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| Status |
Public on Jan 25, 2023 |
| Title |
RS_03 |
| Sample type |
SRA |
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| Source name |
Durian Var. D24 fruit
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| Organism |
Durio zibethinus |
| Characteristics |
age: 127 days
cultivar: D24
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extraction kit namely GeneAll RibospinTM Seed/Fruit RNA mini kit was used to isolate the RNA. RNA samples were extracted according to the manufacturer’s protocols with the minor modifications to increase the yileds and purity. The assesment of RNA quality was carried out using implen nanodrop spectrophotometer, qubit fluorometer, 1% gel agarose electrophoresis, agilent bioanalyzer and agilent tapestation.
Poly-A mRNAs were purified from 1 ug of total RNA using the NEB Next Poly(A) mRNA magnetic isolation module. The first and second strand of cDNA synthesis was performed with purified mRNA using the NEB Next Ultra RNA Library Prep Kit (Ilumina). The index primers 1-9 were used for each of the samples to ensure every samples were having different barcode for pool method of sequencing. To obtain the final library, the cDNA fragments were amplified by PCR as per outlined in the NEB protocol. The purification of PCR reaction were carried out using AmPure XP beads. Nine pre-prepared cDNA libraries were send to NGS service provider (Novogene). The libraries were sequenced with HiSeq Ilumina Platform using 2x 150 bp paired end protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Durio zibethinus Murr.
ripeningstage03_1
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| Data processing |
The sequencing was run by using the Illumina Hiseq 150 PE Run. The expected data output was 16.7 million reads or equivalent to 5 GB per sample. For the total of 9 samples, the amount of the total data was 150.3 M or 45 GB. The total output of data on the sequencer is 58.0 G, and the filtered data (clean data) is 50.0 G. FastQC was run to check the quality of the raw data and the quality of the trimmed data. Comparison was made before and after (twice for each sample) to ensure only the cleaned reads were used for downstream analysis.
Trimmomatic is applied to performs a trimming the Illumina FastQC of paired end data. It is used to remove the adapters that are added during the sequencing process. Perform alignment of RNA-Seq reads to D. zibethinus reference genome sequence (accession number: GCF_00230385.1) using the ultra-high-throughput short read aligner Bowtie (2), and then analyzes the mapping results to identify splice junctions between exons.
Parameter TopHat: Type of data: Paired-end data. Input: RNA-Seq FASTQ file, forward and reverse reads, Mean inner distance between mate pairs: 300, STD. DEV for distance between mate pairs: 20, Report discordant pair alignments: Yes, use built-in reference genome from history,
TopHat setting to use: by default value (20 for maximum number of alignments to be allowed, 2 for final read mismatches and yes to output of unmapped reads in BAM format).
Output: junctions (BED track of junction), insertions, deletions, accepted_hits (BAM format of alignment files) and align summary.
Genome_build: NCBI Durio zibethinus Annotation Release 100. Accession number: GCF_00230385.1.
Supplementary_files_format_and_content: Tab-delimited text files include gene abundance analysis for all samples.
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| Submission date |
Aug 23, 2019 |
| Last update date |
Jan 26, 2023 |
| Contact name |
Nurul Arneida Husin |
| E-mail(s) |
nurul.arnieda@monash.edu
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| Organization name |
Monash University
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| Lab |
Bio Medical Lab
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| Street address |
Jalan Lagoon Selatan
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| City |
Sunway |
| State/province |
Selangor |
| ZIP/Postal code |
47500 |
| Country |
Malaysia |
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| Platform ID |
GPL27140 |
| Series (1) |
| GSE136290 |
Discovery of Novel Genes and Pathways through Comparative Transcriptomics Approach to Elucidate Genes Expressed in Durian (Durio zibethinus Murr) D24 Varieties Fruit Pulp Development and Ripening. |
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| Relations |
| BioSample |
SAMN12629372 |
| SRA |
SRX6756346 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4044054_gene_abundance_rs_03.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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