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| Status |
Public on Nov 23, 2021 |
| Title |
S1_ant |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Adjacent non-tumor
condition: NAFLD
Sex: Female
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Frozen biposies were homgogenized in lysis buffer, filtered and washed, suspended, and processed with a 10X Chromium using the Single Cell 3' v3 library prep.
10X Single Cell 3' v3
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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 |
Template switch oligo, primer, and polyA sequences of at least 20 bp in length were trimmed from the fastq files.
Reads were aligned to the hg38 genome using STARsolo from STAR v2.7.3a.
Empty and contaminated droplets were removed using DIEM. Doublets were removed by clustering and manual identification of doublet clusters.
Clustering was performed using Seurat with SCTransform and CCA integration.
Genome_build: hg38
Supplementary_files_format_and_content: Text files in matrix market format
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| Submission date |
Nov 19, 2021 |
| Last update date |
Nov 23, 2021 |
| Contact name |
Marcus Alvarez |
| E-mail(s) |
malvarez@mednet.ucla.edu
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| Organization name |
UCLA
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| Department |
Human Genetics
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| Lab |
Pajukanta
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| Street address |
695 Charles E Young Dr South, Gonda 6335
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL30982 |
| Series (1) |
| GSE189175 |
Single-nucleus RNA-seq of NASH HCC liver tissue |
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| Relations |
| BioSample |
SAMN23314705 |
| Supplementary data files not provided |
| Processed data are available on Series record |
| Raw data not provided for this record |
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