|
| Status |
Public on Oct 01, 2024 |
| Title |
56, coccyx, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Coccyx
|
| Organism |
Xenopus tropicalis |
| Characteristics |
cell type: Coccyx
genotype: WT
time: stage 56
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Laser capture microdissection of targeted tissues which were frozen in OCT. RNA extractions followed the spatial transcriptomic protocol, Geo-seq using the TAKARA NucleoSpin® RNA XS kit.
cDNA and libraries were generated using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (with the number of amplification cycles set to 18).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequence quality was checked using FastQC and, Adapter sequences were trimmed using Cutadapt (version 1.8.1)
Trimmed sequences were mapped to Xenopus_tropicalis_v9.1 to impelement a normal alignment using HTSeq v.0.13.5.
Read count extraction and normalization were performed using HTSeq2
Assembly: Xenopus_tropicalis_v9.1
Supplementary files format and content: Tab deliminated text files with gene counts for each sample
|
| |
|
| Submission date |
Aug 10, 2023 |
| Last update date |
Oct 01, 2024 |
| Contact name |
Gayani Senevirathne |
| E-mail(s) |
msenevirathne@fas.harvard.edu
|
| Organization name |
Harvard University
|
| Department |
Human Evolutionary Biology
|
| Street address |
11 Divinity Avenue
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL23182 |
| Series (2) |
| GSE240548 |
Molecular basis of Urostyle development [RNA-seq] |
| GSE243236 |
Molecular basis of Urostyle development |
|
| Relations |
| BioSample |
SAMN36935216 |
| SRA |
SRX21329168 |
