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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 16, 2024 |
| Title |
opossum, 3M, 1 |
| Sample type |
SRA |
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| Source name |
testis
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| Organism |
Monodelphis domestica |
| Characteristics |
tissue: testis
age: 3 months
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| Growth protocol |
Animals were grown under standard laboratory conditions and euthanized at the indicated developmental time points.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Bulk RNA-seq libraries were prepared using KAPA mRNA HyperPrep Kit (Roche # 08098123702) and sequenced on an Illumina NovaSeq
Testes from gray short-tailed opossums at Yale or adult (8-16 week old) male C57BL6/J mice purchased from Jackson Laboratories were harvested and dissociated into single-cell suspension for RNA isolation using collagenase and trypsin. Briefly, testes were removed from the scrotum, decapsulated from the tunica albuginea, and incubated in 0.75mg/mL collagenase in Dulbecco’s Modified Eagle Medium (Gibco 11965-09L; Thermo Fisher Scientific, Inc.) at 37oC. DMEM was added to dilute collagenase and samples were centrifuged for 5 minutes at 400 x g at room temperature. Supernatant was discarded and samples were washed in DMEM. Samples were resuspended in 0.05% trypsin-EDTA (Gibco 25300-054; Thermo Fisher Scientific Inc.) with DNAse (1:10,000; Stem Cell Technologies #07900, Vancouver BC, Canada). The reaction was quenched with 10% Cosmic Calf Serum (Sigma-Aldrich #C8056, Burlington, MA, USA) in DMEM (CCS-DMEM) and centrifuged. Samples were resuspended in CCS-DMEM and filtered through a 100-micron filter. Cell concentration was determined by hemocytometer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
polyA RNA-seq
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| Data processing |
Assembly: ASM229v1
RNA-seq libraries were aligned using HISAT 2.2.1 (Kim et al., 2019) with Ensembl (Yates et al., 2020) release 104 as a reference and -data output type. Output files were converted from SAM format to sorted BAM format using SAMtools-1.12 (Danecek et al., 2021; Li et al., 2009; Murat et al., 2021). Raw count values and FPKM were obtained using StringTie 2.1.4 (Pertea et al., 2016) with the -e and -G options and Ensembl (Yates et al., 2020) ASM229 release 104 or GRCM39 release 104 reference files for opossum and mouse, respectively.
Supplementary files format and content: scRNA-seq: filtered index (.tsv), feature (.tsv), and matrix (.mtx) files
Supplementary files format and content: bulk RNA-seq: tab-delimited text files with FPKM values by gene
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| Submission date |
Oct 21, 2022 |
| Last update date |
Aug 16, 2024 |
| Contact name |
Bluma J Lesch |
| Organization name |
Yale University
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| Department |
Genetics
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| Street address |
333 Cedar Street
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06525 |
| Country |
USA |
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| Platform ID |
GPL30856 |
| Series (1) |
| GSE216343 |
Gene regulatory divergence in spermatogenesis between mouse and opossum |
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| Relations |
| BioSample |
SAMN31408350 |
| SRA |
SRX17990200 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6670727_Md3MWTW6_e_abundance.tab.gz |
870.0 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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