Additional data from Milivojev et al., "Light-modulated stem cells in the camera-type eye of an annelid model for adult brain plasticity"
Milivojev, Nadja; Scaramuzza, Federico; Ozorio Brum, Pedro; Velastegui, Camila; Andreatta, Gabriele; Raible, Florian; Tessmar-Raible, Kristin
- Publisher
- Zenodo
- Language
- en
Abstract
The files deposited here represent the data related to the article "Light-modulated stem cells in the camera-type eye of an annelid model for adult brain plasticity" by Milivojev et al. Files included in this repository are as follows: Additional data displaying gating information of fluorescence-activated cell sorting (FACS) and genome-mapping of single cell RNA-sequencing (scRNA-seq) libraries. FACS_plots_1: FACS gating of single cell suspensions obtained from head tissue of (A) immature, (B) premature, (C) female and (D) male worms. FACS_plots_2: FACS gating of single cell suspensions obtained from head tissue of (A) EdU-labeled and (B) unlabeled control worms sampled at the same time. FACS_plots_3: (A-C) FACS gating of single cell suspensions obtained from head tissue of c-ops1Δ8/Δ8 worms; the genotype is presented as three replicated with the suffixes _1, _2 and _3. FACS_plots_4: (A-C) FACS gating of single cell suspensions obtained from head tissue of WT worms corresponsing to c-ops1Δ8/Δ8 mutants; the genotype is presented as three replicated with the suffixes _1, _2 and _3. Genome_mapping_1: Overview of results and statistics of genome-mapping of raw sequencing data of (A) immature, (B) premature and (C) female library. Genome_mapping_2: Overview of results and statistics of genome-mapping of raw sequencing data of (A) male, (B) EdU-labeled and (C) corresponding unlabeled sampling time-matched control library. Genome_mapping_3: (A-C) Overview of results and statistics of genome-mapping of raw sequencing data of c-ops1Δ8/Δ8 worms; the genotype is presented as three replicated with the suffixes _1, _2 and _3. Genome_mapping_4: (A-C) Overview of results and statistics of genome-mapping of raw sequencing data of WT worms corresponding to c-ops1Δ8/Δ8 mutants; the genotype is presented as three replicated with the suffixes _1, _2 and _3. All R code used for processing, analysis and visualization of the data generated in the scope of the study (in the form of an R notebook), as well as all relevant R objects generated as output in this manner (in the form of an RData file). The objects in the RData file are named consistently with their variables in the code.
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7,490 Estimated Number of Cells Sequencing N umber of Reads 370,125,257 N umber of Short Reads Skipped 0 V alid Barcodes 95.5% V alid UMIs 99.7% S equencing Saturation 95.2% Q 30 Bases in Barcode 96.4% Q 30 Bases in RNA Read 92.5% Q 30 Bases in UMI 96.2% Mapping R eads Mapped to Genome 86.7% R eads Mapped Con dently to Genome 79.8% R eads Mapped Con dently to Intergenic Regions 3.6% R eads Mapped Con dently to Intronic Regions 4.2% R eads Mapped Con dently to Exonic Regions 72.0% R eads Mapped Con dently to Transcriptome 71.5% R eads Mapped Antisense to Gene 4.4% Cells E stimated Number of Cells 7,490 F raction Reads in Cells 70.9% M ean Reads per Cell 49,416 M edian UMI Counts per Cell 799 M edian Genes per Cell 460 T otal Genes Detected 47,609 Alert Value Detail Intron mode used This data has been analyzed with intronic reads included in the count matrix. This behavior is di erent from previous Cell Ranger versions. If you would not like to count intronic reads, please rerun with the "include-introns" option set to "false". Please contact [email protected] for any further questions. Summary Gene Expression Cell Ranger • count Male Alerts The analysis detected 1 informational notice . 49,416 Mean Reads per Cell 460 Median Genes per Cell 1 100 10k 1 10 100 1000 10k Cells Background Barcode Rank Plot Barcodes UMI counts 4,981 Estimated Number of Cells Sequencing N umber of Reads 254,918,440 N umber of Short Reads Skipped 0 V alid Barcodes 97.0% V alid UMIs 99.9% S equencing Saturation 90.8% Q 30 Bases in Barcode 96.5% Q 30 Bases in RNA Read 91.3% Q 30 Bases in UMI 95.9% Mapping R eads Mapped to Genome 88.1% R eads Mapped Con dently to Genome 80.5% R eads Mapped Con dently to Intergenic Regions 2.3% R eads Mapped Con dently to Intronic Regions 1.8% R eads Mapped Con dently to Exonic Regions 76.4% R eads Mapped Con dently to Transcriptome 75.4% R eads Mapped Antisense to Gene 2.6% Cells E stimated Number of Cells 4,981 F raction Reads in Cells 72.0% M ean Reads per Cell 51,178 M edian UMI Counts per Cell 1,660 M edian Genes per Cell 818 T otal Genes Detected 44,781 Alert Value Detail Intron mode used This data has been analyzed with intronic reads included in the count matrix. This behavior is di erent from previous Cell Ranger versions. If you would not like to count intronic reads, please rerun with the "include-introns" option set to "false". Please contact [email protected] for any further questions. Summary Gene Expression Cell Ranger • count EdU Alerts The analysis detected 1 informational notice . 51,178 Mean Reads per Cell 818 Median Genes per Cell 1 100 10k 1M 1 10 100 1000 10k 100k Cells Background Barcode Rank Plot Barcodes UMI counts 8,360 Estimated Number of Cells Sequencing N umber of Reads 231,251,008 N umber of Short Reads Skipped 0 V alid Barcodes 97.3% V alid UMIs 99.9% S equencing Saturation 86.3% Q 30 Bases in Barcode 96.5% Q 30 Bases in RNA Read 90.2% Q 30 Bases in UMI 96.0% Mapping R eads Mapped to Genome 87.0% R eads Mapped Con dently to Genome 81.6% R eads Mapped Con dently to Intergenic Regions 2.6% R eads Mapped Con dently to Intronic Regions 2.1% R eads Mapped Con dently to Exonic Regions 76.9% R eads Mapped Con dently to Transcriptome 75.9% R eads Mapped Antisense to Gene 3.0% Cells E stimated Number of Cells 8,360 F raction Reads in Cells 78.8% M ean Reads per Cell 27,662 M edian UMI Counts per Cell 1,451 M edian Genes per Cell 718 T otal Genes Detected 46,895 Alert Value Detail Intron mode used This data has been analyzed with intronic reads included in the count matrix. This behavior is di erent from previous Cell Ranger versions. If you would not like to count intronic reads, please rerun with the "include-introns" option set to "false". Please contact [email protected] for any further questions. Summary Gene Expression Cell Ranger • count EdU control Alerts The analysis detected 1 informational notice . 27,662 Mean Reads per Cell 718 Median Genes per Cell 1 100 10k 1M 1 10 100 1000 10k 100k Cells Background Barcode Rank Plot Barcodes UMI counts A B C Supplementary Data 6
