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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 06, 2022 |
| Title |
S2 mouse, WT |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6N
tissue: spleen
Sex: male
age (months): 2
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| Treatment protocol |
None. Heathly naked mole-rats kept under normal housing conditions (29°C, 50-60% humidity) and healthy mice kept at about 22°C under 55% humidity, 12h light/dark cycle.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Spleens were dissected and fast frozen on dry-ice. Total RNA was extracted from 3 biological replicates per group using RNeasy extraction kit from Qiagen. RNA was sequenced on the Illumina HiSeq2500 platform according to the manufacturer's instruction at Macrogen (Korea)
Illumina TruSeq stranded mRNA LT Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols; library type: Illumina-transcriptome, library: TruSeq stranded mRNA, read length: Illumina 100bp PE
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq
Reads were mapped to mm9 and hetGla2 respectively, using STAR version 2.5.3a
Raw reads were generated using htseq-count version 0.10.0
RNA differential gene expression was performed with DESeq2
Genome_build: hetGla2/hetGla_Female_1.0 and mm9
Supplementary_files_format_and_content: Normalized counts for mouse and naked mole rat samples
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| Submission date |
Jul 02, 2021 |
| Last update date |
Apr 06, 2022 |
| Contact name |
Valerie Begay |
| E-mail(s) |
vbegay@mdc-berlin.de
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| Organization name |
Max Delbrück Center
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| Street address |
Robert-Rössle-Str. 10
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| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE179350 |
RNA sequencing of the spleen of naked mole-rat and mouse |
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| Relations |
| BioSample |
SAMN20010177 |
| SRA |
SRX11342562 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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