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| Status |
Public on Sep 01, 2024 |
| Title |
corpus, fresh tissue, rep4 |
| Sample type |
SRA |
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| Source name |
epididymis
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| Organism |
Felis catus |
| Characteristics |
tissue: epididymis
treatment: fresh
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using an RNAeasy kit (Qiagen)
Libraries were constructed using a TruSeq Stranded mRNA Library Prep Kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
4corpusD0
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| Data processing |
Reads were trimmed using Trimmomatic 0.38. Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
trimmed reads were mapped to the felis catus genome using HISAT2 version 2.1.0, Bowtie2 2.3.4.1
StringTie version 2.1.3b was used to assemble known genes and transcripts
Assembly: NCBI Felis catus genome
Supplementary files format and content: tab-delimited text file includes raw counts for each samples
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| Submission date |
Jun 09, 2024 |
| Last update date |
Sep 01, 2024 |
| Contact name |
Danielle Sosnicki |
| Organization name |
Smithsonian's National Zoo and Conservation Biology Institute
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| Street address |
3001 Connecticut Ave NW
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| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20008 |
| Country |
USA |
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| Platform ID |
GPL28702 |
| Series (1) |
| GSE269443 |
Extracellular vesicles are involved in the paracrine communication between epithelial cells in different regions of the domestic cat epididymis |
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| Relations |
| BioSample |
SAMN41769248 |
| SRA |
SRX24855186 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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