|
| Status |
Public on May 01, 2024 |
| Title |
wt_4d_RNAseq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
bone-marrow-derived macrophage
|
| Organism |
Mus musculus |
| Characteristics |
cell type: bone-marrow-derived macrophage
genotype: WT
treatment: Osteoclastic differentiation
time: Day 4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent kit(Invitrogen). Total RNA transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530)
Genomic DNA was extracted after tagementation of Tn5 transposome. Barcoded libraries were then amplified with PCR reactions (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme)
Genomic DNA was extracted after tagementation of PAG-Tn5 and the libraries were constructed with CUT&Tag Assay Kit (pAG-Tn5) for illumina, (Abclonal)
Total RNA transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530)
ATAC-seq libraries were then amplified with PCR reactions (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme)
CUT&Tag libraries were constructed with CUT&Tag Assay Kit (pAG-Tn5) for illumina, (Abclonal)
RNA-seq; ATAC-seq; CUT&Tag
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired-end 150 bp reads of RNA-seq data were aligned to mm9 genome reference (UCSC) using STAR alignment tool (version 2.7.3a) . Uniquely mapped reads were employed to quantify gene expression using RSEM software (version 1.3.1) . Transcripts per million mapped reads (TPM) were calculated to estimate the gene expression levels, normalized for sequencing depth. Euclidean distance based on TPM values were used to evaluate the similarities across biological replicates. Differential gene expression (DGE) analysis was performed using DESeq2 R package
Raw reads of ATAC-seq data were trimmed using TrimGalore (version 0.6.1). Trimmed reads were aligned to mm9 genome reference (UCSC) using Bowtie2 aligner.uniquely mapped reads were employed to carry out peak calling using MACS2. Genomic distribution of ATAC peaks was annotated by “ChIPseeker” R package
The CUT&Tag reads were aligned to the mm10 genome by using Bowtie2. Low-mapping-quality reads were filtered by SAMtools (v.1.9), and duplicate reads were removed by Picard tools (v1.90).MACS2 (41) was used to call peaks with a q-value < 0.01. BigWig files were generated by deeptools (46) by theRPKM normalization method and visualized in igv (v.2.13.1)
Assembly: mm9，mm10
|
| |
|
| Submission date |
May 08, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Zhaoming Ye |
| E-mail(s) |
yezhaoming@zju.edu.cn
|
| Organization name |
The Second Affiliated Hospital, Zhejiang University School of Medicine
|
| Street address |
88 jiefang road
|
| City |
hangzhou |
| ZIP/Postal code |
310031 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE231933 |
The chromatin remodeling factor Arid1a cooperates with Jun/Fos to promote osteoclastogenesis by epigenetically upregulating Siglec15 expression |
|
| Relations |
| BioSample |
SAMN34998640 |
| SRA |
SRX20253218 |
