 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 31, 2022 |
| Title |
D08_3CI |
| Sample type |
SRA |
| |
|
| Source name |
3D inner ear organoid
|
| Organism |
Mus musculus |
| Characteristics |
cell type: R1E derived Inner ear organoid
treatment: 3 uM CHIR + 4 uM IWP2
induction day: 8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Dissociated organoids in TrypLE. Dissociated cells were filtered through 40µM cell strainer follwed by three washes in 2% BSA/DPBS. Finally, suspended in 2%BSA/DPBS.
Single cell 3’ RNA-seq experiment is conducted using the Chromium single cell system (10x Genomics, Inc) and the NovaSeq 6000 sequencer (Illumina, Inc).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The single cell suspension was first counted on the Countess II FL for cell number, cell viability, and cell size.
Appropriate number of cells were loaded on a multiple-channel micro-fluidics chip of the Chromium Single Cell Instrument (10x Genomics) with a targeted cell recovery of 10,000.
Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v2 single cell reagent kit (10X Genomics).
Following cell capture and cell lysis, cDNA was synthesized and amplified. Illumina sequencing library was then prepared with the amplified cDNA. The resulting library was sequenced using a custom program on Illumina NovaSeq 6000.
CellRanger 3.1.0 was utilized to process the raw sequence data generated. Briefly, CellRanger used bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample-specific FASTQ files
Genome_build: mm10
Supplementary_files_format_and_content: Processed data were analized with the Rpackage Seurat (version 2.3.1) with Rstudio version 1.1.453 and R version 3.5.1
|
| |
|
| Submission date |
Jul 14, 2021 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Pei-Ciao Tang |
| E-mail(s) |
peictang@med.miami.edu
|
| Phone |
3373260631
|
| Organization name |
University of Miami
|
| Department |
Otolayrngology
|
| Street address |
1501 NW 10th Avenue, Miami, FL 33136, 926 F2
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE180062 |
Wnt signaling promotes cell caudalization and inner ear differentiation in mouse stem cell-derived organoids |
|
| Relations |
| BioSample |
SAMN20207158 |
| SRA |
SRX11438999 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5452185_D08_3CI_barcodes.tsv.gz |
77.6 Kb |
(ftp)(http) |
TSV |
| GSM5452185_D08_3CI_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM5452185_D08_3CI_matrix.mtx.gz |
150.4 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
