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| Status |
Public on Jan 01, 2024 |
| Title |
Neonatal microbes shape islet-immune interactions that determine life-long host metabolic capacity [scRNA-seq and bulk RNA-seq]. |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The composition of the resident microbiota changes and diversifies as its host develops. Enrichment of specific taxa early in life is important for immune system development and maturation, but the impact of early life commensals on other host developmental processes is little studied. Here, we describe a critical window of postnatal life when specific microbes are necessary to establish an adequate supply of insulin-producing tissue for lifelong metabolic homeostasis of the host.
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| Overall design |
The main goal is to determine the effect of microbiota presence on developing neonatal pancreatic islets.
Samples are pancreatic islets purified away from acinar tissue by several rounds of hand picking.
scRNA-seq:
Each sample is representative of pooled islets from 20 animals at 15 days old (P15), either Germ-free (GF) or specific pathogen free (SPF).
bulk RNA-seq:
Islets from Germ-free (GF) and specific pathogen free (SPF) mice 10 days old (P10) or 20 days old (P20) are included.
Additionally, a subset of samples from P20 SPF mice were treated with Clodronate to diminish macrophages in order to investigate the effect of macrophages on neonatal islets.
Pacncreatic islets from male and female mice for each group are included.
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| Contributor(s) |
Jennifer HH, Lune RL, W Zac S |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA983325 |
| |
| Submission date |
Sep 21, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
W. Zac Stephens |
| Organization name |
University of Utah
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| Department |
Pathology
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| Lab |
Round Lab
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| Street address |
15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208
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| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84121-3808 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (59)
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| GSM7795354 |
Pancreatic islets, GF, P15 [scRNA-seq] |
| GSM7795355 |
Pancreatic islets, SPF, P15 [scRNA-seq] |
| GSM7798199 |
Pancreatic islet, SPF, P20, Male, biol rep 1 |
| GSM7798200 |
Pancreatic islet, SPF, P20, Female, biol rep 1 |
| GSM7798201 |
Pancreatic islet, SPF, P20, Female, biol rep 2 |
| GSM7798202 |
Pancreatic islet, SPF, P20, Female, biol rep 3 |
| GSM7798203 |
Pancreatic islet, SPF, P20, Female, biol rep 4 |
| GSM7798204 |
Pancreatic islet, SPF, P20, Female, biol rep 5 |
| GSM7798205 |
Pancreatic islet, SPF, P20, Female, biol rep 6 |
| GSM7798206 |
Pancreatic islet, SPF, P20, Male, biol rep 2 |
| GSM7798207 |
Pancreatic islet, SPF, P20, Male, biol rep 3 |
| GSM7798208 |
Pancreatic islet, SPF, P20, Male, biol rep 4 |
| GSM7798209 |
Pancreatic islet, SPF, P20, Male, biol rep 5 |
| GSM7798210 |
Pancreatic islet, SPF, P20, Female, biol rep 7 |
| GSM7798211 |
Pancreatic islet, SPF, P20, Female, biol rep 8 |
| GSM7798212 |
Pancreatic islet, SPF, P20, Female, biol rep 9 |
| GSM7798213 |
Pancreatic islet, SPF, P10, Male, biol rep 1 |
| GSM7798214 |
Pancreatic islet, SPF, P10, Female, biol rep 1 |
| GSM7798215 |
Pancreatic islet, SPF, P10, Female, biol rep 2 |
| GSM7798216 |
Pancreatic islet, SPF, P10, Female, biol rep 3 |
| GSM7798217 |
Pancreatic islet, SPF, P10, Male, biol rep 2 |
| GSM7798218 |
Pancreatic islet, SPF, P10, Male, biol rep 3 |
| GSM7798219 |
Pancreatic islet, SPF, P10, Female, biol rep 4 |
| GSM7798220 |
Pancreatic islet, SPF, P20, Clodronate-treated, Male, biol rep 1 |
| GSM7798221 |
Pancreatic islet, SPF, P20, Clodronate-treated, Male, biol rep 2 |
| GSM7798222 |
Pancreatic islet, SPF, P20, Clodronate-treated, Male, biol rep 3 |
| GSM7798223 |
Pancreatic islet, SPF, P20, Clodronate-treated, Male, biol rep 4 |
| GSM7798224 |
Pancreatic islet, SPF, P20, Clodronate-treated, Male, biol rep 5 |
| GSM7798225 |
Pancreatic islet, SPF, P20, Clodronate-treated, Female, biol rep 2 |
| GSM7798226 |
Pancreatic islet, SPF, P20, Clodronate-treated, Female, biol rep 3 |
| GSM7798227 |
Pancreatic islet, SPF, P20, Clodronate-treated, Female, biol rep 4 |
| GSM7798228 |
Pancreatic islet, SPF, P20, Clodronate-treated, Female, biol rep 5 |
| GSM7798229 |
Pancreatic islet, SPF, P20, Clodronate-treated, Female, biol rep 6 |
| GSM7798230 |
Pancreatic islet, GF, P20, Male, biol rep 1 |
| GSM7798231 |
Pancreatic islet, GF, P20, Male, biol rep 2 |
| GSM7798232 |
Pancreatic islet, GF, P20, Male, biol rep 3 |
| GSM7798233 |
Pancreatic islet, GF, P20, Male, biol rep 4 |
| GSM7798234 |
Pancreatic islet, GF, P20, Female, biol rep 1 |
| GSM7798235 |
Pancreatic islet, GF, P20, Female, biol rep 2 |
| GSM7798236 |
Pancreatic islet, GF, P20, Female, biol rep 3 |
| GSM7798237 |
Pancreatic islet, GF, P20, Female, biol rep 4 |
| GSM7798238 |
Pancreatic islet, GF, P20, Male, biol rep 5 |
| GSM7798239 |
Pancreatic islet, GF, P20, Female, biol rep 6 |
| GSM7798240 |
Pancreatic islet, GF, P20, Female, biol rep 7 |
| GSM7798241 |
Pancreatic islet, GF, P20, Female, biol rep 8 |
| GSM7798242 |
Pancreatic islet, GF, P20, Female, biol rep 9 |
| GSM7798243 |
Pancreatic islet, GF, P10, Male, biol rep 1 |
| GSM7798244 |
Pancreatic islet, GF, P10, Female, biol rep 1 |
| GSM7798245 |
Pancreatic islet, GF, P10, Female, biol rep 2 |
| GSM7798246 |
Pancreatic islet, GF, P10, Male, biol rep 2 |
| GSM7798247 |
Pancreatic islet, GF, P10, Male, biol rep 3 |
| GSM7798248 |
Pancreatic islet, GF, P10, Male, biol rep 4 |
| GSM7798249 |
Pancreatic islet, GF, P10, Male, biol rep 5 |
| GSM7798250 |
Pancreatic islet, GF, P10, Male, biol rep 6 |
| GSM7798251 |
Pancreatic islet, GF, P10, Female, biol rep 3 |
| GSM7798252 |
Pancreatic islet, GF, P10, Female, biol rep 4 |
| GSM7798253 |
Pancreatic islet, GF, P10, Female, biol rep 5 |
| GSM7798254 |
Pancreatic islet, GF, P10, Female, biol rep 6 |
| GSM7798255 |
Pancreatic islet, GF, P10, Female, biol rep 7 |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE243754_RAW.tar |
130.4 Mb |
(http)(custom) |
TAR (of TAR) |
SRA Run Selector |
| Raw data are available in SRA |
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