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| Status |
Public on Apr 30, 2021 |
| Title |
D7_b |
| Sample type |
SRA |
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| Source name |
sciatic nerve
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| Organism |
Rattus norvegicus |
| Characteristics |
treatment: 7 days post sciatic nerve crush
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| Extracted molecule |
total RNA |
| Extraction protocol |
none provided by the submitter
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
mRNA_expression
lncRNA_expression
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| Data processing |
Purified total RNA was subjected to rRNA removal, fragmentation, first and second-strand cDNA synthesis, end repair, poly-A tail addition, ligation, enrichment and other steps to construct sequencing sample library. High-throughput RNA paired-end sequencing was then performed using the Illumina Hiseq Xten platform (Illumina, lnc., CA, USA). The unqualified reads, with low overall or end quality and containing sequencing primers, etc. were removed from the raw reads to obtain clean reads, from which rat ribosomal RNAs were further filtered. The Spliced Mapping algorithm in Hisat2 (version: 2.0.4) was applied to map the above processed reads to the rat reference genome (ftp://ftp.ensembl.org/pub/release-100/fasta/rattus_norvegicus/dna/).
With use of the Stringtie software (version: 1.3.0), the mapped reads were assembled to construct the transcripts, which were then matched to the reference databases (NOCODE and Ensembl) using the GffCompare (version: 0.9.8) software to obtain annotation. The unmatched transcripts were performed the potential novel lncRNA prediction with the criteria as follows: (1) transcript length >= 200 bp AND exon >= 2, (2) the predicted ORF < 300 bp, (3) Coding Potential Calculator (CPC) score < 0 AND Coding-Non-Coding Index (CNCI) score < 0 AND with no significant difference using Pfam comparison. The Perl script was then applied to locate the position of the above novel lncRNAs on the chromosomes and to make annotation.
With use of Stringtie software, the Fragment numbers of each gene were counted, which were then normalized by TMM (trimmed mean of M values) method. Finally the FPKM value of each known or newly predicted lncRNA was counted using perl script, where the lncRNA ID starting with NON is the known lncRNA in the NONCODE database, the ID starting with ENS is the known lncRNA in the Ensembl database, and the ID starting with MSTRG is the newly predicted lncRNA. The edgeR package was then used to analyze the differentially expressed genes between samples (Control vs D4 and Control vs D7). The screening criteria for differentially expressed genes are as follows: (1) q-value (the corrected p-value) < 0.05, (2) the absolute value of fold change >= 2.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include count number and FPKM values of each sample
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| Submission date |
Dec 02, 2020 |
| Last update date |
Apr 30, 2021 |
| Contact name |
Yu-Jing Zhang |
| E-mail(s) |
zhangyj256@mail.sysu.edu.cn
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| Phone |
+86-189-0091-0197
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| Organization name |
Sun Yat-sen University
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| Street address |
No.2 Zhongshan Road #58
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| City |
Guangzhou |
| ZIP/Postal code |
510080 |
| Country |
China |
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| Platform ID |
GPL24688 |
| Series (1) |
| GSE162548 |
Integrated analysis of long noncoding RNAs and mRNA expression profiles reveals the potential role of lncRNAs in early stage of post-peripheral nerve injury in Sprague-Dawley rats |
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| Relations |
| BioSample |
SAMN16982415 |
| SRA |
SRX9620975 |
| 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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