 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 14, 2018 |
| Title |
D8 |
| Sample type |
SRA |
| |
|
| Source name |
the eighth day of subcutaneous preadipocyte differentiation
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Chinese Erhualian pigs
differentiation stage: D8
Sex: male
|
| Treatment protocol |
The different differentiation stages (D0, D2, D4, and D8) of subcutaneous preadipocyte
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Adipocytes at different differentiation stages were subjected to total RNA extraction using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Total RNA from D0, D2, D4, and D8 (3 individuals/group) was pooled in equal amounts to generate mixed sample respectively. Sequencing libraries were prepared using NEB Next Ultra Directional RNA LibraryPrep Kit (NEB, Ispawich, MA, USA).
Libraries were prepared for sequencing using Illumina Solexa transcriptome sequencing protocol after removing ribosomal RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
the eighth day of subcutaneous preadipocyte differentiation
|
| Data processing |
Raw sequencing data was evaluated by FAST-QC
Raw reads after quality control testing were mapped to the reference pig genome version 11.1 (Sscrofa 11.1) using HiSAT2 program (V2.0.5) for mRNAs and lncRNAs, and BWA-MEM for circRNAs
The normalized expression level of each gene was measured by fragments per kilobase of transcript per million reads mapped (FPKM) for mRNAs and lncRNAs, and spliced reads per billion mapping (SRPBM) for circRNAs
Genome_build: Sscrofa 11.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM (for mRNAs and lncRNAs) or SRPBM (for circRNAs) values for each gene
|
| |
|
| Submission date |
May 17, 2018 |
| Last update date |
Nov 14, 2018 |
| Contact name |
Xin Liu |
| E-mail(s) |
965092279@qq.com
|
| Phone |
13260986761
|
| Organization name |
Nanjing Agricultural University
|
| Department |
College of Animal Science and Technology
|
| Street address |
weigang1
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL22918 |
| Series (1) |
| GSE114583 |
Transcriptome analysis of mRNAs, lncRNAs, and circRNAs during the differentiation of porcine subcutaneous preadipocytes |
|
| Relations |
| BioSample |
SAMN09220700 |
| SRA |
SRX4095652 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3145323_D8_FPKM_and_SRPBM.txt.gz |
594.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
