 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 23, 2024 |
| Title |
E10.5, GFP-only, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
hindbrain
|
| Organism |
Mus musculus |
| Characteristics |
cell type: neurons
tissue: hindbrain
strain: C57BL/6J
age: E10.5
condition: GFP-only
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The hindbrains of embryos were dissected in ice-cold HEBG media (0.8X B27, 0.25X GlutaMAX in Hibernate E media). For each timepoint, at least 3 embryos were collected for each two independent replicates. Tissues were incubated with Worthington Papain solution at 37°C for 30 min at 800 rpm. At the end of incubation, the samples were transferred to 15 mL falcon tube, followed by gentle trituration with serologic pipette. The cell pellets were collected by centrifuge at 200 rcf for 3 min at 4°C, washed and resuspended in ice-cold sorting buffer (PBS with 0.05% fetal bovine serum). The single-cell resuspension was loaded to 30 µm cell drainer to remove debris, followed by DAPI staining at RT for 5 min. GFP+DAPI-, GFP+TdTom+DAPI-, or TdTom+DAPI- cells were sorted by Sony SH800S. The cells were pelleted by centrifuge at 200 rcf for 5 min at 4°C and resuspended in sorting buffer to make the final concentration of 1,000 cells/µL.
The cDNA libraries were constructed by 10x Genomics 3’ v3.1 kit following the user guide. Briefly, ~16,500 cells from one sample were mixed with reversed transcription master mix before loaded into Chromium Chip G. GEM containing cells, reversed transcription reagents, and barcoded gel beads were generated by Chromium Controller. The first strand cDNA was amplified, fragmentated, and ligated with sequencing adaptors and sample indices.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 with default settings.
Assembly: customized genome composed of mouse mm10 reference genome and WPRE sequence
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
May 31, 2023 |
| Last update date |
Jun 24, 2024 |
| Contact name |
Huda Zoghbi |
| E-mail(s) |
hzoghbi@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Street address |
1250 Moursund St
|
| City |
Houston |
| State/province |
Tx |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE233856 |
A single cell transcriptomic map of the developing Atoh1-lineage uncovers neural fate decisions and neuronal diversity in the hindbrain.[RNA-Seq] |
| GSE233966 |
A single cell transcriptomic map of the developing Atoh1-lineage uncovers neural fate decisions and neuronal diversity in the hindbrain. |
|
| Relations |
| BioSample |
SAMN35548395 |
| SRA |
SRX20558665 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7438096_E10.5_rep1_barcodes.tsv.gz |
50.2 Kb |
(ftp)(http) |
TSV |
| GSM7438096_E10.5_rep1_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM7438096_E10.5_rep1_matrix.mtx.gz |
161.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
