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| Status |
Public on Apr 20, 2023 |
| Title |
Six1-KO rep3 |
| Sample type |
SRA |
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| Source name |
otic vesicle E10.5
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
developmental stage: E10.5 mouse embryo
tissue: otic vesicle
genotype: Six1-KO
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| Extracted molecule |
total RNA |
| Extraction protocol |
E10.5 mouse embryos were obtained and the otic vesicles were removed with dissection tweezers. Total RNA from pools of vesicles (3 pools with 6 vesicles each for each genotype) was obtained using the Rneasy Micro Kit (Qiagen). Residual DNA was removed using the Turbo DNA Free Kit (Thermofisher). 10-30 ng of total RNA were used per sample for library preparation.
Libraries were constructed using the QuantSeq 3' mRNA-Seq Library Prep Kit (Illumina), following the manufacturer's instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
otic vesicles from E10.5 Six1-/- mouse embryo
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| Data processing |
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina HiSeq Control Software.
Conversion of BCL files to FASTQ format was performed with the bcl2fastq Software (Illumina).
Reads were aligned, counted, and mapped using BlueBee’s STAR-aligner, HTSeq-count, and RSEQC.
Differential gene expression analysis was performed with DESeq2 within Bluebee (Lexogen QuantSeq DE)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file includes normalised counts for each sample.
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| Submission date |
Jan 09, 2022 |
| Last update date |
Apr 20, 2023 |
| Contact name |
Ignacio Palmero |
| E-mail(s) |
ipalmero@iib.uam.es
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| Organization name |
CSIC
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| Street address |
Arturo Duperier, 4.
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| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE193334 |
Gene expression profiling of Six1-null developing inner ear. |
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| Relations |
| BioSample |
SAMN24777265 |
| SRA |
SRX13688172 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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