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| Status |
Public on Oct 31, 2022 |
| Title |
‘Zhongshanyuan poplar’（ZSY)，purple-leaves 1 |
| Sample type |
SRA |
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| Source name |
‘Zhongshanyuan poplar’，leaf
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| Organism |
Populus deltoides |
| Characteristics |
tissue: ‘Zhongshanyuan poplar’，leaf
genotype: WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of the total RNA from leaf samples was performed using the EAZY spin Plus Plant RNA Kit. The contaminated DNA was removed from the extracted RNA using DNase I (TAKARA).
The Dynabeads mRNA Purification Kit (Invitrogen) was used fot the total RNA to generate mRNA, which were furtehr fragmented and reverse transcribed into first strand cDNAs initiated by random hexamer priming.Then the double-stranded cDNAs (ds-cDNA) were generated by the NEBNext Ultra RNA Library Prep Kit (NEB), which were purified, end-repaired, and ligated to adaptors.
Finally, the dscDNAs with adding adaptors were further fragmented and enriched by PCR to construct the final cDNA libraries for Illumina paired-end sequencing. The cDNA library was sequenced using the Illumina NovaSeq 600
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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 |
After filtering out the adapter sequences and low quality sequence reads, the clean reads were were mapped to the poplar reference genome sequence (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCA_015852605.2/) to obtain the unigenes using HISAT2 and StringTie software.
Eight databases, including NR, NR, GO, Swiss-Prot, COG, KOG, Pfam, and KEGG, were used to annotate the unigenes using BLAST (E <10−5).
The expression level of all unigenes were calculated and normalized to fragments per kilobase of transcript per million fragments mapped (FPKM).
Moreover, DEGs between two sample pairs were analyzed using the DESeq R package. The FDR (false discovery rate) of <0.05 and |log2(foldchange)| of ≥1 were applied to identify the significant DEGs.
In addition, GO annotations were conducted using the DAVID online tool on the screened DEGs. KEGG pathway analysis of DEGs was performed using the KOBAS online analysis database (available online: http://kobas.cbi.pku.edu.cn/).
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Oct 28, 2022 |
| Last update date |
Nov 01, 2022 |
| Contact name |
yunfeng wei |
| E-mail(s) |
[email protected]
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| Phone |
14785897041
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| Organization name |
Guizhou University
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| Street address |
Huaxi District, Guiyang City
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| City |
Guiyang |
| ZIP/Postal code |
550000 |
| Country |
China |
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| Platform ID |
GPL32787 |
| Series (1) |
| GSE216754 |
Transcriptome and metabolome analysis reveals anthocyanin biosynthesis pathway associated with poplar (Populus deltoids) leaf color formation |
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| Relations |
| BioSample |
SAMN31499451 |
| SRA |
SRX18057461 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6690507_F_P1.txt.gz |
355.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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