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| Status |
Public on Nov 28, 2018 |
| Title |
La3 |
| Sample type |
SRA |
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| Source name |
juvenile lanceolate leaf
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| Organism |
Populus euphratica |
| Characteristics |
leaf shape: lanceolate
tree age: 4-6 years
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| Growth protocol |
The juvenile linear,lanceolate,ovate and broad-ovate leaf groups were respectively sampled from 0-3, 4-6, 8-12 and over 20 years old P. euphratica in Alar (81°17′56.52″ E, 40°32′36.90″ N), Xinjiang province, China at April 2017
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the mirVanamiRNA Isolation Kit (Ambion) following the manufacturer’s protocol
The strand-specific libraries (dUTP) were constructed using TruSeq Stranded Total RNA LT - (with Ribo-Zero Plant) according to the manufacturer’s instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
strand-specific RNA sequencing
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| Data processing |
The clean reads obtained from sequencing were compared with P. euphratica genome (GCF_000495115.1_ PopEup_1.0_genomic.fna.gz, https://www.ncbi.nlm.nih.gov/genome/13265) by TopHat2
The clean reads were further compared with P. euphratica transcriptome to calculate the expressive abundance of every transcripts by bowtie2 (-k30 -t) and eXpress (---rf-stranded).
The transcripts were rebuilt based on probabilistic model using cufflinks (--no-update-check--library-type fr-firststrand).
All the transcripts were compared with P. euphratica transcriptome to remove known code transcripts and locus. Then these transcripts shorter than 200 bp or exons less than 2 were also removed. Remainder transcripts were analyzed with CPC (default), CNCI (-m pl), Pfam (-e_seq 0.001) and PLEK (default) to remove code transcripts, and lncRNAs of P. euphratica were obtained at last.
The expressive abundance of mRNA and lncRNA were quantified as FPKM (Fragments Per kb Per Million Reads)
Based on the sequencing results, the circRNAs were predicted De Novo with CIRI (command: CIRI_v2.0.1pl-Ialn-pe.sam-O CircRNA.gtf-S 100000-F genome.fa-M Mt-A reference.gtf)
The expressive abundance of circRNA was quantified as RPM (spliced reads per millon).
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and RPM for each Sample
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| Submission date |
Oct 04, 2018 |
| Last update date |
Nov 28, 2018 |
| Contact name |
Shaowei Qin |
| E-mail(s) |
qinshaowei2005@126.com
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| Organization name |
Tarim University
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| Department |
College of Life Sciences
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| Street address |
Hongqiao Road 705
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| City |
Alar |
| State/province |
Xinjiang |
| ZIP/Postal code |
843300 |
| Country |
China |
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| Platform ID |
GPL25640 |
| Series (2) |
| GSE120818 |
Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis [RNA-Seq] |
| GSE120822 |
Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis |
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| Relations |
| BioSample |
SAMN10170283 |
| SRA |
SRX4791933 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3416362_La3circRNA.txt.gz |
37.7 Kb |
(ftp)(http) |
TXT |
| GSM3416362_La3lncRNA.txt.gz |
34.5 Kb |
(ftp)(http) |
TXT |
| GSM3416362_La3mRNA.txt.gz |
345.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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