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| Status |
Public on Mar 16, 2022 |
| Title |
17_Skin_CompoundHetero_rep1 |
| Sample type |
SRA |
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| Source name |
skin
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Col7a1 E2857X mut X Col7a1 5818delC mut
cell type: Live skin cells
age: post natal day 14
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| Extracted molecule |
total RNA |
| Extraction protocol |
After euthanasia, back skins were removed from palm and dissociated into single cells by the Liberase enzyme.
RNA-seq library was constructed using a modified smart-seq2 protocol. Cells were sorted into 384-well plates with barcoded oligo dT primer for each well (1 cell / well). After reverse transcription in each well, cDNA was pre-amplified using the Accel-NGS 1S Plus DNA Library Kit (Swift Biosciences, Ann Arbor, MI, USA). Purified cDNAs were tagmentationed with Amplicon Tagment enzyme (Illumina) and PCR for library construction was done by using NEBNext High-Fidelity 2× PCR Master Mix (NEB).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Description |
SCI239_33_S33
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| Data processing |
Sequencing outputs were demultiplexed using bcl2fastq2 (https://jp.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)
Fastq files were aligned to Mus musculus GRCm38 reference using STAR aligner (2.7.6a; https://github.com/alexdobin/STAR)
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Processed data files are zipped STAR output directory (Solo.out).
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| Submission date |
Aug 02, 2021 |
| Last update date |
Mar 18, 2022 |
| Contact name |
Takashi Shimbo |
| E-mail(s) |
[email protected]
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| Organization name |
Osaka university
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| Street address |
2-2 Yamadaoka
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| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
5650871 |
| Country |
Japan |
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| Platform ID |
GPL30172 |
| Series (1) |
| GSE181357 |
Single cell RNA-seq for a mouse model of recessive dystrophic epidermolysis bullosa |
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| Relations |
| BioSample |
SAMN20524366 |
| SRA |
SRX11633205 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5495194_SCI239_33_S33.tar.gz |
785.1 Kb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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