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Sample GSM7476435

Query DataSets for GSM7476435

Status

Public on Jun 14, 2024

Title

Intramuscular adipocytes, Ad_ lncFABP4 transduction, Day4, rep3 [Ad_ lncFABP4-3]

Sample type

SRA

Source name

Intramuscular adipocytes

Organism

Bubalus bubalis

Characteristics

cell type: Intramuscular adipocytes
genotype: lncFABP4 overexpress
treatment: adipogenic differentiation, Ad_lncFABP4 transduction

Treatment protocol

Intramuscular adipocytes were planted in six-well plates in triplicate. When the cells reach 80% confluence, transduction was performed. Adenovirus were added to cells at the indicated MOI. The culture media was exchanged three hours later. When transduction occurs for 48 hours, cells were treated with an inducing medium. Cells were collected for RNA sequencing after 48 hours of induction.

Growth protocol

Cells were cultured with complete culture medium containing 20% fetal bovine serum and 1% penicillin–streptomycin (Gibco, Grand Island, NY) at 37℃ with 5% CO2.

Extracted molecule

polyA RNA

Extraction protocol

Total RNAs were isolated using a TRIzol regent according to a manufacturer’s protocol (Invitrogen, Carlsbad, CA, USA).
Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; mRNA molecules were fragmented into small pieces; The fragmented mRNA was synthesized into first strand cDNA using random primers; The second strand cDNA was synthesized; The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; PCR amplification and purification; Library quality control; Library circularization; The library was amplified to make DNA nanoball (DNB); Sequencing on DNBSEQ (DNBSEQ Technology) platform.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

DNBSEQ-G400

Data processing

To obtain clean reads, Low-quality reads, adapter reads, and those reads with more than 3% N were removed by SOAPnuke software (Chen et al. 2018).
The buffalo reference genome (GVM000043) and gene model annotation files were downloaded from the Genome Variation Map database (https://ngdc.cncb.ac.cn/gvm).
Clean reads were aligned to the reference genome by HISAT2 (Kim et al. 2019).
Mapped reads were assembled using StringTie (Pertea et al. 2015).
Expression of transcript was analyzed by StringTie (Pertea et al. 2015) and presented as fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: The river buffalo genome was assembled by our team (not published) and can be provided from corresponding authors by e-mail.
Supplementary files format and content: Excel file (.xlsx) include all the identified mRNA with FPKM values for all samples

Submission date

Jun 14, 2023

Last update date

Jun 14, 2024

Contact name

Huang JiePing

E-mail(s)

[email protected]

Organization name

Guangxi University

Street address

Xixiangtang District