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| Status |
Public on May 04, 2024 |
| Title |
THP1_PMA24_rep1_ATACseq |
| Sample type |
SRA |
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| Source name |
THP1 human AML cells
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| Organism |
Homo sapiens |
| Characteristics |
treatment: PMA 100nM
time point: 24h
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| Growth protocol |
Cells were grown in RPMI (Corning, 15-040-CV) with 10% dialyzed fetal bovine serum (Sigma, F0392), 4mM glutamine, and 1% penicillin/streptomycin (Corning, 45000-652).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For THP1 cells, cells were stained with a final concentration of 1 ng/ml DAPI in growth media, and 200,000 live cells were sorted using a BD FACSAria and placed on ice. 50,000 cells were then processed using the Active Motif ATACseq kit (cat. 53150).
For THP1 cells, libraries were constructed using the dual index barcodes included in the Active Motif ATAC-seq kit (cat. 53150), except that after the PCR amplification, libraries were size selected with 1.5X SPRI beads instead of 1.2X SPRI beads in order to retain smaller fragments. Libraries were then quantified using Qubit and Bioanalyzer analysis, pooled, and sequenced using an Illumina NextSeq 500.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ATACseq
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| Data processing |
Mouse and human data were trimmed using Cutadapt (v3.4) (with parameters -m 20 -q 20 -a CTGTCTCTTATA -A CTGTCTCTTATA), then aligned to the mm10 and hg38 genomes with Bowtie2 v2.4.2 (with parameters --dovetail -I 10 -X 1000 --very-sensitive).
Reads in the mitochondrial genome and unannotated chromosomes as well as the UCSC blacklist were removed, then duplicates were removed with samtools markdup (v1.1.2), and the insert size distribution was calculated using Picard CollectInsertSizeMetrics (v2.25.2) and validated to contain nucleosomal peaks. BED file was then constructed with each mate pair as a separate read using bedtools bamtobed (v2.3.0), and peaks were called using MACS2 callpeak (v2.2.7.1) (with parameters --nomodel --shift -100 --extsize 200 --keep-dup all --call-summits). Note that the MACS2 command shifts each read by 100 base pairs towards the 5’ end and extends the read length to 200 base pairs, thus treating the 5’ end of the original read (the Tn5 cut site) as the center of a new “fragment” that is then used for peak calling and other downstream analysis.
To normalize tracks, reads overlapping shared peaks were counted for each BAM file using featureCounts (with parameters -M -O) and normalization factors were calculated from these counts using the calcNormFactors function in the edgeR package (v3.32.1) in R. Visualization was performed using the bedGraphToBigWig utility and the igv-jupyter package in Python.
Genome_build: hg38
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files for each sample
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| Submission date |
Apr 19, 2021 |
| Last update date |
May 04, 2024 |
| Contact name |
Brian Do |
| E-mail(s) |
bdo311@gmail.com
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| Organization name |
MIT
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| Department |
Biology
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| Lab |
Vander Heiden
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| Street address |
500 Main St
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE172299 |
A myeloid maturation program initiated by nucleotide depletion during S phase [ATAC-Seq] |
| GSE172335 |
Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress |
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| Relations |
| BioSample |
SAMN18795067 |
| SRA |
SRX10632338 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5252086_THP1_PMA24_rep1_ATACseq.bw |
211.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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