{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Daniel Caffrey"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14504"],"description":["The goal of the study was to determine the role of CNBP in spleenic tissue when mice are infected with Plasmodium chabaudi."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Samples were sequence on a Illumina NovaSeq as paired-end 150 reads.","Sample Collection - Wild-type (CNBP vav-iCre -/- ) and  knockout (CNBP vav-iCre +/+) mice were grouped into infected and uninfected cohorts, total four groups. Mice in the infected groups were injected intraperitoneally with 1 x 10^6 Plasmodium chabaudi-infected red blood cells, while uninfected controls received an injection of sterile 1X PBS. Seven days post-infection (7dpi), all mice were euthanized, and spleens were harvested.","Nucleic Acid Extraction - Approximately 15 mg of splenic tissue was homogenized in RLT buffer from the RNeasy Kit (Qiagen) using a TissueLyser at 25 Hz for a total of 2 minutes, with a 30-second incubation on ice between cycles. The homogenates were centrifuged at 10,000 g for 10 min at 4C  to remove cells and debris, and the Qiagen RNeasy Kit protocol was followed for RNA extraction. On-column DNase treatment was included during RNA isolation. RNA integrity was assessed using a Fragment Analyzer.","Library Construction - 1ug total RNA was used on magnetic bead for capture of polyA mRNA.   Illumina Stranded mRNA Prep Kit was used for library preparation according to manufacturers protocol. All samples were sized, quantified, and validated on a Bioanalyzer to ensure high quality for sequencing.","Sample Treatment - C57BL/6 mice (Jackson Laboratory, Bar Harbor, ME) were maintained in specific pathogen-free conditions and used in accordance with the Institutional Animal Care and Use Committee.  Intra-peritoneal injection of 1 x10e6 P.chabaudi infected Red Blood Cells."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - We used Bowtie2 (via RSEM) to align RNA-Seq reads to the mouse genome (assembly GRCm38 MM10, Ensembl version 100). The RSEM package was used to calculate transcripts per million (TPM) mapped reads for each sample with the command. rsem-calculate-expression  -p 16  --output-genome-bam --bowtie-chunkmbs 400 --bowtie2  --paired-end --forward-prob 0 r1.fq r2.fq mus_musculus.ensembl.100 accepted_hits"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Daniel Caffrey"],"additional_accession":[]},"is_claimable":false,"name":"Comparison of wild type and CNBPKO mice infected with Plasmodium chabaudi","description":"The goal of the study was to determine the role of CNBP in spleenic tissue when mice are infected with Plasmodium chabaudi.","dates":{"release":"2026-06-06T00:00:00Z","modification":"2026-06-06T01:01:10.876Z","creation":"2024-10-07T12:29:35.273Z"},"accession":"E-MTAB-14504","cross_references":{"ENA":["ERP164809"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003738","EFO_0004184","EFO_0003969"]}}