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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 04, 2023 |
| Title |
mouse_brain_SIMPLE |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: brain
cell line: brain cells
cell type: brain cells
genotype: WT
treatment: No treatment
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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 deplation; 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).
The formaldehyde fixed cells are collected and re-suspended in ice cold NIB buffer for nucleosome deplation; 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 |
Illumina HiSeq 2500 |
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| Data processing |
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
Assembly: mm10
Supplementary files format and content: The genome browser track file showing the modification levels of each cluster of mouse brain cells.
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| Submission date |
May 03, 2023 |
| 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 |
GPL17021 |
| Series (1) |
| GSE197740 |
Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq |
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| Relations |
| BioSample |
SAMN34571625 |
| SRA |
SRX20210760 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7291623_Brain_5hmC_CHG_bs100kb_matrix.tar.gz |
232.6 Mb |
(ftp)(http) |
TAR |
| GSM7291623_Brain_5hmC_CPG_bs100kb_matrix.tar.gz |
166.1 Mb |
(ftp)(http) |
TAR |
| GSM7291623_Brain_5mC_CHG_bs100kb_matrix.tar.gz |
280.7 Mb |
(ftp)(http) |
TAR |
| GSM7291623_Brain_5mC_CPG_bs100kb_matrix.tar.gz |
220.5 Mb |
(ftp)(http) |
TAR |
| GSM7291623_Brain_wig.tar.gz |
606.5 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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