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| Status |
Public on Feb 26, 2021 |
| Title |
LW_2W_2_Duodenum_RNA |
| Sample type |
SRA |
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| Source name |
Duodenum
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| Organism |
Sus scrofa |
| Characteristics |
breed: Large White
tissue: duodenum
age: 2 weeks
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each tissue sample using TRIzol reagent, and RNA was further purified by removing the rRNA. These rRNA depleted RNA samples were used for the construction of sequencing libraries.
The strand-specific RNA-seq libraries using the protocol provided by Ilumina. The libraries were sequenced using the illumina Hiseq X ten PE150 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
individual 2
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| Data processing |
The adapter was firstly removed from the raw data and the clean data was obtained after removing low quality reads.
The reads were mapped to the susScr11.1 reference genome using TopHat (v2.1.1). The transcript assembly of each sample was separately performed by using BAM file as input file for Cufflinks (v2.2.1). The resulting individual transcript assemblies were further merged to a single transcript assembly using Cuffcompare.
To identify lncRNA of the pig genome, the transcripts from the single transcript assembly were filtered as the following steps: (i) the identified transcripts which must be with class code “x”, “i” or “.” in at least two samples, and do not overlap with any known transcripts or with class code “u” ; (ii) transcripts with length ≥ 200, exon number ≥ 2; (iii) transcripts with FPKM ≥ 1 and reads ≥ 5 in at least 2 replicates; (iv) the identified transcripts without potential coding regions which were filtered using CNCI and CPC2.
For identification of other types of novel transcripts, the transcripts which were assembled in two replicates in the transcript assembly file of each sample were selected firstly. Then the filtered transcript assembly files were merged by Cuffmerge. Next, Cuffcompare was applied again to integrate the merged transcript assembly file and the lncRNA gtf file. This new gtf was used to calculate transcript expression levels (FPKM value) by RSEM (v1.3.0). The last step was to filter the transcripts to identify novel transcripts by the following criteria: (i) transcripts on the same strand of known transcripts and exon overlapped with any known transcripts were omitted; (ii) lncRNAs which were identified before were removed; (iii) transcripts with class code “x”, “i” and “u” and with FPKM ≥ 5 at least in any 2 replicates.
Finally, The gtf file of lncRNA and novel transcripts was integrated with the annotation file from UCSC for calculating gene expression level(TPM value) by RSEM.
Genome_build: susScr11.1
Supplementary_files_format_and_content: Bed file of each Sample include TPM (Transcripts Per Million) values calculated by RSEM.
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| Submission date |
Jan 08, 2020 |
| Last update date |
Feb 27, 2021 |
| Contact name |
Shuhong Zhao |
| E-mail(s) |
shzhao@mail.hzau.edu.cn
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| Organization name |
Huazhong Agricultural University
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| Street address |
No.1,Shizishan Street, Hongshan District
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| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platform ID |
GPL22918 |
| Series (1) |
| GSE143288 |
A compendium map of Cis-Regulatory Elements in the Pig Genome and epigenetic comparison with the human Genome |
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| Relations |
| SRA |
SRX7438609 |
| BioSample |
SAMN13676591 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4256245_LW_2W_2_Duodenum_RNA_TPM.bed.gz |
398.1 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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