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Sample GSM5719324 Query DataSets for GSM5719324
Status Public on Nov 09, 2022
Title alveolar macrophage, NC-2, ATAC-seq
Sample type SRA
 
Source name NC-2
Organism Sus scrofa
Characteristics cell type: alveolar macrophage
treatment: control
Treatment protocol The cell viability of porcine alveolar macrophages (3D4/21) cells treated with different concentrations (0, 10, 20, 30, 40, 50, and 60μg/mL) of FB1 at different culture time points (24, 48, and 72 h) was measured on a Tecan Infinit 200 microplate reader (Tecan) platform using the Cell CountingKit-8 (CCK-8) kit (Dojindo), and finally 50μg/mL FB1 was induced for 24 h as the optimal treatment concentration and action time to investigate the cytotoxicity of FB1 on 3D4/21 cells. Porcine alveolar macrophages were seeded in 6-well plates at a density of 5 × 105 cells/mL and cultured in a 5% CO2 incubator at 37℃ for 24 h. FB1 at a final concentration of 50 µg/mL was added to the culture medium of the experimental wells, and the same amount of enzyme-free water was added to the culture medium of the control wells.
Growth protocol Porcine alveolar macrophages (3D4/21) were cultured in RPMI-1640 (Gibco) medium containing 10% fetal bovine serum (Gibco) and 1% antibiotics (penicillin (100 U/mL), streptomycin (0.1 mg/mL) (Beijing Solarbio Science & Technology Co., Ltd.) at 37℃ in a saturated humidity constant temperature incubator continuously supplied with 5% CO2.
Extracted molecule genomic DNA
Extraction protocol The cell samples were collected and the nuclei were extracted, and the transposable mixture containing Tn5 transposase was added to the nuclear suspension for transposable reaction.
Tn5 transposase entered the nucleus and preferentially cleaved exposed DNA in the open region of chromatin, while ligating specific sequencing adaptor. The DNA fragments ligated with adaptors were amplified by PCR, and the amplified PCR products were purified with the Qiagen MinElute kit and sequenced by Gene Denovo Biotechnology Company (Guangzhou, China).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description ATAC-seq.NC_2ca
Data processing Data quality control was performed on ATAC-seq raw reads obtained from the sequencer before information analysis, and low-quality reads containing adapter reads, reads containing more than 10% unknown nucleotides (N), and low-quality reads containing more than 50% low quality (Q-value≤20) bases were removed to obtain high quality clean reads. The processed reads were aligned to the pig reference genome (release Sscrofa11.1) using Bowtie2 v2.2.8 with reads aligned to mitochondrial genome discarded, and reads that are uniquely aligned were used for subsequent analysis. The distribution map of insert fragments of each sample was drawn by ATACseqQC. DeepTools was used to visualize the read distribution flanking transcription start sites (TSSs). Peak calling was performed using MACS v2.1.2 with a threshold of q-value < 0.05. Only the common peaks among replicates (with overlap more than 50%) were retained for analysis. Peak annotation was performed using ChIPseeker v1.16.1.
We used fastp v0.18.0for quality control and data filtering of raw reads from rRNA-depleted library, to remove reads containing adapters, with a N-containing proportion greater than 10%, with all A bases, or with bases with Q-value≤20 accounting for more than 50% of the whole reads. The processed reads were aligned to the pig reference genome (release Sscrofa11.1) using HISAT2 v2.1.0. To examine the relationship among different samples, Principal component analysis (PCA) was performed using R package gmodels (http://www.rproject.org/). Differentially expressed genes were identified by DESeq2, with cut-off: FDR<0.05 and foldChange≥2. The raw data of small RNA library was filtered to remove low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides (N) in the data, to filter out reads without 3 'adapters, to filter out reads containing 5' adapters, and to filter out reads containing poly A. All clean tags were searched to identify known porcine miRNAs (exist miRNAs) using the miRbase database (release 22).
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Peak calling was performed using MACS v2.1.2. Peak annotation was performed using ChIPseeker v1.16.1
Supplementary_files_format_and_content: LncRNA_CodeGenesExpression_fpkm.csv
Supplementary_files_format_and_content: all_mirna_tpm.xlsx
 
Submission date Dec 06, 2021
Last update date Nov 09, 2022
Contact name 靳 健
E-mail(s) jiayao.jiang7@gmail.com
Phone 18860895953
Organization name 扬州大学
Street address 扬州大学荷花池校区
City 扬州
State/province 江苏
ZIP/Postal code 225000
Country China
 
Platform ID GPL22475
Series (1)
GSE190291 Transcriptomic and chromatin accessibility analyses of porcine alveolar macrophages exposed to Fumonisin B1
Relations
BioSample SAMN23705695
SRA SRX13328057

Supplementary file Size Download File type/resource
GSM5719324_NC_2ca_peaks.csv.gz 888.6 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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