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| Status |
Public on Jan 15, 2024 |
| Title |
Zebrafish_batch2_male1 |
| Sample type |
SRA |
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| Source name |
Whole body, wild-type strain AB, 4 month-old
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| Organism |
Danio rerio |
| Characteristics |
tissue: whole body
strain: strain AB
genotype: wild-type
age: 4 months
Sex: male
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| Treatment protocol |
Hypothermal shocked
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were subjected to manual pulverization via grinded in liquid nitrogen. The pulverized tissues were aliquoted into 1.5 ml lysis buffer [10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sangon Biotech), 0.1% IGEPAL-CA630 (Sigma Aldrich) and 0.01% Digitonin (Thermo Scientific) in water], and followed by incubation for 3 minutes on ice for nuclei extraction.
Library preparations were performed with the CH ATAC-seq protocol
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| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
DNBSEQ-T7 |
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| Description |
CH ATAC-seq
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| Data processing |
For each sequenced CHATAC-seq library, we obtained two FASTQ files, one of which contained combinatorial index for HY(768 indices) and Tn5 (384 indices) in specific base positions. We filtered reads with more than one mismatch in each index and trimmed adaptor sequences using trimmomatic(version 0.3.8). After that, reads from zebrafish were aligned to D. rerio danRer11 genome(UCSC) using BWA (version 0.7.15). Taking the 9-bp duplication caused by Tn5 transposase into account, we shifted aligned reads + 4bp and -5bp for each positive and negative strand using alignmentSieve(deeptools 3.5.1).Then we used snaptools(version 1.4.8) to keep nonduplicate fragments with high mapping quality (MAPQ > 30) and proper length(<1000 bp) and extracted fragment files from the snap files. Subsequent analysis was performed by ArchR (version 1.0.2). We created arrow files from fragment files by ‘createArrowFiles function’ and constructed customized genome using ‘createGenomeAnnotation’ and ‘createGeneAnnotation function’.
Assembly: D. rerio danRer11 genome(UCSC)
Supplementary files format and content: BED files recording coordinates of fragments captured by scATAC-seq
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| Submission date |
May 09, 2023 |
| Last update date |
Jan 15, 2024 |
| Contact name |
Guoji Guo |
| Organization name |
Center for Stem Cell and Regenerative Medicine
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| Department |
Zhejiang University School of Medicine
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| Street address |
Yuhangtang street 866
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| City |
Hanzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL30277 |
| Series (2) |
| GSE232043 |
Construction of zebrafish chromatin accessibility landscape at a single-cell level using CH-ATAC-seq |
| GSE232162 |
Construction of a cross-species chromatin accessibility landscape at a single-cell level using CH-ATAC-seq |
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| Relations |
| BioSample |
SAMN35007766 |
| SRA |
SRX20263976 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7310838_Zebrafish_batch2_male1_fragment.bed.gz |
911.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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