|
| Status |
Public on Mar 02, 2022 |
| Title |
Spatial Transcriptomics 384 well plate (Spatial_T_H6B) |
| Sample type |
SRA |
| |
|
| Source name |
Plasmodium pieces
|
| Organism |
Physarum polycephalum |
| Characteristics |
life cycle stage: Plasmodium
individual: T3
|
| Growth protocol |
Physarum polycephalum was cultivated as Microplasmodia in a liquid culture and 100-500 uL of microplasmodia suspension was placed on Agar to induce plasmodium network formation as recently described (Bauerle et al. 2017 Journal of Physics D: Applied Physics).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SmartSeq2 (Wollny et al. 2016 bioRxiv / Picelli et al. 2013 Nat Methods)
Illumina Nextera
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
bulk RNA-seq
Spatial_T.RDS
|
| Data processing |
10xGenomics' Cellranger software package (v3.0.2) was used for all preprocessing steps for 10xGenomics data.
The basecaller "freeIbis" was used for SmartSeq2 samples (Bioinformatics. 2013 May 1;29(9):1208-9) and "leeHom" was used to trim adapters and merge Illumina sequencing reads afterwards (Nucleic Acids Res. 2014 Oct;42(18):e141). "deML" was used for robust demultiplexing of Illumina sequences for SmartSeq2 samples (Bioinformatics. 2015 Mar 1;31(5):770-2).
Sequencing reads were mapped against the Physarum polycephalum reference transcriptome (Glockner & Marwan 2017 Sci Rep) using STAR with either Cellranger's built in function for 10xGenomics samples or with a local STAR installation for SmartSeq2 samples (Dobin et al. 2013 Bioinformatics).
Gene expression levels were estimated by custom Perl scripts as TPM values for SmartSeq2 samples or based on UMI counts for 10x Genomics samples, respectively.
Genes without an UniProt annotation (Glockner & Marwan 2017 Sci Rep) were removed from all sample/gene matrices and final data sets were loaded and analyzed using Seurat (Stuart et al. 2019 Cell).
Genome_build: Physarum polycephalum transcriptome (Glockner & Marwan 2017 Sci Rep)
Supplementary_files_format_and_content: Matrix and tsv files are cellranger outputs ready to be loaded by Seurat (Stuart et al. 2019 Cell)
Supplementary_files_format_and_content: RDS files are Seurat objects containing all relevant information for Spatial Transcriptomics data files.
|
| |
|
| Submission date |
May 04, 2021 |
| Last update date |
Mar 02, 2022 |
| Contact name |
Tobias Gerber |
| E-mail(s) |
tobias.gerber@embl.de
|
| Organization name |
MPI for Evolutionary Anthropology
|
| Department |
Genetics
|
| Lab |
Barbara Treutlein
|
| Street address |
Deutscher Platz 6
|
| City |
Leipzig |
| ZIP/Postal code |
04103 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30072 |
| Series (1) |
| GSE173809 |
Spatial transcriptomic and single-nucleus analysis reveals heterogeneity in a gigantic single-celled syncytium |
|
| Relations |
| BioSample |
SAMN19008836 |
| SRA |
SRX10769075 |
