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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 29, 2024 |
| Title |
Genetic and Environmental interactions contribute to immune variation in rewilded mice |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The relative and synergistic contributions of genetics and environment to inter-individual immune response variation remain unclear, despite its implications for understanding both evolutionary biology and medicine. We used single cell RNA sequencing (scRNA-seq) to quantify the interactive effects of genotype and environment on immune traits by investigating three inbred mouse sttrain rewilded in an outdoor enclosure and infected with the parasite, Trichuris muris
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| Overall design |
Single cell suspensions from the mesenteric lymph node were prepared by mashing the tissues individually through a 70μm cell strainer and washed with RPMI from murine mesenteric lymph nodes. 2000 cells from each individual mouse (Block 1 (n = 51); Block 2 (n = 71)) were labelled with the Ab-Hash Tag Oligonucleoutides (HTO) and analyzed using scRNAseq.
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| Contributor(s) |
Oyesola O, Howard N, Zaldana K, Kiwanuka K, Downie A, Graham A, Loke P |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jul 03, 2023 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Yongmei Zhao |
| E-mail(s) |
zhaoyong@mail.nih.gov
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| Organization name |
Frederick National Labroatory for Cancer Research
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| Department |
Biomedical Informatics and Data Science (BIDS) Directorate
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| Street address |
Post Office Box B
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| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21702 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (14)
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| GSM7528301 |
primary cells, lymph nodes [Rewild1_GEX] |
| GSM7528302 |
primary cells, lymph nodes [Rewild2_GEX] |
| GSM7528303 |
primary cells, lymph nodes [Rewild3_GEX] |
| GSM7528304 |
primary cells, lymph nodes [Rewild4_GEX] |
| GSM7528305 |
primary cells, lymph nodes [Rewild5_GEX] |
| GSM7528306 |
primary cells, lymph nodes [Rewild6_GEX] |
| GSM7528307 |
primary cells, lymph nodes [Rewild7_GEX] |
| GSM7528308 |
primary cells, lymph nodes [Rewild8_GEX] |
| GSM7528309 |
primary cells, lymph nodes [Rewild9_GEX] |
| GSM7528310 |
primary cells, lymph nodes [Rewild10_GEX] |
| GSM7528311 |
primary cells, lymph nodes [Rewild11_GEX] |
| GSM7528312 |
primary cells, lymph nodes [Rewild12_GEX] |
| GSM7528313 |
primary cells, lymph nodes [Rewild13_GEX] |
| GSM7528314 |
primary cells, lymph nodes [Rewild14_GEX] |
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| Relations |
| BioProject |
PRJNA990675 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE236347_RAW.tar |
306.3 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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