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Series GSE232438 Query DataSets for GSE232438
Status Public on Apr 01, 2024
Title Transcriptional control of the Cryptosporidium lifecycle
Organism Cryptosporidium parvum
Experiment type Expression profiling by high throughput sequencing
Summary The parasite Cryptosporidium is a leading agent of diarrheal disease in young children, and a cause and consequence of chronic malnutrition. There are no vaccines and only limited treatment options. The parasite infects enterocytes, where it engages in asexual and sexual replication, both of which are essential to continued infection and transmission. However, their molecular mechanisms remain largely unknown. Here we use single-cell RNA sequencing to reveal the gene expression program of the entire C. parvum life cycle in culture and infected animals. Diverging from the prevailing model, we find support for only three intracellular stages: asexual type-I meronts, male gamonts, and female gametes. We uncover a highly organized program for the assembly of components at each stage. Dissecting the underlying regulatory network, we identify the transcription factor Myb-M as the earliest determinant of male fate, in an organism that lacks genetic sex determination. Conditional expression of this factor overrides the developmental program and induces widespread maleness, while conditional deletion ablates male development. Both have a profound impact on the infection. A large set of stage-specific genes now provides the opportunity to understand, engineer, and disrupt parasite sex and life cycle progression to advance the development of vaccines and treatments.
Overall design Bulk and single-cell RNA sequencing (scRNA-seq) data were generated in this study. Samples for scRNA-seq and stage-specific bulk RNA sequencing were flow sorted to enrich for infected cells. For bulk analysis of stage-specific reporters, asexual and female datasets were already available (GEO:GSE129267) while the male in vitro dataset, consisting of four biological replicates, was produced in this study. For bulk analysis of Myb-M gain-of-function mutants, three biological replicates were used for each strain and condition collected at 30 hours after 6 hours of vehicle or Shield-1 treatment. For scRNA-seq analysis, infected cells were captured from culture or a mouse. In vitro samples were collected at 24, 36, 42, 46, and 54 hours while the in vivo sample was collected from an acutely infected mouse on day 6.
Contributor(s) Walzer KA, Tandel J, Byerly JH, Daniels AM, Gullicksrud JA, Whelan EC, Carro SD, Krespan E, Beiting DP, Striepen B
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Submission date May 12, 2023
Last update date Apr 01, 2024
Contact name Katelyn Ann Walzer
Organization name University of Pennsylvania
Department Pathobiology
Lab Striepen
Street address 380 South University Avenue
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (2)
GPL26382 Illumina NextSeq 500 (Cryptosporidium parvum)
GPL34324 NextSeq 2000 (Cryptosporidium parvum)
Samples (22)
GSM7334348 Male_in_vitro_1
GSM7334349 Male_in_vitro_2
GSM7334350 Male_in_vitro_3
BioProject PRJNA971984

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE232438_24hrs_barcodes.tsv.gz 8.9 Kb (ftp)(http) TSV
GSE232438_24hrs_matrix.mtx.gz 3.3 Mb (ftp)(http) MTX
GSE232438_24hrs_with_lncRNAs_barcodes.tsv.gz 8.6 Kb (ftp)(http) TSV
GSE232438_24hrs_with_lncRNAs_matrix.mtx.gz 3.1 Mb (ftp)(http) MTX
GSE232438_36hrs_barcodes.tsv.gz 9.7 Kb (ftp)(http) TSV
GSE232438_36hrs_matrix.mtx.gz 3.7 Mb (ftp)(http) MTX
GSE232438_36hrs_with_lncRNAs_barcodes.tsv.gz 9.2 Kb (ftp)(http) TSV
GSE232438_36hrs_with_lncRNAs_matrix.mtx.gz 3.6 Mb (ftp)(http) MTX
GSE232438_42hrs_barcodes.tsv.gz 4.1 Kb (ftp)(http) TSV
GSE232438_42hrs_matrix.mtx.gz 1.4 Mb (ftp)(http) MTX
GSE232438_42hrs_with_lncRNAs_barcodes.tsv.gz 3.9 Kb (ftp)(http) TSV
GSE232438_42hrs_with_lncRNAs_matrix.mtx.gz 1.3 Mb (ftp)(http) MTX
GSE232438_46hrs_barcodes.tsv.gz 11.8 Kb (ftp)(http) TSV
GSE232438_46hrs_matrix.mtx.gz 2.0 Mb (ftp)(http) MTX
GSE232438_46hrs_with_lncRNAs_barcodes.tsv.gz 11.4 Kb (ftp)(http) TSV
GSE232438_46hrs_with_lncRNAs_matrix.mtx.gz 1.9 Mb (ftp)(http) MTX
GSE232438_54hrs_barcodes.tsv.gz 3.0 Kb (ftp)(http) TSV
GSE232438_54hrs_matrix.mtx.gz 414.1 Kb (ftp)(http) MTX
GSE232438_54hrs_with_lncRNAs_barcodes.tsv.gz 3.0 Kb (ftp)(http) TSV
GSE232438_54hrs_with_lncRNAs_matrix.mtx.gz 415.4 Kb (ftp)(http) MTX
GSE232438_Asexual_metadata.csv.gz 70.4 Kb (ftp)(http) CSV
GSE232438_Crypto_atlas_lncRNAs_included_metadata.csv.gz 149.7 Kb (ftp)(http) CSV
GSE232438_Crypto_atlas_metadata.csv.gz 183.9 Kb (ftp)(http) CSV
GSE232438_all_features.tsv.gz 22.9 Kb (ftp)(http) TSV
GSE232438_all_features_with_lncRNAs.tsv.gz 50.0 Kb (ftp)(http) TSV
GSE232438_in_vivo_barcodes.tsv.gz 18.9 Kb (ftp)(http) TSV
GSE232438_in_vivo_matrix.mtx.gz 8.8 Mb (ftp)(http) MTX
GSE232438_in_vivo_with_lncRNAs_barcodes.tsv.gz 17.3 Kb (ftp)(http) TSV
GSE232438_in_vivo_with_lncRNAs_matrix.mtx.gz 8.8 Mb (ftp)(http) MTX
GSE232438_normData_CryptoDB_46_bulk.txt.gz 440.2 Kb (ftp)(http) TXT
GSE232438_normData_CryptoDB_MybM_OE_30hrs.txt.gz 32.0 Kb (ftp)(http) TXT
GSE232438_seurat.object.crypto.asexual.rds.gz 117.6 Mb (ftp)(http) RDS
GSE232438_seurat.object.crypto.atlas.all.lncRNAs.rds.gz 796.5 Mb (ftp)(http) RDS
GSE232438_seurat.object.crypto.atlas.all.rds.gz 481.4 Mb (ftp)(http) RDS
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