|
| Status |
Public on Jul 18, 2022 |
| Title |
Male_Pistillode_S3_R1 |
| Sample type |
SRA |
| |
|
| Source name |
Pistillode of pre-meiotic male flower bud (size 4.5-6.5 mm)
|
| Organism |
Carica papaya |
| Characteristics |
tissue: Pistillode of pre-meiotic male flower bud (size 4.5-6.5 mm)
genotype: AU9
Sex: Male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction
Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw read quality was analyzed using FastQC (Version 0.11.5).
Adapters and low-quality reads were removed using Trimmomatic (Version 0.36).
Clean paired reads were aligned to a reference containing both the MSY and the X pseudomolecules using Hisat2 (Version 2.0.5).
SAM files were converted to BAM files using samtools (Version 1.3.1).
BAM files were used to count reads aligned to the X and Y alleles using featureCounts (Version 1.5.2). Reads aligned to exons were counted and summarized per gene ID.
Assembly: Fasta file containing the "X_pseudomolecule-5.4M-091211.fasta" and "MaleY_reassembly_pseudomolecule_6-29-12.fasta" sequences for Carica papaya.
Supplementary files format and content: .txt' files containing read counts for each gene.
|
| |
|
| Submission date |
Jul 15, 2022 |
| Last update date |
Jul 18, 2022 |
| Contact name |
Dessiree Patricia Zerpa Catanho |
| E-mail(s) |
dpz2@illinois.edu
|
| Organization name |
University of Illinois at Urbana-Champaign
|
| Street address |
1201 W. Gregory Dr, 279 ERML
|
| City |
Urbana |
| State/province |
Illinois |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL26326 |
| Series (1) |
| GSE208265 |
Characterization and analysis of the promoter region of Monodehydroascorbate reductase 4 (CpMDAR4) in papaya |
|
| Relations |
| BioSample |
SAMN29762572 |
| SRA |
SRX16252464 |
