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Status |
Public on Aug 03, 2023 |
Title |
intramuscular adipocytes, NC-4 |
Sample type |
SRA |
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Source name |
goat intramuscular preadipocyte
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Organism |
Capra hircus |
Characteristics |
cell type: goat intramuscular preadipocyte genotype: WT
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Treatment protocol |
The negative control groups was treated with negative control interfering RNA (NC) and the experimental groups treated with interfering RNA that silences CPT1B gene (si-CPT1B).
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
The sample-4 of negative control nc4
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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
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Submission date |
Jul 28, 2023 |
Last update date |
Aug 03, 2023 |
Contact name |
Yinggui Wang |
E-mail(s) |
YingguiWang326@outlook.com
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Phone |
18788705310
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Organization name |
Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province
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Lab |
2-31
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Street address |
2-31, Jingwenyuan, South District, Airport Campus, Southwest University for Nationalities, Chengdu, Sichuan
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City |
chengdu |
State/province |
sichuan |
ZIP/Postal code |
610000 |
Country |
China |
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Platform ID |
GPL21299 |
Series (1) |
GSE239570 |
CPT1B regulates goat intramuscular preadipocyte lipid deposition through p38MAPK signaling pathway |
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Relations |
SRA |
SRX20572227 |
BioSample |
SAMN35553898 |
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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