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| Status |
Public on Jul 21, 2017 |
| Title |
Lamb 1 |
| Sample type |
SRA |
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| Source name |
longissimus dorsi muscle
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| Organism |
Ovis aries |
| Characteristics |
breed: Hu sheep
developmental stage: 5-day lamb
tissue: longissimus dorsi muscle
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| Extracted molecule |
total RNA |
| Extraction protocol |
muscle samples were collected and immediately frozen in liquid nitrogen, then total RNA was isolated with TRIzol reagent.
The strand-specific sequencing libraries were separately prepared using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) according to the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Clusters were generated on the acBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS (Illumia) according to the manufacturer’s instructions and further sequenced on an Illumina HiseqX Ten platform. Reads that passed the quality control were then mapped to the Ovis Aries reference genome (Oar_v3.1). Based on it, the transcripts were assembled with Cufflinks (version 2.1.1) and Scripture
The Coding Potential Calculator, the Coding-Non-Coding Index, the Protein Families Database and the Coding-Potential Assessment Tool, which have the power to sort lncRNAs from putative protein-coding RNAs were combined to screen the lncRNAs. The transcripts from the intersection of the four methods with fragments per kilo base of exon per million fragments mapped (FPKM) greater than 0.1 were kept and predicted to be lncRNA transcripts.
Transcript abundance was measured by FPKM using Cuffdiff. Differential expression analysis of the groups was performed using the DESeq packages (1.10.1) . LncRNAs or protein-coding genes with a false discovery rate (FDR) < 5% and an absolute value of log2 (fold change) > 1 were assigned as differentially expressed.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: Excel files include lncRNA FPKM values in each Sample and differential analysis results of lncRNA and genes in each comparison, and a fastq file include lncRNA sequence information .
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| Submission date |
Jul 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Caifang Ren |
| E-mail(s) |
rencaifang@hotmail.com
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| Organization name |
Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University
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| Street address |
1 Weigang
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
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| Platform ID |
GPL23810 |
| Series (1) |
| GSE101669 |
Genome-wide Analysis Reveals Extensive Changes in LncRNAs during Skeletal Muscle Development in Hu sheep |
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| Relations |
| BioSample |
SAMN07372123 |
| SRA |
SRX3021699 |
| 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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