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| Status |
Public on Sep 23, 2024 |
| Title |
Larvae, 42 hours post fertilization |
| Sample type |
SRA |
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| Source name |
Larvae
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| Organism |
Heliocidaris erythrogramma |
| Characteristics |
tissue: Larvae
age: 42 hours post fertilization
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspensions were prepared, to do this, larvae were washed twice in calcium-free artificial seawater (CFASW) then resuspended in dissociation buffer [1.0 M glycine and 0.25 mM EDTA (pH 8.0)] at 4°C. The embryos were then dissociated by gentle trituration. Following dissociation, cells were resuspended in CFASW, and fixed at a final concentration of 80% methanol in CFASW for 1 h, at 4°C. Following fixation, cells were stored at −20°C and all cell libraries were processed within 1 month of dissociation.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kits v3.1 (10X Genomics) according to the manufacturer's protocol. Briefly, single cells were encapsulated into Gel Bead-In-Emulsions (GEMs) using the Chromium Controller, followed by reverse transcription, cDNA amplification, and library construction.
Libraries were titered and pooled at Duke University’s Sequencing and Genomic Technologies Core Facility, then sequenced in one S1 flow cell on an Illumina NovaSeq 6000 with 28 x 8 x 91 bp.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10X Genomics
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| Data processing |
Raw sequencing data was processed using the Cellranger 3.1.0 pipeline (10X Genomics) to generate FASTQ files.
FASTQ files were aligned to the reference genome (H. erythrogramma 1.0 Genome) and gene expression matrices were generated using Cell Ranger.
Quality control, normalization, and clustering were performed using Seurat (v4.0).
Differential expression analysis was conducted using the FindMarkers function in Seurat.
Assembly: GCA_025617745.1 (Davidson et al., 2022)
Supplementary files format and content: Processed data files are provided in TSV and MTX format, containing gene expression matrices. TSV files include files with cell metadata and gene annotations.
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| Submission date |
Sep 18, 2024 |
| Last update date |
Sep 23, 2024 |
| Contact name |
Alejandro Berrio |
| E-mail(s) |
alebesc@gmail.com
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| Phone |
5123489070
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| Organization name |
Duke University
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| Department |
Biology
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| Lab |
Wray
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| Street address |
124 Science Dr
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| City |
DURHAM |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platform ID |
GPL34915 |
| Series (1) |
| GSE277518 |
Contrasting the development of larval and adult body plans during the evolution of biphasic lifecycles in sea urchins |
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| Relations |
| BioSample |
SAMN43816518 |
| SRA |
SRX26119858 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8523872_He_42hpf_barcodes.tsv.gz |
22.5 Kb |
(ftp)(http) |
TSV |
| GSM8523872_He_42hpf_features.tsv.gz |
288.4 Kb |
(ftp)(http) |
TSV |
| GSM8523872_He_42hpf_matrix.mtx.gz |
12.8 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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