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| Status |
Public on Nov 27, 2024 |
| Title |
adult_green_anole_lizard_saccule_snATAC |
| Sample type |
SRA |
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| Source name |
inner ear saccule
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| Organism |
Anolis carolinensis |
| Characteristics |
tissue: inner ear saccule
cell type: mixed
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For 14 dpf zebrafish, heads from converted Sox10:Cre; ubb:LOXP-EGFP-LOXP-mCherry fish were decapitated at the level of the pectoral fin with eyes and brains removed. For 12 mpf zebrafish, utricle, saccule, and lagena were extracted from converted Sox10:Cre; ubb:LOXP-EGFP-LOXP-mCherry fish after brains and otolith crystals were removed. For adult lizard, saccules were extracted from lizard heads and otoconia crystals were removed. Dissected heads and otic sensory patches were then incubated in fresh Ringer’s solution for 5–10 min, followed by mechanical and enzymatic dissociation by pipetting every 5 min in protease solution (0.25% trypsin (Life Technologies, 15090-046), 1 mM EDTA, and 400 mg/mL Collagenase D (Sigma, 11088882001) in PBS) and incubated at 28.5 °C for 20–30 min or until full dissociation. Reaction was stopped by adding 6× stop solution (6 mM CaCl2 and 30% fetal bovine serum (FBS) in PBS). Cells were pelleted (376 × g, 5 min, 4 °C) and resuspended in suspension media (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, and 0.05 mg/mL streptomycin (Sigma-Aldrich, St. Louis, MO) in phenol red-free Leibovitz’s L15 medium (Life Technologies)) twice. Final volumes of 500 μL resuspended cells were placed on ice and fluorescence-activated cell sorted (FACS) to isolate live cells that excluded the nuclear stain DAPI
10X Genomics Chromium Next GEM Single Cell ATAC Library and Gel Bead Kit v1.1 (14 dpf zebrafish) or Single Cell Multiome ATAC + Gene Expression kit (12 mpf zebrafish and adult lizard)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
10x Genomics multiome snATAC library
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| Data processing |
Base calling and sample were demultiplexed by bcl2fastq performed by the single cell sequencing and CyTOF core at Chilren's Hospital Los Angeles
Zebrafish sequences were alinged to danRer11 and UMI counts were created using cellranger-atac count v2 (14dpf) or cellranger-arc count v2.0.0 (12mpf). Lizard sequences were aligned to AnoCar2.0v2 and UMI counts were created using cellranger-arc count v2.0.0
Downstream analysis was performed in R using Seurat v5.0.1 and Signac v1.12.0 and in Unix Shell using deepTools
Assembly: danRer11/GRCz11 and AnoCar2.0v2
Supplementary files format and content: .h5 files of filtered barcode feature count matrix for each individual library
Supplementary files format and content: .bigwig files of 14 dpf and 12 mpf zebrafish hair and supporting cell pseudo-bulk ATAC tracks
Supplementary files format and content: .tsv and .tbi files of snATAC fragments required to visualize ATAC coverage in R
Library strategy: snATAC-seq (14dpf zebrafish) and Single Cell Multiome ATAC + Gene Expression (12 mpf zebrafish and adult lizard)
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| Submission date |
Aug 01, 2024 |
| Last update date |
Nov 27, 2024 |
| Contact name |
Tuo Shi |
| E-mail(s) |
[email protected]
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| Phone |
6264913123
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| Organization name |
University of Southern California
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| Street address |
1425 San Pablo St BCC 403
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| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90033 |
| Country |
USA |
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| Platform ID |
GPL34767 |
| Series (1) |
| GSE273764 |
Long-range Atoh1 enhancers maintain competency for hair cell regeneration in the inner ear |
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| Relations |
| BioSample |
SAMN42993086 |
| SRA |
SRX25568222 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8436611_lizard_atac_fragments.tsv.gz |
2.6 Gb |
(ftp)(http) |
TSV |
| GSM8436611_lizard_atac_fragments.tsv.gz.tbi.gz |
817.9 Kb |
(ftp)(http) |
TBI |
SRA Run Selector |
| Raw data are available in SRA |
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