E-MTAB-10399:Sample 46

text: MEMORIAL SLOAN KETTERING CANCER CENTER

text: public

text: E-MTAB-10399:Sample 46

text: ArrayExpress

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text: adult

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text: lung cancer

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text: Homo sapiens

text: Homo sapiens

text: lung

text: small cell lung carcinoma

text: Homo sapiens

text: female

text: frozen specimen

text: Sample 46

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E-MTAB-10399:Sample 47

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text: Protocols: We identified 11 formalin-fixed paraffin-embedded (FFPE) tumors with combined LUAD and SCLC histology, from which independent isolation of both histological components was possible. We identified an additional 1 pre-transformation LUAD and 1 post-transformation SCLC cases for which tissue material was available. As controls we included a group of never-transformed LUADs and a set of de novo SCLC samples. RNA/DNA dual extraction from FFPE sections were deparaffinized in mineral oil. Briefly, 800µL mineral oil (Fisher Scientific, #AC415080010) and 180µL Buffer PKD were mixed with the sections, Proteinase K was added for tissue digestion, and the sample was incubated at 56°C for 15 minutes. Phase separation was encouraged with centrifugation, and the aqueous phase was chilled 3 minutes to precipitate RNA. After centrifugation for 15 minutes at 20,000g, RNA-containing supernatant was removed for extraction, while DNA remained in the pellet. Nucleic acids were subsequently extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN, #80204) according to the manufacturer’s instructions. RNA was eluted in nuclease-free water and DNA in 0.5X Buffer ATE. RNA/DNA dual extraction from frozen tissue Frozen tissues were weighed and homogenized in RLT and nucleic acids were extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN, #80204) according to the manufacturer’s instructions. RNA was eluted in nuclease-free water and DNA in 0.5X Buffer EB. Approximately 500ng of FFPE RNA or 100ng of fresh frozen RNA per sample were used for RNA library construction using the KAPA RNA Hyper library prep kit (Roche, Switzerland) per the manufacturer’s instructions with minor modifications. Customized adapters with unique molecular indexes (UMI) (Integrated DNA Technologies, US) and Sample-specific dual-indexes primers (Integrated DNA Technologies, US) were added to each library. The quantity of libraries was measured with Qubit (Thermo Fisher Scientific, US) and quality measured by TapStation Genomic DNA Assay (Agilent Technologies, US). Equal amounts of each RNA library (around 500ng) were pooled for hybridization capture with IDT Whole Exome Panel V1 (Integrated DNA Technologies, US) using a customized capture protocol modified from NimbleGen SeqCap Target Enrichment system (Roche, Switzerland).

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text: Sample 47


E-MTAB-10399:Sample 48

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text: Viollier AG; Hagmattstrasse 14, 4123 Allschwil

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text: Chaoran Chen, Sarah Nadeau, Catharine Aquino, Ivan Topolsky, Kim Philipp Jablonski, Lara Fuhrmann, Daniel Ehrsam, Isabel Stürmer, Andreia Cabral de Gouvea, Maria Domenica Moccia, Simon Grüter, Timothy Sykes, Lennart Opitz, Griffin White, Laura Neff, Doris Popovic, Andrea Patrignani, Jay Tracy, Ralph Schlapbach, Christiane Beckmann, Maurice Redondo, Olivier Kobel, Christoph Noppen, Niko Beerenwinkel, Tanja Stadler

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text: Severe acute respiratory syndrome coronavirus 2


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text: Protocols: BC neurospheres derived from space cells and earth controls were grown in stem cell medium for one to four weeks after space voyage. RNA was extracted using an RNAEasy Plus Micro kit (Qiagen), according to the manufacturer’s instructions. Concentrations were measured using an ND-1000 spectrophotometer (NanoDrop Technologies) and subsequently, RNA integrity was controlled by using an Agilent 2100 Bioanalyzer. Ten ng of RNA was used for each sample. The libraries were prepared for sequencing on the Ion Chef System and sequenced on the Ion S5 XL on 540 chips using IonCode adapters. Sequencing libraries for 16 individual samples pre-pared from 180-280 ng total RNA using the Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit (Cat. Nos. A36553, A36554, and A36555, Thermo Fischer Scientific) according to the manufacturer’s protocol.

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text: Mus musculus

text: Mus musculus

text: neural crest

characteristic: organism part

text: Mus musculus

text: BTBR mouse

characteristic: strain

text: Microgravity


E-MTAB-10543:Normal culture

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E-MTAB-10543:Outside incubator

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E-MTAB-10543:Space cells

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E-MTAB-10543:Space mimic

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characteristic: External Id

text: ETH ZURICH D-BSSE

characteristic: INSDC center name

text: public

text: SIB

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: SG

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: ETH ZURICH D-BSSE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: Switzerland

text: SZ

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

characteristic: host subject id

characteristic: isolate

characteristic: organism


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GISAID Accession ID

text: ETH ZURICH D-BSSE

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: Switzerland

text: SO

characteristic: geographic location (region and locality)

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: ETH ZURICH D-BSSE

characteristic: INSDC center name

text: public

text: SIB

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: BS

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ETH ZURICH D-BSSE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: Switzerland

text: GR

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

characteristic: host subject id

characteristic: isolate

characteristic: organism


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: GISAID Accession ID

text: ETH ZURICH D-BSSE

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: Switzerland

text: TI

characteristic: geographic location (region and locality)

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ETH ZURICH D-BSSE

characteristic: INSDC center name

text: public

text: SIB

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VS

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: TEL AVIV UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:TEL AVIV UNIVERSITY

text: ArrayExpress

text: Protocols: Strains were maintained at -80˚C. Strains were streaked on YPD plates. The plates were incubated at 37˚C overnight. Then several colonies were picked up and suspended in deuterium-depleted water (DDW). Cell density was adjusted to 10,000 cells/ml, then 100µl of cell suspension was plated on YPD plates. The plates were incubated at 37˚C overnight. Colonies were picked up and suspended in DDW, then cell pellets were obtained by centrifuging at highest speed for 1min. We used the phenol-chloroform method to extract Genomic DNA. Cell pellets were suspended in 200µl of lysis buffer, add 100µl of acid washed glass beads, and 0,2ml phenol:chloroform:isoamyl alcohol (25:24:1). Vortex for 30min at 4˚C. Add 200µl TE pH7.5. Centrifuge for 5min at maximum speed. Transfer aqueous layer to a new 1.5ml EP tube. Add 1ml 100% ethanol. Precipitate 1h at -20˚C. Pellet DNA by centrifuging for 10min at maximum speed. Discard the supernatant. Add 400µl TE pH 7.5. Add 3ul of RNase A (10mg/ml). Incubate at 37˚C for 30min. Add 10µl of 3M NaOAc and 1ml of 100% ethanol. Mix by inversion. Precipitate 30min at -20˚C. Pellet DNA by centrifuging for 10min at maximum speed. Discard supernatant. Air-dry the pellet overnight. Resuspend in 50µl water. 1µg Genomic DNA was randomly fragmented by Covaris, followed by fragments selection by Agencourt AMPure XP-Medium kit to an average size of 200~400 bp. Selected fragments were end repaired and 3\adenylate, then the adaptors were ligated to the end of these 3\adenylate fragments. The products were amplified by PCR and purified by the Agencourt AMPure XP-Medium kit. The purified double stranded PCR products were heat denatured to single strand, then circularised by the splint oligo sequence. The single strand circle DNA (ssCirDNA) were formatted as the final library and qualified by QC.

characteristic: description

text: euploid; diploid

characteristic: genotype

text: YPD medium with 8 microgram per milliliter of tunicamycin

characteristic: growth condition

text: Candida auris

characteristic: organism

text: [Candida] auris

text: whole organism

characteristic: organism part

text: [Candida] auris

text: clade III isolate B12039

characteristic: strain

text: Parent


E-MTAB-10549:Sample 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TEL AVIV UNIVERSITY

characteristic: INSDC center name

text: public

text: E-MTAB-10549:Sample 1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 1

characteristic: title


E-MTAB-10549:Sample 10

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 10

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 10


E-MTAB-10549:Sample 11

text: TEL AVIV UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10549:Sample 11

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 11


E-MTAB-10549:Sample 13

text: TEL AVIV UNIVERSITY

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10549:Sample 13

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 13


E-MTAB-10549:Sample 12

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 12

text: ArrayExpress

characteristic: description

text: aneuploid

characteristic: genotype

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 12


E-MTAB-10549:Sample 14

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 14

text: ArrayExpress

text: aneuploid

characteristic: growth condition

text: Candida auris

characteristic: organism

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 14


E-MTAB-10549:Sample 15

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 15

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

characteristic: organism part

text: [Candida] auris

text: clade III isolate B12039

characteristic: strain

text: Sample 15


E-MTAB-10549:Sample 16

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 16

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 16


E-MTAB-10549:Sample 17

text: TEL AVIV UNIVERSITY

characteristic: INSDC center name

text: public

text: E-MTAB-10549:Sample 17

characteristic: Submitter Id

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 17


E-MTAB-10549:Sample 18

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 18

text: ArrayExpress

characteristic: broker name

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 18

characteristic: title


E-MTAB-10549:Sample 19

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 19

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 19


E-MTAB-10549:Sample 2

text: TEL AVIV UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10549:Sample 2

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 2


E-MTAB-10549:Sample 20

text: TEL AVIV UNIVERSITY

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10549:Sample 20

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 20


E-MTAB-10549:Sample 21

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 21

text: ArrayExpress

characteristic: description

text: aneuploid

characteristic: genotype

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 21


E-MTAB-10549:Sample 22

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 22

text: ArrayExpress

text: aneuploid

characteristic: growth condition

text: Candida auris

characteristic: organism

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 22


E-MTAB-10549:Sample 23

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 23

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

characteristic: organism part

text: [Candida] auris

text: clade III isolate B12039

characteristic: strain

text: Sample 23


E-MTAB-10549:Sample 24

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 24

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 24


E-MTAB-10549:Sample 25

text: TEL AVIV UNIVERSITY

characteristic: INSDC center name

text: public

text: E-MTAB-10549:Sample 25

characteristic: Submitter Id

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 25


E-MTAB-10549:Sample 26

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 26

text: ArrayExpress

characteristic: broker name

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 26

characteristic: title


E-MTAB-10549:Sample 27

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 27

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 27


E-MTAB-10549:Sample 3

text: TEL AVIV UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10549:Sample 3

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 3


E-MTAB-10549:Sample 4

text: TEL AVIV UNIVERSITY

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10549:Sample 4

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 4


E-MTAB-10549:Sample 5

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 5

text: ArrayExpress

characteristic: description

text: aneuploid

characteristic: genotype

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 5


E-MTAB-10549:Sample 6

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 6

text: ArrayExpress

text: aneuploid

characteristic: growth condition

text: Candida auris

characteristic: organism

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 6


E-MTAB-10549:Sample 7

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 7

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

characteristic: organism part

text: [Candida] auris

text: clade III isolate B12039

characteristic: strain

text: Sample 7


E-MTAB-10549:Sample 8

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TEL AVIV UNIVERSITY

text: public

text: E-MTAB-10549:Sample 8

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 8


E-MTAB-10549:Sample 9

text: TEL AVIV UNIVERSITY

characteristic: INSDC center name

text: public

text: E-MTAB-10549:Sample 9

characteristic: Submitter Id

text: ArrayExpress

text: aneuploid

text: Candida auris

text: [Candida] auris

text: whole organism

text: [Candida] auris

text: clade III isolate B12039

text: Sample 9