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| Status |
Public on Feb 22, 2023 |
| Title |
colorectal cancer, primary tumor, sample 4 |
| Sample type |
SRA |
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| Source name |
colorectal tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: colorectal tissue
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| Extracted molecule |
total RNA |
| Extraction protocol |
For scRNA-seq, freshly resected tumors were rinsed with 1×PBS for three times, cut into small pieces and transferred to 15 mL digestion medium containing collagenase IV (1 mg/mL, C5138, Sigma-Aldrich) in DME/F-12 1:1 (70100300, Biosharp). Tissues were digested for 45 minutes at 37 ℃ under agitation at 120 rpm, afterwards, the samples were filtered using a 150 μm nylon mesh. Following the centrifugation at 450 g for 5 minutes, the supernatants were discarded and the cell pellets were resuspended in 3 mL red blood cell lysis buffer (C3702, Beyotime) at 4 ℃ for 10 minutes. After washing with 1×PBS, the cell pellets were suspended in 1×PBS containing 0.2% bovine serum albumin (4240GR500, BioFroxx) and filtered using a 74 μm nylon mesh. Single cell suspensions were stained with APC/Cy7-CD45 (HI30, BioLegend) and 7-aminoactinomycin D (7-AAD, B226396, BioLegend) for fluorescence-activated cell sorting using BD Aria ⅡI (BD Biosciences). Non-immune cells were sorted as 7-AAD-CD45-, and immune cells as 7-AAD-CD45+. For spatial transcriptome sequencing (ST-seq), The tissues were obtained from patients after resection, fixed by formalin and embedded in the paraffin. 10x FFPE gene expression slide (PN-1000185, 10x Genomics) was used for ST. Slide with 5μm FFPE section was dewaxed with xylene (214736, Sigma-Aldrich) and stained with hematoxylin (51275, Sigma-Aldrich) and eosin (HT110116, Sigma-Aldrich). After visualizing and scanning the whole slide, decrosslinking was performed using the TE buffer (10-0046, GeneMed) to release the RNA. Forward and reverse human transcriptome probes (PN-1000364, 10x Genomics) were used for probe hybridization overnight.
Single-cell library preparation was carried out according to the BD Rhapsody™ Single-Cell Whole transcriptome analysis alpha protocol (https://www.bdbiosciences.com/) and ST library were constructed according to the 10x protocol (CG000407_VisiumSpatialGeneExpressionforFFPE_UserGuide_RevA)
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
For scRNA-seq, the BD Genomics Rhapsody Targeted Analysis pipeline was used to demultiplex cellular barcodes, map reads to the reference genome.
For ST-seq, raw sequencing reads were processed with CellRanger V3 and aligned to human genome
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw UMI counts and metadata for every cells
Supplementary files format and content: H&E staining images for ST-seq tissues
Library strategy: Spatial Transcriptomics
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| Submission date |
Feb 22, 2023 |
| Last update date |
Sep 22, 2023 |
| Contact name |
Jie Long |
| E-mail(s) |
lj9358@mail.ustc.edu.cn
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| Organization name |
Guangdong Provincial People's Hospital
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| Street address |
No.106 Zhongshan 2nd Road
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| City |
Guangzhou |
| ZIP/Postal code |
510080 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE225857 |
Single-cell and spatial transcriptome analysis reveals the cellular heterogeneity of liver metastatic colorectal cancer |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM7058759_C4.barcodes.tsv.gz |
22.3 Kb |
(ftp)(http) |
TSV |
| GSM7058759_C4.features.tsv.gz |
151.6 Kb |
(ftp)(http) |
TSV |
| GSM7058759_C4.matrix.mtx.gz |
24.9 Mb |
(ftp)(http) |
MTX |
| GSM7058759_C4_aligned_fiducials.jpg.gz |
2.3 Mb |
(ftp)(http) |
JPG |
| GSM7058759_C4_detected_tissue_image.jpg.gz |
2.5 Mb |
(ftp)(http) |
JPG |
| GSM7058759_C4_scalefactors_json.json.gz |
163 b |
(ftp)(http) |
JSON |
| GSM7058759_C4_tissue_hires_image.png.gz |
6.5 Mb |
(ftp)(http) |
PNG |
| GSM7058759_C4_tissue_lowres_image.png.gz |
598.3 Kb |
(ftp)(http) |
PNG |
| GSM7058759_C4_tissue_positions_list.csv.gz |
63.9 Kb |
(ftp)(http) |
CSV |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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