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| Status |
Public on Nov 09, 2022 |
| Title |
NBG-1-Month-2 |
| Sample type |
SRA |
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| Source name |
longissimus dorsi muscle
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| Organism |
Capra hircus |
| Characteristics |
tissue: longissimus dorsi muscle
breed: Nubian
age: 1-Month
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh adipose tissues were collected and stored in liquid nitrogen at −80 ℃, and RNA was harvested using Trizol reagent(Invitrogen，Carlsbad，CA，USA). A total amount of 3 μg RNA per sample was used as an initial material for the RNA sample preparation. The library was prepared according to the method and process of lncRNA sample preparation kit (Illumina, NEB) and Small RNA Sample Preparation Kit (Illumina, RS-200-0048) at Annoroad Gene Technology Corporation (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
NBG_2
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to capra hircus whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments per Kilobase per Million Mapped Fragments (FPKM)were calculated using a protocol from Trapnell, C. et al, 2010.Spliced Reads per Billion Mapping (SRPBM) calculated using a protocol from Li, et al. 2015 . In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
MiRNA cannot be directly enriched and analyzed; so two *DEG_GO_enrichment_result.xls files represent target genes of DEM.
Assembly: ARS1.2
Supplementary files format and content: tab-delimited text files include FPKM/TPM/SRPBM values for each Sample
Supplementary files format and content: Matrix table with raw miRNA counts for every miRNA and every sample
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| Submission date |
Nov 02, 2022 |
| Last update date |
Nov 09, 2022 |
| Contact name |
Sanbao Zhang |
| E-mail(s) |
gxuzsb@126.com
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| Phone |
18447055384
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| Organization name |
Guangxi University
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| Street address |
No.100,Daxue East Road
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| City |
Nanning |
| ZIP/Postal code |
530004 |
| Country |
China |
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| Platform ID |
GPL15473 |
| Series (1) |
| GSE217092 |
Differential expression and correlation analysis of miRNA–mRNA profiles in longissimus dorsi of different stage goats |
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| Relations |
| BioSample |
SAMN31572388 |
| SRA |
SRX18120609 |
| 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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