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| Status |
Public on May 01, 2024 |
| Title |
Mouse_KI_E14.5_Pinna_rep2 |
| Sample type |
SRA |
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| Source name |
pinna
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| Organism |
Mus musculus |
| Characteristics |
tissue: pinna
genotype: Knock-In (KI)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Forming pinna prominences from E14.5 embryos (both wild type and mEC1dup/dup) were microdissected, washed with cold 1× PBS, and homogenized using a Tissue-Tearor. RNA extraction was performed according to the manufacturer’s protocol (RNeasy Mini Kit, Qiagen, 74104).
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
E145KI2
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| Data processing |
RNA sequencing reads were initially processed using fastp for trimming of the paired-end data, with quality assessment performed via FASTQC. Subsequently, the reads were aligned to the mouse reference genome (GRCm39) using the STAR aligner. Quantification of the alignment files was carried out using featureCounts, incorporating the gene model parameter. Differential gene expression analysis was conducted utilizing the limma, Glimma, and edgeR packages
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
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| Submission date |
Apr 02, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Xu Xiaopeng |
| E-mail(s) |
xu_xiaopeng@gzlab.ac.cn
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| Organization name |
Guangzhou National Laboratory
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| Street address |
96 Xingdao South Road, Guangzhou International Bio Island, Haizhu District
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| City |
Guangzhou |
| ZIP/Postal code |
510320 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE263086 |
Regulatory Functional Landscape of the HMX1 Gene for Normal Ear Development [RNA-seq] |
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| Relations |
| BioSample |
SAMN40731261 |
| SRA |
SRX24137038 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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