|
| Status |
Public on Aug 07, 2023 |
| Title |
snRNA-seq of 6hpf S. purpuratus embryos |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo nuclar extract
|
| Organism |
Strongylocentrotus purpuratus |
| Characteristics |
tissue: whole embryo nuclear extract
developmental stage: 6hpf
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclear isolation protocol adapted from Omni-ATAC-seq protocol (Corces et al., 2017). Full protocol in Meyer et al 2021, biorxiv
Single nuclei libraries were created using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 RevD (10X Genomics) and the Chromium X instrument (10X Genomics) using manufacturer protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10X Genomics
|
| Data processing |
Cell Ranger V4.0.0 (Zheng et al., 2017) was used to create aligned to a pre- mRNA indexes for P. miniatagenome V3.0 (GenBank assembly accession: GCA_015706575.1) andS. purpuratusgenome V5.0 (GenBank assembly accession: GCA_000002235.4). The pre-mRNA indices were constructed using gene annotation files modified by an in-house script to remove intron annotations. Read were aligned using the cellranger count command. The raw, unfiltered count files are presented in this GEO entry. In the P. miniata entries, note that when applicable, the gene names are consistant with the names of their 1:1 othologs in S. purpuratus, as is consistant with the gene page naming system of echinobase.org
A Standard Seurat processing pipeline (V4.2.0 ) was used to prepare the final .RDS atlases provided in this entry.
Assembly: P miniatagenome V3.0 (GenBank assembly accession: GCA_015706575.1); S. purpuratusgenome V5.0 (GenBank assembly accession: GCA_000002235.4)
Supplementary files format and content: annotated and processed S. purpuratus developmental atlas in .RDS format
|
| |
|
| Submission date |
Aug 04, 2023 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Hinman Veronica |
| E-mail(s) |
veronica@cmu.edu
|
| Organization name |
Carnegie Mellon University
|
| Department |
Biological Sciences
|
| Lab |
Hinman Lab
|
| Street address |
587 S Negley Ave, Apt 17
|
| City |
PITTSBURGH |
| State/province |
PA |
| ZIP/Postal code |
15232 |
| Country |
USA |
| |
|
| Platform ID |
GPL29871 |
| Series (2) |
| GSE240144 |
single nucleus RNA-seq of early development S. purpuratus |
| GSE240146 |
single nucleus RNA-seq of early development in P. miniata and S. purpuratus |
|
| Relations |
| BioSample |
SAMN28492965 |
| SRA |
SRX15625923 |
