 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 17, 2023 |
| Title |
NC-2 |
| Sample type |
SRA |
| |
|
| Source name |
goat intramuscular preadipocyte
|
| Organism |
Capra hircus |
| Characteristics |
cell type: goat intramuscular preadipocyte
genotype: WT
treatment: Adipose differentiation
|
| Treatment protocol |
The negative control groups was treated with negative control interfering RNA (NC) and the experimental groups treated cells with interfering RNA that silences LIPG (si-LIPG).
|
| Growth protocol |
Goat intramuscular precursor adipocytes were cultured using DMEM medium (containing 10% fetal bovine serum, 1% double antibody) at 37°C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
A_2
|
| Data processing |
fastp
Sequence readswere trimmed for adaptor sequnce/low-quality sequence using fastp
Trimmed sequnence reads wrere mapped to ARS1 using hisat2 samtools
The transcript was assembled using htseq-count.
Assembly: ARS1
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jun 14, 2023 |
| Last update date |
Jul 10, 2023 |
| Contact name |
Yinggui Wang |
| E-mail(s) |
YingguiWang326@outlook.com
|
| Phone |
18788705310
|
| Organization name |
Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province
|
| Lab |
2-31
|
| Street address |
2-31, Jingwenyuan, South District, Airport Campus, Southwest University for Nationalities, Chengdu, Sichuan
|
| City |
chengdu |
| State/province |
sichuan |
| ZIP/Postal code |
610000 |
| Country |
China |
| |
|
| Platform ID |
GPL21299 |
| Series (1) |
| GSE234932 |
LIPG regulates goat intramuscular preadipocyte proliferation and lipid deposition through PPARα signaling pathway |
|
| Relations |
| SRA |
SRX19746002 |
| BioSample |
SAMN33835702 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7479485_A2counts.txt.gz |
87.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
