|
| Status |
Public on Sep 11, 2024 |
| Title |
WNTi (batch A) |
| Sample type |
SRA |
| |
|
| Source name |
Brain organoid
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain organoid
cell line: HMGU1
cell type: Neural progenitors and neurons
treatment: control
|
| Treatment protocol |
FGF8 100ng/ML in culture medium; See Materials and Merthods in original paper
|
| Growth protocol |
See Materials and Merthods in original paper
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Organoids were freshly collected at day 69 and dissociated with Papain; See Materials and Merthods in original paper
scRNA-seq libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit v.2 (10x Genomics, PN-120237). Final cDNA libraries were checked for quality and quantified using 2100 Bioanalyzer (High Sensitivity DNA Assay; Agilent Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
FastQ files of each sample were processed with Cell Ranger count pipeline (10X Genomics) version 6.1.1, that performs alignment, filtering, barcode counting, and UMI counting, using the pre-processed Homo sapiens reference GRCh38-2020-A (GENCODE v32/Ensembl 98) from 10X Genomics.
See Materials and Merthods in original paper for further details
Assembly: Homo sapiens reference GRCh38-2020-A (GENCODE v32/Ensembl 98)
Supplementary files format and content: Tab separated values files and matrix files
|
| |
|
| Submission date |
Sep 06, 2024 |
| Last update date |
Sep 11, 2024 |
| Contact name |
Michele Bertacchi |
| E-mail(s) |
mbertacchi@unice.fr, Michele.BERTACCHI@univ-cotedazur.fr
|
| Phone |
+33489150721
|
| Organization name |
iBV - Institut de Biologie Valrose
|
| Lab |
Studer Lab
|
| Street address |
28, avenue Valrose
|
| City |
Nice |
| State/province |
Provence Alpes Côte d Azur |
| ZIP/Postal code |
06108 |
| Country |
France |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE276558 |
FGF8-mediated gene regulation affects regional identity in human cerebral organoids |
|
| Relations |
| BioSample |
SAMN43524165 |
| SRA |
SRX25998052 |
