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| Status |
Public on Oct 31, 2021 |
| Title |
S4 stage root rep2 |
| Sample type |
SRA |
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| Source name |
Root
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| Organism |
Ipomoea batatas |
| Characteristics |
tissue: Root
developmental stage: S4 stage (diameter 1.5 mm)
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-sequencing analysis, total RNA was isolated from the middle sections of fibrous roots (S4 and S8), pencil roots (S10 and S12) and storage roots (S14, S16 and S20) using the RNeasy Mini Kit (Qiagen) with manufacturer’s instruction. Quality of RNAs were checked by determining the RNA Integrity Number (RIN) using an Agilent 2100 Bioanalyzer and Nanodrop 2000 (Thermo Scientific, Waltham, United States).
All the 28 libraries (7 samples in four biological replicates) were prepared using the Illumina TruSeq RNA Sample Prep Kit with 1μg of total RNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
S4_2
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| Data processing |
The raw sequence data were assessed for various quality parameters, and high-quality reads were filtered using NGS QC Toolkit (v2.3) (Patel and Jain, 2012).
The filtered high-quality reads were mapped on the sweet potato genome (http://public-genomes-ngs.molgen.mpg.de/cgi-bin/hgGateway?hgsid=9052&clade=plant&org=Ipomoea+batatas&db=ipoBat4) using TopHat (v2.0.0).
The mapped output was processed via RSEM (v1.3.1) to obtain TPM for all the sweet potato genes in each sample.
Genome_build: sweet potato genome (http://public-genomes-ngs.molgen.mpg.de/cgi-bin/hgGateway?hgsid=9052&clade=plant&org=Ipomoea+batatas&db=ipoBat4)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
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| Submission date |
Apr 19, 2021 |
| Last update date |
Oct 31, 2021 |
| Contact name |
Shutao He |
| E-mail(s) |
shutao.he@sibcb.ac.cn
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| Organization name |
Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences
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| Street address |
320 Yue Yang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL30016 |
| Series (1) |
| GSE172378 |
Dynamic network biomarker analysis discovers IbNAC083 in initiation and regulation of sweet potato root tuberization |
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| Relations |
| BioSample |
SAMN18803132 |
| SRA |
SRX10638248 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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