protocol (1). In brief, one pair of oligos is designed for each amplicon. Hybridization of oligos to genomic DNA occurs in a 96-well plate, followed by extension and ligation to form DNA templates consisting of the regions of interest flanked by universal primer sequences. Using indexed primers supplied with the kit, DNA templates are amplified by PCR and elongated with barcodes and sequencing adapters. In addition to the 22 gDNA samples, a control DNA (2800M) provided with the kit and a Non-template control (NTC) were processed in parallel in order to control the complete library preparation process. The DNA 1000 LabChip Kit (Agilent Technologies) was used on the 2100 Bioanalyzer (Agilent Technologies) to analyze the quality and fragment distribution of the generated libraries. The expected PCR product size including adapter sequences is ~ 350 bp for the targeted amplicon size of 250 bp. Furthermore, all libraries were quantified using the highly sensitive fluorescent dye-based Qubit® ds DNA HS Assay Kit (Invitrogen). Afterwards, the single TruSeq Custom Amplicon libraries were pooled together in equimolar ratios into a final sequencing library. The final pooled sequencing library was quantified again using the highly sensitive fluorescent dye-based Qubit® ds DNA HS Assay Kit (Invitrogen). After quantification, the final sequencing library pool was diluted to 2 nM, followed by denaturation with NaOH. This ensures the presence of single stranded DNA fragments for cluster generation. The final sequencing library pool consists of single stranded fragments with sequencing adapters, sequencing primer binding sites and indices.

text: adult

characteristic: developmental stage

text: glioblastoma multiforme

characteristic: disease

text: primary glioblastoma cell culture

characteristic: growth condition

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: brain

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Neurosurgical Research, Department of Neurosurgery, University Hospital, LMU Munich, Germany

text: public

text: adult

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: glioblastoma multiforme

text: primary glioblastoma cell culture

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: brain

text: Homo sapiens

text: female


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: adult

text: ArrayExpress

text: human

text: adult

text: glioblastoma multiforme

text: primary glioblastoma cell culture

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: male


text: public

text: adult

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: glioblastoma multiforme

characteristic: disease

text: primary glioblastoma cell culture

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF CAMBRIDGE

text: public

tag: Namespace:UNIVERSITY OF CAMBRIDGE

text: ArrayExpress

text: naive pluripotent stem cell

characteristic: cell type

text: white-tufted-ear marmoset

text: Protocols: Cells were dissociated in Accutase for 5 min and pipetted vigorously to obtain a single cell suspension in normal culture media. Single cells were picked by mouth pipette using a blunted microcapillary with internal diameter 15 μM and under a dissection microscope. Cells were collected into 0.2 mL tubes with 4 μL lysis buffer and immediately snap frozen on dry ice. RNA separation was performed using biotinylated oligo-dT30VN-tailed oligonucleotides (IDT) conjugated to Dynabeads Streptavidin C1 in an RNAse-inhibitor supplemented buffer solution. Sequencing libraries were prepared according to an adapted version of the G&T protocol previously described. Samples were transferred to a 96-well plate and prepared for both transcriptome and methylome sequencing, by physical separation of genomic DNA (gDNA) from messenger RNA (mRNA).

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

characteristic: organism part

text: pass

characteristic: post analysis well quality

text: Callithrix jacchus

text: OK

characteristic: single cell well quality


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

characteristic: common name

text: embryo stage

text: Callithrix jacchus

characteristic: organism

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK


text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9349:SLX-10821.N701_N502.C854JANXX.s_7.r

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-10821.N701_N503.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

characteristic: description

text: embryo stage

characteristic: developmental stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-10821.N701_N504.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

characteristic: cell type

text: white-tufted-ear marmoset

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

characteristic: organism part

text: pass

characteristic: post analysis well quality

text: Callithrix jacchus

text: OK


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC center name

text: public

text: E-MTAB-9349:SLX-10821.N701_N517.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK

characteristic: single cell well quality


text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9349:SLX-10821.N702_N502.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

characteristic: common name

text: embryo stage

text: Callithrix jacchus

characteristic: organism

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK


text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9349:SLX-10821.N702_N503.C854JANXX.s_7.r

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-10821.N702_N504.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

characteristic: description

text: embryo stage

characteristic: developmental stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-10821.N702_N517.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

characteristic: cell type

text: white-tufted-ear marmoset

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

characteristic: organism part

text: pass

characteristic: post analysis well quality

text: Callithrix jacchus

text: OK


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC center name

text: public

text: E-MTAB-9349:SLX-10821.N703_N502.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK

characteristic: single cell well quality


text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9349:SLX-10821.N703_N503.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

characteristic: common name

text: embryo stage

text: Callithrix jacchus

characteristic: organism

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK


text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9349:SLX-10821.N703_N504.C854JANXX.s_7.r

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-10821.N703_N517.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

characteristic: description

text: embryo stage

characteristic: developmental stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-10821.N704_N502.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

characteristic: cell type

text: white-tufted-ear marmoset

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

characteristic: organism part

text: pass

characteristic: post analysis well quality

text: Callithrix jacchus

text: OK


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC center name

text: public

text: E-MTAB-9349:SLX-10821.N704_N503.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK

characteristic: single cell well quality


text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9349:SLX-10821.N704_N504.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

characteristic: common name

text: embryo stage

text: Callithrix jacchus

characteristic: organism

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK


text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9349:SLX-10821.N704_N517.C854JANXX.s_7.r

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-10821.N705_N502.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

text: Protocols: Cells were dissociated in Accutase for 5 min and pipetted vigorously to obtain a single cell suspension in normal culture media. Single cells were picked by mouth pipette using a blunted microcapillary with internal diameter 15 μM and under a dissection microscope. Cells were collected into 0.2 mL tubes with 4 μL lysis buffer and immediately snap frozen on dry ice. RNA separation was performed using biotinylated oligo-dT30VN-tailed oligonucleotides (IDT) conjugated to Dynabeads Streptavidin C1 in an RNAse-inhibitor supplemented buffer solution. Sequencing libraries were prepared according to an adapted version of the G&T protocol previously described. Samples were transferred to a 96-well plate and prepared for both transcriptome and methylome sequencing, by physical separation of genomic DNA (gDNA) from messenger RNA (mRNA).

characteristic: description

text: embryo stage

characteristic: developmental stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-10821.N705_N503.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

characteristic: cell type

text: white-tufted-ear marmoset

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

characteristic: organism part

text: pass

characteristic: post analysis well quality

text: Callithrix jacchus

text: OK


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC center name

text: public

text: E-MTAB-9349:SLX-10821.N705_N504.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK

characteristic: single cell well quality


text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9349:SLX-10821.N705_N517.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

characteristic: common name

text: embryo stage

text: Callithrix jacchus

characteristic: organism

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK


text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9349:SLX-10821.N706_N502.C854JANXX.s_7.r

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-10821.N706_N504.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

text: white-tufted-ear marmoset

characteristic: description

text: embryo stage

characteristic: developmental stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

text: pass

text: Callithrix jacchus

text: OK

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-10821.N706_N517.C854JANXX.s_7.r

text: ArrayExpress

text: primed pluripotent stem cell

characteristic: cell type

text: white-tufted-ear marmoset

text: embryo stage

text: Callithrix jacchus

text: Callithrix jacchus

text: blastocyst

characteristic: organism part

text: pass

characteristic: post analysis well quality

text: Callithrix jacchus

text: OK


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC center name

text: public

text: E-MTAB-9349:SLX-12168.N701_S502.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

text: neonate

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK

characteristic: single cell well quality


text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9349:SLX-12168.N701_S503.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

characteristic: common name

text: neonate

text: Callithrix jacchus

characteristic: organism

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK


text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9349:SLX-12168.N701_S504.C9JGJANXX.s_8.r

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: forebrain-derived cell

text: white-tufted-ear marmoset

text: neonate

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-12168.N701_S517.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

characteristic: description

text: neonate

characteristic: developmental stage

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-12168.N702_S502.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

characteristic: cell type

text: white-tufted-ear marmoset

text: neonate

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

characteristic: organism part

text: pass

characteristic: post analysis well quality

text: Callithrix jacchus

text: OK


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC center name

text: public

text: E-MTAB-9349:SLX-12168.N702_S503.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

text: neonate

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK

characteristic: single cell well quality


text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9349:SLX-12168.N702_S504.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

characteristic: common name

text: neonate

text: Callithrix jacchus

characteristic: organism

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK


text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9349:SLX-12168.N702_S517.C9JGJANXX.s_8.r

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: forebrain-derived cell

text: white-tufted-ear marmoset

text: neonate

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-12168.N703_S502.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

characteristic: description

text: neonate

characteristic: developmental stage

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-12168.N703_S503.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

characteristic: cell type

text: white-tufted-ear marmoset

text: neonate

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

characteristic: organism part

text: pass

characteristic: post analysis well quality

text: Callithrix jacchus

text: OK


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC center name

text: public

text: E-MTAB-9349:SLX-12168.N703_S504.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

text: Protocols: Cells were dissociated in Accutase for 5 min and pipetted vigorously to obtain a single cell suspension in normal culture media. Single cells were picked by mouth pipette using a blunted microcapillary with internal diameter 15 μM and under a dissection microscope. Cells were collected into 0.2 mL tubes with 4 μL lysis buffer and immediately snap frozen on dry ice. RNA separation was performed using biotinylated oligo-dT30VN-tailed oligonucleotides (IDT) conjugated to Dynabeads Streptavidin C1 in an RNAse-inhibitor supplemented buffer solution. Sequencing libraries were prepared according to an adapted version of the G&T protocol previously described. Samples were transferred to a 96-well plate and prepared for both transcriptome and methylome sequencing, by physical separation of genomic DNA (gDNA) from messenger RNA (mRNA).

text: neonate

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK

characteristic: single cell well quality


text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9349:SLX-12168.N703_S517.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

characteristic: common name

text: neonate

text: Callithrix jacchus

characteristic: organism

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK


text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9349:SLX-12168.N704_S502.C9JGJANXX.s_8.r

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: forebrain-derived cell

text: white-tufted-ear marmoset

text: neonate

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-12168.N704_S503.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

characteristic: description

text: neonate

characteristic: developmental stage

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-12168.N704_S504.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

characteristic: cell type

text: white-tufted-ear marmoset

text: neonate

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

characteristic: organism part

text: pass

characteristic: post analysis well quality

text: Callithrix jacchus

text: OK


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC center name

text: public

text: E-MTAB-9349:SLX-12168.N704_S517.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

text: neonate

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK

characteristic: single cell well quality


text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9349:SLX-12168.N705_S502.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

characteristic: common name

text: neonate

text: Callithrix jacchus

characteristic: organism

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK


text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9349:SLX-12168.N705_S503.C9JGJANXX.s_8.r

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: forebrain-derived cell

text: white-tufted-ear marmoset

text: neonate

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-12168.N705_S504.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

characteristic: description

text: neonate

characteristic: developmental stage

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-12168.N705_S517.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

characteristic: cell type

text: white-tufted-ear marmoset

text: neonate

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

characteristic: organism part

text: pass

characteristic: post analysis well quality

text: Callithrix jacchus

text: OK


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC center name

text: public

text: E-MTAB-9349:SLX-12168.N706_S502.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

text: neonate

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK

characteristic: single cell well quality


text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-9349:SLX-12168.N706_S503.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

characteristic: common name

text: neonate

text: Callithrix jacchus

characteristic: organism

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK


text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9349:SLX-12168.N706_S504.C9JGJANXX.s_8.r

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: forebrain-derived cell

text: white-tufted-ear marmoset

text: neonate

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF CAMBRIDGE

text: public

text: E-MTAB-9349:SLX-12168.N706_S517.C9JGJANXX.s_8.r

text: ArrayExpress

text: forebrain-derived cell

text: white-tufted-ear marmoset

characteristic: description

text: neonate

characteristic: developmental stage

text: Callithrix jacchus

text: Callithrix jacchus

text: frontal lobe

text: pass

text: Callithrix jacchus

text: OK

characteristic: title


E-MTAB-9352:Sample 1

characteristic: ENA-FIRST-PUBLIC

text: Indian Institute of Science

text: public

text: E-MTAB-9352:Sample 1

tag: Namespace:Indian Institute of Science

text: ArrayExpress

characteristic: cell line

text: neuroblastoma

characteristic: cell type

text: house mouse

text: Protocols: Cells were rinsed with ice-cold PBS containing 100ug/ml cycloheximide. Dishes were submerged in a liquid nitrogen reservoir for 10s followed by scraping over dry ice in polysome lysis buffer (20mM Tris-HCl pH 7.5, 150mM NaCl, 5mM MgCl2, 1mM DTT, 1% (v/v) Triton X-100, 100ug/ml cycloheximide and 25U/ml TURBO DNase I (Life Technologies)). Neuro2a cells were maintained in Dulbecco's modification of Eagle's medium (DMEM, Himedia) supplemented with 10% (v/v) foetal bovine serum (FBS, Gibco) and 1% (v/v) Penicillin-Streptomycin (Sigma). Cells were grown to 70% confluence in 10cm dishes and infected with 5 plaque forming units (PFU) per cell of JEV P20778 Vellore strain (AF080251) or Dimethyl sulfoxide (DMSO, mock) in plain DMEM. After 60 min at 37 degrees, inoculum was removed, and monolayer was extensively washed with phosphate buffered saline (PBS) before replacing with complete media (DMEM with 10% FBS). At 18 hours post infection (hpi), cells were treated with either cycloheximide (Sigma-Aldrich, 100ug/ml, 5min) or harringtonine (LKT laboratories, 2ug/ml, 2min) followed by cycloheximide treatment for 5min. Cells were collected and triturated with a 26G needle 20 times and clarified by centrifugation (13000g, 20min, 4degrees). Supernatant was collected and treated with 100U/ul of RNase I (Ambion) for 1h at room temperature with gentle mixing followed by inactivation with 40U of SUPERase-In RNase inhibitor (Ambion). Cell extracts were passed through Sephacryl S400 spin columns (GE) after pre-equilibration with polysome lysis buffer and ribosome-bound mRNA eluates were collected by centrifugation at 600g, 1min, 4degrees. For RNA-Seq, total RNA was fragmented using 10x fragmentation reagent (Ambion) according to manufacturer's protocol. RNA was extracted from eluates and total lysate using TRIzol reagent (ThermoScientific). Purified RNA was size selected for a broader range of fragments (25 to 70 nucleotides) and subjected to RiboSeq and RNASeq library preparation based on original protocols (Ingolia et al., 2012). Final amplicons were PCR amplified for 6, 8 and 10 cycles and pooled before sequencing.

text: mock

characteristic: infect

text: Mus musculus

text: Mus musculus

characteristic: sampling time point

text: Mus musculus

text: Sample 1


E-MTAB-9352:Sample 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Indian Institute of Science

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-9352:Sample 2

text: ArrayExpress

text: neuroblastoma

text: house mouse

text: Japanese encephalitis virus P20778

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 2


E-MTAB-9352:Sample 3

text: Indian Institute of Science

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-9352:Sample 3

text: ArrayExpress

text: neuroblastoma

text: house mouse

characteristic: common name

text: Japanese encephalitis virus P20778

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Sample 3


E-MTAB-9352:Sample 4

characteristic: ENA-CHECKLIST

text: Indian Institute of Science

text: public

characteristic: SRA accession

text: E-MTAB-9352:Sample 4

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: neuroblastoma

text: house mouse

text: Japanese encephalitis virus P20778

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 4


characteristic: ENA-FIRST-PUBLIC

text: Neurosurgical Research, Department of Neurosurgery, University Hospital, LMU Munich, Germany

text: public

text: ArrayExpress

text: house mouse

text: Protocols: Murine glioblastoma cell cultures were maintained under stem cell cultivation conditions in DMEM-F12 (Cat. 11320-074) supplemented with 1× B27 (Cat. 17504-044) containing 5% penicillin-streptomycin (Cat. 151140-122; all ThermoFisher Scientific, Waltham, MA, USA), 10 ng/ml epidermal growth factor (EGF; Cat. 236-EG; Biotechne; Minneapolis, MN, USA) and 10 ng/ml fibroblast growth factor (FGF; Cat. 100-18B PeproTech, Hamburg, Germany). All cells were maintained at 37°C in a humidified atmosphere of 95% O2 and 5% CO2. For the experiment, cells were treated with 10 microM CBD dissolved in DMSO or 0.01% DMSO only. Total RNA was isolated from the cells using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions including on-column DNase digestion. Total RNA was eluted in 30 μl RNase-free water. An aliquot of each total RNA sample was used to determine RNA concentration and purity on the NanoDrop ND-1000 spectral photometer (Peqlab). All samples were analyzed on the 2100 Bioanalyzer (Agilent Technologies) using RNA 6000 Nano and Pico LabChip Kits (Agilent Technologies). Library preparation was performed with the RNA samples using the TruSeq® Stranded mRNA HT technology, according to the manufacturer´s protocol (Illumina Inc. TruSeq® Stranded mRNA Sample Preparation Guide - Catalog # RS-122-9004DOC - Part # 15031047 Rev. E. 2013). The protocol started with a RNA fragmentation step using divalent cations. Samples were then introduced into a reverse transcription to generate first strand cDNA. In the second strand cDNA synthesis dUTP is incorporated instead of dTTP, to avoid amplification by the DNA polymerase in the subsequent PCR and thus guarantee strandedness. 3’-ends were adenylated and sequencing adapters were ligated. Those comprise sequencing primer- and flow cell-binding sites, as well as indices for multiplexed sequencing of pooled libraries. Adapter-ligated fragments were amplified during a limited-cycle PCR reaction. After the limited cycle PCR and at the end of the library preparation all samples were quality controlled using the DNA 1000 LabChip kits on the 2100 Bioanalyzer (Agilent Technologies). Furthermore, all libraries were quantified using the highly sensitive fluorescent dye-based Qubit® ds DNA HS Assay Kit (Invitrogen). Afterwards, all single libraries were pooled into a final sequencing library with an equal DNA amount per sample. The final sequencing library, generated by pooling was quantified again using the highly sensitive fluorescent dye-based Qubit® ds DNA HS Assay Kit (Invitrogen). After quantification, the final library was diluted to 2 nM, followed by denaturation with NaOH. This ensures the presence of single stranded DNA fragments for cluster generation. The final sequencing library consists of single stranded fragments with sequencing adapters, sequencing primer binding sites and indices.

characteristic: description

text: neonate

characteristic: developmental stage

text: glioblastoma multiforme

characteristic: disease

characteristic: genotype

text: primary glioblastoma cell culture

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: brain

characteristic: organism part

text: p65 knockout

characteristic: phenotype

text: Mus musculus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: house mouse

text: neonate

text: glioblastoma multiforme

text: primary glioblastoma cell culture

text: Mus musculus

text: Mus musculus

text: brain

text: wild type

text: Mus musculus


E-MTAB-9359:GS9 MVMi

characteristic: ENA-CHECKLIST

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-9359:GS9 MVMi

tag: Namespace:Centro de Biologia Molecular Severo Ochoa (CBMSO CSIC-UAM)

text: ArrayExpress

text: patient derived cancer stem cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Infected GSCs growing as neurospheres in CSC medium (see Growth Protocol section, below) were harvested at 3 days post-infection, in parallel to the respective uninfected controls. The GSCs were selected for the Pp53 and NS1 phenotypes outlined above by fluorescence-activated cell sorting (FACS) as follows. Neurospheres were centrifuged (F15, Falcon) for 5 min at 10.000xg at 4 ºC, dissociated into isolated cells by a mild trypsin-EDTA digestion at room temperature, diluted in PBS and placed on ice. Cells recovered from neurospheres (either Mock or MVM infected) were washed in cold diethylpyrocarbonate-treated (DEPC) phosphate-buffered saline (PBS) prepared with nuclease-free water (Gifco, distilled water DNase/RNase free 10977-035), thoroughly dispersed by flushing through a 0.45 mm needle, fixed with ethanol at -20 °C added dropwise while stirring, and then left to complete fixation for 24 hours at 4 °C. To stain with antibodies, washed cells were permeabilized with PBS-0.1% Tritón, which was also the buffer used in the washes. Antibody staining was performed in autoclaved PBS, 0.1% Triton, 1% gelatin, supplemented with 20 mM Vanadyl Ribonucleoside Complexes (VRC, Sigma) for RNase inhibition, and micro-precipitates removed by filtration through 0.22 m. Incubations with primary (anti-Pp53S15 and anti-NS1; 1/400) and secondary (anti-mouse-Cy5 and anti-rabbit-FITC; 1/500) antibodies were for 16 and 4 hours respectively with rotary agitation at 4 ºC. Finally the cell suspension was washed in PBS-0.1% Triton, clumps removed by filtration (30 ), and concentration adjusted to 106 cell/ml in cold PBS-DEPC, 1% autoclaved gelatin, and 20 mM VRC. Before fluorescence-activated cell sorting (FACS), the equipment circuit was extensively washed with autoclaved PBS-DEPC pre-cooled at 4 °C, and sorting was performed with autoclaved sheath fluid The glioblastoma stem cells (GSCs) were isolated and growth from human brain tumours. Fresh surgical biopsies minced and incubated in 0,1% trypsin and 0,04% DNase (type II, Sigma) in PBS for 45 min at 37 ºC were mechanically dissociated by passing through fire-polished Pasteur pipettes. The cell suspension was filtered through a 40 mm cell strainer (BD), number and viability measured by trypan blue exclusion, and stored frozen in aliquots in liquid nitrogen at this stage. To be grown as Neurospheres, GSCs were seeded at a density of 1x105 viable cells/ml in Cancer Stem Cells proliferation medium (CSC medium) consisting of DMEM:F12 (1:1) supplemented with glutamax (Gibco), 0,5% Albumax I (Gibco), 5 mM Hepes (Gibco), 0,6% Glucose (Sigma), N2 (1x, Invitrogen), 2 mg/ml heparin (Sigma), 20 ng/ml of both epidermal growth factor (EGF) and basic fibroblast growth factor (FGF-2) (Peprotech), aminoacids (L-Ala 44 mM, L-Asn 45 mM, L-Asp 40 mM, L-Glu 40 mM, L-Pro 30 mM) and gentamicine (0,055 mg/ml) Viral infection, GSC neurospheres grown and fed twice a week with 20% volume of fresh CSC medium until reaching 200-300 mm in size, were dissociated into isolated cells by a mild trypsin-EDTA digestion at room temperature together with mechanically passing through micropipette tips. Cells were washed in CSC and resuspended in the same medium at a density of 1x107 viable cells/ml. The virus was immediately added at a multiplicity of 5-10 PFU/cell and adsorption proceeded under shaking at 37 ºC for 1 h. For the infection we used exclusively purified stocks of the MVMp and MVMi parvovirus strains devoid of empty capsids by two rounds of CsCl centrifugation, dialyzed against phosphate- buffered saline (PBS), and sterile filtered (0.22 m). At the end of the adsorption period cells were washed again and seeded onto P100 dishes at a density of 1x105 viable cells/ml in CSC medium. The FACS-sorted cells were collected on sterile tubes (F15, Falcon) on ice and the TRIzol reagent (Ambion; Invitrogen) was immediately added. Total RNA isolation was performed with chloroform, isopropanol and ethanol, according to the instructions of the manufacturer cDNA was synthetized from 250ng of RNA using the High Capacity cDNA Archive Kit (Applied Biosystems, Thermo Fisher) following the manufacturer´s instructions in a GeneAmp PCR Systems 9700 (Applied Biosystems, Thermo Fisher). From cDNAs we perform a first PCR of 30 cycles with Q5® Hot Start High-Fidelity DNA Polymerase (New England Biolabs) in the presence of 500nM primers for p53 amplification For each primer pair we optimized the PCR doing a temperature gradient to obtain the optimal annealing temperatures. After the first PCR, a second PCR of 13 cycles was performed with Q5® Hot Start High-Fidelity DNA Polymerase (New England Biolabs) in the presence of 400nM of primers of the Access Array Barcode Library for Illumina Sequencers (Fluidigm).

text: glioblastoma multiforme

text: neurosphere culture

text: Parvovirus Immunosuppressive strain Minute Virus of Mice (MVMi)

characteristic: infect

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: brain

text: Homo sapiens

text: GS9 MVMi