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| Status |
Public on Jan 01, 2024 |
| Title |
WT+CDAHFD |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
treatment: CDAHFD
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| Extracted molecule |
total RNA |
| Extraction protocol |
Pulmonary artery tissues were placed in DMEM/F12(Gibco), and cut into small fragments and digested them with collagenase II (Invitrogen) for 2h at 37℃. After digestion, the obtained cells were filtered through a 70μm filter and collect it into a collection tube.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria: MT% < 10%; Cell Gene Number < Median Gene Number * 2; Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: Single cell matrix files
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| Submission date |
Sep 13, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Jiangtao Fu |
| E-mail(s) |
yczxfjt@hotmail.com
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| Organization name |
Naval medical university
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| Street address |
Guohe Road 325
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| City |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
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| Relations |
| BioSample |
SAMN37384606 |
| SRA |
SRX21768196 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7779062_WT-NASH.barcodes.tsv.gz |
50.3 Kb |
(ftp)(http) |
TSV |
| GSM7779062_WT-NASH.features.tsv.gz |
245.4 Kb |
(ftp)(http) |
TSV |
| GSM7779062_WT-NASH.matrix.mtx.gz |
81.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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