|
| Status |
Public on Sep 01, 2022 |
| Title |
Section (A->P) 33 |
| Sample type |
SRA |
| |
|
| Source name |
UiPSM
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: UiPSM
|
| Treatment protocol |
UiSomitoid were forzened with liquid nitrogen after OCT embedded, and then forzen sectioned 110 slices along their anteroposterior axis
|
| Growth protocol |
Uisomitoid elongated in an Advanced DMEM/F12 supplemented with 3uM CHIR99021 and 5uM SB431542
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
he mRNA content of each interval section was extracted using Geo-seq.(Jun Chen, 2017)(Peng Guangdun's group provided experimental platform )
spatial bulk RNA-seq libraries were prepared by Geo-seq(Jun Chen, 2017)(Peng Guangdun's group provided experimental platform )
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
GEO-seq
|
| Data processing |
bcl2fastq conversion software v2.17 used for basecalling.
Raw reads were trimmed with TrimGalore (v.0.6.4)
Reads were aligned to hg38 ensembl v101 transcriptome using rsem (v1.3.1) and bowtie2 (v2.4.1) (—bowtie2—bowtie2-sensitivity-level very_sensitive— no-bam-output—estimate-rspd).
The gene expression level was calculated by using RSEM
Genome_build: hg38
|
| |
|
| Submission date |
Jul 30, 2021 |
| Last update date |
Sep 01, 2022 |
| Contact name |
Xingnan Huang |
| E-mail(s) |
huangxingnan1994@gmail.com
|
| Organization name |
Westlake University
|
| Street address |
No.18 Shilongshan Road
|
| City |
Hangzhou |
| ZIP/Postal code |
310024 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE181181 |
Human Somitoids Generated by Reprogramming Pax8+ Urine Cells [GEO-Seq] |
|
| Relations |
| BioSample |
SAMN20502643 |
| SRA |
SRX11609894 |
