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| Status |
Public on Aug 14, 2023 |
| Title |
WT CLP ATAC-seq Rep 1 |
| Sample type |
SRA |
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| Source name |
bone marrow
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| Organism |
Mus musculus |
| Characteristics |
cell type: CLP
genotype: WT
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq libraries were generated using 1000 sorted cells
ATAC-seq barcoded libraries were constructed as previously described (Wu et al., 2018)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
For ATAC-seq and RNA-seq data, quality assessment of raw reads was achieved with FastQC and contaminants were removed using Trimgalore with parameters ‘-q 30 --length 30 --stringency 5’.
ATAC-seq: The clean paired-end reads were aligned to the mm10 reference genome by Bowtie2 with the parameters -D 20 -R 3 -N 0 -L 20 -i S,1,0.50. All unmapped reads, reads mapped to the mitochondrial genome, PCR duplicates and nonuniquely mapped reads were discarded. Peaks were called using the above filtered reads by MACS with the parameters --nolambda–nomodel.
RNA-seq: The clean paired-end reads were aligned to the mm10 reference genome by Tophat with the parameter --no-novel-juncs. Gene expression levels and differentially expressed genes between samples were calculated with Cuffdiff and visualized with the R package cummeRbund.
For scRNA-seq data, sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads. TopHat was applied to align clean reads to the mm10 reference genome. Uniquely aligned reads were counted by the tool ‘htseq-count’ of HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: text files include FPKM values for each sample
Supplementary_files_format_and_content: text files include UMI counts for each single cell
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| Submission date |
Jul 04, 2020 |
| Last update date |
Aug 14, 2023 |
| Contact name |
Zihan Xu |
| E-mail(s) |
xuzihan0910@gmail.com
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| Organization name |
Peking University
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| Street address |
No.5 Yiheyuan Road Haidian District
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE153804 |
PTEN regulates chromatin accessibility and hematopoietic lineage plasticity via the transcription factor PU.1 |
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| Relations |
| BioSample |
SAMN15448140 |
| SRA |
SRX8666892 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4654380_macs2_s6_peaks.narrowPeak.gz |
1.4 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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