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Source Data and Code for "GPSeq maps the radial organization of eukaryotic genomes along the nuclear periphery-center axis"
No full textHere contains the source data (in .rds) and source code (in .r) to reproduce the figures of manuscript of Genomics loci Positioning by Sequencing (GPSeq) submitted to Nature Protocols. All supplied codes are written in R language. Each script uses the corresponding data as input and generate plots described in the manuscript.
Figure 4. Examples of successful gradual radial DNA digestion in cells and nuclei.
This figure shows the fluorescence signal intensity of nuclei labelled by YFISH from the periphery to the centre after being digested by DpnII at various time points (8 timepoints, from 30 sec to 64 min).
Figure 5. Representative TapeStation profiles for the main QC steps during GPSeq library preparation
This figure shows the DNA or RNA analysed on Tapestation at different steps during GPSeq protocols. These steps include (gDNA extraction, sonication, in vitro transcription and final libraries). This aims to guide the user to obtain optimal size distribution of GPSeq library.
Figure 6. Workflow and representative outputs from the GPSeq data analysis pipeline
This figure shows an exampbletary output of the nextflow-gpseq pipline using the raw data. It includes a barplot describing the amount of reads after various steps of the pipeline, a heatmap describing the reproducibility of two biological replicates using Spearman's correlation coefficient and a pizza plot and boxplot illustrating the distribution of GPSeq score (from 0 at the nuclear periphery to 1 at the nuclear centre).
Figure 7. Comparison of GPSeq performed on cells, nuclei and swelling of cells and nuclei
This figures focuses on demonstrating the robustness and high reproducibility of samples prepared in different conditions (intact cells grown on coverslip, swollen cells grown on coverslip, extracted nuclei spotted on coverslip and swollen extracted nuclei spotted on coverslip)
Kubord 2: Ordrelationer Östgöta Correspondenten 2024
No full textKubord 2 is an updated version of Kubord and contains both token frequencies and word relations from modern newspaper texts from the The National Library of Sweden.Kubord 2 är en uppdaterad version av Kubord och innehåller utöver ordfrekvenser även ordrelationer från moderna tidningstexter från Kungliga biblioteket
Meteorological data from Skogaryd Central, Mast-1
No full textAutomatic weather station data from locations within the distributed Swedish research infrastructure SITES. Check preview or file for the specific parameters included at this location. Data has been quality controlled and cleaned from outliers and other events producing unrealistic data. Gaps have not been filled.
Skogaryd Research Catchment (2025). Meteorological data from Skogaryd Central, Mast-1, 2017-01-01–2017-12-31 [Data set]. Swedish Infrastructure for Ecosystem Science (SITES). https://hdl.handle.net/11676.1/XtHwLNp2xjfVAA4G9MoiGQX
Supplementary Fig. 5c & 6b | Western blots of FUS and TARDBP in iPSC lysates
No full textThis item is part of the Figshare Project:
Early mitochondrial dysfunction revealed across FUS- and TARDBP-ALS at single cell resolution (https://su.figshare.com/projects/Early_mitochondrial_dysfunction_revealed_across_FUS-_and_TARDBP-ALS_at_single_cell_resolution/163252)
From Data Availability Statement for the forthcoming paper in Nature Communications entitled:
Single-cell RNA sequencing reveals early mitochondrial dysfunction unique to motor neurons shared across FUS- and TARDBP-ALS
"We have deposited all raw and processed RNA sequencing data generated in this study on the NCBI Gene Expression Omnibus (GEO) under the accession number GSE226482. The C9orf72-ALS bulk RNA sequencing data was retrieved directly from the authors of the study.
[Items under this Figshare Project contain:] "Scans of fluorescent western blots, raw imaging files from confocal microscopy, the analysis files from Opera Phenix, qPCR data sets, and Seahorse assay result files."
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[Item specific description:]
This data belong to Supplementary Fig. 5 and 6.
Western blots in iPSC lines with various FUS and TARDBP M337V mutations for FUS and TDP-43 protein expression.
The assembled western blots are presented in the PPTX file.
The fluorescent signal were scanned on a Odyssey CLx scanner (LI-COR) and exported as Image Studio ZIP archives. More information about the Image Studio software can be obtained here: https://www.licorbio.com/image-studio
The raw images are given as TIF files, thumbnails as PNG, and aquisition meta information as TXT files within the exported archives
Meteorological data from Mycklemossen, S-mast-2
No full textAutomatic weather station data from locations within the distributed Swedish research infrastructure SITES. Check preview or file for the specific parameters included at this location. Data has been quality controlled and cleaned from outliers and other events producing unrealistic data. Gaps have not been filled.
Skogaryd Research Catchment (2025). Meteorological data from Mycklemossen, S-mast-2, 2013 [Data set]. Swedish Infrastructure for Ecosystem Science (SITES). https://hdl.handle.net/11676.1/4un63ki3hKeUtdn-BkUI1gn
Meteorological data from Mycklemossen, S-mast-2
No full textAutomatic weather station data from locations within the distributed Swedish research infrastructure SITES. Check preview or file for the specific parameters included at this location. Data has been quality controlled and cleaned from outliers and other events producing unrealistic data. Gaps have not been filled.
Skogaryd Research Catchment (2025). Meteorological data from Mycklemossen, S-mast-2, 2016-01-01–2016-12-31 [Data set]. Swedish Infrastructure for Ecosystem Science (SITES). https://hdl.handle.net/11676.1/RcTjvTnkWxIzxG39EvBwcdL
Växt-bladlöss interaktioner efter behandling av vetefröer med kemiska elicitorer
No full textThe data contains counts of number of bird cherry-oat aphids (Rhopalosiphum padi) that settle on wheat (Triticum aestivum) plants after seed treatment with chemical elicitors and control plants (treated with water/wetter), and measures of the size of aphid populations on plants after treatment. Data were collected in glasshouse/growth chambers. Data were collected as part of the Swedish Research Council Formas project 2018-00706 to assess the potential of chemical elicitors methyl salicylate, methyl jasmonate and cis-jasmone for improving plant a health.
Aphid plant colonization: Ten aphids (Rhopalosiphum padi) were placed onto wheat plants (treated with elicitors or water control) at 2-leaf stage and the number of aphids settled on the plants after 2 hours was recorded.
Aphid population development: One adult aphid (Rhopalosiphum padi) was placed onto wheat plants (treated with elicitors or water control) and after it had produced nymphs, all but one nymph were removed. The number of days for each nymph to become adult and produce a first nymph (d) was recorded and the number of nymphs produced in a time equal to d (M) was recorded. The intrinsic rate of aphid population increase (Rm) was calculated using the formula Rm=0.74(LnM)/d
Aphid population development- Variable List:
Treatment (Control, MeSa= methyl salicylate, MeJa= methyl jasmonate, CJ= cis-jasmone), Concentration (concentration of elicitor mM (millimolar)), days to repr (d)= number of days between aphid birth and first reproduction no. offspring (M)= number of aphid offspring produced in time equivalent to d, no. offsring/day= M/d, Rm intrinsic rate of population increase calculated by Rm=0.74(LnM)/d. Experiment code A= MeSa vs control, B= MeJa vs control, C= CJ vs control.
This data file consists of 171 rows and 7 columns
Aphid plant colonization- Variable List:
Treatment (Control, MeSa= methyl salicylate, MeJa= methyl jasmonate, CJ= cis-jasmone), Conc (concentration of elicitor mM millimolar), no. aphids settled after 2 hrs, Experiment code (indicates which control treatment to compare with which elicitor treatment)
This data file consists of 240 rows and 5 columns. Identical values may appear on more than one row, so a unique data value identifier is included in the first column (Data point ID)Data innehåller räkningar av antalet bladlöss (Rhopalosiphum padi) som koloniserar veteplantor (Triticum aestivum) efter fröbehandling med kemiska substanser samt på kontrollväxter (behandlade med vatten/vätare), och mått på storleken på bladluspopulationer på växter efter behandling. Data samlades in i växthus/tillväxtkammare. Se engelsk beskrivning för mer information
Meteorological data from Mycklemossen, S-mast-2
No full textAutomatic weather station data from locations within the distributed Swedish research infrastructure SITES. Check preview or file for the specific parameters included at this location. Data has been quality controlled and cleaned from outliers and other events producing unrealistic data. Gaps have not been filled.
Skogaryd Research Catchment (2025). Meteorological data from Mycklemossen, S-mast-2, 2023 [Data set]. Swedish Infrastructure for Ecosystem Science (SITES). https://hdl.handle.net/11676.1/DeTGXA4Bu3MGZ20dzABPkdi
Data för: Semiochemically assisted trap cropping to reduce broad bean beetle (Bruchus rufimanus) infestation in faba bean
No full textWe conducted a field experiment in south central Sweden over two years, in 2021 and 2023, in a total of 24 faba bean fields to test if a trap crop in combination with semiochemical traps can reduce broad bean beetle infestation in faba bean. Fields were paired, such that each pair (n=12) contained one treated field with a perimeter strip of an early flowering faba bean cultivar used as a trap crop in combination with semiochemical traps, and one control field with just the faba bean main crop without a trap crop or semiochemical traps. In a subset of semiochemical traps in each field, trapped broad bean beetle adults were counted and sexed. Crop damage data was taken along three transects in both field pairs.
The dataset contains egg count (3600 data rows), proportion of bean damage (72 data rows), trap catches (3512 data rows) as well as yield and yield components (72 data rows)
More information about the data can be found in the readme.txt. file.Vi genomförde ett fältexperiment i Östergötland under två år, 2021 och 2023, i totalt 24 fält för att testa om doftfällor i kombination med en fångstgröda kan minska angrepp av bönsmyg i åkerböna. Fälten parades ihop så att varje par (n=12) innehöll ett behandlat fält med en remsa av en tidigblommande åkerbönsort som användes som fångstgröda i kombination med doftfällor, och ett kontrollfält med bara åkerböna utan fångstgröda eller fällor. I en delmängd av doftfällorna i varje fält räknades och könsbestämdes de vuxna bönsmygarna som fångats. Data om bönskador och avkastning togs längs tre transekter i alla fält.
Datasetet innehåller äggräkning (3600 datarader), andel skadade bönor (72 datarader), fångst i fällor (3512 datarader) samt avkastning och avkastningskomponenter (72 datarader)
Mer information om data finns i filen readme.txt
Vector collection_OH surveillance project_Sweden
No full textData set containing the records of vectors collected under the One Health surveillance project in Sweden