text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein RC3H1 on an HTR-SELEX process. This sample corresponds to selection Cycle2

text: synthetic construct

text: synthetic construct


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF TORONTO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:UNIVERSITY OF TORONTO

characteristic: Submitter Id

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein RC3H1 on an HTR-SELEX process. This sample corresponds to selection Cycle3

characteristic: description

text: synthetic construct

characteristic: organism

text: synthetic construct

characteristic: title


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein RC3H1 on an HTR-SELEX process. This sample corresponds to selection Cycle4

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein slbp on an HTR-SELEX process. This sample corresponds to selection Cycle1

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein slbp on an HTR-SELEX process. This sample corresponds to selection Cycle2

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein slbp on an HTR-SELEX process. This sample corresponds to selection Cycle3

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein slbp on an HTR-SELEX process. This sample corresponds to selection Cycle4

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein SNRPA on an HTR-SELEX process. This sample corresponds to selection Cycle1

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein SNRPA on an HTR-SELEX process. This sample corresponds to selection Cycle2

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein SNRPA on an HTR-SELEX process. This sample corresponds to selection Cycle3

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein SNRPA on an HTR-SELEX process. This sample corresponds to selection Cycle4

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein SNU13 on an HTR-SELEX process. This sample corresponds to selection Cycle1

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein SNU13 on an HTR-SELEX process. This sample corresponds to selection Cycle2

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein SNU13 on an HTR-SELEX process. This sample corresponds to selection Cycle3

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein SNU13 on an HTR-SELEX process. This sample corresponds to selection Cycle4

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein SRSF1 on an HTR-SELEX process. This sample corresponds to selection Cycle1

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein SRSF1 on an HTR-SELEX process. This sample corresponds to selection Cycle2

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein SRSF1 on an HTR-SELEX process. This sample corresponds to selection Cycle3

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein SRSF1 on an HTR-SELEX process. This sample corresponds to selection Cycle4

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein Vts1 on an HTR-SELEX process. This sample corresponds to selection Cycle1

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein Vts1 on an HTR-SELEX process. This sample corresponds to selection Cycle2

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein Vts1 on an HTR-SELEX process. This sample corresponds to selection Cycle3

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein Vts1 on an HTR-SELEX process. This sample corresponds to selection Cycle4

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein ZNF326 on an HTR-SELEX process. This sample corresponds to selection Cycle1

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein ZNF326 on an HTR-SELEX process. This sample corresponds to selection Cycle2

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein ZNF326 on an HTR-SELEX process. This sample corresponds to selection Cycle3

text: synthetic construct

text: synthetic construct


text: UNIVERSITY OF TORONTO

text: public

text: randomised nucleotide library that has been selected for binding sites of RNA binding protein ZNF326 on an HTR-SELEX process. This sample corresponds to selection Cycle4

text: synthetic construct

text: synthetic construct


text: public

tag: Namespace:West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Scotland

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

text: active surveillance in response to outbreak

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

text: not provided

text: not provided

text: United Kingdom

text: Scotland

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

text: not provided

characteristic: title

text: not provided


text: ROTHAMSTED RESEARCH

text: public

tag: Namespace:ROTHAMSTED RESEARCH

characteristic: collection date

text: Enterobacter endosymbiont genome of Chilo suppressalis. Single individual taken for CLR PacBio, Hi-C (Arima kit) and 10X illumina sequencing. Insecticide suseptible. Syngenta received this strain from Aventis in April 2000

characteristic: description

text: unidentified bacterial endosymbiont

text: unidentified bacterial endosymbiont

text: Unidentified endosymbiont of Chilo suppressalis from the Pest Genomics Initiative.


text: UMCG

text: public

text: human

characteristic: common name

text: Patient 1 Matched blood control

text: True

characteristic: germline

text: Homo sapiens

text: Homo sapiens

text: Blood sample

characteristic: tissue type


characteristic: ENA-CHECKLIST

text: UMCG

text: public

text: human

text: Patient 1 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


characteristic: ENA-FIRST-PUBLIC

text: UMCG

text: public

text: human

text: Patient 2 Matched blood control

text: True

text: Homo sapiens

text: Homo sapiens

text: Blood sample


characteristic: ENA-LAST-UPDATE

text: UMCG

text: public

text: human

text: Patient 2 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


characteristic: External Id

text: UMCG

text: public

text: human

text: Patient 3 Matched blood control

text: True

text: Homo sapiens

text: Homo sapiens

text: Blood sample


text: UMCG

characteristic: INSDC center name

text: public

text: human

text: Patient 3 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

characteristic: INSDC first public

text: public

text: human

text: Patient 4 Matched blood control

text: True

text: Homo sapiens

text: Homo sapiens

text: Blood sample


text: UMCG

characteristic: INSDC last update

text: public

text: human

text: Patient 4 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

text: public

characteristic: INSDC status

text: human

text: Patient 5 Matched blood control

text: True

text: Homo sapiens

text: Homo sapiens

text: Blood sample


text: UMCG

text: public

characteristic: SRA accession

text: human

text: Patient 5 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

text: public

characteristic: Submitter Id

text: human

text: Patient 6 Matched blood control

text: True

text: Homo sapiens

text: Homo sapiens

text: Blood sample


text: UMCG

text: public

text: human

text: Patient 6 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

text: public

text: human

text: Patient 7 Matched blood control

text: True

text: Homo sapiens

text: Homo sapiens

text: Blood sample

characteristic: title


text: UMCG

text: public

text: human

text: Patient 7 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

text: public

text: human

text: Patient 8 Matched blood control

text: True

text: Homo sapiens

text: Homo sapiens

text: Blood sample


text: UMCG

text: public

text: human

text: Patient 8 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

text: public

text: human

text: Patient 9 Matched blood control

text: True

text: Homo sapiens

text: Homo sapiens

text: Blood sample


text: UMCG

text: public

text: human

text: Patient 9 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

text: public

text: human

text: Patient 10 Matched blood control

text: True

text: Homo sapiens

text: Homo sapiens

text: Blood sample


text: UMCG

text: public

text: human

text: Patient 10 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

text: public

text: human

text: Patient 11 Matched blood control

text: True

text: Homo sapiens

text: Homo sapiens

text: Blood sample


text: UMCG

text: public

text: human

text: Patient 11 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

text: public

text: human

text: Patient 12 Matched blood control

text: True

text: Homo sapiens

text: Homo sapiens

text: Blood sample


text: UMCG

text: public

text: human

text: Patient 12 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

text: public

text: human

text: Patient 13 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

text: public

text: human

text: Patient 14 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

text: public

text: human

text: Patient 15 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

text: public

text: human

text: Patient 16 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

text: public

text: human

text: Patient 17 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


text: UMCG

text: public

text: human

text: Patient 18 B-cell non-Hodgkin's lymphoma Mucosa Associated Lymphoid tissue

text: False

text: Homo sapiens

text: Homo sapiens

text: Mucosa Associated Lymphoid tissue


E-MTAB-11137:Sample 1

text: public

text: E-MTAB-11137:Sample 1

tag: Namespace:Laboratory of Molecular Medicine and Genomics

text: ArrayExpress

characteristic: broker name

text: U-87 MG

characteristic: cell line

text: human

text: Protocols: Human glioblastoma cells (U87MG) were obtained from the American Type Culture Collection (Manassas, Va.). Cells were cultured in Dulbeccos Modified Eagle Medium supplemented with 10% fetal bovine serum (Gibco Fetal Bovine Serum South America, Thermo Scientific Fisher-US), 2mM L-glutamine, 50 U/ml penicillin, 50 ?g/ml streptomycin, at 37o C, 5% CO2 and 95% of humidity U87MG glioblastoma cells have been transfected, in biological triplicate, with a siRNA targeting praja2 gene or control siRNA. Cells were collected and homogenized in Trizol Reagent. Total RNA extraction was performed with a RNA Clean and Concentrator Kit (Zymo Research Corp., Irvine, CA, USA), following the manufacturers instructions. RNA purity and integrity were assessed with a Nanodrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and a 4200 TapeStation instrument (Agilent Technologies, Santa Clara, CA, USA), respectively. For RNA purity, an A260/280 ratio of ?2.0 and a A260/230 ratio of 2.0-2.2 were considered acceptable; for RNA integrity, an RNA Integrity Number (RIN) of 9.0-10.0 has been obtained for all samples, indicating the absence of degradation and high integrity of RNA samples. For a precise estimation of the RNA concentration, a Qubit 2.0 fluorometer assay (Thermo Fisher Scientific, Waltham, MA, USA) has been employed

text: glioblastoma multiforme

characteristic: disease

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: brain

characteristic: organism part

text: Homo sapiens

text: Sample 1


E-MTAB-11137:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Laboratory of Molecular Medicine and Genomics

text: public

text: E-MTAB-11137:Sample 2

text: ArrayExpress

text: U-87 MG

text: human

characteristic: common name

characteristic: description

text: glioblastoma multiforme

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: Sample 2


E-MTAB-11137:Sample 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11137:Sample 3

text: ArrayExpress

text: U-87 MG

text: human

text: glioblastoma multiforme

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: Sample 3


E-MTAB-11137:Sample 4

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11137:Sample 4

characteristic: Submitter Id

text: ArrayExpress

text: U-87 MG

text: human

text: glioblastoma multiforme

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: Sample 4


E-MTAB-11137:Sample 5

text: public

text: E-MTAB-11137:Sample 5

text: ArrayExpress

characteristic: broker name

text: U-87 MG

characteristic: cell line

text: human

text: glioblastoma multiforme

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: brain

text: Homo sapiens

text: Sample 5

characteristic: title


E-MTAB-11137:Sample 6

text: public

text: E-MTAB-11137:Sample 6

text: ArrayExpress

text: U-87 MG

text: human

text: glioblastoma multiforme

characteristic: disease

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: brain

characteristic: organism part

text: Homo sapiens

text: Sample 6


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: universita degli studi di verona

text: public

tag: Namespace:universita degli studi di verona

text: IRCCS Ospedale Sacro Cuore Don Calabria

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: mRNA

characteristic: description

characteristic: dev stage

text: Italy

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host scientific name

text: Strongyloides stercoralis

text: Strongyloides stercoralis


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: universita degli studi di verona

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: IRCCS Ospedale Sacro Cuore Don Calabria

text: miRNA

text: Italy

text: Homo sapiens

text: Strongyloides stercoralis

text: Strongyloides stercoralis


characteristic: ENA-CHECKLIST

text: West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research

text: public

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: not provided

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

text: Scotland

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

text: active surveillance in response to outbreak

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

characteristic: title

text: not provided

characteristic: virus identifier


E-MTAB-11142:Sample 1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LabMedMolGe

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11142:Sample 1

unit: year

characteristic: age

text: ArrayExpress

characteristic: cell line

text: human

characteristic: common name

text: Protocols: Human Breast cell lines ERa-positive MCF-7 and tamoxifen resistant MCF-7 tam 1 (ATCC HTB-22; ATCC-CRL-3435) were purchased from the American Type Culture Collection (ATCC) while ICI-resistant MCF-7/182R-6 cells (16022506) were purchased from European Collection of Authenticated cell cultures. All cell lines were cultured according to manufacture protocol. Tamoxifen and Fulvestrant resistant cells medium was supplemented, respectively, with 1 µM 4-hydroxytamoxifen (4-OH TAM) or 100 nM fulvestrant (ICI 182,780) (Sigma-Aldrich). MCF-7 wt stably transfected by ERE-TK-LUC plasmid (ref) containing the luciferase reporter gene under the control of the estrogen-responsive element was cultured in in Dulbecco's modified Eagle's medium (Sigma-Aldrich) supplemented with 10% FBS (HyClone, Milan, Italy) and 100 U/ml penicillin, 100 mg/mL streptomycin, and 250 ng/mL Amfotericin-B. Functional assays and RNA sequencing experiment were performed after BAZ1B knock-down. MCF-7 cells were seeded into 96-well plates (1,4 × 103 cells per well) in standard growth medium and transiently transfected by using Lipofectamine RNAiMax (13778-150, Invitrogen) diluted in Optimem medium, according to the manufacturer's instructions. 0.5 pM/well of two validated BAZ1B siRNAs (s17208, s17210) or Silencer Select Negative Control (SiSel_NC1) (Ambion, Thermo Fisher Scientific) were added in sixfold each one and incubated for 72h at 37 °C/5% CO2. Total RNA was extracted using TRIzol (Thermofisher Scientific, Waltham, MA, USA), according to the manufacturers instructions. Furthermore, 0.31 mL of TRIzol Reagent per 1,4 X 103 cells was added directly to the culture dish to lyse the cells by pipetting several times to homogenize. Before use, RNA concentration was determined by using Quant-IT RNA Assay Kit-High Sensitivity and a Qubit Fluorometer (Life Technologies, Monza, Italy) and its quality and integrity assessed with the Agilent 4200 Tapestation System (Agilent Technologies, Milan, Italy). For RNA sequencing, cell lines silencing with siRNA BAZ1B 1 and 2 or treated with 10-6 M ICI 182,7800 were prepared in sixfold and pooled. Negative control (scramble, nontargeting) was used as control. Indexing libraries were prepare starting to 150 ng of total RNA according to Illumina Stranded Total RNA prep Ligation with Ribo-Zero Plus kit (Illumina Inc., San Diego, CA, USA).

characteristic: description

text: adult

characteristic: developmental stage

text: breast cancer

characteristic: disease

text: European

characteristic: ethnic group

text: wild type genotype

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

text: Sample 1


E-MTAB-11142:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: LabMedMolGe

text: public

characteristic: SRA accession

text: E-MTAB-11142:Sample 2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: breast cancer

text: European

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

text: Sample 2

characteristic: title


E-MTAB-11142:Sample 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LabMedMolGe

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11142:Sample 3

characteristic: age

text: ArrayExpress

characteristic: cell line

text: human

text: adult

text: breast cancer

text: European

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

text: Sample 3


E-MTAB-11142:Sample 4

text: LabMedMolGe

text: public

text: E-MTAB-11142:Sample 4

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: breast cancer

characteristic: disease

text: European

characteristic: ethnic group

text: wild type genotype

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

text: Sample 4


E-MTAB-11142:Sample 5

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: LabMedMolGe

text: public

characteristic: SRA accession

text: E-MTAB-11142:Sample 5

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: MCF-7 tam 1

text: human

text: adult

text: breast cancer

text: European

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

text: Sample 5

characteristic: title


E-MTAB-11142:Sample 6

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LabMedMolGe

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11142:Sample 6

characteristic: age

text: ArrayExpress

text: MCF-7 tam 1

characteristic: cell line

text: human

text: adult

text: breast cancer

text: European

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

text: Sample 6


E-MTAB-11142:Sample 7

text: LabMedMolGe

text: public

text: E-MTAB-11142:Sample 7

text: ArrayExpress

text: MCF-7 tam 1

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: breast cancer

characteristic: disease

text: European

characteristic: ethnic group

text: wild type genotype

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

text: Sample 7


E-MTAB-11142:Sample 8

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: LabMedMolGe

text: public

characteristic: SRA accession

text: E-MTAB-11142:Sample 8

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: MCF-7 tam 1

text: human

text: adult

text: breast cancer

text: European

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

text: Sample 8

characteristic: title


E-MTAB-11142:Sample 9

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LabMedMolGe

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11142:Sample 9

characteristic: age

text: ArrayExpress

characteristic: cell line

text: human

text: adult

text: breast cancer

text: European

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

text: Sample 9


E-MTAB-11142:Sample 10

text: LabMedMolGe

text: public

text: E-MTAB-11142:Sample 10

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: breast cancer

characteristic: disease

text: European

characteristic: ethnic group

text: wild type genotype

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

text: Sample 10


E-MTAB-11142:Sample 11

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: LabMedMolGe

text: public

characteristic: SRA accession

text: E-MTAB-11142:Sample 11

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: breast cancer

text: European

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

text: Sample 11

characteristic: title


E-MTAB-11142:Sample 12

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LabMedMolGe

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11142:Sample 12

characteristic: age

text: ArrayExpress

characteristic: cell line

text: human

text: adult

text: breast cancer

text: European

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

text: Sample 12


E-MTAB-11790:CL1 H3K27ac 1

text: MRC Cancer Unit

text: public

text: E-MTAB-11790:CL1 H3K27ac 1

tag: Namespace:MRC Cancer Unit

text: ArrayExpress

text: Fh1 -/- CL1

text: epithelial cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: 1x106 Fh1 fl/fl or 2x106 Fh1 -/- cells were plated onto 15-cm dishes (Nunc) and allowed to reach 80% confluency. Cells were then washed twice in PBS and detached using trypsin (Gibco, 0.25% in PBS-EDTA). After inactivating trypsin with complete medium, cells were filtered through 70μm cell strainers (Fisher Scientific) and counted with Cell Counter CASY (OmniLife Sciences). Following an additional wash in PBS, 7x106 cells were resuspended in 500 μl of PBS and crosslinked using formaldehyde (Thermo Fisher) at 1% final concentration. Crosslinking was stopped using glycine solution after 10 min and 3 washes were carried in cold PBS before storing the pellets at -80˚C. Cells were processed using iDeal ChIP-seq kit for Histones (Diagenode, C01010051) DNA Library was generated using NEB Next Ultra II DNA library kit (NEB, E7645S) following the manufacturer’s protocol

characteristic: description

text: adult

characteristic: developmental stage

text: hereditary leiomyomatosis and renal cell cancer

characteristic: disease

text: Fh1 knockout

characteristic: genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: kidney

characteristic: organism part

characteristic: replicate

text: Mus musculus

text: CL1 H3K27ac 1


E-MTAB-11790:CL1 H3K27ac 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MRC Cancer Unit

text: public

characteristic: SRA accession

text: E-MTAB-11790:CL1 H3K27ac 2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Fh1 -/- CL1

text: epithelial cell

text: house mouse

text: adult

text: Fh1 knockout

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: kidney

text: Mus musculus

text: CL1 H3K27ac 2

characteristic: title


E-MTAB-11790:CL1 H3K27ac 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MRC Cancer Unit

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11790:CL1 H3K27ac 3

text: ArrayExpress

text: Fh1 -/- CL1

characteristic: cell line

text: epithelial cell

text: house mouse

text: adult

text: Fh1 knockout

text: not applicable

text: Mus musculus

text: Mus musculus

text: kidney

text: Mus musculus

text: CL1 H3K27ac 3


E-MTAB-11790:CL1 input

text: MRC Cancer Unit

text: public

text: E-MTAB-11790:CL1 input

text: ArrayExpress

text: Fh1 -/- CL1

text: epithelial cell

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

characteristic: disease

text: Fh1 knockout

characteristic: genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: kidney

characteristic: organism part

text: Mus musculus

text: CL1 input


E-MTAB-11790:CL19 H3K27ac 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MRC Cancer Unit

text: public

characteristic: SRA accession

text: E-MTAB-11790:CL19 H3K27ac 1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Fh1 -/- CL19

text: epithelial cell

text: house mouse

text: adult

text: Fh1 knockout

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: kidney

characteristic: replicate

text: Mus musculus

text: CL19 H3K27ac 1


E-MTAB-11790:CL19 H3K27ac 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MRC Cancer Unit

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11790:CL19 H3K27ac 2

text: ArrayExpress

text: Fh1 -/- CL19

text: epithelial cell

text: house mouse

text: adult

text: Fh1 knockout

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: kidney

text: Mus musculus

text: CL19 H3K27ac 2

characteristic: title


E-MTAB-11790:CL19 H3K27ac 3

text: MRC Cancer Unit

text: public

characteristic: INSDC status

text: E-MTAB-11790:CL19 H3K27ac 3

text: ArrayExpress

text: Fh1 -/- CL19

characteristic: cell line

text: epithelial cell

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

characteristic: disease

text: Fh1 knockout

text: not applicable

text: Mus musculus

text: Mus musculus

text: kidney

text: Mus musculus

text: CL19 H3K27ac 3


E-MTAB-11790:CL19 input

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MRC Cancer Unit

text: public

characteristic: SRA accession

text: E-MTAB-11790:CL19 input

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Fh1 -/- CL19

text: epithelial cell

text: house mouse

text: adult

text: Fh1 knockout

characteristic: genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: kidney

characteristic: organism part

text: Mus musculus

text: CL19 input


E-MTAB-11790:pFH H3K27ac 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MRC Cancer Unit

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11790:pFH H3K27ac 1

text: ArrayExpress

text: Fh1 -/- +pFH

text: epithelial cell

text: house mouse

text: adult

text: Fh1 knockout

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: kidney

characteristic: replicate

text: Mus musculus

text: pFH H3K27ac 1


E-MTAB-11790:pFH H3K27ac 2

text: MRC Cancer Unit

text: public

characteristic: INSDC status

text: E-MTAB-11790:pFH H3K27ac 2

text: ArrayExpress

text: Fh1 -/- +pFH

characteristic: cell line

text: epithelial cell

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: Fh1 knockout

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: kidney

text: Mus musculus

text: pFH H3K27ac 2

characteristic: title


E-MTAB-11790:pFH H3K27ac 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MRC Cancer Unit

text: public

characteristic: SRA accession

text: E-MTAB-11790:pFH H3K27ac 3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Fh1 -/- +pFH

text: epithelial cell

text: house mouse

text: adult

characteristic: developmental stage

characteristic: disease

text: Fh1 knockout

text: not applicable

text: Mus musculus

text: Mus musculus

text: kidney

text: Mus musculus

text: pFH H3K27ac 3


E-MTAB-11790:pFH input

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MRC Cancer Unit

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11790:pFH input

text: ArrayExpress

text: Fh1 -/- +pFH

text: epithelial cell

text: house mouse

text: adult

text: Fh1 knockout

characteristic: genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: kidney

characteristic: organism part

text: Mus musculus

text: pFH input


E-MTAB-11790:FLFL H3K27ac 1

text: MRC Cancer Unit

text: public

characteristic: INSDC status

text: E-MTAB-11790:FLFL H3K27ac 1

text: ArrayExpress

text: Fh1 fl/fl

characteristic: cell line

text: epithelial cell

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: wild type genotype

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: kidney

characteristic: replicate

text: Mus musculus

text: FLFL H3K27ac 1


E-MTAB-11790:FLFL H3K27ac 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MRC Cancer Unit

text: public

characteristic: SRA accession

text: E-MTAB-11790:FLFL H3K27ac 2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Fh1 fl/fl

text: epithelial cell

text: house mouse

text: adult

text: wild type genotype

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: kidney

text: Mus musculus

text: FLFL H3K27ac 2

characteristic: title


E-MTAB-11790:FLFL H3K27ac 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MRC Cancer Unit

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11790:FLFL H3K27ac 3

text: ArrayExpress

text: Fh1 fl/fl

text: epithelial cell

text: house mouse

text: adult

characteristic: developmental stage

characteristic: disease

text: wild type genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: kidney

text: Mus musculus

text: FLFL H3K27ac 3


E-MTAB-11790:FLFL input

text: MRC Cancer Unit

text: public

characteristic: INSDC status

text: E-MTAB-11790:FLFL input

text: ArrayExpress

text: Fh1 fl/fl

characteristic: cell line

text: epithelial cell

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: wild type genotype

characteristic: genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: kidney

characteristic: organism part

text: Mus musculus

text: FLFL input


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Cambridge Stem Cell Institute

text: public

characteristic: SRA accession

tag: Namespace:Cambridge Stem Cell Institute

characteristic: Submitter Id

text: gestational day 7

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: rabbit

text: Protocols: Embryos dissected from the same time-points for transcriptional profiling were flash frozen by placing embryos into Corning® Cryogenic Vials and immediately submerging the vials in liquid nitrogen. Embryos were stored in -80C and then shortly processed to extract nuclei following a 10X genomics demonstrated protocol for nuclei isolation for single cell ATAC on frozen tissues (CG000212). GD9 embryo was split into the extraembryonic portion for one well and the embryo portion was split across four wells of the 10X chip. 10X ATAC (v1.1 chemistry) according to manufacturers instructions 10X ATAC (v1.1 chemistry) according to manufacturers instructions

text: embryo

text: normal

text: wild type genotype

text: 1 + 2

characteristic: individual

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus

text: whole organism

text: Oryctolagus cuniculus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Cambridge Stem Cell Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: gestational day 8

text: ArrayExpress

text: rabbit

text: embryo

text: normal

text: wild type genotype

text: Oryctolagus cuniculus

characteristic: organism

text: Oryctolagus cuniculus

text: whole organism

text: Oryctolagus cuniculus

characteristic: title


text: Cambridge Stem Cell Institute

text: public

characteristic: INSDC status

text: gestational day 9

text: ArrayExpress

text: rabbit

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus

text: extraembryonic tissue

text: Oryctolagus cuniculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Cambridge Stem Cell Institute

text: public

characteristic: SRA accession

text: gestational day 9

text: ArrayExpress

text: rabbit

text: embryo

text: normal

text: wild type genotype

characteristic: genotype

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus

text: whole organism

characteristic: organism part

text: Oryctolagus cuniculus


E-MTAB-11783:Sample 1

characteristic: ENA-LAST-UPDATE

text: MEMORIAL SLOAN KETTERING CANCER CENTER

text: public

text: E-MTAB-11783:Sample 1

tag: Namespace:MEMORIAL SLOAN KETTERING CANCER CENTER

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: We performed RNA sequencing of meso PDXs. Patient samples 17 samples from the 17 patients reported in this study were collected with informed consent from patients under protocols approved by the MSKCC (MSK IMPACT Protocol 12-245; PDX Protocol 14-091; Biospecimen Protocol 06-107). Metadata for each patient can be found in Supplementary Table 1. Patient-derived xenografts All animal experiments were approved by the Memorial Sloan Kettering Cancer Center (MSKCC) Animal Care and Use Committee and mice were housed in accredited facilities under pathogen-free conditions. PDX models were generated from primary tumors and whole blood samples as described previously (Daniel, V. C. et al. Cancer Res 69, 3364-3373, doi:10.1158/0008-5472.CAN-08-4210 (2009). Xenograft protocol as follows: Generation and maintenance of primary xenografts and cell lines. Over an 18-mo period, discarded tissues from three chemo-naive SCLC patients undergoing therapeutic bronchoscopy for acute bronchial obstruction were obtained fresh and transported to the laboratory in 1× PBS at 4°C. All samples were anonymized and obtained in accordance with the Johns Hopkins University Institutional Review Board. Due to the small amount of material available, the entire sample was used to generate a xenograft. Under aseptic conditions, tumor samples were finely minced with razor blades, vigorously triturated in 1× PBS, passed through a 60-μm filter, centrifuged, and then resuspended in 500 μL of Matrigel (BD Biosciences) at 4°C. Cells were then injected s.c. in the flanks of five nonobese diabetic/severe combined immunodeficient mice that were monitored for tumor growth. When the P0 tumors reached 1 cm in diameter, the mouse was sacrificed and the tumor divided into sections for snap freezing, frozen tissue sectioning, formalin fixation, conventional cell culture, or serial passage. All animal studies were done in accordance with protocols approved by the Johns Hopkins University Animal Care and Use Committee. Serial passage in vivo was done by disaggregating the tumor as described above. Aliquots of cells were then injected into the flanks of athymic nude mice in Matrigel or cryopreserved in 90% RPMI (Invitrogen)/10% DMSO (Sigma). Conventional cell lines were established by seeding an aliquot of disaggregated cells in culture with advanced RPMI (Invitrogen)/1% bovine calf serum (Invitrogen). Cell lines were passaged and cryopreserved in standard fashion for SCLC cultures. Publicly available SCLC cell lines were obtained from American Type Culture Collection (ATCC) and cultured in advanced RPMI (Invitrogen)/1% bovine calf serum. Xenografts derived from these conventional cell lines were grown in the flanks of nude mice as described above. Orthotopic xenografts were generated by dorsoscapular, transcutaneous injection of cells suspended in Matrigel into the right lung of nude mice, essentially as described RNA extraction and sequencing was done in collaboration with Genewiz. Total RNA was extracted from fresh frozen cell pellet samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). Sample preparation for RNA sequencing and subsequent analysis was performed as in 26. Briefly, Illumina HiSeq instrument (4000 or equivalent; a 2x150bp Paired End (PE)) according to manufacturer’s instructions was used for RNA sequencing in collaboration with Genewiz.

text: adult

text: mesothelioma

text: patient derived mesothelial xenograft grown in vivo in mouse until neoplasm

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: female

characteristic: sex

text: Sample 1


E-MTAB-11783:Sample 10

characteristic: External Id

text: MEMORIAL SLOAN KETTERING CANCER CENTER

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11783:Sample 10

text: ArrayExpress

text: human

text: adult

text: mesothelioma

text: patient derived xenograft grown in vivo in mouse until neoplasm

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

text: Homo sapiens

text: female

text: Sample 10

characteristic: title


E-MTAB-11783:Sample 12

characteristic: ENA-CHECKLIST

text: MEMORIAL SLOAN KETTERING CANCER CENTER

text: public

characteristic: INSDC status

text: E-MTAB-11783:Sample 12

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: mesothelioma

characteristic: disease

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: female

text: Sample 12


E-MTAB-11783:Sample 13

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MEMORIAL SLOAN KETTERING CANCER CENTER

text: public

characteristic: SRA accession

text: E-MTAB-11783:Sample 13

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: mesothelioma

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: lung

characteristic: organism part

text: Homo sapiens

text: female

text: Sample 13


E-MTAB-11783:Sample 15

characteristic: External Id

text: MEMORIAL SLOAN KETTERING CANCER CENTER

text: public

text: E-MTAB-11783:Sample 15

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: mesothelioma

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: female

characteristic: sex

text: Sample 15


E-MTAB-11783:Sample 17

text: MEMORIAL SLOAN KETTERING CANCER CENTER

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11783:Sample 17

text: ArrayExpress

text: human

text: adult

text: mesothelioma

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

text: Homo sapiens

text: female

text: Sample 17

characteristic: title


E-MTAB-11783:Sample 2

characteristic: ENA-CHECKLIST

text: MEMORIAL SLOAN KETTERING CANCER CENTER

text: public

characteristic: INSDC status

text: E-MTAB-11783:Sample 2

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: mesothelioma

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: female

text: Sample 2


E-MTAB-11783:Sample 3

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MEMORIAL SLOAN KETTERING CANCER CENTER

text: public

characteristic: SRA accession

text: E-MTAB-11783:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: mesothelioma

characteristic: disease

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: female

text: Sample 3


E-MTAB-11783:Sample 4

characteristic: External Id

text: MEMORIAL SLOAN KETTERING CANCER CENTER

text: public

text: E-MTAB-11783:Sample 4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: mesothelioma

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: lung

characteristic: organism part

text: Homo sapiens

text: female

text: Sample 4


E-MTAB-11783:Sample 5

text: MEMORIAL SLOAN KETTERING CANCER CENTER

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11783:Sample 5

text: ArrayExpress

text: human

text: adult

text: mesothelioma

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

text: Homo sapiens

text: female

characteristic: sex

text: Sample 5


E-MTAB-11783:Sample 6

characteristic: ENA-CHECKLIST

text: MEMORIAL SLOAN KETTERING CANCER CENTER

text: public

characteristic: INSDC status

text: E-MTAB-11783:Sample 6

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: adult

text: mesothelioma

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: female

text: Sample 6

characteristic: title


E-MTAB-11783:Sample 7

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MEMORIAL SLOAN KETTERING CANCER CENTER

text: public

characteristic: SRA accession

text: E-MTAB-11783:Sample 7

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

characteristic: developmental stage

text: mesothelioma

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: female

text: Sample 7


E-MTAB-11783:Sample 8

characteristic: External Id

text: MEMORIAL SLOAN KETTERING CANCER CENTER

text: public

text: E-MTAB-11783:Sample 8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: mesothelioma

characteristic: disease

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: female

text: Sample 8


E-MTAB-11783:Sample 9

text: MEMORIAL SLOAN KETTERING CANCER CENTER

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11783:Sample 9

text: ArrayExpress

text: human

text: adult

text: mesothelioma

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

characteristic: organism part

text: Homo sapiens

text: female

text: Sample 9


characteristic: ENA-CHECKLIST

text: Wageningen University & Research

text: public

characteristic: INSDC status

tag: Namespace:Wageningen University & Research

characteristic: collection date

text: potato

characteristic: common name

text: Solanum tuberosum AltusxColumba offspring genotype

characteristic: description

characteristic: estimated size

characteristic: genotype

text: Netherlands

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: isolation and growth condition

characteristic: number of replicons

text: Solanum tuberosum

text: potato

characteristic: organism common name

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

characteristic: plant structure

characteristic: ploidy

text: Solanum tuberosum

characteristic: subspecific genetic lineage name

text: Potato AxC offspring


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Suzhou Ninth People's Hospital

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Suzhou Ninth People's Hospital

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: peridontal ligament stem cell

characteristic: cell type

text: human

text: Protocols: GMSCs and PDLSCs were separated from the surface of the middle third of the root, and were digested with α-minimum essential medium (α-MEM, Gibco, Carlsbad, CA, USA) containing 3 mg/mL collagenase (type I) and 4 mg/mL dispase (both from Sigma-Aldrich, Billerica, MA, USA) for 15 min at 37 °C. Single-cell suspensions were obtained by passing the digested tissues through a 70-μm cell strainer (BD Bioscience, Franklin Lakes, NJ, USA). Then the cell suspensions were seeded into 10-cm culture dishes (Corning, USA) containing α-MEM supplemented with 15% fetal bovine serum (FBS, Hyclone, New York City, NY, USA), and 1 x GlutaMAX (Thermo Fisher Scientific, Waltham, MA, USA). The cells were incubated at 37 °C in a humidified atmosphere containing 5% CO2, and medium was changed twice a week. Cells were used at passages 3-5 for subsequent experiments. SP600125 (MedChemExpress LLC, Shanghai, China) were dissolved in dimethyl sulfoxide (DMSO). Unless otherwise indicated, cells were pre-incubated with serum-free medium containing same dose of DMSO (0.2%) or 10 μM SP600125 for 2 h. Here, we collected GMSCs and PDLSCs from systemically healthy patients due to the premolars and extracted for orthodontic reasons, and treated with tobacco smoke (G1, P1), E-cig smoke with original flavor (G2, P2), E-cig smoke with menthol flavor (G3, P3), E-cig liquid with original flavor (G4, P4), and E-cig liquid with menthol flavor (G5, P5) by the optimal conditions of LC50, and conducted RNA-seq to compare with untreated control (G0, P0). All followed iso smoking model. Total RNA of 5 x 107 GMSCs or PDLSCs were extracted using TRIZOL (Thermo Fisher Scientific). Nanodrop 2000 (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100 (Agilent) were used to evaluate RNA concentration and quality. 5 μg of RNA from different experimental groups was prepared cDNA library using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s instructions, and sequenced on an Illumina Hiseq 4000 platform.

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: premolar tooth

characteristic: organism part

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Suzhou Ninth People's Hospital

text: public

text: ArrayExpress

text: dental papilla cell

text: human

characteristic: common name

characteristic: description

text: adult

text: normal

text: wild type genotype

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: premolar tooth

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TEAGASC FOOD RESEARCH CENTRE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:TEAGASC FOOD RESEARCH CENTRE

text: spiked milk metagenome

text: milk metagenome

text: milk metagenome

text: spiked milk metagenome


text: TEAGASC FOOD RESEARCH CENTRE

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: heat inactivated mock community

text: milk metagenome

text: milk metagenome

text: heat inactivated mock community


text: TEAGASC FOOD RESEARCH CENTRE

text: public

text: live mock community

text: milk metagenome

text: milk metagenome

text: live mock community


text: public

tag: Namespace:Roche Pharmaceutical Research and Early Development (pRED) Roche Innovation Center Basel

characteristic: batch

text: ArrayExpress

characteristic: broker name

text: CD8-positive, alpha-beta T cell

characteristic: cell type

text: house mouse

text: Protocols: Tumour were digested as previously described and 1-10 Mio cells were stored in liquid nitrogen in Ibidi freezing medium. The samples were randomised and processed in 2 different batches with 10 samples each. After thawing a batch of samples, the cells were stained with a mix of FACS and oligo-labelled antibodies and sorted for CD8+ T cells before performing scRNA-seq. The cell number and viability of the sorted cells was determined using a Nexcelom Cellometer Auto 2000 and a total of 10,000 viable cells per sample were loaded into the 10x Genomics Chromium controller. cDNA and library preparation was performed according to the manufacturer’s indications (scRNA-seq 5’ v2 kit with TCR and feature barcoding).

text: adult

characteristic: developmental stage

text: pancreatic cancer

characteristic: disease

characteristic: individual

text: Mus musculus

text: Mus musculus

text: pancreas

text: neoplasm

characteristic: sampling site

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Roche Pharmaceutical Research and Early Development (pRED) Roche Innovation Center Basel

text: public

text: ArrayExpress

text: CD8-positive, alpha-beta T cell

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: pancreatic cancer

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: pancreas

characteristic: organism part

text: neoplasm

text: Mus musculus

text: female

characteristic: title


characteristic: External Id

text: MAX PLANCK INSTITUTE FOR BIOLOGY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:MAX PLANCK INSTITUTE FOR BIOLOGY

characteristic: Submitter Id

text: 16S rRNA gene amplicons from plant leaves

text: 16S rRNA gene amplicons, using 341F and 806R primers

text: collection

text: collection


text: T.officinale

text: MAX PLANCK INSTITUTE FOR BIOLOGY

text: public

text: collection

text: collection


text: UCSDMI

text: public

text: TRUE

text: BLANK

characteristic: elevation

text: meters

text: Control

text: Negative

text: Sterile water blank

text: urban biome

characteristic: env biome

text: research facility

characteristic: env feature

text: misc environment

characteristic: env package

text: sterile water

text: USA:CO:Denver

characteristic: geo loc name

characteristic: host subject id

text: years

text: cm

text: kg

text: Caltech

characteristic: latitude

text: decimal degrees

characteristic: longitude

text: decimal degrees

text: metagenome

text: Caltech

text: FALSE

text: control blank

characteristic: sample type

text: metagenome

text: PD Shotgun Metagenomics


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Seoul National University Bundang Hospital

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens


characteristic: External Id

text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:GHENT UNIVERSITY

characteristic: collection date

text: Anthidium florentinum 1

characteristic: description

text: solitary bee

characteristic: environment (biome)

text: Anthidium florentinum

characteristic: environment (feature)

text: whole gut

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: insect gut metagenome

text: 16S rRNA amplicon sequencing of Megachile sculpturalis from native and invaded regions, Anthidium florentinum and Halictus scabiosae

characteristic: project name

text: insect gut metagenome

text: Illumina

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: V3-V4 region

characteristic: target subfragment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Anthidium florentinum 2

text: solitary bee

text: Anthidium florentinum

text: whole gut

text: France

text: host-associated

text: metagenome

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


text: GHENT UNIVERSITY

text: public

characteristic: INSDC status

characteristic: collection date

text: Anthidium florentinum 3

characteristic: description

text: solitary bee

characteristic: environment (biome)

text: Anthidium florentinum

characteristic: environment (feature)

text: whole gut

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: insect gut metagenome

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

text: public

text: Anthidium florentinum 4

text: solitary bee

text: Anthidium florentinum

text: whole gut

text: France

text: host-associated

text: metagenome

characteristic: investigation type

text: insect gut metagenome

characteristic: project name

text: insect gut metagenome

text: Illumina

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: V3-V4 region

characteristic: target subfragment

characteristic: title


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Anthidium florentinum 5

characteristic: description

text: solitary bee

characteristic: environment (biome)

text: Anthidium florentinum

text: whole gut

text: France

text: host-associated

text: metagenome

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

text: public

text: Anthidium florentinum 6

text: solitary bee

text: Anthidium florentinum

characteristic: environment (feature)

text: whole gut

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: insect gut metagenome

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Anthidium florentinum 7

text: solitary bee

text: Anthidium florentinum

text: whole gut

text: France

text: host-associated

text: metagenome

characteristic: investigation type

text: insect gut metagenome

characteristic: project name

text: insect gut metagenome

text: Illumina

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: V3-V4 region

characteristic: target subfragment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Anthidium florentinum 8

characteristic: description

text: solitary bee

characteristic: environment (biome)

text: Anthidium florentinum

text: whole gut

text: France

text: host-associated

text: metagenome

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Anthidium florentinum 9

text: solitary bee

text: Anthidium florentinum

characteristic: environment (feature)

text: whole gut

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: insect gut metagenome

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

text: public

text: Anthidium florentinum 10

text: solitary bee

text: Anthidium florentinum

text: whole gut

text: France

text: host-associated

text: metagenome

characteristic: investigation type

text: insect gut metagenome

characteristic: project name

text: insect gut metagenome

text: Illumina

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: V3-V4 region

characteristic: target subfragment

characteristic: title


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Anthidium florentinum 11

characteristic: description

text: solitary bee

characteristic: environment (biome)

text: Anthidium florentinum

text: whole gut

text: France

text: host-associated

text: metagenome

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

text: public

text: Anthidium florentinum 12

text: solitary bee

text: Anthidium florentinum

characteristic: environment (feature)

text: whole gut

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: insect gut metagenome

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Anthidium florentinum 13

text: solitary bee

text: Anthidium florentinum

text: whole gut

text: France

text: host-associated

text: metagenome

characteristic: investigation type

text: insect gut metagenome

characteristic: project name

text: insect gut metagenome

text: Illumina

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: V3-V4 region

characteristic: target subfragment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Anthidium florentinum 14

characteristic: description

text: solitary bee

characteristic: environment (biome)

text: Anthidium florentinum

text: whole gut

text: France

text: host-associated

text: metagenome

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Anthidium florentinum 15

text: solitary bee

text: Anthidium florentinum

characteristic: environment (feature)

text: whole gut

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: insect gut metagenome

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

text: public

text: Halictus scabiosae 1

text: solitary bee

text: Halictus scabiosae

text: whole gut

text: France

text: host-associated

text: metagenome

characteristic: investigation type

text: insect gut metagenome

characteristic: project name

text: insect gut metagenome

text: Illumina

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: V3-V4 region

characteristic: target subfragment

characteristic: title


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Halictus scabiosae 2

characteristic: description

text: solitary bee

characteristic: environment (biome)

text: Halictus scabiosae

text: whole gut

text: France

text: host-associated

text: metagenome

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

text: public

text: Halictus scabiosae 3

text: solitary bee

text: Halictus scabiosae

characteristic: environment (feature)

text: whole gut

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: insect gut metagenome

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Halictus scabiosae 4

text: solitary bee

text: Halictus scabiosae

text: whole gut

text: France

text: host-associated

text: metagenome

characteristic: investigation type

text: insect gut metagenome

characteristic: project name

text: insect gut metagenome

text: Illumina

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: V3-V4 region

characteristic: target subfragment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Halictus scabiosae 5

characteristic: description

text: solitary bee

characteristic: environment (biome)

text: Halictus scabiosae

text: whole gut

text: France

text: host-associated

text: metagenome

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Halictus scabiosae 6

text: solitary bee

text: Halictus scabiosae

characteristic: environment (feature)

text: whole gut

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: insect gut metagenome

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

text: public

text: Halictus scabiosae 7

text: solitary bee

text: Halictus scabiosae

text: whole gut

text: France

text: host-associated

text: metagenome

characteristic: investigation type

text: insect gut metagenome

characteristic: project name

text: insect gut metagenome

text: Illumina

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: V3-V4 region

characteristic: target subfragment

characteristic: title


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Halictus scabiosae 8

characteristic: description

text: solitary bee

characteristic: environment (biome)

text: Halictus scabiosae

text: whole gut

text: France

text: host-associated

text: metagenome

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

text: public

text: Halictus scabiosae 9

text: solitary bee

text: Halictus scabiosae

characteristic: environment (feature)

text: whole gut

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: insect gut metagenome

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Megachile sculpturalis 1

text: solitary bee

text: Megachile sculpturalis

text: whole gut

text: France

text: host-associated

text: metagenome

characteristic: investigation type

text: insect gut metagenome

characteristic: project name

text: insect gut metagenome

text: Illumina

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: V3-V4 region

characteristic: target subfragment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Megachile sculpturalis 2

characteristic: description

text: solitary bee

characteristic: environment (biome)

text: Megachile sculpturalis

text: whole gut

text: France

text: host-associated

text: metagenome

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Megachile sculpturalis 3

text: solitary bee

text: Megachile sculpturalis

characteristic: environment (feature)

text: whole gut

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

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characteristic: geographic location (country and/or sea)

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characteristic: ENA-CHECKLIST

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text: GHENT UNIVERSITY

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text: Megachile sculpturalis 16

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text: GHENT UNIVERSITY

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text: Megachile sculpturalis 18

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characteristic: environment (feature)

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characteristic: geographic location (country and/or sea)

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characteristic: Submitter Id

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text: Megachile sculpturalis 20

characteristic: description

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text: V3-V4 region


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characteristic: environment (feature)

text: whole gut

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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characteristic: host-associated environmental package

text: metagenome

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text: V3-V4 region


characteristic: ENA-CHECKLIST

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text: GHENT UNIVERSITY

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text: Megachile sculpturalis 22

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characteristic: Submitter Id

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text: Megachile sculpturalis 23

characteristic: description

text: solitary bee

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text: Megachile sculpturalis

text: whole gut

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characteristic: organism

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


characteristic: ENA-CHECKLIST

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characteristic: ENA-LAST-UPDATE

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text: GHENT UNIVERSITY

text: public

text: Megachile sculpturalis 24

text: solitary bee

text: Megachile sculpturalis

characteristic: environment (feature)

text: whole gut

characteristic: environment (material)

text: Japan

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: insect gut metagenome

text: insect gut metagenome

text: Illumina

text: 16S rRNA

text: V3-V4 region


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

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text: Megachile sculpturalis 25

text: solitary bee

text: Megachile sculpturalis

text: whole gut

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characteristic: project name

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characteristic: target subfragment

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characteristic: ENA-CHECKLIST

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characteristic: External Id

text: MAX F. PERUTZ LABORATORIES

text: public

characteristic: SRA accession

tag: Namespace:MAX F. PERUTZ LABORATORIES

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: RNA seq (quantseq protocol) of R1 wt or IRF1 KO samples, cultured under 2iLIF conditions (ESC) or differentiated for 48 h (EpiLC)

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus


tag: attribute

text: MAX F. PERUTZ LABORATORIES

characteristic: INSDC center name

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text: public

text: house mouse

text: RNA seq of IRF1 overexpression in SunTag overexpressing cells. All samples were cultured in 2iLIF (ESC). Samples were transfected with guides targeting the Irf1 promoter (IRF1OE), or as controls no guides (noOE). Overexpression was induced by dox induction for 48h (dox), no induction (nodox) was used as control

text: Mus musculus

text: Mus musculus


text: public

characteristic: INSDC status

tag: Namespace:Unit of Viral Infection and Immunity, National Center for Microbiology, Institute of Health Carlos III

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: Whole peripheral blood was isolated and processed within the first 4 h after extraction. Plasma fraction was pre-clarified at 15.000 rpm 15 min at 4°C, and stored at – 80°C. Extracellular vesicles (EVs isolation and RNA purification was performed using the ExoRNeasy Serum/Plasma Midi kit (QIAGEN, Cat #77044). EVs were phenol-lysed and total RNA was purified by ethanol-based membrane binding into spin columns. Quality and integrity were evaluated by the Bioanalyzer 2100 with Agilent RNA 6000 Nano kit (Agilent). Small RNA library was constructed with NEBNext Multiplex Small RNA Library Prep Kit (NewEngland BioLabs).

text: adult

characteristic: developmental stage

text: HIV-1 coinfection with hepatitis C virus infection

characteristic: disease

text: extracellular vesicles

characteristic: fraction

characteristic: individual

text: Human immunodeficiency virus 1; Hepatitis C virus

characteristic: infect

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: blood

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: Unit of Viral Infection and Immunity, National Center for Microbiology, Institute of Health Carlos III

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: extracellular vesicles

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

text: extracellular vesicles

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: male