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| Status |
Public on Apr 14, 2024 |
| Title |
SPATAC-seq with zebrafish embryogenesis well-ZB2SL07B (DNBSEQ-T7) |
| Sample type |
SRA |
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| Source name |
zebrafish embryos
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| Organism |
Danio rerio |
| Characteristics |
tissue: zebrafish embryos
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryo nuclei were extracted via previously described methods (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019) with some modifications. Briefly, frozen embryos were transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 1 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 200 μl NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB.
Bulk ATAC-seq, 10x Genomics scATAC-seq, and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-T7 |
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| Description |
ZB2SL07B_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file
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| Data processing |
Raw Read1 Fastq files within genome DNA (position from 66-121 nucleotide) were extracted and renamed as new Read1 file. Similarly, raw Read2 Fastq files within genome DNA (position from 51-101 nucleotide) were extracted and renamed as new Read2 file. Round 1, round2 and round3 barcodes are extracted from Read1 and Read2 Fastq files, and are merged and were added into the header of new Read1 and Read2 files. New Read1 and Read2 files were aligned to the reference zebrafish GRCz11 genome assemblyby BWA. The scATAC-seq fragment files were created by sinto (https://timoast.github.io/sinto/index.html) according to standard procedure. Barcodes in fragment file of each sublibrary were tagged with Round4 barcodes (PCR wells), then all sublibrary fragment files were merged into one big fragment file, which were further split into stage-specific fragment files based on Round1 barcodes. For the bulk ATAC-seq data from zebrafish embryos, reads were trimmed with to remove the Nextera sequencing adaptors by trim_galore. The trimmed reads were mapped to the reference zebrafish (GRCz11) genome using BWA. Reads with mapping quality less than 30 and duplication were removed by samtools. BigWig files were generated by bamCoverage. Fastq files of 10x Genomics scATAC-seq were processed Cell Ranger ATAC Pipeline (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac, v.1.2.0).
Assembly: GRCz11
Supplementary files format and content: bed files, the fragment file of SPATAC-seq, the information of each unique fragment of SPATAC within each sublibrary, including the chromsome number, start site, end site and frequency.
Supplementary files format and content: bed files, the fragment file of 10x Genomics scATAC-seq, the information of each unique fragment within each sample, including the chromsome number, start site, end site and frequency.
Supplementary files format and content: bed files, the fragment file of bulk ATAC-seq, the information of each unique fragment, including the chromsome number, start site, end site
Supplementary files format and content: excel file, cell metadata information for the atlas of zebrafish development, including cell types, coordinate and quality metric of each cell
Supplementary files format and content: bigWig file, genome-wide signal for 604 cell types of scATAC-seq datasets
Supplementary files format and content: bigWig file, genome-wide signal for bulk ATAC-seq of zebrafish embryos
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| Submission date |
Sep 14, 2023 |
| Last update date |
Apr 14, 2024 |
| Contact name |
Keyong Sun |
| E-mail(s) |
keyongsuntsinghua@gmail.com
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| Organization name |
tsinghua university
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| Department |
School of Medicine
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| Street address |
Hai Dian street
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| City |
beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL30277 |
| Series (1) |
| GSE243256 |
Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq |
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| Relations |
| BioSample |
SAMN37412997 |
| SRA |
SRX21788221 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7782249_ZB2SL07B_SPATACseq_Batch2.bed.gz |
250.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
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