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| Status |
Public on Mar 27, 2024 |
| Title |
Crypts, High-fat diet, Vertical sleeve gastrectomy |
| Sample type |
SRA |
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| Source name |
Small intestinal epithelial crypts
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| Organism |
Mus musculus |
| Characteristics |
tissue: Small intestinal epithelial crypts
diet: High-fat diet
treatment: Vertical sleeve gastrectomy
strain: Wildtype C57BL/6J
Sex: Male
age: ~ 30-weeks-old
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| Extracted molecule |
total RNA |
| Extraction protocol |
Small intestinal epithelial samples were freshly collected and flushed with ice-cold PBS to remove luminal contents. Intestinal segments were opened longitudinally and placed in individual tubes containing cold DMEM before immediate processing with a solution of 3mM EDTA in PBS for cell dissociation. During processing in the EDTA/PBS solution, the intestinal segments were manually scrapped and subsequently filtered through a 70 µm cell strainer to separate crypts from villi. For single-cell dissociation, the crypts and villi were resuspended separately in a cold solution of 0.04% bovine serum albumin (BSA)/PBS, followed by processing with 0.3 U/ml dispase/HBSS, DNAse1/FBS, and 0.04% BSA/PBS solutions. The viability of and number of dissociated crypt and villus cells were measured using the ThermoFisher ViCell counter, with an average viability of 71% for crypts and 66% for villus cells. Approximately 3.0 x 10^7 crypt cells and 3.5 x 10^7 villus cells from each sample were pooled (n=3 for LFD-sham and HFD-sham, n=2 for HFD-VSG) and diluted to a concentration of 1000 cells/µL.
Single-cell library preparation was performed using the 10x Genomics Chromium Next GEM 3' v3.1 kit following the manufacturer's instructions.
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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 |
Demultiplexing, FASTQ generation and alignment, barcode/UMI processing, and gene counting were performed using Cell Ranger v.6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values (.tsv) and matrix (.mtx) files from raw and filtered feature-barcode matrices generated by Cell Ranger v.6.0.0
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| Submission date |
Jun 05, 2023 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Kieran Koch-Laskowski |
| E-mail(s) |
klk246@cornell.edu
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| Organization name |
Cornell University
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| Department |
Biomedical Sciences
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| Lab |
Sethupathy Lab
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| Street address |
618 Tower Road, VRT #T7006
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE234189 |
Intestinal epithelial adaptations to vertical sleeve gastrectomy defined at single-cell resolution |
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| Relations |
| BioSample |
SAMN35625903 |
| SRA |
SRX20595920 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7453707_HFD_VSG_Crypts_filtered-barcodes.tsv.gz |
49.9 Kb |
(ftp)(http) |
TSV |
| GSM7453707_HFD_VSG_Crypts_filtered-features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM7453707_HFD_VSG_Crypts_filtered-matrix.mtx.gz |
91.2 Mb |
(ftp)(http) |
MTX |
| GSM7453707_HFD_VSG_Crypts_raw-barcodes.tsv.gz |
8.7 Mb |
(ftp)(http) |
TSV |
| GSM7453707_HFD_VSG_Crypts_raw-features.tsv.gz |
254.1 Kb |
(ftp)(http) |
TSV |
| GSM7453707_HFD_VSG_Crypts_raw-matrix.mtx.gz |
204.4 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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