|
| Status |
Public on Jun 03, 2024 |
| Title |
section3_infected_12h |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organisms |
Plasmodium berghei ANKA; Mus musculus |
| Characteristics |
tissue: liver
timepoint: 12h
treatment: infected
sample id: 200302-G-C-12h
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Livers were dissected at the respective timepoints, divided into approxmately 6x6mm large pieces and frozen in Methylbutane at -30°C for 5-10 seconds and embedded in OCT before sectioning them in 10µm thick sections.
Libraries were constructed as previously described in Hildebrandt et al. (2021), https://doi-org.ezp.sub.su.se/10.1038/s41467-021-27354-w
Spatial Transcriptomics
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Raw sequencing data (.fastq) were processes using the stpipeline to generate count matrices
H&E and CY3 images were aligned using the spotdetector tool
Assembly: mm10 (GRCm38.101), PlasmoDB-48_PbergheiANKA
Supplementary files format and content: stdata.tsv.gz: gene expression count-data
Supplementary files format and content: spotfiles_0.1.tsv.gz, spot-coordinate data
Supplementary files format and content: .jpg, images from spatial transcrptomics analysis (Fluoercence or Hematoxylin&Eosin)
|
| |
|
| Submission date |
May 21, 2024 |
| Last update date |
Jun 03, 2024 |
| Contact name |
Franziska Hildebrandt |
| E-mail(s) |
franziska.hildebrandt@su.se
|
| Phone |
0702186657
|
| Organization name |
Stockholm University
|
| Street address |
Svante Arrhenius Väg 20C, Stockholm
|
| City |
Stockholm |
| ZIP/Postal code |
11418 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL34496 |
| Series (1) |
| GSE268018 |
Host-Pathogen Interactions in the Plasmodium-Infected Mouse Liver at Spatial and Single-Cell Resolution (Spatial Transcriptomics 2k) |
|
| Relations |
| BioSample |
SAMN41478957 |
| SRA |
SRX24625152 |
