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| Status |
Public on Oct 23, 2024 |
| Title |
StrokeofGenus: RNA-seq in five tissues of the hibernating 13-lined ground squirrel |
| Organism |
Ictidomys tridecemlineatus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Identify shifts in gene expression relevant to torpor phenotypes and recovery following torpor in five tissues of the 13-lined ground squirrel. Sampled tissues and time points overlap with prior hibernation RNA-seq studies in 13-lined ground squirrel and other species, allowing for the analysis of conserved gene expression patterns in torpor.
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| Overall design |
RNA-seq from the Cortex, Hypothalamus, Retina, Retinal pigment epithelium (RPE), and Liver of 13-lined ground squirrel taken at five points surrounding and during hibernation: euthermia, prehibernation (RT torpor), torpor, three days post torpor euthermia, and fourteen days post torpor euthermia. Tissue was collected from three specimens for each time point, though two liver samples for the prehibernation time point and two RPE sample samples for the euthermia time point failed quality checks and were not sequenced.
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| Contributor(s) |
Weir K, Sadjak B, Kallestad L, Carroll J, Palczewsk K, Blackshaw S |
| Citation(s) |
39420030 |
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| Submission date |
Nov 29, 2023 |
| Last update date |
Oct 23, 2024 |
| Contact name |
Kurt Weir |
| E-mail(s) |
[email protected]
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| Organization name |
Johns Hopkins School of Medicine
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| Street address |
733 North Broadway
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| City |
Baltimore |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platforms (1) |
| GPL29082 |
Illumina NextSeq 500 (Ictidomys tridecemlineatus) |
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| Samples (101)
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| GSM7923118 |
Cortex, Prehibernation, Rep1 |
| GSM7923119 |
Cortex, Prehibernation, Rep2 |
| GSM7923120 |
Cortex, Prehibernation, Rep3 |
| GSM7923121 |
Cortex, Torpor, Rep1 |
| GSM7923122 |
Cortex, Torpor, Rep2 |
| GSM7923123 |
Cortex, Torpor, Rep3 |
| GSM7923124 |
Cortex, 3 days post torpor, Rep1 |
| GSM7923125 |
Cortex, 3 days post torpor, Rep2 |
| GSM7923126 |
Cortex, 3 days post torpor, Rep3 |
| GSM7923127 |
Cortex, 14 days post torpor, Rep1 |
| GSM7923128 |
Cortex, 14 days post torpor, Rep2 |
| GSM7923129 |
Cortex, 14 days post torpor, Rep3 |
| GSM7923130 |
Hypothalamus, Euthermia, Rep1 |
| GSM7923131 |
Hypothalamus, Euthermia, Rep2 |
| GSM7923132 |
Hypothalamus, Euthermia, Rep3 |
| GSM7923133 |
Hypothalamus, Prehibernation, Rep1 |
| GSM7923134 |
Hypothalamus, Prehibernation, Rep2 |
| GSM7923135 |
Hypothalamus, Prehibernation, Rep3 |
| GSM7923136 |
Hypothalamus, Torpor, Rep1 |
| GSM7923137 |
Hypothalamus, Torpor, Rep2 |
| GSM7923138 |
Hypothalamus, Torpor, Rep3 |
| GSM7923139 |
Hypothalamus, 3 days post torpor, Rep1 |
| GSM7923140 |
Hypothalamus, 3 days post torpor, Rep2 |
| GSM7923141 |
Hypothalamus, 3 days post torpor, Rep3 |
| GSM7923142 |
Hypothalamus, 14 days post torpor, Rep1 |
| GSM7923143 |
Hypothalamus, 14 days post torpor, Rep2 |
| GSM7923144 |
Hypothalamus, 14 days post torpor, Rep3 |
| GSM7923145 |
Retina, Euthermia, Rep1 |
| GSM7923146 |
Retina, Euthermia, Rep2 |
| GSM7923147 |
Retina, Euthermia, Rep3 |
| GSM7923148 |
Retina, Euthermia, Rep4 |
| GSM7923149 |
Retina, Euthermia, Rep5 |
| GSM7923150 |
Retina, Euthermia, Rep6 |
| GSM7923151 |
Retina, Prehibernation, Rep1 |
| GSM7923152 |
Retina, Prehibernation, Rep2 |
| GSM7923153 |
Retina, Prehibernation, Rep3 |
| GSM7923154 |
Retina, Prehibernation, Rep4 |
| GSM7923155 |
Retina, Prehibernation, Rep5 |
| GSM7923156 |
Retina, Prehibernation, Rep6 |
| GSM7923157 |
Retina, Torpor, Rep1 |
| GSM7923158 |
Retina, Torpor, Rep2 |
| GSM7923159 |
Retina, Torpor, Rep3 |
| GSM7923160 |
Retina, Torpor, Rep4 |
| GSM7923161 |
Retina, Torpor, Rep5 |
| GSM7923162 |
Retina, Torpor, Rep6 |
| GSM7923163 |
Retina, 3 days post torpor, Rep1 |
| GSM7923164 |
Retina, 3 days post torpor, Rep2 |
| GSM7923165 |
Retina, 3 days post torpor, Rep3 |
| GSM7923166 |
Retina, 3 days post torpor, Rep4 |
| GSM7923167 |
Retina, 3 days post torpor, Rep5 |
| GSM7923168 |
Retina, 3 days post torpor, Rep6 |
| GSM7923169 |
Retina, 14 days post torpor, Rep1 |
| GSM7923170 |
Retina, 14 days post torpor, Rep2 |
| GSM7923171 |
Retina, 14 days post torpor, Rep3 |
| GSM7923172 |
Retina, 14 days post torpor, Rep4 |
| GSM7923173 |
Retina, 14 days post torpor, Rep5 |
| GSM7923174 |
Retina, 14 days post torpor, Rep6 |
| GSM7923175 |
RPE, Euthermia, Rep1 |
| GSM7923176 |
RPE, Euthermia, Rep2 |
| GSM7923177 |
RPE, Euthermia, Rep3 |
| GSM7923178 |
RPE, Euthermia, Rep4 |
| GSM7923179 |
RPE, Prehibernation, Rep1 |
| GSM7923180 |
RPE, Prehibernation, Rep2 |
| GSM7923181 |
RPE, Prehibernation, Rep3 |
| GSM7923182 |
RPE, Prehibernation, Rep4 |
| GSM7923183 |
RPE, Prehibernation, Rep5 |
| GSM7923184 |
RPE, Prehibernation, Rep6 |
| GSM7923185 |
RPE, Torpor, Rep1 |
| GSM7923186 |
RPE, Torpor, Rep2 |
| GSM7923187 |
RPE, Torpor, Rep3 |
| GSM7923188 |
RPE, Torpor, Rep4 |
| GSM7923189 |
RPE, Torpor, Rep5 |
| GSM7923190 |
RPE, Torpor, Rep6 |
| GSM7923191 |
RPE, 3 days post torpor, Rep1 |
| GSM7923192 |
RPE, 3 days post torpor, Rep2 |
| GSM7923193 |
RPE, 3 days post torpor, Rep3 |
| GSM7923194 |
RPE, 3 days post torpor, Rep4 |
| GSM7923195 |
RPE, 3 days post torpor, Rep5 |
| GSM7923196 |
RPE, 3 days post torpor, Rep6 |
| GSM7923197 |
RPE, 14 days post torpor, Rep1 |
| GSM7923198 |
RPE, 14 days post torpor, Rep2 |
| GSM7923199 |
RPE, 14 days post torpor, Rep3 |
| GSM7923200 |
RPE, 14 days post torpor, Rep4 |
| GSM7923201 |
RPE, 14 days post torpor, Rep5 |
| GSM7923202 |
RPE, 14 days post torpor, Rep6 |
| GSM7923203 |
Liver, Euthermia, Rep1 |
| GSM7923204 |
Liver, Euthermia, Rep2 |
| GSM7923205 |
Liver, Euthermia, Rep3 |
| GSM7923206 |
Liver, Prehibernation, Rep1 |
| GSM7923207 |
Liver, Torpor, Rep1 |
| GSM7923208 |
Liver, Torpor, Rep2 |
| GSM7923209 |
Liver, Torpor, Rep3 |
| GSM7923210 |
Liver, 3 days post torpor, Rep1 |
| GSM7923211 |
Liver, 3 days post torpor, Rep2 |
| GSM7923212 |
Liver, 3 days post torpor, Rep3 |
| GSM7923213 |
Liver, 14 days post torpor, Rep1 |
| GSM7923214 |
Liver, 14 days post torpor, Rep2 |
| GSM7923215 |
Liver, 14 days post torpor, Rep3 |
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| Relations |
| BioProject |
PRJNA1046472 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE248932_13LGS_Blackshaw_countsframe.Robj.gz |
22.1 Mb |
(ftp)(http) |
ROBJ |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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