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| Status |
Public on Jul 19, 2022 |
| Title |
Day5_DTR_Utricle_scATACseq |
| Sample type |
SRA |
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| Source name |
Regenerating adult zebrafish utricle
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| Organism |
Danio rerio |
| Characteristics |
strain: myo6b:hDTR
embryo age: 6-10 month old adult zebrafish
treatment: 0.05 ng/ul Diphtheria Toxin
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For single-cell experiments, non-regenerating (untreated) and regenerating inner ears (saccule and utricle) were dissected at consecutive time-points and dissociated into single-cells using trypsin and collagenase. For bulk ATAC-seq experiments, untreated inner ears (saccule and utricle) were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers.
For scRNA-seq, cDNA libraries were generatated with Chromium Controller and Chromium Single Cell 3' GEM, Library and Gel Bead Kit V3 (10x Genomics). For scATAC-seq, libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit (1000111, 10X Genomics). For bulk ATAC-seq, libraries were generated using Nextera DNA Library Preparation Kit (Catalog # FC-121-1030). Transposed DNA were amplified by PCR with indexed primers and libraries were purified.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Data processing |
Binary Base Call (BCL) files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 (10x Genomics). Cell Ranger Version 3.0.2 (10x Genomics) was used to demultiplex, for barcode processing, for single cell gene counts, for single-cell accessibility counts, and aggregating files. For bulk ATAC-seq, libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC-seq reads were aligned to reference zebrafish genome (danRer11) using bowtie2. Peaks were called by MACS2 from individual replicate.
Genome_build: danRer11
Supplementary_files_format_and_content: scRNA-seq and scATAC-seq outputs were generated using the 10x Cell Ranger pipeline. scRNA-seq H5 (filtered feature bc matrix) files contain the UMI counts for each cell. scATAC-seq processed data files include three file formats per sample: CSV, TBI, and H5. CSV (singlecell.csv) files contain per barcode QC information associated with the fragments per barcode, ATAC signal per barcode, and cell calling information. TBI (Fragments.tsv.gz.tbi) files are tabix index of the fragment intervals. H5 (filtered peak bc matrix.h5) files contain only detected cellular barcodes. For bulk ATAC-seq, narrowPeak files contain MACS2 called peaks in BED format.
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| Submission date |
Jan 03, 2022 |
| Last update date |
Jul 19, 2022 |
| Contact name |
Erin Jimenez |
| E-mail(s) |
erin.jimenez@nih.gov, erinjimenez9@gmail.com
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| Phone |
4433702563
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| Organization name |
NIH
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| Department |
NHGRI
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| Lab |
Shawn Burgess
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| Street address |
50 South Drive
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL25922 |
| Series (1) |
| GSE192947 |
A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish |
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| Relations |
| BioSample |
SAMN24588408 |
| SRA |
SRX13584935 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5769461_Day5_DTR_U_filtered_peak_bc_matrix.h5 |
11.0 Mb |
(ftp)(http) |
H5 |
| GSM5769461_Day5_DTR_U_fragments.tsv.gz.tbi.gz |
297.2 Kb |
(ftp)(http) |
TBI |
| GSM5769461_Day5_DTR_U_singlecell.csv.gz |
2.5 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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