|
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 |