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Multivariate models improve accuracy of genomic prediction for spring frost tolerance in Norway spruce
No full textGenomic (SNP data) and phenotype information (measurements of spring frost tolerance, bud burst and height) of the manuscript "Multivariate models improve accuracy of genomic prediction for spring frost tolerance in Norway spruce" are included in attached files. See README for more details about the files.
Abstract
Background
Warming spring temperatures are expected to increase the risk of frost damage to emerging buds of Norway spruce by advancing their spring phenology and increasing the likelihood of damaging stochastic frost event. Current methods for assessing spring frost tolerance rely on field phenotyping after frost, which limits the ability to measure basal frost tolerance due to the sporadic nature of frost events, thereby limiting large-scale sampling. Quantitative phenotyping data are essential for genomic selection (GS) approaches that combine genomic information with phenotypic data to predict complex traits.
Results
In this study, we introduce a field sampling method to assess basal frost tolerance in Norway spruce using an ion leakage assay, and evaluate the effectiveness of multivariate GS models for predicting spring frost tolerance. We phenotyped 38 families across three consecutive springs at a predetermined early bud-burst stage to assess frost damage. The narrow-sense heritability of spring frost tolerance was estimated at 0.23. A strong genetic correlation between bud burst and frost damage (-0.63) improved prediction accuracy when using a multivariate model that included bud burst as an assisting trait. Additionally, we found that optimizing prediction models by increasing the number of clones in the training set further improved the accuracy of frost tolerance predictions. The observed genetic correlation between basal frost tolerance and bud burst suggests that early-flushing genotypes exhibit higher tolerance to spring frost, providing a new trait to consider in the Norway spruce breeding programs against frost damage.
Conclusion
The novel phenotyping method provides highly quantitative data for assessing basal frost tolerance among Norway spruce genotypes. Our study emphasizes the role of basal frost tolerance in the breeding programs of Norway spruce, particularly in the context of a warming climate, where relying solely on frost avoidance through late bud-burst timing may be insufficient. The use of multi-trait genomic prediction models for frost tolerance, incorporating assisting traits and optimized model parameters, enhances prediction accuracy and provides a promising approach for improving frost tolerance in Norway spruce
U25006 Utvecklingen av dödsorsaksrapporteringen i Sverige 1749–1950
No full textDenna studie består av två delar, den första har som målsättning att beskriva dödsorsaksrapporteringens olika aktörer och deras roller, den andra beskriver innehållet i källorna och i CEDAR:s databaser avseende dödsorsaker, vilken forskning som gjorts och som möjliggörs med dessa data. De två delarna kommer att utgöra bidrag till två temanummer i tidskriften Historical Lifecourse Studies.
Syftet med datauttaget är att studera de historiska dödsorsaker som finns registrerade i CEDAR:s databas samt undersöka vem som ställde diagnos vid dödsfall. Från 1860 i Sveriges städer skulle samtliga dödsfall attesteras av en läkare. Från 1911 gällde detta för hela landet även på landsbygden. Avsikten är att undersöka vem som egentligen ställde dödsorsaksdiagnos, samt hur denna utveckling såg ut över tiden 1860–1950.
Information om vem som utfärdat dödsattesten finns angiven i död- och begravningsböckerna för den period som studeras i projektet. Datauttaget består av aggregerad statistik och summerade uppgifter på församlingsnivå, som hämtas från databasen KBGRUND
3D-modell av medeltida lavett från fartygsvraket Gribshunden (1495) (DC78_ BLM 28314:6)
No full textThis dataset contains a 3D model of a wooden gun bed (lavett), which served as the support for a wrought-iron breech-loading swivel gun (skerpentine). The bed is carved from a square oak beam with a hemispherical recess along the upper side that formed a channel for the gun barrel. A hole through the middle of the beam was mounted an iron fork, allowing the gun to be trained and elevated.
The artefact comes from an underwater archaeological investigation carried out in 2002 by Kalmar County Museum at the shipwreck Gribshunden at St. Ekön (Ekösund), south of Saxemara in the Ronneby archipelago, Blekinge, Sweden. The investigation focused on documenting and salvaging loose finds at risk of looting. The archaeological activities including localisation, identification, measurement, documentation of loose finds, and recovery of the material. The assemblage from this campaign included a capstan and nine gun carriages, which carried three styles of breech-loading wrought-iron guns.
In the Blekinge Museum catalogue this object is registered as Blm 28314:6 (object number 28314, sub-number 6). It is classified as an archaeological find (jordfynd) and weapon (vapen) and is assigned to the medieval period. The manufacturing period is given as the 1400s before 1495 and the use period as the 1400s up to 1495. The historical country context is listed as Denmark. The carriage is made of wood (oak), with recorded dimensions of 2570 mm in length, 200 mm in width, and 200 mm in height.
Find circumstances and provenance are documented under RAÄ number Ronneby 728. The find was made in 2002 at St. Ekön (Ekösund) in Saxemara, Ronneby municipality, Blekinge county, Sweden, and the object was acquired by Blekinge Museum in the same year. The site is registered as a shipwreck find spot within the municipality of Ronneby, Blekinge, Sweden. The find context is described as a marine archaeological investigation in 2002.
The object has been conserved by impregnation with PEG 400 and freeze-drying under vacuum. A dendrochronological sample was taken from this carriage, but the result for this specific piece was inconclusive.
Link to the Dynamic Collection platform
https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=78Detta dataset innehåller en 3D-modell av en lavett till en smidd bakladdad svängbössa. Lavetten är tillverkad ur en fyrkantig ekstok med en halvrund ränna längs ovansidan, avsedd att fungera som bädd för eldröret. Genom ett genomborrat hål i stockens mittparti har en järngaffel varit monterad, vilket möjliggjorde rikting och höjning av vapnet.
Föremålet påträffades vid en marinarkeologisk undersökning som Kalmar läns museum utförde år 2002 på det danska örlogsfartyget Gribshunden, beläget vid S:t Ekön (Ekösund) söder om Saxemara i Ronneby skärgård, Blekinge. Undersökningen inriktades på dokumentation och bärgning av lösfynd som riskerade att utsättas för plundring. Arbetet omfattade lokalisering, identifiering, inmätning, dokumentation och upptagning av lösfynd. Bland materialet från kampanjen ingick ett gångspel (capstan) samt nio lavetter till tre olika typer av smidda bakladdade eldrör.
I Blekinge museums katalog är lavetten registrerad som Blm 28314:6 (objektnummer 28314, delnummer 6). Den är klassificerad som arkeologiskt fynd (jordfynd) och vapen, och är daterad till medeltiden. Tillverkningsperioden anges till 1400-talet före 1495, och brukningsperioden till 1400-talet fram till 1495. Den historiska landskontexten är Danmark. Lavetten är tillverkad av ek, med uppmätta mått 2570 mm (längd), 200 mm (bredd) och 200 mm (höjd).
Fyndomständigheterna är registrerade under RAÄ Ronneby 728. Fyndet gjordes 2002 vid S:t Ekön (Ekösund) i Saxemara, Ronneby kommun, Blekinge län, och införlivades i Blekinge museums samlingar samma år. Platsen är registrerad som en fartygslämning inom Ronneby kommun. Fyndkontexten anges som en marinarkeologisk undersökning 2002.
Föremålet har konserverats genom impregnering med PEG 400 och därefter frystorkats under vakuum. Ett dendrokronologiskt prov togs från lavetten, men resultatet var inte avgörande.
Länk till Dynamic Collection-plattformen:
https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=7
Mediebarometern 1999
No full textThe first Media Barometer was conducted in 1979 and since then the survey has been carried out annually. The purpose is to explore how the Swedish population is using different media during an average day. In 1999 the respondents were asked about their usage of different media equipment such as television, text-television, radio, video recorder, CD-player/record player, and tape recorder, the day before the interview. Respondents using any of these equipments were asked about time spent using the equipment. For equipment not used the day before the respondents were asked when it was last used. Television watchers were asked about which channels they had watched. Video watchers were asked if they watched a recorded program, a rented movie or a movie they had bought. All respondents were asked if they had been reading any of the following the day before: morning paper, evening paper, weekly magazine, comics or any other magazine, or book. If so, they were asked how many and for how long period. Readers of morning and evening papers were asked if they read the printed version or the internet version. Book readers were also asked what kind of literature they were reading, and paper and magazine readers were asked about what kind of paper/magazine they read. Those respondents who answered that they did not read any paper, magazine or book the day before were asked when they last did so. The survey also includes detailed information on at what time the day before the respondent spent time reading morning paper, evening paper, listening to the radio or watching television. There is also more detailed information on which news magazines the respondent watched. The respondents also had to state what kind of advertisments they had been reading/looking to during the last week. A number of questions dealt with computer usage at home and at work respectively, and the usage of Internet at home and at work. Background variables includes information on age, gender, education, occupation, and household composition. Questions about which radio channels the respondent listened to are not asked in the main survey. These questions are put in a separate survey.
Purpose:
Describe the trends and changes in people's use of mass media.Mediebarometern genomfördes första gången 1979 och har sedan dess genomförts varje år. Undersökningen avser att belysa hur stor andel av den svenska befolkningen som en genomsnittlig dag tagit del av ett antal enskilda medier. Syftet är att beskriva tendenser och förändringar i människors utnyttjande av massmedier.
Syfte:
Beskriva tendenser och förändringar i människors nyttjande av massmedier
Samhällskunskapsundervisning om tillit för ett aktivt och kritiskt medborgarskap
No full textStudent panel data from a project on trust. Conducted at two upper secondary schools 2021-2022.
Survey data from "Social Science Education on Trust for an Active and Critical Citizenship" (Swedish Research Council, 2019-03439_VR). https://www.vr.se/english/swecris.html#/project/2019-03439_VR .
Access to SurveyResponses file (in Swedish) on request after processing in accordance with Swedish Public Access to Information and Secrecy Act. File format .sav (SPSS) - can be opened with RStudio; also available as .csv (with potential minor file format conversion errors).Paneldata från undersökning om tillit. Utförd på två gymnasieskolor 2021-2022.
Från forskningsprojektet "Vem kan man lita på? Samhällskunskapsundervisning om tillit för ett aktivt och kritiskt medborgarskap." (Vetenskapsrådet, 2019-03439_VR) . https://www.vr.se/swecris.html#/project/2019-03439_VR
SurveyResponses filen (på svenska) utlämnas på begäran efter prövning enligt OSL. Filformat .sav (SPSS) - kan öppnas i RStudio ; finns även som .csv (med ev. mindre konverteringsfel)
Data för: A Morphology-Based Machine Learning Model for Scoring Epithelial-Mesenchymal Plasticity using Organelle Dynamics
No full textProject Description:
This project is aimed at modelling dynamic organelle morphology changes in a cellular model of epithelial-mesenchymal transition (EMT). EMT is a developmental process, which is re-activated in cancer and promotes invasion, metastasis and resistance to various therapies.
The repository contains raw microscopy images (.nd2 files) and numerical data outputs of all the experiments performed on a variety of cell lines (breast cancer, lung cancer). Cells were stained with the CellPainting kit. Experiments codes are listed below.
Categories:
Translational and applied bioinformatics; Cellular interactions (incl. adhesion, matrix, cell wall)
Numerical Data Source_wet lab + database (782.78 KB)
(1 excel file with numerical data source for MS experiments; 1 pdf file with WB uncropped membranes images)
Numerical Source Data_all CP experiments (microscopy): (14.47 GB)
- CP015/016/018: NMuMG training set (cellprofiler outputs)
- CP017: NMuMG reversal experiment
- CP019:NMuMG model validation
- CP020: breast cancer cells
- CP_INT_03_Normoxia: A549 Normoxia
- CP_INT_03_Hypoxia: A549 Hypoxia
Images (.ND2 files):
- CP015_nd2 (37.24 GB): NMuMG training set.1
- CP016_nd2 (37.24 GB): NMuMG training set.2
- CP018_nd2 (37.24 GB): NMuMG training set.3
- CP017_nd2 (37.24 GB): NMuMG reversal experiment
- CP019_nd2 (37.24 GB): NMuMG model validation
- CP020_nd2 (37.24 GB): breast cancer cells
- CP_INT_03_Normoxia_nd2 (18.62 GB): A549 Normoxia
- CP_INT_03_Hypoxia_nd2 (18.62 GB): A549 Hypoxia
Image files are in nd2 format, which is Nikon's proprietary format, but can be viewed with open source tools such as ImageJ.Project Description:
This project is aimed at modelling dynamic organelle morphology changes in a cellular model of epithelial-mesenchymal transition (EMT). EMT is a developmental process, which is re-activated in cancer and promotes invasion, metastasis and resistance to various therapies.
The repository contains raw microscopy images (.nd2 files) and numerical data outputs of all the experiments performed on a variety of cell lines (breast cancer, lung cancer). Cells were stained with the CellPainting kit. Experiments codes are listed below.
Categories:
Translational and applied bioinformatics; Cellular interactions (incl. adhesion, matrix, cell wall)
Numerical Data Source_wet lab + database (782.78 KB)
(1 excel file with numerical data source for MS experiments; 1 pdf file with WB uncropped membranes images)
Numerical Source Data_all CP experiments (microscopy): (14.47 GB)
- CP015/016/018: NMuMG training set (cellprofiler outputs)
- CP017: NMuMG reversal experiment
- CP019:NMuMG model validation
- CP020: breast cancer cells
- CP_INT_03_Normoxia: A549 Normoxia
- CP_INT_03_Hypoxia: A549 Hypoxia
Images (.ND2 files):
- CP015_nd2 (37.24 GB): NMuMG training set.1
- CP016_nd2 (37.24 GB): NMuMG training set.2
- CP018_nd2 (37.24 GB): NMuMG training set.3
- CP017_nd2 (37.24 GB): NMuMG reversal experiment
- CP019_nd2 (37.24 GB): NMuMG model validation
- CP020_nd2 (37.24 GB): breast cancer cells
- CP_INT_03_Normoxia_nd2 (18.62 GB): A549 Normoxia
- CP_INT_03_Hypoxia_nd2 (18.62 GB): A549 Hypoxia
Image files are in nd2 format, which is Nikon's proprietary format, but can be viewed with open source tools such as ImageJ
ETC L2 ARCHIVE from Hyltemossa
No full textArchive Product for ICOS Ecosystem data. It is the most complete data collection for the ICOS ecosystem station and it contains all the data (continuous fluxes and meteo and ancillary) and metadata collected and produced.
Heliasz, M., Kljun, N., Biermann, T., Holst, J., Holst, T., Kornacher, P., Linderson, M., Molder, M., Rinne, J. (2025). ETC L2 ARCHIVE from Hyltemossa, 2018-01-01–2025-10-01, ICOS RI, https://hdl.handle.net/11676/TZ238Cd2oU7G-uKzHGjZLqJ
Data för "Hypergammaglobulinemia in treated and untreated people with HIV"
No full textThis dataset contains pseudo-anonymized information on sex, age and blood samples (n = 821), of which 750 samples are from 584 adult (age ≥ 18 years) persons with HIV (PWH) and 71 from HIV-negative controls.
The blood samples from the PWH were collected in a standardized manner during outpatient clinic visits as part of "the Gothenburg HIV CSF Study Cohort" at the Department of Infectious Diseases, at the Sahlgrenska University Hospital, Gothenburg, Sweden. Data became available at the time of sample collection and were compiled for analysis between 13/11/1985 and 14/03/2023.
The samples from the HIV-positive participants were categorized according to eight categories representing immunologically different stages of HIV infection: primary HIV infection (PHI; within 12 months of initial HIV infection), five groups characterized by CD4+ T cell counts (≥ 500; 350−499; 200−349, 50−199 and < 50 cells/μL), ongoing infection or malignancy (OIM), and those on ART.
The diagnosis of PHI was based on a combination of clinical histories and seroconversion, nucleic acid testing or enzyme-linked immunosorbent assay (ELISA) testing. OIM was defined as the presence of an opportunistic or non-opportunistic bacterial, viral or parasitic infection or active cancer in association with or within two weeks of blood sampling. ART suppression was defined as ongoing ART with plasma HIV-RNA < 50 copies/mL for ≥ 6 months and included antiretroviral regimens with two or more active agents (non-nucleoside reverse transcriptase inhibitors, nucleoside reverse transcriptase inhibitors, integrase inhibitors and/or protease inhibitors) according to guidelines existing at the time of inclusion.
The HIV-negative control group (n = 71) consisted of 44 individuals receiving HIV preexposure prophylaxis (PrEP) with tenofovir disoproxil fumarate (TDF)/emtricitabine (FTC) and 27 volunteers (healthcare workers, students and their relatives) without PrEP.
The blood samples were analyzed for IgG, neopterin, β2-microglobulin, albumin, HIV-RNA, CD4+, and CD4+ nadir. Additionally, information on antiretroviral therapy, the duration of viral suppression as well as hepatitis C status are provided. Data on hepatitis C status were extracted from the Swedish InfCareHIV cohort.Detta dataset innehåller pseudoanonymiserad data för kön, ålder och blodprover (n = 821), varav 750 prover är från 584 vuxna (≥ 18 år) personer med HIV (persons with HIV; PWH) och 71 från HIV-negativa kontroller. Blodproverna insamlades på ett standardiserat sätt i samband med mottagningsbesök som en del av "the Gothenburg HIV CSF Study Cohort" vid Avdelningen för infektionssjukdomar vid Sahlgrenska Universitetssjukhuset, Göteborg, Sverige. Data blev tillgänglig i samband med provtagningen och sammanställdes för analys mellan 13/11/1985 och 14/3/2023.
Proverna från HIV-positiva deltagare kategoriserades i åtta kategorier motsvarande immunologiskt olika stadier av HIV-infektion: primär HIV-infektion (PHI; inom 12 månader från initial HIV-infektion), fem grupper karaktäriserade av CD4+ T cells-tal (≥ 500; 350−499; 200−349, 50−199 and < 50 celler/μL), pågående infektion eller malignitet (OIM) och deltagare med ART. PHI diagnos baserades på en kombination av anamnes och serokonversion, HIV-RNA eller enzyme-linked immunosorbent assay (ELISA)-testning. OIM definierades som förekomst av opportunistisk eller icke-opportunistisk bakteriell, viral eller parasitinfektion eller aktiv cancer i samband med eller inom två veckor från provtagning. ART suppression definierades som pågående ART med plasma HIV-RNA < 50 kopiopr/mL i ≥ 6 months och innebar antiretroviral terapi med två eller fler aktiva läkemedel (nukleosid omvänt transkriptashämmare, non-nukleosid omvänt transkriptashämmare, proteashämmare, integrashämmare) enligt aktuella riktlinjer vid inklusionstillfället.
Den HIV-negativa kontrollgruppen (n = 71) bestod av 44 individer med HIV preexponeringsprofylax (PrEP) med tenofovir disoproxil fumarate (TDF)/emtricitabine (FTC) och 27 frivilliga (sjukvårdspersonal, studenter och deras släktingar) utan PrEP.
Blodproverna analyserades avseende IgG, neopterin, β2-microglobulin, albumin, HIV-RNA , CD4+, and CD4+ nadir. Därutöver finns information om antiretroviral terapi, varaktighet av viral suppression och hepatit C status. Data på hepatit C status erhölls från den svenska InfCareHIV kohorten
Dissecting CAF subtypes in Pancreatic Cancer
No full textWithin the stroma of pancreatic ductal adenocarcinoma (PDAC), mesenchymal cells differentiate into cancer-associated fibroblast (CAF) subtypes that differentially mediate disease progression. Defining the regulatory mechanism and diversity of CAF subtypes could identify potential therapeutic strategies to harness the tumor suppressive activities of CAFs. To address this, we utilized single-cell RNA sequencing to profile fibroblast activation protein-alpha (FAP) expressing mesenchymal cells in human PDAC. The mesenchymal subpopulations in PDAC reflected mesenchymal cell heterogeneity found in the normal developing pancreas. In addition to characterizing inflammatory CAF (iCAF) and myofibroblastic CAF (myCAF) subpopulations in detail, the analysis uncovered a previously undescribed interferon-response CAF (ifCAF) subtype. Tumor-derived signals induced specific CAF subtypes from pancreatic stellate cells (PSCs) in an organoid-based co-culture model, and time-course experiments revealed regulatory mechanisms that govern subtype formation. STING agonists promoted an ifCAF phenotype in vivo and in vitro. Importantly, induction of an ifCAF phenotype suppressed tumor cell invasiveness and induced an anti-tumor phenotype in tumor-associated neutrophils. Together, this study resolves FAP+ stromal cell heterogeneity in PDAC and identifies an ifCAF subtype that can be induced to suppress pro-tumorigenic features of PDAC (Cumming et al., 2025).
This dataset contains the following data and metadata files:
1. Six pairs of fastq files that contain the actual sequencing data. The total size is 230 GB. Each pair represents a paired-end single-cell RNA sequencing from an individual patient sample. The fastq files are text files with genomic sequence and sequence quality metrics. They are stored as compressed gzip-ed files.
2. A metadata file with sample information. The variables included are: Sample name, sequencing library ID, sequencing depth, sequencing index, number of cells, barcode set, patient pseudo ID (P1-P5), pathologic diagnosis, gender, age, surgical procedure, pathological classification, tumour location, histological status (desmoplasia). This is an Excel file (xlsx).
3. A metadata file with sample information according to the Federated European Genome-Phenome Archive Sweden (FEGA-sweden) template format. This is an Excel file (xlsx).
4. Twelve processed data tables with raw read (UMI) count; Six files for quality filtered cells, and six files with all cells. Each table corresponds to a separate sample. This corresponds to gene expression levels after mapping to the reference genome. The data is stored in MEX format, i.e. three tab-delimited text files in sparse matrix format. The files are compressed with gzip.
5. Two cell annotation tables for the single-cell data. The tables describe read count, gene count, cluster number, and cell type annotation for 30786/26733 single cells from the 6 samples described in the sample information metadata file. The tables are submitted as tab-delimited text files.
6. Two binary files written in R programming language containing an object readable by the Seurat package. The files contain processed data in the form of read count (i.e. gene expression levels) and also as transformed (normalized and scaled) data and analysis results. The files are in RDS format and can be loaded in R.
For more information about the data files, please read the documentation files that accompany this data description. If you would like to submit a request to access data of this dataset, please read the document Readme_before_submission_of_an_access_request.Inom stroman av duktalt adenokarcinom hos pankreas (PDAC) differentierar mesenkymala celler till cancerassocierade fibroblastsubtyper (CAF) som successivt medierar sjukdomsprogression. Att definiera den reglerande mekanismen och mångfalden av CAF-subtyper kan identifiera potentiella terapeutiska strategier för att utnyttja CAFs tumörhejdande aktiviteter. För att undersöka detta använde vi RNA-sekvensering hos enskilda celler för att karakterisera mesenkymala celler hos human PDAC som utrycker fibroblastaktiveringsprotein-alfa (FAP). De mesenkymala subpopulationerna i PDAC reflekterade mesenkymal cellheterogenitet som finns i normalt utvecklande pankreas. Förutom en detaljerad karakterisering av subpopulationer av inflammatorisk CAF (iCAF) och myofibroblastisk CAF (myCAF), avslöjade analysen en tidigare okänd subtyp av en interferon-respons CAF (ifCAF). Signaler från tumören inducerade specifika CAF-subtyper från pankreatiska stellatceller (PSCs) i en organoidbaserad samodlingsmodell, och tidsförloppsexperiment avslöjade regulatoriska mekanismer som styr subtypbildning. STING-agonister främjade en ifCAF-fenotyp in vivo och in vitro. Viktigt är att induktion av en ifCAF-fenotyp hejdade tumörcellinvasivitet och inducerade en antitumörfenotyp i tumörassocierade neutrofiler. Sammanfattningsvis ger denna studie detaljerad insyn i FAP+ stromacellsheterogenitet i PDAC och identifierar en ifCAF-subtyp som kan induceras för att bromsa tumörfrämjande egenskaper hos PDAC (Cumming m. fl. 2025).
Detta dataset innehåller följande data- och metadatafiler:
1. Sex par fastq-filer som innehåller den faktiska sekvenseringsdatan. Den totala storleken är 230 Gb. Varje fastq par representerar singel-cell RNA-sekvensering från ett separat patientprov. Fastq-filer är textfiler med genomsekvens och sekvenskvalitetsmått. De är lagrade som komprimerade gzip-filer.
2. En metadatafil med provinformation. De inkluderade variablerna är: Provnamn, sekvenseringsbiblioteks-ID, sekvenseringsdjup, sekvenseringsindex, antal celler, barcode set, patientens pseudo-ID (P1-P5), patologisk diagnos, kön, ålder, kirurgiskt ingrepp, patologisk klassificering, tumörens läge, histologisk status (desmoplasi). Detta är en Excelfil (xlsx).
3. En metadatafil med provinformation enligt Federated European Genome-Phenome Archive Sweden (FEGA-Sweden) mallformat. Detta är en Excelfil (xlsx).
4. Tolv bearbetade datatabeller med råa sekvens-reads (UMI) count; Sex filer med kvalitetsfiltrerade celler, och sex filer med alla celler. Detta motsvarar genuttrycksnivåer efter mappning till referensgenomet. Datan är lagrad i MEX-format, dvs tre tabbavgränsade textfiler i gles matrisformat. Filerna är komprimerade med gzip.
5. Två cellannoteringstabeller för singel-cell datan. Tabellerna beskriver read count, genantal, klusternummer och celltypannotering för 30786/26733 celler från de 6 proverna som beskrivs i metadatafilen med provinformation. Tabellerna är i tabbavgränsade textfiler.
6. Två binära filer skrivna i R-programmeringsspråket som innehåller ett objekt läsbart av Seurat-paketet. Filerna innehåller processad data i form av read-count (dvs genuttrycksnivåer) samt transformerad (normaliserad och skalad) data och analysresultat. Filerna är i RDS-format och kan laddas in i R.
För mer information om datafilerna, vänligen läs dokumentationsfilerna som medföljer denna databeskrivning. Om du vill skicka in en begäran om åtkomst till data i denna datauppsättning, vänligen läs dokumentet Readme_before_submission_of_an_access_request
ETC L2 Fluxnet (half-hourly) from Degero
No full textHalf-hourly Fluxes and Meteo measurements processed with the standard FLUXNET procedure used for the FLUXNET2015 collection (ONEFlux suite).
Nilsson, M., Peichl, M., Marklund, P., Boschetti, F., De Simon, G., Holst, J., Smith, P., Kozii, N., Dignam, R., Larmanou, E., Lofvenius, P., Molder, M., Andersson, T., Linderson, M., Lindgren, K. (2025). ETC L2 Fluxnet (half-hourly) from Degero, 2018-12-31–2025-09-30, ICOS RI, https://hdl.handle.net/11676/UDOWzX6TB-dgQI-yCUSTPYu