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| Status |
Public on Jul 05, 2024 |
| Title |
VHMF001_18196 PBMCs, 4h, Dex |
| Sample type |
SRA |
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| Source name |
peripheral blood mononuclear cells
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| Organism |
Suricata suricatta |
| Characteristics |
cell type: peripheral blood mononuclear cells
treatment: Dex
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| Treatment protocol |
Purified PBMCs from each sample were cultured for 4 hours in (i) media only (control condition), (ii) media with 10 ng/mL lipopolysaccharide (LPS from the E. coli O111:B4 strain), to mimic bacterial exposure; (iii) media plus 1.0 μg/mL Gardiquimod (Gard), which activates Toll-like receptor 7 signaling; or (iv) media plus 1.0 μM Dexamethasone (Dex), a synthetic glucocorticoid. The cells were then incubated in parallel for 4 hours (37 C and 5% CO2), washed with 1× PBS, lysed, and stored immediately at -80° C until library preparation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
We prepared RNA-sequencing libraries for each sample (control, Dex-challenged, Gard-challenged, LPS-challenged) by purifying mRNA using the miRNeasy Mini Kit (Qiagen).
Libraries were generated following the Transposase Mediated 3′ RNAseq (TM3’seq) protocol (Pallares, Picard, & Ayroles, 2020) with an input of 50 ng total RNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
SSUR1581
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| Data processing |
TM-3’-seq data were first filtered with trimmomatic (version 0.38, Bolger, Lohse, & Usadel, 2014) to remove adapter sequence and stretches of low-quality bases, as well as reads <20 bp following trimming.
Remaining trimmed reads were mapped to the meerkat genome (GCF_006229205.1, https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_006229205.1/) using the STAR two-pass method (version 2.7.10ac, Dobin, Davis et al., 2013)
Mapped reads were aggregated to the gene level using HTseq (version 2.0, Putri, Anders et al., 2022) based on overlap with annotated gene exons. As expected based on the library preparation method we used, mapped reads were highly biased towards the 3’ end of genes
Assembly: meerkat - GCF_006229205.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
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| Submission date |
Nov 11, 2023 |
| Last update date |
Jul 05, 2024 |
| Contact name |
C. Ryan Campbell |
| E-mail(s) |
c.ryan.campbell@duke.edu
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| Organization name |
Duke University
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| Department |
Evolutionary Anthropology
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| Lab |
Tung
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| Street address |
130 Science Dr
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platform ID |
GPL33926 |
| Series (1) |
| GSE247525 |
A female-biased gene expression signature of dominance in cooperatively breeding meerkats |
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| Relations |
| BioSample |
SAMN38209044 |
| SRA |
SRX22489897 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7891795_SSUR1581.count.txt.gz |
114.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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