The LungMAP scRNA-Seq reference associated with the Lung CellCards resource. The initial reference integrated 259k cells from 72 donors from five published (PMIDs: 32726565, 32427931, 30554520, 32832599, 32832598) and one unpublished single cell RNA-seq cohort. Non-diseased adult and pediatric healthy lung single-cell 10x Genomics captures (3��� v2 and v3). Cells from different donors were integrated using Batchlor. Preliminary cell types were called based on Leiden clustering analysis and expression patterns of LungMAP cell card markers. UMAP embeddings were generated using monocle3. This reference, along with a corresponding single-nucleus specific version of this atlas, is under active construction. We expect to release the beta version of the reference in November 2021. Conforms to Azimuth reference data structure described at https://github.com/satijalab/azimuth/wiki/Azimuth-Reference-Format.

When analyzing scRNA-seq data with clustering algorithms, annotating the clusters with cell types is an essential step toward biological interpretation of the data. Annotations can be performed manually using known cell type marker genes. Annotations can also be automated using knowledge-driven or data-driven machine learning algorithms. Majority of cell type annotation algorithms are designed to predict cell types for individual cells in a new dataset. Since biological interpretation of scRNA-seq data is often made on cell clusters rather than individual cells, several algorithms have been developed to annotate cell clusters. In this study, we compared five cell type annotation algorithms, Azimuth, SingleR, Garnett, scCATCH, and SCSA, which cover the spectrum of knowledge-driven and data-driven approaches to annotate either individual cells or cell clusters. We applied these five algorithms to two scRNA-seq datasets of peripheral blood mononuclear cells (PBMC) samples from COVID-19 patients and healthy controls, and evaluated their annotation performance. From this comparison, we observed that methods for annotating individual cells outperformed methods for annotation cell clusters. We applied the cell-based annotation algorithm Azimuth to the two scRNA-seq datasets to examine the immune response during COVID-19 infection. Both datasets presented significant depletion of plasmacytoid dendritic cells (pDCs), where differential expression in this cell type and pathway analysis revealed strong activation of type I interferon signaling pathway in response to the infection.

Single-cell RNA sequencing has revolutionized the study of cellular heterogeneity, yet accurate cell type annotation remains a significant challenge. Inconsistent labels, technological variability, and limitations in transferring annotations from reference datasets hinder precise annotation. This study presents a novel approach for accurate cell type annotation in scRNA-seq data using unique marker gene sets. By manually curating cell type names and markers from 280 publications, we verified marker expression profiles across these datasets and unified nomenclatures to consistently identify 166 cell types and subtypes. Our customized algorithm, which builds on the AUCell method, achieves accurate cell labeling at single-cell resolution and surpasses the performance of reference-based tools like Azimuth, especially in distinguishing closely related subtypes. To enhance accessibility and practical utility for researchers, we have also developed a user-friendly application that automates the cell typing process, enabling efficient verification and supporting comprehensive downstream analyses. The desktop application can be accessed at https://omnibusx.com.

PAZ Image Products can be acquired in 8 image modes with flexible resolutions (from 1 m to 40 m) and scene sizes. Thanks to different polarimetric combinations and processing levels the delivered imagery can be tailored specifically to meet the requirements of the application. Available modes are: • StripMap mode (SM) in single and dual polarisation: The ground swath is illuminated with a continuous train of pulses while the antenna beam is pointed to a fixed angle, both in elevation and in azimuth. • ScanSAR mode (SC) in single polarisation: the swath width is increased respecting to the StripMap mode, it is composed of four different sub-swaths, which are obtained by antenna steering in elevation direction. • Wide ScanSAR mode (WS), in single polarisation: the usage of six sub-swaths allows to obtain a higher swath coverage product. • Spotlight modes: in single and dual polarisation: Spotlight modes take advantage of the beam steering capability in the azimuth plane to illuminate for a longer time the area of interest: a sensible improvement of the azimuth resolution is achieved at the expense of a shorter scene size. Spotlight mode (SL) is designed to maximise the azimuth scene extension at the expense of the spatial resolution, and High Resolution Spotlight mode (HS) is designed to maximize the spatial resolutions at the expense of the scene extension. • Staring Spotlight mode (ST), in single polarisation: The virtual rotation point coincides with the center of the beam: the image length in the flight direction is constrained by the projection on- ground of the azimuth beamwidth and it leads to a target azimuth illumination time increment and to achieve the best azimuth resolution. There are two main classes of products: • Spatially Enhanced products (SE): designed with the target of maximize the spatial resolution in pixels with squared size, so the larger resolution value of azimuth or ground range determines the square pixel size, and the smaller resolution value is adjusted to this size and the corresponding reduction of the bandwidth is used for speckle reduction. • Radiometrically Enhanced products (RE): designed with the target of maximize the radiometry, so the range and azimuth resolutions are intentionally decreased to significantly reduce speckle by averaging several looks. The following geometric projections are offered: • Single Look Slant Range Complex (SSC): single look product of the focused radar signal: the pixels are spaced equidistant in azimuth and in slant range. No geocoding is available, no radiometric artifacts included. Product delivered in the DLR-defined binary COSAR format. The SSC product is intended for applications that require the full bandwidth and phase information, e.g. for SAR interferometry and polarimetry. • Multi Look Ground Range Detected (MGD): detected multi look product in GeoTiff format with reduced speckle and approximately square resolution cells on ground. The image coordinates are oriented along flight direction and along ground range; the pixel spacing is equidistant in azimuth and in ground range. A simple polynomial slant to ground projection is performed in range using a WGS84 ellipsoid and an average, constant terrain height parameter. No image rotation to a map coordinate system is performed and interpolation artifacts are thus avoided. • Geocoded Ellipsoid Corrected (GEC): multi look detected product in GeoTiff format. It is projected and re-sampled to the WGS84 reference ellipsoid assuming one average terrain height. No terrain correction performed. UTM is the standard projection, for polar regions UPS is applied. • Enhanced Ellipsoid Corrected (EEC): multi look detected product in GeoTiff format. It is projected and re-sampled to the WGS84 reference ellipsoid. The image distortions caused by varying terrain height are corrected using an external DEM; therefore the pixel localization in these products is highly accurate. UTM is the standard projection, for polar regions UPS is applied. StripMap Single Mode ID: SM-S Polarizations: HH, VV, HV, VH Scene size (Range x Azimuth) [km]: 30 x 50 Range Resolution [m]: - MGD, GEC, EEC (SE)[Ground range] 2.99 - 3.52 at (45° - 20°) - MGD, GEC, EEC (RE)[Ground range] 6.53 - 7.65 at (45° - 20°) - SSC[Slant range] 1.1 (150 MHz bandwidth) 1.7 (100 MHz bandwidth) Azimuth Resolution [m]: - MGD, GEC, EEC (SE) 3.05 - MGD, GEC, EEC (RE) 6.53 - 7.60 at (45° - 20°) - SSC 3.01 StripMap Dual Mode ID: SM-D Polarizations: HH/VV, HH/HV, VV/VH Scene size (Range x Azimuth) [km]: 15 x 50 Range Resolution [m]: - MGD, GEC, EEC (SE)[Ground range] 6 - MGD, GEC, EEC (RE)[Ground range] 7.51 - 10.43 at (45° - 20°) - SSC[Slant range] 1.18 Azimuth Resolution [m]: - MGD, GEC, EEC (SE) 6.11 - MGD, GEC, EEC (RE) 7.52 - 10.4 at (45° - 20°) - SSC ScanSAR Mode ID: SC Polarizations: HH, VV, HV, VH Scene size (Range x Azimuth) [km]: 100 x 150 Range Resolution [m]: - MGD, GEC, EEC (SE)[Ground range] N/A - MGD, GEC, EEC (RE)[Ground range] 16.79 - 18.19 at (45° - 20°) - SSC[Slant range] 1.17 - 3.4 (depending on range bandwidth) Azimuth Resolution [m]: - MGD, GEC, EEC (SE) N/A - MGD, GEC, EEC (RE) 17.66 - 18.18 at (45° - 20°) - SSC 18.5 Wide ScanSAR Mode ID: WS Polarizations: HH, VV, HV, VH Scene size (Range x Azimuth) [km]: [273-196] x 208 Range Resolution [m]: - MGD, GEC, EEC (SE)[Ground range] N/A - MGD, GEC, EEC (RE)[Ground range] 35 - SSC[Slant range] 1.75 - 3.18 (depending on range bandwidth) Azimuth Resolution [m]: - MGD, GEC, EEC (SE) N/A - MGD, GEC, EEC (RE) 39 - SSC 38.27 Spotlight Single Mode ID: SL-S Polarizations: HH, VV, HV, VH Scene size (Range x Azimuth) [km]: 10 x 10 Range Resolution [m]: - MGD, GEC, EEC (SE)[Ground range] 1.55 - 3.43 at (55° - 20°) - MGD, GEC, EEC (RE)[Ground range] 3.51 - 5.43 at (55° - 20°) - SSC[Slant range] 1.18 Azimuth Resolution [m]: - MGD, GEC, EEC (SE) 1.56 - 2.9 at (55° - 20°) - MGD, GEC, EEC (RE) 3.51 - 5.4 at (55° - 20°) - SSC 1.46 Spotlight Dual Mode ID: SL-D Polarizations: HH/VV, HH/HV, VV/VH Scene size (Range x Azimuth) [km]: 10 x 10 Range Resolution [m]: - MGD, GEC, EEC (SE)[Ground range] 3.09 - 3.5 at (55° - 20°) - MGD, GEC, EEC (RE)[Ground range] 4.98 - 7.63 at (55° - 20°) - SSC[Slant range] 1.17 Azimuth Resolution [m]: - MGD, GEC, EEC (SE) 3.53 - MGD, GEC, EEC (RE) 4.99 - 7.64 at (55° - 20°) - SSC 3.1 HR Spotlight Single Mode ID: HS-S Polarizations: HH, VV, HV, VH Scene size (Range x Azimuth) [km]: 10-6 x 5 (depending on incident angle) Range Resolution [m]: - MGD, GEC, EEC (SE)[Ground range] 1 - 1.76 at (55° - 20°) - MGD, GEC, EEC (RE)[Ground range] 2.83 - 3.11 at (55° - 20°) - SSC[Slant range] 0.6 Azimuth Resolution [m]: - MGD, GEC, EEC (SE) 1 - 1.49 at (55 °- 20°) - MGD, GEC, EEC (RE) 2.83 - 3.13 at (55° - 20°) - SSC 1.05 HR Spotlight Dual Mode ID: HS-D Polarizations: HH/VV, HH/HV, VV/VH Scene size (Range x Azimuth) [km]: 10 x 5 Range Resolution [m]: - MGD, GEC, EEC (SE)[Ground range] 2 - 3.5 at (55° - 20°) - MGD, GEC, EEC (RE)[Ground range] 4 - 6.2 at (55° - 20°) - SSC[Slant range] 1.17 Azimuth Resolution [m]: - MGD, GEC, EEC (SE) 2.38 - 2.93 at (55° - 20°) - MGD, GEC, EEC (RE) 4 - 6.25 at (55° - 20°) - SSC 2.16 Staring Spotlight Mode ID: ST Polarizations: HH, VV, HV, VH Scene size (Range x Azimuth) [km]: [9-4.6] x [2.7-3.6] Range Resolution [m]: - MGD, GEC, EEC (SE)[Ground range] 0.96 - 1.78 at (45°- 20°) - MGD, GEC, EEC (RE)[Ground range] 0.97 - 1.78 at (45°-20°) - SSC[Slant range] 0.59 Azimuth Resolution [m]: - MGD, GEC, EEC (SE) 0.38 - 0.7 at (45°-20°) - MGD, GEC, EEC (RE) 0.97 - 1.42 at (45°-20°) - SSC 0.22 All details about the data provision, data access conditions and quota assignment procedure are described into the Terms of Applicability available in Resources section. For archive data, the user is invited to search PAZ products by using the USP (User Service Provider) web portal (http://www.geos.hisdesat.es/) (self registration required) in order to verify the availability over the Area of Interest in the Time of Interest.

ICEYE full archive and new tasking products are available in Strip, Spot, SLEA (Spot Extended Area), Scan, and Dwell modes: • Strip instrument mode: the ground swath is illuminated with a continuous sequence of pulses while the antenna beam is fixed in its orientation. This results in a long image strip parallel to the flight direction: the transmitted pulse bandwidth is adjusted to always achieve a ground range resolution of 3 m • Spot instrument mode: the radar beam is steered to illuminate a fixed point to increase the illumination time, resulting in an extended Synthetic aperture length, which improves the azimuth resolution. Spot mode uses a 300 MHz pulse bandwidth and provides a slant plane image with a resolution of 0.5 m (range) by 0.25 m (azimuth); when translated into the ground, the products has 1 m resolution covering an area of 5 km x 5 km. Due to multi-looking, speckle noise is significantly reduced • As an evolution of Spot mode, SLEA (Spot Extended Area) products are available with the same resolution of Spot data but a scene size of 15 km x 15 km • Scan Instrument mode: the phased array antenna is used to create multiple beams in the elevation direction which allows to acquire a large area (100km x 100km) with resolution better than 15m. To achieve the finest image quality of its Scan image, ICEYE employs a TOPSAR technique, which brings major benefits over the quality of the images obtained with conventional SCANSAR imaging. With the 2-dimensional electronic beam steering, TOPSAR ensures the maximum radar power distribution in the scene, providing uniform image quality. • Dwell mode: with the satellite staring at the same location for up to 25 seconds, Dwell mode is a very long Spot mode SAR collection. This yields a very fine azimuth resolution and highly-reduced speckle. The 25 second collection time allows the acquired image stack to be reconstructed as a video to give insight into the movement of objects. Two different processing levels can be requested: • Single Look Complex (SLC): Single Look Complex (SLC) Level 1a products consist of focused SAR data geo-referenced using orbit and attitude data from the satellite and the scenes are stored in the satellite's native image acquisition geometry which is the slant-range-by-azimuth imaging plane and with zero-Doppler SAR coordinates. The pixels are spaced equidistant in azimuth and in slant range. The products include a single look in each dimension using the full transmit signal bandwidth and consist of complex magnitude value samples preserving both amplitude and phase information. No radiometric artefacts induced by spatial resampling or geocoding. The product is provided in Hierarchical Data Format (HDF5) plus a xml file with selected metadata • Ground Range Detected (GRD): Ground Range Detected (GRD) Level 1b products consist of focused SAR data that has been detected, multi-looked and projected to ground range using an Earth ellipsoid model. The image coordinates are oriented along the flight direction and along the ground range. Pixel values represent detected magnitude, the phase information is lost. The resulting product has approximately square spatial resolution pixels and square pixel spacing with reduced speckle due to the multi-look processing at the cost of worse spatial resolution. No image rotation to a map coordinate system has been performed and interpolation artefacts are thus avoided. The product is provided in GeoTiff plus a xml file with selected metadata. Strip Spot SLEA Scan Dwell Ground range resolution (GRD) 3 m 1 m 1 m 15 m 1 m Ground azimuth resolution (GRD) 3 m 1 m 1 m 15 m 1 m Slant range resolution (SLC) 0.5 m - 2.5 m 0.5 m 0.5 m 0.5 m Slant azimuth resolution (SLC) 3 m 0.25 m 1 m 0.05 m Scene size (W x L) 30 x 50 km2 5 x 5 km2 15 x 15 km2 100 x 100 km2 5 x 5 km2 Incident angle 15 - 30° 20 - 35° 20 - 35° 21 - 29° 20 - 35° Polarisation VV

All details about the data provision, data access conditions and quota assignment procedure are described in the _\(ICEYE Terms of Applicability\) https://earth.esa.int/eogateway/documents/20142/37627/ICEYE-Terms-Of-Applicability.pdf . In addition, ICEYE has released a _\(public catalogue\) https://www.iceye.com/lp/iceye-18000-public-archive that contains nearly 18,000 thumbnails under a creative common license of radar images acquired with ICEYE's SAR satellite constellation all around the world from 2019 until October 2020. Access to the catalogue requires registration.

The SAR SLC product is a single look complex acquired in Image Mode. It is a digital image, with slant range and phase preserved, generated from raw SAR data using up-to-date auxiliary parameters. The products are intended for use in SAR quality assessment, calibration and interferometric applications. A minimum number of corrections and interpolations are performed on the data. Absolute calibration parameters (when available) are provided in the product annotation. Product characteristics: - Pixel size: 8 m (range - across track) x 4 m (azimuth - along track – varying slightly depending on acquisition Pulse Repetition Frequency) - Scene area: 100 km (range) x at least 102.5 km (azimuth) - Scene size: 5000 samples (range) x at least 30000 lines (azimuth) - Pixel depth: 32 bits signed integer (16 bits I, 16 bits Q) - Total product volume: 575 MB - Projection: Slant range - Number of looks: 1

BackgroundThe human genome contains approximately 3,200 near full-length autonomous human endogenous retroviral (HERV) genomes distributed across the 23 chromosomes. These autonomous HERV proviral genomes include long terminal repeats (LTRs) capable of promoting RNA transcription. In quiescent cells, most HERV loci remain transcriptionally silent. However, environmental changes, such as epigenetic remodeling of chromatin, can activate these silenced loci.MethodsTo study HERV reactivation, we previously analyzed autonomous HERV expression patterns in monocytes isolated from peripheral blood mononuclear cells (PBMCs) identified in single-cell RNA sequencing (scRNA-seq) databases using the Azimuth application. We developed a Window-based HERV Alignment (WHA) method, which analyzes aligned DNA sequences using sequential, non-overlapping windows of defined lengths. Samples were scored as positive (>= 9 good/usable windows) or negative (

This ERS Medium Resolution stripline product is generated from the Image Mode Level 0 Product. Stripline image products contain image data for an entire segment, up to a maximum size of 10 minutes per product for IM mode. The processor concatenates together several sub-images called 'slices' that were processed separately on a dataset-by-dataset basis in order to form the entire stripline image. The product is processed to an approximately 150 m x 150 m resolution and has a radiometric resolution that is good enough for ice applications. This product has a lower spatial resolution than the SAR_IMP_1P and SAR_IMS_1P products. Product Characteristics: Pixel size: 5 m (ground range – across track) x 75 m (azimuth – along track) Scene area: 100 km (range) x at least 102.5 km Scene Size: 1300 pixels (range) x at least 1350 lines (azimuth) Pixel depth: 16 bits unsigned integer- Total product volume: at least 3.5 MB Projection: Ground-range Number of looks: 8 (azimuth) x 7 (range).

Additional file 2: Table S1. Summary of scRNA-seq and scATAC-seq dataset. Table S2. Marker genes of each cell type. Table S3. Cattle PBMC cell type annotation under three resolutions using Azimuth. Table S4. Cattle PBMC cell type annotation using SingleR. Table S5. The expression of 93 cell cycle-related genes in each cell. Table S6. The summary information of TF identified by SCENIC. Table S7. Single cell’s pseudotime value obtained from Monocle2. Table S8. Gene list of each module identified by WGCNA. Table S9. Enrichment results of each module identified by WGCNA.