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| Status |
Public on Feb 28, 2023 |
| Title |
PBMC_SIMPLE |
| Sample type |
SRA |
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| Source name |
human PBMCs
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| Organism |
Homo sapiens |
| Characteristics |
cell type: human peripheral blood mononuclear cells
treatment: untreated
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| Growth protocol |
Naive mouse Embryonic Stem Cells (mESCs ) were regularly maintained on the pre-gelatinized dishes without feeders, supplemented with two inhibitors (2i): 1 mM PD0325901 (Selleckchem), 3 mM CHIR99021 (Selleckchem) in the presence of 1,000 U/ml leukemia inhibitory factor (LIF, Millipore) and 20% fetal bovine serum (FBS, GIBCO) in Dulbecco’s modified eagle’s medium (DMEM/F-12, GIBCO). Primed mouse Embryonic Stem Cells (mESCs) were cultured with DMEM F12 (GIBCO) with 20% FBS (GIBCO) and 1,000 U/ml LIF (Millipore). Human PBMCs were purchased form AllCells. Cultured cells or PBMCs are harvested and washed with fresh media, then re-suspended in 10mL no-serum media before proceeding to SIMPLE-seq experiments
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The formaldehyde fixed cells are collected and re-suspended in ice cold NIB buffer for nucleosome depilation; the nuclei pellets were tagmentated with identical barcoded assembled Tn5 followed 2 rounds of Ligation-based combinatorial barcoding; nuclei were lysed and gDNA purified with 1X SPRI beads; next, performs Second adaptor tagging and 5hmC transition and hmC-to-T recording; after the primer extension reaction, the dsDNA is subjected into 5mC specific labelling; the final library is amplified by Kapa HiFi uracil plus DNA polymerase and used 1.8X Ampure XP beads to purify the product. The final libraries were sequenced using a MGI-2000 platform (MGI) with the following read lengths: PE 150 + 8 + 150 (Read 1 + Index 1 + Read 2).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
MGISEQ-2000RS |
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| Description |
SIMPLE-seq
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| Data processing |
library strategy: SIMPLE-seq
Cut adapter step: The raw FASTQ files are firstly but the sequencing adapters with cutadapt software
Alignment step: After the cut adapter step, all the FASTQ files are mapped to the reference genome
BAM convert step:The alignment SAM results are converted to sorted BAM files with samtools software
5hmC_CPG_bs100kb_matrix.tar.gz is the cell-to-modification levels matrix for individual cells, each row is a genomic region and each column is a cell, the value in the matrix is the average modification levels of all 5hmCPG in the genomic region. This file is generated by custom script by calculating the average modification levels in each single cell.
5mC_CHG_bs100kb_matrix.tar.gz is the cell-to-modification levels matrix for individual cells, each row is a genomic region and each column is a cell, the value in the matrix is the average modification levels of all 5mCHG in the genomic region. This file is generated by custom script by calculating the average modification levels in each single cell.
5mC_CPG_bs100kb_matrix.tar.gz is the cell-to-modification levels matrix for individual cells, each row is a genomic region and each column is a cell, the value in the matrix is the average modification levels of all 5mCPG in the genomic region. This file is generated by custome script by calculating the average modification levels in each single cell.
The 5hmC_CHG_bs100kb_matrix.tar.gz is the cell-to-modification levels matrix for individual cells, each row is a genomic region and each column is a cell, the value in the matrix is the average modification levels of all 5hmCHG in the genomic region. This file is generated by custom script by calculating the average modification levels in each single cell.
The PBMC_10_states.tar.gz is generated with chromHMM software, by integrating 5mC and 5hmC modification levels in CPG, CHG and CHH contents in 5-kb non-overlapping bins.
wig.tar.gz are wig files showing the 5mC/5hmC modification levels of invididual sites that can be visuallized with genomic browser. This is file is generated by custom script by calculating the average modification levels of individual sites in all cells.
Genome_build: hg39,mm10
Supplementary_files_format_and_content: mESC_5hmC_CHG_bs100kb_matrix.tar.gz: The cell-to-modification levels matrix for 5hmCHG sites in mES cells. mESC_5hmC_CPG_bs100kb_matrix.tar.gz: The cell-to-modification levels matrix for 5hmCPG sites in mES cells. mESC_5mC_CHG_bs100kb_matrix.tar.gz: The cell-to-modification levels matrix for 5mCHG sites in mES cells. mESC_5mC_CPG_bs100kb_matrix.tar.gz: The cell-to-modification levels matrix for 5mCPG sites in mES cells. mESC_wig.tar.gz: The genome browser track file showing the modification levels of each cluster of mES cells. PBMC_10_states.tar.gz: The processed cytosine state files generated by chromHMM software. PBMC_5hmC_CHG_bs100kb_matrix.tar.gz: The cell-to-modification levels matrix for 5hmCHG sites in PBMC cells. PBMC_5hmC_CPG_bs100kb_matrix.tar.gz: The cell-to-modification levels matrix for 5hmCPG sites in PBMC cells. PBMC_5mC_CHG_bs100kb_matrix.tar.gz: The cell-to-modification levels matrix for 5mCHG sites in PBMC cells. PBMC_5mC_CPG_bs100kb_matrix.tar.gz: The cell-to-mod ification levels matrix for 5mCPG sites in PBMC cells. PBMC_wig.tar.gz: The genome browser track file showing the modification levels of each cluster of PBMC cells.
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| Submission date |
Mar 02, 2022 |
| Last update date |
Apr 10, 2024 |
| Contact name |
Dongsheng Bai |
| E-mail(s) |
baidongsheng@pku.edu.cn
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| Phone |
13261502638
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| Organization name |
Peking University
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| Department |
School of Life Sciences
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| Lab |
Chengqi Yi
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| Street address |
Yiheyuan Road,No 5
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL30209 |
| Series (1) |
| GSE197740 |
Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq |
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| Relations |
| BioSample |
SAMN26365943 |
| SRA |
SRX14353267 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5929313_PBMC_5hmC_CHG_bs100kb_matrix.tar.gz |
119.7 Mb |
(ftp)(http) |
TAR |
| GSM5929313_PBMC_5hmC_CPG_bs100kb_matrix.tar.gz |
97.7 Mb |
(ftp)(http) |
TAR |
| GSM5929313_PBMC_5mC_CHG_bs100kb_matrix.tar.gz |
138.7 Mb |
(ftp)(http) |
TAR |
| GSM5929313_PBMC_5mC_CPG_bs100kb_matrix.tar.gz |
142.8 Mb |
(ftp)(http) |
TAR |
| GSM5929313_PBMC_wig.tar.gz |
762.9 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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