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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 25, 2021 |
| Title |
SPA 5 |
| Sample type |
SRA |
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| Source name |
subcutaneous preadipocyte
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| Organism |
Capra hircus |
| Characteristics |
tissue: subcutaneous preadipocyte
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| Treatment protocol |
Wash with PBS (Hyclone, Logan, UT, USA)three times
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| Growth protocol |
DMEM/F12 (Hyclone, Logan, UT, USA) with 10% fetal bovine serum (FBS) (Hyclone, Logan, UT, USA)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA from sequenced samples using Trizol reagent (Takara, Dalian, China)
The lncRNA library is constructed using a chain-specific library. The method for synthesizing the first strand of cDNA by reverse transcription is the same as the normal method of NEB library construction. The difference is that when the second strand is synthesized, dTTP in dNTPs is replaced by dUTP. After that, cDNA end repair, A-tailing, ligation of sequencing adapters, and length screening were also performed, and then the second strand of cDNA containing U was degraded by USER enzyme, and then PCR amplification was performed to obtain a library. Finally, twenty libraries were sequenced at Novogene Co. Ltd. (Beijing, China) on Illumina HiSeq Sequencing System.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
HISAT 2.0.4 Chain specificity parameter:--rna-strandness RF
rMATS 3.2.5 Default parameters
GATK v2.6-5 Default Parameters
StringTie v1.3.1 Default parameters
CNCI v2 default parameters, CPC2 default parameters, Pfam-scan v1.3 default parameters, PhyloCSF orf=ATGStop --frames=3
Genome_build: Capra hircus ARS1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Nov 02, 2021 |
| Last update date |
Dec 25, 2021 |
| Contact name |
changsheng he |
| E-mail(s) |
hcs0903@126.com
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| Phone |
13890753825
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| Organization name |
southwest minzu university
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| Street address |
No. 16, South Section, 1st Ring Roa
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| City |
Chengdu |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platform ID |
GPL15473 |
| Series (1) |
| GSE186988 |
Integrative analysis of lncRNA-miRNA-mRNA regulatory network reveals candidate lncRNAs responsible for meat quality in goats |
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| Relations |
| BioSample |
SAMN22837255 |
| SRA |
SRX12895855 |
| 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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