status: PUBLIC

characteristic: ENA first public

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: External Id

text: SAMSUNG MEDICAL CENTER

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:SAMSUNG MEDICAL CENTER

characteristic: Submitter Id

text: human

characteristic: common name

text: Lung adenocarcinoma is one of the most common cancer types with various treatment modalities. However, better biomarkers to predict therapeutic response are still needed to improve precision medicine. S3 was characterized by dependency on CDK4, immune-related expression patterns, and altered MET signaling; experimental validation showed that S3-associated cell lines responded to MET inhibitors, leading to increased PD-L1 expression. Patients with S3 tumors were also enriched with responders to immune checkpoint blockade (ICB) in a real world patient dataset. We further identified genomic features in S3 and S163 as biomarkers for enabling clinical diagnosis of these subtypes.

characteristic: description

text: eukaryote

characteristic: investigation type

text: Homo sapiens

characteristic: organism

characteristic: project name

text: Homo sapiens

text: NGS

characteristic: sequencing method

text: High-resolution lung adenocarcinoma expression subtypes

characteristic: title


text: SAMSUNG MEDICAL CENTER

text: public

text: human

text: Lung adenocarcinoma is one of the most common cancer types with various treatment modalities. However, better biomarkers to predict therapeutic response are still needed to improve precision medicine. S3 was characterized by dependency on CDK4, immune-related expression patterns, and altered MET signaling; experimental validation showed that S3-associated cell lines responded to MET inhibitors, leading to increased PD-L1 expression. Patients with S3 tumors were also enriched with responders to immune checkpoint blockade (ICB) in a real world patient dataset. We further identified genomic features in S3 and S164 as biomarkers for enabling clinical diagnosis of these subtypes.

text: eukaryote

text: Homo sapiens

text: Homo sapiens

text: NGS


text: SAMSUNG MEDICAL CENTER

text: public

text: human

text: Lung adenocarcinoma is one of the most common cancer types with various treatment modalities. However, better biomarkers to predict therapeutic response are still needed to improve precision medicine. S3 was characterized by dependency on CDK4, immune-related expression patterns, and altered MET signaling; experimental validation showed that S3-associated cell lines responded to MET inhibitors, leading to increased PD-L1 expression. Patients with S3 tumors were also enriched with responders to immune checkpoint blockade (ICB) in a real world patient dataset. We further identified genomic features in S3 and S165 as biomarkers for enabling clinical diagnosis of these subtypes.

text: eukaryote

text: Homo sapiens

text: Homo sapiens

text: NGS


text: SAMSUNG MEDICAL CENTER

text: public

text: human

text: Lung adenocarcinoma is one of the most common cancer types with various treatment modalities. However, better biomarkers to predict therapeutic response are still needed to improve precision medicine. S3 was characterized by dependency on CDK4, immune-related expression patterns, and altered MET signaling; experimental validation showed that S3-associated cell lines responded to MET inhibitors, leading to increased PD-L1 expression. Patients with S3 tumors were also enriched with responders to immune checkpoint blockade (ICB) in a real world patient dataset. We further identified genomic features in S3 and S166 as biomarkers for enabling clinical diagnosis of these subtypes.

text: eukaryote

text: Homo sapiens

text: Homo sapiens

text: NGS


text: public

text: ena-SAMPLE-TAB-29-06-2022-11:48:38:426-51710

tag: Namespace:Department of Biology - University of Padova

characteristic: collection date

text: Ribodepleted RNA extracted from sediment samples at the Chioggia inlet, Venice Lagoon

text: marine sediment

characteristic: environment (biome)

text: lagoon sediment

characteristic: environment (feature)

text: surface sediment

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metatranscriptome

text: marine sediment metagenome

text: Transcriptional profiles of Venice lagoon microbial communities

text: marine sediment metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina NovaSeq


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Department of Biology - University of Padova

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-29-06-2022-11:50:25:676-51712

characteristic: Submitter Id

text: marine sediment

text: lagoon sediment

text: surface sediment

text: Italy

text: metatranscriptome

text: marine sediment metagenome

text: marine sediment metagenome

text: sediment

text: Illumina NovaSeq


text: public

text: ena-SAMPLE-TAB-29-06-2022-11:51:32:776-51479

characteristic: collection date

characteristic: description

text: marine sediment

characteristic: environment (biome)

text: lagoon sediment

text: surface sediment

text: Italy

text: metatranscriptome

characteristic: investigation type

text: marine sediment metagenome

characteristic: organism

characteristic: project name

text: marine sediment metagenome

text: sediment

text: Illumina NovaSeq

characteristic: sequencing method

characteristic: title


text: public

text: ena-SAMPLE-TAB-29-06-2022-11:52:48:683-51714

text: marine sediment

text: lagoon sediment

characteristic: environment (feature)

text: surface sediment

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metatranscriptome

text: marine sediment metagenome

text: marine sediment metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina NovaSeq


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-29-06-2022-11:53:56:953-51716

characteristic: Submitter Id

text: marine sediment

text: lagoon sediment

text: surface sediment

text: Italy

text: metatranscriptome

text: marine sediment metagenome

text: marine sediment metagenome

text: sediment

text: Illumina NovaSeq


text: public

text: ena-SAMPLE-TAB-29-06-2022-11:54:37:822-51831

characteristic: collection date

text: Ribodepleted RNA extracted from sediment samples at Marghera, Venice Lagoon

characteristic: description

text: marine sediment

characteristic: environment (biome)

text: lagoon sediment

text: surface sediment

text: Italy

text: metatranscriptome

characteristic: investigation type

text: marine sediment metagenome

characteristic: organism

characteristic: project name

text: marine sediment metagenome

text: sediment

text: Illumina NovaSeq

characteristic: sequencing method

characteristic: title


text: public

text: ena-SAMPLE-TAB-29-06-2022-11:55:08:450-51833

text: marine sediment

text: lagoon sediment

characteristic: environment (feature)

text: surface sediment

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metatranscriptome

text: marine sediment metagenome

text: marine sediment metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina NovaSeq


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-29-06-2022-11:56:43:643-51835

characteristic: Submitter Id

text: marine sediment

text: lagoon sediment

text: surface sediment

text: Italy

text: metatranscriptome

text: marine sediment metagenome

text: marine sediment metagenome

text: sediment

text: Illumina NovaSeq


text: public

text: ena-SAMPLE-TAB-29-06-2022-11:57:23:161-51837

characteristic: collection date

characteristic: description

text: marine sediment

characteristic: environment (biome)

text: lagoon sediment

text: surface sediment

text: Italy

text: metatranscriptome

characteristic: investigation type

text: marine sediment metagenome

characteristic: organism

characteristic: project name

text: marine sediment metagenome

text: sediment

text: Illumina NovaSeq

characteristic: sequencing method

characteristic: title


text: public

text: ena-SAMPLE-TAB-29-06-2022-11:58:07:930-51481

text: marine sediment

text: lagoon sediment

characteristic: environment (feature)

text: surface sediment

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metatranscriptome

text: marine sediment metagenome

text: marine sediment metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina NovaSeq


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-29-06-2022-11:59:11:878-51483

characteristic: Submitter Id

text: Ribodepleted RNA extracted from sediment samples at Palude della Rosa, Venice Lagoon

text: marine sediment

text: lagoon sediment

text: surface sediment

text: Italy

text: metatranscriptome

text: marine sediment metagenome

text: marine sediment metagenome

text: sediment

text: Illumina NovaSeq


text: public

text: ena-SAMPLE-TAB-29-06-2022-11:59:48:524-51839

characteristic: collection date

characteristic: description

text: marine sediment

characteristic: environment (biome)

text: lagoon sediment

text: surface sediment

text: Italy

text: metatranscriptome

characteristic: investigation type

text: marine sediment metagenome

characteristic: organism

characteristic: project name

text: marine sediment metagenome

text: sediment

text: Illumina NovaSeq

characteristic: sequencing method

characteristic: title


text: public

text: ena-SAMPLE-TAB-29-06-2022-12:00:31:793-51485

text: marine sediment

text: lagoon sediment

characteristic: environment (feature)

text: surface sediment

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metatranscriptome

text: marine sediment metagenome

text: marine sediment metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina NovaSeq


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-29-06-2022-12:01:11:290-51487

characteristic: Submitter Id

text: marine sediment

text: lagoon sediment

text: surface sediment

text: Italy

text: metatranscriptome

text: marine sediment metagenome

text: marine sediment metagenome

text: sediment

text: Illumina NovaSeq


text: public

text: ena-SAMPLE-TAB-29-06-2022-12:01:49:239-51841

characteristic: collection date

characteristic: description

text: marine sediment

characteristic: environment (biome)

text: lagoon sediment

text: surface sediment

text: Italy

text: metatranscriptome

characteristic: investigation type

text: marine sediment metagenome

characteristic: organism

text: Transcriptional profiles of Venice lagoon microbial communities

characteristic: project name

text: marine sediment metagenome

text: sediment

text: Illumina NovaSeq

characteristic: sequencing method

characteristic: title


text: Department of Biology - University of Padova

text: public

text: ena-SAMPLE-TAB-29-06-2022-12:02:44:803-51489

text: Ribodepleted RNA extracted from the 0.22-3 µm surface water fraction sampled at the Chioggia inlet, Venice Lagoon

text: water surface

text: lagoon

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metatranscriptome

text: marine plankton metagenome

text: marine plankton metagenome

text: Illumina NovaSeq

text: water

characteristic: water environmental package


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-29-06-2022-12:03:42:302-51491

text: water surface

text: lagoon

text: water

text: Italy

text: metatranscriptome

text: marine plankton metagenome

text: marine plankton metagenome

text: Illumina NovaSeq

text: water


text: public

text: ena-SAMPLE-TAB-29-06-2022-12:04:23:222-51493

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: water surface

characteristic: environment (biome)

text: lagoon

text: water

text: Italy

text: metatranscriptome

characteristic: investigation type

text: marine plankton metagenome

characteristic: organism

characteristic: project name

text: marine plankton metagenome

text: Illumina NovaSeq

text: water


text: public

text: ena-SAMPLE-TAB-29-06-2022-12:04:48:109-51843

text: water surface

text: lagoon

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metatranscriptome

text: marine plankton metagenome

text: marine plankton metagenome

text: Illumina NovaSeq

characteristic: sequencing method

characteristic: title

text: water


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ena-SAMPLE-TAB-29-06-2022-12:05:33:068-51845

text: Ribodepleted RNA extracted from the 0.22-3 µm surface water fraction sampled at Marghera, Venice Lagoon

text: water surface

text: lagoon

text: water

text: Italy

characteristic: geographic location (longitude)

text: metatranscriptome

text: marine plankton metagenome

text: marine plankton metagenome

text: Illumina NovaSeq

text: water

characteristic: water environmental package


text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-29-06-2022-12:06:01:554-51495

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: water surface

characteristic: environment (biome)

text: lagoon

text: water

text: Italy

text: metatranscriptome

characteristic: investigation type

text: marine plankton metagenome

text: marine plankton metagenome

text: Illumina NovaSeq

text: water


text: public

text: ena-SAMPLE-TAB-29-06-2022-12:06:44:519-51847

text: water surface

text: lagoon

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metatranscriptome

text: marine plankton metagenome

characteristic: organism

characteristic: project name

text: marine plankton metagenome

text: Illumina NovaSeq

text: water


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ena-SAMPLE-TAB-29-06-2022-12:07:12:875-51497

text: water surface

text: lagoon

text: water

text: Italy

text: metatranscriptome

text: marine plankton metagenome

text: marine plankton metagenome

text: Illumina NovaSeq

characteristic: sequencing method

characteristic: title

text: water


text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-29-06-2022-12:07:55:700-51849

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: water surface

text: lagoon

text: water

text: Italy

characteristic: geographic location (longitude)

text: metatranscriptome

text: marine plankton metagenome

text: marine plankton metagenome

text: Illumina NovaSeq

text: water

characteristic: water environmental package


text: public

text: ena-SAMPLE-TAB-29-06-2022-12:08:38:588-51499

text: Ribodepleted RNA extracted from the 0.22-3 µm surface water fraction sampled at Palude della Rosa, Venice Lagoon

text: water surface

characteristic: environment (biome)

text: lagoon

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metatranscriptome

characteristic: investigation type

text: marine plankton metagenome

text: marine plankton metagenome

text: Illumina NovaSeq

text: water


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ena-SAMPLE-TAB-29-06-2022-12:09:07:262-51851

text: water surface

text: lagoon

text: water

text: Italy

text: metatranscriptome

text: marine plankton metagenome

characteristic: organism

characteristic: project name

text: marine plankton metagenome

text: Illumina NovaSeq

text: water


text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-29-06-2022-12:09:39:137-51853

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: water surface

text: lagoon

text: water

text: Italy

text: metatranscriptome

text: marine plankton metagenome

text: marine plankton metagenome

text: Illumina NovaSeq

characteristic: sequencing method

characteristic: title

text: water


text: public

text: ena-SAMPLE-TAB-29-06-2022-12:10:09:128-51501

text: water surface

characteristic: environment (biome)

text: lagoon

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (longitude)

text: metatranscriptome

text: marine plankton metagenome

text: Transcriptional profiles of Venice lagoon microbial communities

text: marine plankton metagenome

text: Illumina NovaSeq

text: water

characteristic: water environmental package


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Department of Biology - University of Padova

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ena-SAMPLE-TAB-29-06-2022-12:10:36:149-51855

text: water surface

text: lagoon

text: water

text: Italy

characteristic: geographic location (latitude)

text: metatranscriptome

characteristic: investigation type

text: marine plankton metagenome

text: marine plankton metagenome

text: Illumina NovaSeq

text: water


text: positive

characteristic: ArrayExpress-Phenotype

text: unknown

characteristic: ArrayExpress-Sex

text: metagenome

characteristic: ArrayExpress-Species

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: metagenome

characteristic: common name

text: metagenome

characteristic: organism

text: metagenome

characteristic: strain


text: School of Biological Sciences

text: public

tag: Namespace:School of Biological Sciences

text: Genomic DNA from adult female

characteristic: description

text: Procambarus virginalis

text: Procambarus virginalis

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: public

tag: Namespace:FEDERAL INSTITUTE FOR RISK ASSESSMENT (BFR)

text: human

text: CD154+CD4+ memory T cells

text: homo sapiens

characteristic: host scientific name

text: PMBC

text: Homo sapiens

text: Homo sapiens

text: peripheral blood


characteristic: External Id

text: FEDERAL INSTITUTE FOR RISK ASSESSMENT (BFR)

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: human

text: CD154+CD4+ memory T cells

text: homo sapiens

text: PMBC

text: Homo sapiens

text: Homo sapiens

text: peripheral blood


text: public

tag: Namespace:INSERM U1242 OSS (Oncogenesis, Stress and Signaling) - Universite de Rennes1

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: Mice were anesthetized by intra-peritoneal route with a mixture of ketamine and xylazine. Opening of the animals was performed by a laparotomy and then a thoracotomy to reveal the heart. Blood was collected via the right atrium and tumors were removed with a scalpel, cut in two pieces and snap-frozen in liquid nitrogen. Xenograft tumors were then stored at -80°C until tissue homogenization and RNA extraction. Xenograft tumors were cut into smaller pieces in a Petri dish placed on ice and transferred into 2mL tubes containing 2.8mm ceramic beads (P000911-LYSK0-A, Bertin Corp) filled with 1 ml Qiazol. Homogenization of the tumors was performed using the Precellys 24 homogenizer (5500 rpm, 20s x 2, pause: 20s). Then, the homogenate was transferred to new tubes and subjected to RNA extraction using the RNeasy Lipid Tissue Mini Kit (74804, Qiagen), according to the instructions by the manufacturer. The library construction method and sequencing process are carried out according to the following steps: 1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB);

text: cholangiocarcinoma

characteristic: disease

text: wild type genotype

characteristic: genotype

text: human HuCC-T1 cells injected in mice to induce xenograft tumors

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: xenograft tumor

characteristic: sampling site

text: Homo sapiens

text: human HuCC-T1 cell line grafted into mice

characteristic: xenograft


text: INSERM U1242 OSS (Oncogenesis, Stress and Signaling) - Universite de Rennes1

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: cholangiocarcinoma

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: xenograft tumor

text: Homo sapiens


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

text: human

characteristic: description

text: cholangiocarcinoma

text: LINC313 overexpression

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: xenograft tumor

text: Homo sapiens

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: 100,000 HuCCT1 pcDNA3.1 (empty vector) and pcLINC00313 over-expressing cells were used per ATAC reaction. Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay. cells were then thawed in a 37°C water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems)

text: adult

characteristic: developmental stage

text: intrahepatic cholangiocarcinoma

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: wild type

characteristic: phenotype

text: Homo sapiens

text: male

characteristic: sex

text: EV


text: public

characteristic: INSDC status

text: ArrayExpress

text: human

text: adult

text: intrahepatic cholangiocarcinoma

characteristic: disease

text: overexpress LINC00313

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: LINC00313 overexpression

text: Homo sapiens

text: male

text: LINC


characteristic: ENA first public

text: public

characteristic: SRA accession

tag: Namespace:Laboratory for Molecular Infection Medicine Sweden Umeå university Department of molecular biology

characteristic: Submitter Id

text: 8 to 12

unit: week

text: ArrayExpress

text: CD4-positive helper T cell

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

text: Protocols: CD4cre+HDAC1f/f mice were crossed to IL-13 dtTomato reporter mice. Between 8 to 10 weeks old CD4cre-HDAC1f/f dtTomato+ and CD4cre+HDAC1f/f dtTomato+ mice on C57BL/6 background were sensitized by intratracheal injection on day 0 and day 5 with 10 µg House dust mite (HDM) extract, challenged intranasally on day 12 and 14 with 25 µg of HDM, and sacrificed on day 16. After bronchoalveolar lavage, lungs were perfused with PBS, homogenized, digested and IL-13+, IL-13- effector (CD44hiCD62L-) and naive (CD44loCD62L+) CD4+ T cells were sorted by FACS. As control, IL-13- effector and naive cells were sorted from untreated CD4cre-HDAC1f/f dtTomato+ and CD4cre+HDAC1f/f dtTomato+ mice. Sorted cells from WT and KO mice were incubated with different DNA-barcoded antibodies for sample demultiplexing. Nucleic acids extracted as an integrated part of the single cell library construction protocol. All single-cell suspensions were counted and diluted according to manufacturer recommendations before loading onto a Chromium Controller (10X Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were generated using the Next GEM Single Cell 3’ Reagent Kit (v3.1, 10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s instructions aiming for a maximum cell recovery of 10,000 cells.

text: adult

text: mixed CD4cre-HDAC1f/f dtTomato+ and CD4cre+HDAC1f/f dtTomato+

text: not collected

characteristic: geographic location (country and/or sea)

text: mixed

characteristic: individual

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: lung

text: feature barcoding

characteristic: readout

text: Mus musculus

text: female

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Laboratory for Molecular Infection Medicine Sweden Umeå university Department of molecular biology

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: 8 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: CD4-positive helper T cell

text: not collected

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

text: not collected

text: mixed

text: not applicable

text: Mus musculus

text: Mus musculus

text: lung

text: gene expression profiling

text: Mus musculus

text: female

characteristic: title


characteristic: ENA first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 8 to 12

text: ArrayExpress

text: CD4-positive helper T cell

text: not collected

text: house mouse

text: adult

characteristic: genotype

text: not collected

text: mixed

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: lung

characteristic: organism part

text: feature barcoding

text: Mus musculus

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

text: public

text: ena-SAMPLE-TAB-14-11-2023-15:56:42:607-107295

tag: Namespace:IFOM - ISTITUTO FONDAZIONE DI ONCOLOGIA MOLECOLARE ETS

text: U-2 OS

text: epithelial

characteristic: collection date

text: human

characteristic: common name

text: Osteosarcoma

text: Italy

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Straight


characteristic: External Id

text: IFOM - ISTITUTO FONDAZIONE DI ONCOLOGIA MOLECOLARE ETS

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ena-SAMPLE-TAB-14-11-2023-15:56:42:607-107296

text: U-2 OS

text: epithelial

text: human

text: Osteosarcoma

text: Italy

text: Homo sapiens

text: Homo sapiens

text: Constriction


text: DKFZ Heidelberg

text: public

tag: Namespace:DKFZ Heidelberg

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: house mouse

text: Protocols: All mice used in this study were derived from colonies maintained inhouse, at around 8 weeks of age after spermatogenesis is fully established. For the cross-species analysis, we used animals from the C57BL/6, CAST/EiJ and CAROLI/EiJ strains. For the F1 analysis, we used C57BL/6-Ly5.1 and CAST/EiJ strains as well as F1 mice derived from a C57BL/6-Ly5.1 (female) x CAST/EiJ (male) cross. scRNA-Seq of murine testicular tissue using the 10x Genomics platform was performed similarly to Ernst et al, 2019. For the cross-species dataset, single-cell suspensions were generated by enzymatic digestion using 25 mg/ml Collagenase A (Sigma, 10103578001), 25 mg/ml Dispase II (Sigma, D4693) and 2.5 mg/ml DNAse I (Sigma, 10104159001) I for 30 min at 37C. For the F1 dataset, digestion was performed using 5mg/ml Collagenase A, 5 mg/ml Dispase II and 2.5 mg/ml DNAse I. After generation of single-cell suspensions, libraries were generated using 10x library construction kits according to the manufacturers instructions. For the cross-species dataset, for each sample, 10,000 cells were loaded into one channel of the Chromium™ Single Cell A Chip (10X Genomics ®, 1000009) and scRNA-Seq libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics ®, 120237). For the F1 dataset, libraries were generated using the Chromium™ Single Cell B Chip (10X Genomics ® 1000073) and Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics ®, 1000075). After generation of single-cell suspensions, libraries were generated using 10x library construction kits according to the manufacturers instructions. For the cross-species dataset, for each sample, 10,000 cells were loaded into one channel of the Chromium™ Single Cell A Chip (10X Genomics ®, 1000009) and scRNA-Seq libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics ®, 120237). For the F1 dataset, libraries were generated using the Chromium™ Single Cell B Chip (10X Genomics ® 1000073) and Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics ®, 1000075).

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

text: not collected

characteristic: individual

text: not applicable

text: DKFZ Heidelberg

characteristic: laboratory

text: Mus musculus

text: Mus musculus

text: testis

text: Mus musculus

text: male

characteristic: strain

characteristic: title


characteristic: ENA first public

text: DKFZ Heidelberg

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: house mouse

text: adult

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: DKFZ Heidelberg

text: Mus musculus

text: Mus musculus

text: testis

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: CAST/EiJ


characteristic: ENA-CHECKLIST

characteristic: External Id

text: BioSpyder

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: collection date

characteristic: common name

text: USA

characteristic: geographic location (country and/or sea)

text: eukaryotic synthetic construct

characteristic: organism

text: TempO-Seq data of sample C16_rep2

text: eukaryotic synthetic construct

text: TempO-Seq data of sample C16_rep2


text: BioSpyder

text: public

text: USA

text: eukaryotic synthetic construct

text: TempO-Seq data of sample C19_rep1

text: eukaryotic synthetic construct

text: TempO-Seq data of sample C19_rep1

characteristic: title


characteristic: ENA first public

text: BioSpyder

text: public

text: USA

text: eukaryotic synthetic construct

text: TempO-Seq data of sample C19_rep2

text: eukaryotic synthetic construct

text: TempO-Seq data of sample C19_rep2


text: BioSpyder

text: public

characteristic: INSDC status

text: USA

text: eukaryotic synthetic construct

text: TempO-Seq data of sample C19_rep3

text: eukaryotic synthetic construct

text: TempO-Seq data of sample C19_rep3


text: BioSpyder

text: public

characteristic: SRA accession

text: USA

text: eukaryotic synthetic construct

text: TempO-Seq data of sample C20_rep2

text: eukaryotic synthetic construct

text: TempO-Seq data of sample C20_rep2


E-MTAB-11573:Psoriasis patient 3

text: public

text: E-MTAB-11573:Psoriasis patient 3

tag: Namespace:Post-doc, Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: endothelial cell of lymphatic vessel

text: PASI 1.6

characteristic: clinical information

text: human

text: Protocols: Primary dermal lymphatic endothelial cells (CD31+PDPN+) isolated from chronic psoriatic plaques or healthy human skin were used for RNA-Seq RNA was extracted from primary dermal lymphatic endothelial cells using the NucleoSpin RNA kit (Machery Nagel) according to manufacturer’s instructions Libraries were generated from 100ng of high-quality RNA

characteristic: description

text: adult

characteristic: developmental stage

text: psoriasis vulgaris

characteristic: disease

text: psoriasis patient 3

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: abdomen

characteristic: sampling site

text: Homo sapiens

text: male

text: Psoriasis patient 3


E-MTAB-11573:Psoriasis patient 5

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Post-doc, Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: E-MTAB-11573:Psoriasis patient 5

text: ArrayExpress

text: endothelial cell of lymphatic vessel

text: PASI 2.2

text: human

text: adult

text: psoriasis vulgaris

text: psoriasis patient 5

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

text: not available

text: Homo sapiens

text: female

characteristic: sex

text: Psoriasis patient 5


E-MTAB-11573:Psoriasis patient 2

characteristic: ENA first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11573:Psoriasis patient 2

text: ArrayExpress

text: endothelial cell of lymphatic vessel

text: PASI 4.6

text: human

characteristic: common name

text: adult

text: psoriasis vulgaris

text: psoriasis patient 2

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: not available

text: Homo sapiens

text: male

text: Psoriasis patient 2

characteristic: title


E-MTAB-11573:Psoriasis patient 4

text: public

text: E-MTAB-11573:Psoriasis patient 4

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: endothelial cell of lymphatic vessel

text: PASI 4.9

characteristic: clinical information

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: psoriasis vulgaris

text: psoriasis patient 4

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: leg

text: Homo sapiens

text: male

text: Psoriasis patient 4


E-MTAB-11573:Psoriasis patient 1

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-11573:Psoriasis patient 1

text: ArrayExpress

text: endothelial cell of lymphatic vessel

text: PASI 8

text: human

text: adult

text: psoriasis vulgaris

characteristic: disease

text: psoriasis patient 1

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: not available

characteristic: sampling site

text: Homo sapiens

text: male

text: Psoriasis patient 1


E-MTAB-11573:Healthy donor 3

characteristic: ENA first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11573:Healthy donor 3

text: ArrayExpress

text: endothelial cell of lymphatic vessel

text: not applicable

text: human

text: adult

text: normal

text: healthy donor 3

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

text: leg

text: Homo sapiens

text: female

characteristic: sex

text: Healthy donor 3


E-MTAB-11573:Healthy donor 2

text: public

characteristic: SRA accession

text: E-MTAB-11573:Healthy donor 2

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: endothelial cell of lymphatic vessel

text: not applicable

text: human

characteristic: common name

text: adult

text: normal

text: healthy donor 2

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: breast

text: Homo sapiens

text: female

text: Healthy donor 2

characteristic: title


E-MTAB-11573:Healthy donor 4

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: E-MTAB-11573:Healthy donor 4

text: ArrayExpress

characteristic: broker name

text: endothelial cell of lymphatic vessel

text: not applicable

characteristic: clinical information

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: healthy donor 4

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: breast

text: Homo sapiens

text: female

text: Healthy donor 4


E-MTAB-11573:Healthy donor 5

characteristic: ENA first public

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: E-MTAB-11573:Healthy donor 5

text: ArrayExpress

text: endothelial cell of lymphatic vessel

text: not applicable

text: human

text: adult

text: normal

characteristic: disease

text: healthy donor 5

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: breast

characteristic: sampling site

text: Homo sapiens

text: female

text: Healthy donor 5


E-MTAB-11573:Healthy donor 1

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11573:Healthy donor 1

characteristic: Submitter Id

text: ArrayExpress

text: endothelial cell of lymphatic vessel

text: not applicable

text: human

text: adult

text: normal

text: healthy donor 1

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

text: abdomen

text: Homo sapiens

text: female

characteristic: sex

text: Healthy donor 1


E-MTAB-11573:Healthy donor 6

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: E-MTAB-11573:Healthy donor 6

characteristic: age

text: ArrayExpress

text: endothelial cell of lymphatic vessel

text: not applicable

text: human

characteristic: common name

text: adult

text: normal

text: healthy donor 6

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: abdomen

text: Homo sapiens

text: female

text: Healthy donor 6

characteristic: title


E-MTAB-11573:Psoriasis patient 6

characteristic: ENA first public

characteristic: INSDC center name

text: public

text: E-MTAB-11573:Psoriasis patient 6

text: ArrayExpress

characteristic: broker name

text: endothelial cell of lymphatic vessel

text: not available

characteristic: clinical information

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: psoriasis vulgaris

text: psoriasis patient 6

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: arm

text: Homo sapiens

text: male

text: Psoriasis patient 6


text: Center of Allergy and Environment

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

characteristic: batch

text: ncISD

characteristic: disease

text: male

characteristic: gender

text: Homo sapiens

characteristic: patient id

text: non-lesional skin


characteristic: External Id

text: Center of Allergy and Environment

text: live

text: Generic

characteristic: age

text: ncISD

text: male

text: Homo sapiens

characteristic: organism

text: lesional skin

characteristic: title


text: Center of Allergy and Environment

characteristic: INSDC center name

text: live

text: Generic

text: ncISD

text: female

text: Homo sapiens

text: non-lesional skin


text: Center of Allergy and Environment

text: live

text: Generic

text: ncISD

text: female

text: Homo sapiens

text: lesional skin