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Status |
Public on Feb 06, 2024 |
Title |
LTS1_LTS |
Sample type |
SRA |
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Source name |
root
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Organism |
Ipomoea batatas |
Characteristics |
tissue: root treatment: 4 C
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Extracted molecule |
total RNA |
Extraction protocol |
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Data processing |
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value. Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways. Assembly: GT4SP_v3 Supplementary files format and content: excel files include count values for each sample
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Submission date |
Feb 06, 2024 |
Last update date |
Feb 08, 2024 |
Contact name |
Jiahao Zhu |
E-mail(s) |
f2694635698@gmail.com
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Phone |
13281253315
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Organization name |
Jiangsu Normal University
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Street address |
Shanghai Road 101
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City |
Xuzhou |
ZIP/Postal code |
221000 |
Country |
China |
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Platform ID |
GPL30016 |
Series (1) |
GSE255226 |
High throughput sequencing identifies chilling responsive genes in sweetpotato (Ipomoea batatas Lam.) during storage |
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Relations |
BioSample |
SAMN39848489 |
SRA |
SRX23575693 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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