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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 19, 2024 |
| Title |
Fn-1 |
| Sample type |
SRA |
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| Source name |
Fn administration
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| Organism |
Mus musculus |
| Characteristics |
the mice model: C57BL/6J wild-type mice
treatment type: colorectal tumor tissues Fn administration
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| Treatment protocol |
C57BL/6J wild-type (WT) mice were housed and reared in specific pathogen free and barrier conditions with autoclaved food and water. The body weight of mice was measured every week. For AOM/DSS model, 6- to 7-week-old male mice were treated with metronidazole(2mg/ml) in drinking water for 5 consecutive days to ensure the consistency of regular microbiota and facilitate Fn colonization. PBS-resuspended 109 CFU Fn or PBS were administrated into mice by gavage every other day. Then mice were given a single intraperitoneal injection of carcinogen azoxymethane at 12 mg/kg body weight. After 8 days of intraperitoneal injection, 2% dextran sodium sulfate (DSS) was added in the drinking water for 7 consecutive days. Then mice were given regular drinking water. After a week, mice were again given 2% dextran sodium sulfate in drinking water for 7 consecutive days. During the DSS intervention, the bacteria administration was suspended. Bacteria, or PBS administration was given for a period of 10 weeks. To investigate the effect of related therapy on the Fn induced gut tumor progression, At the indicated time intervals, the mice were anaesthetized with 40 mg/kg pentobarbital sodium and sacrificed for tumor statistics.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Chromium™ Single Cell 3'Solution is a microfluidics platform built on GemCode technology that combines gel beads with barcodes and primers. Individual cells are encapsulated in oil droplets to form GEM(Gel bead in emulsion).The gel beads in the GEM dissolve and the cells cleave to release mRNA, which is then reverse transcribed to produce cDNA with barcodes for sequencing. After the liquid oil layer is destroyed, cDNA amplification reaction is carried out. After purification, quality inspection is carried out.
Enzymatic digestion interrupted the fragments, end patching was carried out, and base A was added to connect the joints, and the target size fragments were recovered for library quality inspection and quantification.
10X scRNA-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Mouse CRC tissue was obtained from wild-type C57 mice with AOM/DSS model
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| Data processing |
Using Cell, the official 10X Genomics analysis software Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) to the raw data to identify the data filtering, alignment, quantitative, recycling cells, Finally, the gene expression matrix of each cell was obtained.
The Seurat (https://satijalab.org/seurat/) for further cell filtration, standardization, the classification of the cells, each subgroup analysis and Marker gene screening differentially expressed genes.
Genome_build: Mus_musculus.GRCm38.96
Supplementary_files_format_and_content: Sample name.gz:contains three files:barcodes.tsv.gz,features.tsv.gz and matrix.mtx.gz.
Supplementary_files_format_and_content: cell_batch.tsv.gz:includes cell - sample correspondence.
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| Submission date |
Apr 19, 2021 |
| Last update date |
Apr 19, 2024 |
| Contact name |
Xie qin |
| E-mail(s) |
qxie@lc-bio.com
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| Phone |
15618926050
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| Organization name |
LC sciences
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| Street address |
Minchi first road, pujiang town, minhang district, Shanghai
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| City |
shanghai |
| ZIP/Postal code |
200000 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE172334 |
Fusobacterium nucleatum Induces PD-L1 Expression by Tumor-Associated Macrophages and Inhibits Anti-Tumor Immunity in Colorectal Cancer. |
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| Relations |
| BioSample |
SAMN18796591 |
| SRA |
SRX10635693 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5252780_Fn-1.tar.gz |
66.6 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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