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| Status |
Public on Mar 10, 2023 |
| Title |
RNA-seq based transcriptome profiles of the human testis tissues across multiple conditions, with an intention to mainly study non-obstructive azoospermia |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To study alternatively spliced isoforms expressed differently in the testis of donors with Non-Obstructive Azoospermia (NOA), testicular biopsies were collected from donors with NOA condition (as identified by cytological examination) and Obstructive Azoospermia (OA), and Varicocele (VA) conditions. The biopsy samples were stored in RNA-later solution (Ambion, cat # AM7024), according to the manufacturer's guidelines. RNA was extracted using the RiboPure kit (Ambion cat # AM1924). Two normal commercial testicular RNA (Clontech cat. no.: 636533, Asian: lot no: 1105041; Caucasian: lot. no.: LOT1105214A) samples were also used. The RNA quality was checked with formaldehyde agarose gel electrophoresis as well as a micro-volume spectrophotometer. For NGS, testicular RNA from 8 NOA, 2 OA and 2 Varicocele donors were used. Paired-end library preparation was carried out using Illumina TruSeq RNA Library Prep Kit v2, and sequencing was done using the Illumina HiSeq 2000. After quality checks, seqtk (https://github.com/lh3/seqtk) was used for trimming low-quality reads. Alignments, identification of transcripts and the chimeric/transplice molecules, and their quantification were performed by Kallisto software. Sample segregation according to the corresponding donor condition was confirmed via clustering RNA-seq data from the samples.
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| Overall design |
Transcriptome profiles from eight NOA samples were compared with those from 15 control samples (six sequenced newly, and nine public datasets). The control samples included 4 from donors with disorders with complete testicular spermatogenesis (two each with OA and VA).
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| Contributor(s) |
Kshitish KA, Govindkumar B, Kavyashree B |
| Citation(s) |
36883778 |
| BioProject |
PRJNA556935 |
| Submission date |
Oct 31, 2022 |
| Last update date |
Mar 11, 2023 |
| Contact name |
Kshitish K Acharya |
| E-mail(s) |
kshitish@ibab.ac.in
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| Organization name |
Institute of Bioinformatics and Applied Biotechnology
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| Street address |
Electronic City Ph 1
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| City |
Bengaluru |
| State/province |
Karnataka |
| ZIP/Postal code |
560100 |
| Country |
India |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (14)
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