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| Status |
Public on Dec 31, 2021 |
| Title |
Beta2 |
| Sample type |
SRA |
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| Source name |
beta cells
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| Organism |
Danio rerio |
| Characteristics |
cell type: beta cells
developmental stage: 3mpf
genotype: Tg(ins:Brainbow1.0L)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Enzymatic Dissociation
ATAC-Seq. was carried out using 50,000 cells collected using FACS. For ATAC-Seq. of beta-cells, primary islet for dissociation was collected from Tg(ins:BB1.0L; cryaa:RFP) line and beta-cells sorted using the red fluorescence. For hepatocytes, liver for dissociation was collected from Tg(fabp10:dsRed, ela3l:GFP) line and cells collected using the red fluorescence. Cells were processed according to the protocol outlined in Buenrostro et al., Nature Methods, 2013. In brief, cells were homogenized in a 2 ml Dounce homogenizer with 5 strokes in 1X homogenization buffer on ice. The nuclei suspension was centrifuged at 500g for 10 min at 4 °C. After removing the supernatant, transposition was carried out by incubating the nuclei in the transposition reaction mix for 30 min at 37 °C. Transposed DNA was purified using Qiagen MinElute Reaction Cleanup Kit. Barcoded libraries were generated from the isolated DNA by PCR amplification for 11 cycles. Libraries were sequenced on llumina HiSeq2500 in 2 X 75 bp paired-end mode.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The raw sequencing data was trimmed using Trim Galore and mapped to GRCz11 using Bowtie2.
The sorted bam file obtained from mapping was filtered for high-quality reads (greater than or equal to 30 and Paired) and for removal of mitochrondrial reads. In addition, duplicate reads were removed using Picard MarkDuplicates.
Peak Calling was performed using Genrich.
Genome_build: Zebrafish GRCz11
Supplementary_files_format_and_content: bedGraph format, obtained from Genrich Peak Calling
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| Submission date |
Jun 10, 2020 |
| Last update date |
Dec 31, 2021 |
| Contact name |
Sumeet Pal Singh |
| E-mail(s) |
sumeetpalsingh@gmail.com
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| Phone |
+32-473-125019
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| Organization name |
ULB
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| Department |
IRIBHM
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| Lab |
Regeneration and Stress Biology
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| Street address |
Route de Lennik 808, Anderlecht
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| City |
Brussels |
| ZIP/Postal code |
1070 |
| Country |
Belgium |
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| Platform ID |
GPL18413 |
| Series (1) |
| GSE152199 |
ATAC sequencing of zebrafish pancreatic beta-cells |
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| Relations |
| BioSample |
SAMN15198495 |
| SRA |
SRX8518689 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4608942_Beta2.bedgraph.gz |
41.0 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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