|
| Status |
Public on Feb 22, 2024 |
| Title |
TH-_3 |
| Sample type |
SRA |
| |
|
| Source name |
ammocete trunk
|
| Organism |
Petromyzon marinus |
| Characteristics |
tissue: ammocete trunk
cell type: TH- control
|
| Treatment protocol |
Tissues were dissociated and fixed in paraformaldehyde followed by antibody-based selection for TH+ and TH- cells. Samples underwent reverse crosslinking prior to RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the NucleoSpin RNA SX kit (Takara), and cDNAs were synthesized using the SMARTseq v4 ultra low input kit (Takara)
RNA libraries for RNA-seq were prepared using NEBext Ultra II Kit (NEB) following manufacturer's protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were mapped to the Stowers Institute SIMRBASE Petromyzon marinus reference genome, kPetMar1.0 (https://simrbase.stowers.org/sealamprey?pane=resource-1) using Kallisto
Differential expression was determined using the DEseq2 package in R
Assembly: kPetmar1
Supplementary files format and content: tab-separated values file includes counts for each sample
|
| |
|
| Submission date |
Oct 25, 2023 |
| Last update date |
Feb 22, 2024 |
| Contact name |
Brittany Megan Edens |
| Organization name |
Caltech
|
| Street address |
1200 E California Blvd
|
| City |
Pasadena |
| State/province |
CA |
| ZIP/Postal code |
91125 |
| Country |
USA |
| |
|
| Platform ID |
GPL24751 |
| Series (1) |
| GSE246248 |
Neural crest origin of sympathetic neurons at the dawn of vertebrates |
|
| Relations |
| BioSample |
SAMN37984767 |
| SRA |
SRX22224954 |
