BUSCADOR RECOLECTA

A) Overview of the different clusters identified through SOTA analysis. B) Behavior of total RNAP II (RNAp ChIP) and active RNAP II (GRO) in each identified cluster. mRNA expression and mRNA decay data from Eser et al. [17] are also presented. Genes included in each cluster, along with all transcriptomic data, are listed in S1 Table. To determine the proportion of active polymerases, we performed a linear regression analysis using GRO as the dependent variable and RNAp ChIP as the predictor, without an intercept term. The resulting regression coefficient represents the fraction of RNA polymerases actively engaged in transcription. By interpreting this coefficient as the efficiency of polymerase engagement, we estimate the percentage of active polymerases relative to the total chromatin-bound population. C) Distribution of cell cycle genes according to their peak of maximal expression (CellCycleBase 3.0) [18] in each of the clusters identified. Green arrows indicate groups in which the enrichment or depletion of cell cycle genes is statistically significant (logistic regression with Benjamini-Hochberg correction). D) Transcription factors known to regulate genes belonging to the clusters described in A. Only transcription factors significantly enriched in one or two clusters (Yeastrack [25], hypergeometric test p < 10 ⁻ ⁵), according to DNA binding or expression evidence, are shown. Other transcription factors significantly enriched in three or more clusters include: Bas1, Cst6, Tec1, Gat1, Cbf1, Met28, Pdr1, Gcn4, Met31, Met32, Pdr3, Rpn4, and Yap1., Peer reviewed

A) Schematic representation of the time points and samples taken for the analysis of total and active RNAP II. B) Plot representing total (RNAp ChIP) and active RNAP II (GRO) present at each gene at each time point analyzed. Black line: Overall tendency. Dashed blue line: Cycling genes. C) Behavior of total (RNAp ChIP) and active RNAP II (GRO) of cyclically expressed genes, classified according to the phase of maximal expression (G1, G1/S, S, S/G2, G2/M, and M) using CycleBase 3.0 as a reference (S1 Table). Total mRNA expression and mRNA decay values from Eser et al. [17] are also shown., Peer reviewed

Results of the gene ontology analyses performed with each gene cluster. (XLSX), Peer reviewed

GRO, RNAp ChIP, mRNA expression and mRNA decay data for all genes, indicating the cluster where each genes is located, whether the gene has been previously described as cell-cycle regulated, and whether it belongs to RiBi or RP regulons. mRNA expression and decay data are from Cramer´s lab [17]. (XLSX), Peer reviewed

Gene ontology analysis highlights a strong enrichment of cluster A in RP and RIBI genes. Manual validation of mRNA levels obtained for selected RiBi and RP genes in synchronized cells released from a G1 arrest with alpha factor (10 minutes interval sampling). (PDF), Peer reviewed

A) Examples of G1-expressed genes (AMS1, ARA1, CHS1, GPD1, TPS1 and YDL023C) belonging to cluster D. B) Examples of G1- (ALD4, HXT4 and HXT5) and G1/S-expressed genes (IDH2, HEM15 and YLR327C) from cluster F. C) Examples of S/G2- (ARP10) and G2/M-expressed genes (FKH2, STB5, TUB2, YOR246C and YTH1) from cluster I. (PDF), Peer reviewed

Green arrows represent groups in which the enrichment or depletion of clusters is statistically significant (logistic regression with BF correction). (PDF), Peer reviewed

A) Plot representing total RNA pol II and active RNA pol II present in each gene at each time point analysed. B) Plot representing clusters identified with SOTA. (PDF), Peer reviewed

Representative example of the budding index and the FACS profile of samples in which stages in which active and total RNA pol II were analysed. (PDF), Peer reviewed

[Notes] A total of 67 samples were obtained from the farm, out of which sufficient DNA was extracted from 63 samples for 16S sequencing.The type of samples analyzed were environmental and animal samples: air, surfaces, water, animal skin and animal feces. Sequencing libraries were generated using TruSeq® DNA PCR-Free Sample Preparation Kit (Illumina, USA), according to the manufacturer’s instructions, and index codes were added. Library quality was assessed using the Qubit@ 2.0 Fluorometer (Thermo Scientific) and the Agilent Bioanalyzer 2100 system. Finally, sequencing was performed on an Illumina NovaSeq platform, generating 250 bp paired-end reads. The sequencing of the 16S region was performed to assess the microbial composition of the collected samples., [Materia] Ciencias de la tierra y el medioambiente., Metagenomic study of environmental samples collected at a pig farm in Spain. This study is part of the HE-FARM project under the Horizon Europe programme, which aims to improve biosecurity on farms. Bacterial genera present in several areas of a pig farm were analyzed using high-throughput sequencing techniques. Samples were collected from the skin and feces of animals, as well as from surfaces, water, and air. The analyses revealed a strong cor-relation between air and skin samples, supporting the idea that bacterial growth on skin is potentially a mechanism of aerosolization and airborne transport. A water–air trans-mission route also appears to be present, although the direction of the transport mecha-nism cannot yet be determined. Other potential routes, such as contact with surfaces or feces, seem to be less efficient. This data contains the raw data used for metagenomic analyses (16S) of environmental samples in a pig farm. It includes the genomic data for each sample analyzed and compared in the study titled 'Skin Aerosolisation Predominance in a Pig Farm'. The data is organized in a way that facilitates further exploration and analysis, ensuring that researchers can effectively utilize it for their own studies., European Union: PROYECTO HORIZON-CL6-2022-FARM2FORK-01-HE-FARM-101084097 HE-FARM, Peer reviewed