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| Status |
Public on May 31, 2019 |
| Title |
R1E_D35-WT |
| Sample type |
SRA |
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| Source name |
3D inner ear organoid
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| Organism |
Mus musculus |
| Characteristics |
cell type: Inner ear organoid
developmental stage: Day 35
derived strain: 129X1x129S1
genotype/variation: Wild-Type_R1/E
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| Extracted molecule |
total RNA |
| Extraction protocol |
Dissociated organoids in TrypLE. Dissociated cells were filtered through 40µM cell strainer followed by three washes in 2% BSA/DPBS. Finally, suspended in 2%BSA/DPBS.
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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
scRNA-seq
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| Data processing |
Single cell 3’ RNA-seq experiment is conducted using the Chromium single cell system (10x Genomics, Inc) and the NovaSeq 6000 sequencer (Illumina, Inc).
Cell Ranger 2.1.0 was utilized to process the raw sequence data generated. Briefly, Cell Ranger used bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample-specific FASTQ files.
Processed data were analyzed with the R package Seurat (version 2.3.1) with RStudio version 1.1.453 and R version 3.5.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx files.
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| Submission date |
May 02, 2019 |
| Last update date |
Jun 01, 2019 |
| Contact name |
Pei-Ciao Tang |
| E-mail(s) |
peictang@med.miami.edu
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| Phone |
3373260631
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| Organization name |
University of Miami
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| Department |
Otolayrngology
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| Street address |
1501 NW 10th Avenue, Miami, FL 33136, 926 F2
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| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE130649 |
Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids |
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| Relations |
| BioSample |
SAMN11567346 |
| SRA |
SRX5783494 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3746280_R1E_D35-WT_barcodes.tsv.gz |
35.7 Kb |
(ftp)(http) |
TSV |
| GSM3746280_R1E_D35-WT_genes.tsv.gz |
212.7 Kb |
(ftp)(http) |
TSV |
| GSM3746280_R1E_D35-WT_matrix.mtx.gz |
39.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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