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| Status |
Public on Feb 08, 2023 |
| Title |
Ventral skin 2 |
| Sample type |
SRA |
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| Source name |
Finger
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| Organism |
Homo sapiens |
| Characteristics |
tissue type: skin
tissue location: Finger
tissue type: Ventral
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| Extracted molecule |
total RNA |
| Extraction protocol |
Collected tissue was flash frozen and stored at -80C. Nuclei were isolated by homogenization in EZ Nuclei Lysis Buffer, washed, and prepared for cDNA library generation.
NextSeq 1000/2000 P3 Reagents (100 cycles) v3 Kit (#20040559)
Libraries were pooled in equimolar quantities and PhiX Control v3 (#FC-110-3001) library was spiked in to the run at a concentration of ~1% to help with cluster resolution and facilitate troubleshooting in case of any problems with the run. Sequencing was run on NextSeq 2000 platform (Illumina Inc, #SY-415-1002)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Basecall data generated by the NextSeq 1000/2000 Control Software (Version 1.4.1.39716)
cellranger mkfastq was used go generated fastq
cellranger count (--include-introns --expect-cells=10,000) was used for generating the processed data files
Genome_build: GRCh38 (version 2020-A; pre-built index provided by 10x Genomics)
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, and matrix.mtx
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| Submission date |
Jan 28, 2022 |
| Last update date |
Feb 05, 2024 |
| Contact name |
Barbara Bo-Ju Shih |
| E-mail(s) |
b.shih@lancaster.ac.uk
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| Organization name |
Lancaster University
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| Department |
Biomedical and Life Sciences
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| Street address |
Bailrigg
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| City |
Lancaster |
| ZIP/Postal code |
LA1 4YW |
| Country |
United Kingdom |
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| Platform ID |
GPL30173 |
| Series (1) |
| GSE195657 |
Single nucelus RNA sequencing of 14 week EGA fetal skin |
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| Relations |
| BioSample |
SAMN25384028 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5844685_V_barcodes.tsv.gz |
12.2 Kb |
(ftp)(http) |
TSV |
| GSM5844685_V_features.tsv.gz |
325.6 Kb |
(ftp)(http) |
TSV |
| GSM5844685_V_matrix.mtx.gz |
21.6 Mb |
(ftp)(http) |
MTX |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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