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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 06, 2023 |
| Title |
Rete testis cell, 3 |
| Sample type |
SRA |
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| Source name |
Rete testis cell culture
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| Organism |
Mus musculus |
| Characteristics |
cell type: Rete testis cell culture
genotype: WT
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using ExtractRNA kit (Evrogen). Samples were treated with recombinant duplex-specific nuclease (Eurogen) to remove genomic DNA impurities.
Poly(A) enrichment of the total RNA, cDNA synthesis and preparation of cDNA libraries were performed using TruSeq mRNA Stranded (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
RT3
gene_count_matrix.csv
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| Data processing |
bcl2fastq v2.20 Conversion Software (Illumina) was used to obtain FASTQ files
Sequence reads were trimmed using Trim Galore and Cutadapt
Reads were mapped using the HiSat2 algorithm
Read summarization was performed using FeatureCounts v.2.0.1
The R package EdgeR v.3.42.4 was used for normalization of data and differential expression analysis
Assembly: GRCm38
Supplementary files format and content: Comma Separated Spreadsheet includes raw counts for each sample
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| Submission date |
Sep 06, 2023 |
| Last update date |
Dec 06, 2023 |
| Contact name |
Valeru Mun |
| E-mail(s) |
[email protected]
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| Organization name |
IDB RAS
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| Street address |
st. Vavilova, 26
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| City |
Moscow |
| ZIP/Postal code |
119334 |
| Country |
Russia |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE242442 |
Analysis of genes differentially expressed between rete testis cells and Sertoli cells of the mouse testis |
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| Relations |
| BioSample |
SAMN37299065 |
| SRA |
SRX21645349 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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