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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 01, 2022 |
| Title |
S9Rosa26A-P8 |
| Sample type |
SRA |
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| Source name |
Inner ear
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| Organism |
Mus musculus |
| Characteristics |
genotype: Reporter expressing ATOH1 induced P8 cochlear cells
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| Treatment protocol |
Tamoxifen administered at P1 samples analyzed at P8, Tamoxifen administered at P8 samples analyzed at P15,
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| Growth protocol |
Sox9CreER; Rosa26-tdtomato; Rosa26 A/GA/GAP/+ mice were bred
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| Extracted molecule |
total RNA |
| Extraction protocol |
Papain dissociation of cells, FACS on red channel
In brief, a single cell suspension was loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) in which full length cDNA was synthesized and barcoded. Subsequently the GEMS are broken and cDNAs from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads (Thermo Fisher, 370020), cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Finally, PCR amplification was carried out to produce the library.
Single cell 3’ RNA seq libraries were prepared using the Chromium single cell 3’ reagent kit v3 (10x Genomics).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
S9Rosa26A-P8
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| Data processing |
The libraries were sequenced on the NovaSeq 6000 System using a S1 flowcell. Library quantification by qPCR and Bioanalyzer - A qPCR assay was performed on the libraries to determine the concentration of adapter ligated fragments using the Applied Biosystems ViiA 7 Quantitative PCR instrument and a KAPA Library Quant Kit (p/n KK4824). All samples were pooled at equimolar amounts and re-quantitated by qPCR, and re-assessed on the Bioanalyzer. Using the concentration from the ViiA7 TM qPCR machine above, 300pM of pooled library was loaded onto a NovaSeq S1 flowcell (Illumina p/n 20012865), using the Standard Workflow loading conditions designated by the manufacturer and amplified by exclusion amplification (ExAMP) for patterned flowcells using the Illumina NovaSeq 6000 sequencing instrument. PhiX Control v3 adapter-ligated library (Illumina p/n FC110-3001) was spiked-in at 1% by weight to ensure balanced diversity and to monitor clustering and sequencing performance. A paired end run, using 28 cycles for Read 1, 8 cycles for Index 1 Read and 91 cycles for Read 2 was set to sequence the flowcell on a NovaSeq 6000 Sequencing System to achieve a minimum of approximately 300M reads per sample. FastQ file generation and QC assessment was achieved using the 10X Cell Ranger software for 10X Chromium Platforms.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Aug 16, 2021 |
| Last update date |
Aug 01, 2022 |
| Contact name |
Andrew K Groves |
| Organization name |
Baylor College of Medicine
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| Street address |
One Baylor Plaza, Baylor College of Medicine
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE182202 |
Single cell transcriptomic analysis of P8 and P15 mouse cochlea (control and three overexpression conditions) and simultaneous single cell transcriptomic and accessible chromatin analysis of P1 and P8 mouse cochlea (wildtype) |
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| Relations |
| BioSample |
SAMN20811219 |
| SRA |
SRX11780892 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5520357_s9_rosa26A_p8.tar.gz |
106.5 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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