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| Status |
Public on Nov 28, 2024 |
| Title |
AD3 |
| Sample type |
SRA |
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| Source name |
terminal ileum tissues
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| Organism |
Homo sapiens |
| Characteristics |
tissue: terminal ileum tissues
disease state: atopic dermatitis
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples were processed as follows: First, they were washed with phosphate-buffered saline (PBS) and then minced into small pieces (approximately 1mm3) on ice. Next, they were enzymatically digested using 285 U/mL collagenase I (Worthington), 355 U/mL collagenase II (Worthington), 0.5 U/mL Dispase II (Sigma), and 50 U/mL DNase I (Worthington) for 45 min at 37°C with agitation. After digestion, the samples were sieved through a 70µm cell strainer and then centrifuged at 300g for 5 min. Following the removal of the supernatant, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse any remaining red blood cells. The cell pellets were then washed with PBS containing 0.04% BSA and re-suspended in the same buffer. The samples were then re-filtered through a 35μm cell strainer to ensure single-cell dissociation. The dissociated single cells were stained with AO/PI to assess cell viability using the Countstar Fluorescence Cell Analyzer.
For the scRNA-Seq libraries, the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10X Genomics, Pleasanton, CA) were used.
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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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| Description |
10x Genomics
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| Data processing |
Single-cell RNA-seq data analysis was performed by NovelBio Co.,Ltd. with NovelBrain Cloud Analysis Platform (www.novelbrain.com).
Assembly: mm10
Supplementary files format and content: Supplementary_files
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| Submission date |
Mar 24, 2023 |
| Last update date |
Nov 28, 2024 |
| Contact name |
yalan wu |
| E-mail(s) |
[email protected]
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| Phone |
+8618520264095
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| Organization name |
guang zhou university of China medicine
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| Street address |
guangzhou
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| City |
guangzhou |
| ZIP/Postal code |
00000 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE228148 |
Gene expression profile at single cell level of terminal ileum tissues from healthy humans and atopic dermatitis |
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| Relations |
| BioSample |
SAMN33905386 |
| SRA |
SRX19766583 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7115129_AD3_barcodes.tsv.gz |
32.2 Kb |
(ftp)(http) |
TSV |
| GSM7115129_AD3_features.tsv.gz |
290.3 Kb |
(ftp)(http) |
TSV |
| GSM7115129_AD3_matrix.mtx.gz |
31.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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