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| Format: | Recurso digital |
| Language: | English |
| Published: |
Zenodo
2025
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| Online Access: | https://doi.org/10.5281/zenodo.17496937 |
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Table of Contents:
- <p> </p> <h1>Supplementary Files</h1> <h3>Supplementary Section 1.</h3> <p>General Feature Format File of AgamP4.61_Embryo transcriptome annotation and InterproScan output of potential novel genes.</p> <p>File/s:</p> <p>-AgamP4.61_Embryo.gtf</p> <p>-NovelGenes_interproScan.xlsx</p> <h3>Supplementary Section 2. </h3> <p>DESeq2 counts generated from the short-read dataset across all conditions and timepoints and PCA output across all conditions and timepoints.</p> <p>File/s:</p> <p>-PCA_data.xlsx</p> <h3>Supplementary Section 3. </h3> <p>Differential transcript expression (DESeq2) across timepoints for each experimental condition. Data are not filtered for significance.</p> <p>File/s:</p> <p>-DTE_acrossTime_Males.xlsx</p> <p>-DTE_acrossTime_WT.xlsx</p> <p>-DTE_acrossTime_Females.xlsx</p> <h3>Supplementary Section 4. </h3> <p>Z-score values across all conditions and timepoints used to perform k-mean analysis and list of gene IDs used for GO enrichment analysis performed using ShinyGo(v0.8).</p> <p>File/s:</p> <p>-Cluster_analysis_z_scores.xlsx</p> <h3>Supplementary Section 5.</h3> <p>Conservation scores value obtained using <em>An. gambiae </em>conservation score tool. Pkl files containing per-base Cs values (3kb upstream, TSS,TED, 3kb downstream) for each transcript category (potential novel genes, potential novel transcript, 5000 random annotated transcripts) and for the embryonic clusters.</p> <p>-Plotting_cs_clusters (Python script to plot conservation score values across different embryonic clusters)</p> <p>-Plotting_cs_transcriptome_categories (Python script to plot conservation score values of transcript belonging to different annotation categories).</p> <p>Pkl files containing per-base Cs values:</p> <p>transcriptome_cs_cluster_0.pkl<br>transcriptome_cs_cluster_1.pkl<br>transcriptome_cs_cluster_2.pkl<br>transcriptome_cs_cluster_3.pkl<br>transcriptome_cs_cluster_4.pkl<br>transcriptome_cs_cluster_5.pkl<br>transcriptome_cs_cluster_6.pkl<br>transcriptome_cs_potenial_novel_genes.pkl<br>transcriptome_cs_potenial_novel_isoforms.pkl<br>transcriptome_cs_real_matching_5000.pkl</p> <h3>Supplementary Section 6. </h3> <p>DenoiSex pipeline output. The file contains sex-corrected estimated transcript counts (generated using Kallisto) alongside with the original counts. The file also contains boolean values that indicating transcript above/below quantification noise treshold.</p> <p>File/s:</p> <p>-DenoiSex_corrected_counts_booleans.xlsx</p> <h3>Supplementary Section 7. </h3> <p>Differential transcripts expression across timepoints and between Male and Female embryo pools (DESeq2). Data are annotated based on AgamP4.61_Embryo transcriptome and are not filtered for significance. The file also incorporate information from the DenoiSex pipeline (Boolean value for quantificaiton noise tresholds).</p> <p>File/s:</p> <p>-DTE_acrossTime_Female.xlsx</p> <p>-DTE_acrossTime_Male.xlsx</p> <p>-DTE_acrossTime_WT.xlsx</p> <p>-DTE_Male_versus_Female.xlsx</p> <h3>Supplementary Section 8.</h3> <p>Differential splicing analysis output (splicing events) across timepoints for all the experimental conditions and between Male and Female embryo pools (SUPPA2). Transcript are annotated based on AgamP4.61_Embryo transcriptome and are filtered for significance as explained in the main text.</p> <p>File/s:</p> <p>-Differential_splicing_events_time_sex.xlsx</p> <h3>Supplementary Section 9.</h3> <p>The folder contains the output of a Motif enrichment analysis on splicing events during <em>An. gambiae</em> embryogenesis. Transcripts were selected based on SUPPA2 results used to identify differential splicing between male and female embryogenesis and across developmental stages. This file contains the output of SEA (<a href="https://doi.org/10.1101/2021.08.23.457422" target="_new" rel="noopener">https://doi.org/10.1101/2021.08.23.457422</a>) performed on transcript regions involved in splicing across time and between sexes selected using MoSEA (<a href="https://github.com/comprna/MoSEA" target="_new" rel="noopener">https://github.com/comprna/MoSEA</a>). The folder also contains the input sequences (fasta) for each splicing event category used as input for the SEA analysis. Control fasta sequences are also provided.</p> <p>File/s:</p> <p>-Plotting_SEA_output (script to plot merged SEA output files)</p> <p>-all_events_merged_sequences_Anopheles_sex (merged SEA sequences output files. differential splicing between sexes)</p> <p>-all_events_merged_sequences_Anopheles_time (merged SEA sequences output files, differential splicing across time)</p> <p>Sex:</p> <p>-SEA_output (contains folders for each SEA analysis on each splicing event category).</p> <p>-Male_versus_Female_a3_tot.fasta<br>-Male_versus_Female_a5_tot.fasta<br>-Male_versus_Female_af_tot.fasta<br>-Male_versus_Female_al_tot.fasta<br>-Male_versus_Female_control.fasta<br>-Male_versus_Female_mx_tot.fasta<br>-Male_versus_Female_ri_tot.fasta<br>-Male_versus_Female_se_tot.fasta</p> <p>Time: </p> <p>-SEA_output (contains folders for each SEA analysis on each splicing event category).</p> <p>-splicing_WT_time_a3_tot.fasta<br>-splicing_WT_time_a5_tot.fasta<br>-splicing_WT_time_af_tot.fasta<br>-splicing_WT_time_al_tot.fasta<br>-splicing_WT_time_control.fasta<br>-splicing_WT_time_mx_tot.fasta<br>-splicing_WT_time_ri_tot.fasta<br>-splicing_WT_time_se_tot.fasta</p> <p> </p> <h3>Supplementary Section 10.</h3> <p>Fle binding motif scan using FIMO. The folder contains FIMO output on differentially expressed transcripts and differential spliced transcripts between Male and Female embryos across development.</p> <p>-FIMO_Differential_splicing_Fle_motif (folder containing FIMO output)<br>-FIMO_Differential_transcript_Fle_motif (folder containing FIMO output)</p> <h3>Supplementary Section 11.</h3> <p>List of Primers used for experimental validation of novel genes, sex-specific splicing and qPCR.</p> <p>-List_of_primers </p> <p> </p>