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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 11, 2022 |
| Title |
FST-1 |
| Sample type |
SRA |
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| Source name |
cochlea
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| Organism |
Mus musculus |
| Characteristics |
cell type: cochlear epithelial cell
treatment: FST overexpression
time point: expansion for 7 days
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| Treatment protocol |
To induce and maintain FST and or LIN28B transgene expression, expansion media contained doxycycline hyclate (0.5 μg/mL)
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| Growth protocol |
Dissociated cochlear epithelial cells isolated from 5-day old mice were cultured at high density within a drop of Matrigel matrix in expansion medium prepared with DMEM/F12 , N2 supplement , B-27 supplement, EGF, FGF2, CHIR99021, VPA, and penicillin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Organoids were washed once with 1x PBS, after which they were treated with Cell Recovery solution to dissolve Matrigel matrix. Organoids were pelleted and total RNA was extracted using the miRNeasy Micro Kit (Qiagen, no. 217084).
Samples were processed using Illumina's TruSeq stranded Total RNA kit, per manufacturer's recommendations, using the UDI indexes. The samples were sequenced on the Illumina NovaSeq 6000, paired end, 2x50 bp reads
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Basecalling using Illumina NovaSeq 6000 RTA3
RNAseq reads were aligned to the GRCm38 mouse transcriptome using Kallisto v0.46.1
RNAseq read abundance quantifications were performed using Kallisto v0.46.1
Genome_build: GRCm38 mouse transcriptome
Supplementary_files_format_and_content: h5 abundance files
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| Submission date |
May 13, 2021 |
| Last update date |
Feb 11, 2022 |
| Contact name |
Angelika Doetzlhofer |
| E-mail(s) |
[email protected]
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| Organization name |
Johns Hopkins University School of Medicine
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| Department |
Neuroscience
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| Street address |
855 North Wolfe St
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE174406 |
Follistatin promotes LIN28B mediated supporting cell reprogramming and hair cell regeneration in the murine cochlea |
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| Relations |
| BioSample |
SAMN19160808 |
| SRA |
SRX10869584 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5294986_Fst1_abundance.h5 |
58.8 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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