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| Status |
Public on May 06, 2024 |
| Title |
Mesentery, 9 dpi with WT H18N11, bat 1 |
| Sample type |
SRA |
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| Source name |
Mesentery
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| Organism |
Artibeus jamaicensis |
| Characteristics |
tissue: Mesentery
breed: outbreed
Sex: male
health condition: healthy
treatment: infected with WT H18N11
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| Extracted molecule |
total RNA |
| Extraction protocol |
The small and large intestines were cut longitudinally to expose the lumen, intestines were then cut into 0.5 to 1.0 cm pieces and washed four times with 10 mL wash solution consisting of 1×PBS, 5 mM EDTA under vigorous shaking. Subsequently, 20mL of predigestion buffer (Hanks' balanced salt solution (HBSS) containing 20mM HEPES, 5mM EDTA, 5% fetal calf serum (FCS) and 1mM Dithiothreitol (DTT)) were added and incubated at 37°C for 20minutes with constant rotation. After vortexing for 10 sec, the pieces were drained through a 70-µm cell strainer and the supernatant was saved. Cells in the supernatant were washed three times by adding wash solution and subsequent centrifugation at 350g for 5min. The predigestion step was then repeated as described above. After the second round of predigestion, 20mL of HBSS containing 20mM HEPES was added to the intestinal pieces and incubated for 20 min under continuous rotation followed by vigorous vortexing for 10sec. The pieces were sieved through a 70-µm cell strainer, and the supernatant was washed with wash solution as described above. All cell fractions contained epithelial cells and were pooled. Intestinal pieces were resuspended in digestion buffer (HBSS with 20mM HEPES, 1.25mM CaCl2, 1mM MgCl2, 5mM EDTA, 5% FCS, Lamina Propria Dissociation Kit enzymes D, R, and A, were added according to the manufacture’s protocol) and incubated at 37°C for 30 min with constant rotation. The intestinal tissue was transferred into a gentleMACS C Tube and processed with a gentleMACS using the manufacturer’s program. Perfusion solution was added and the pieces were strained through a 70-µm cell strainer. The supernatant was processed and washed as described above. This second fraction contained the cells of the lamina propria. Intraepithelial and lamina propria fractions of each bat were counted using trypan blue and cells were mixed in a 1:1 ratio for each bat. To prepare a single-cell suspension of the mesentery, the mesentery was tamped through a cell strainer in a Petri dish containing 5 mL of perfusion solution.
A total of 12,000 cells per sample were processed with a Chromium Next GEM Single Cell 5' Kit v2 (10x Genomics) to achieve a recovery of at least 8000 cells.
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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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| Data processing |
A custom reference genome, appending H18N11 sequences to the Artibeus jamaicensis genome (Cold Spring Harbor Laboratories genome, NCBI RefSeq assembly GCF_021234435.1), was built with cellranger (v 6.1.2) using mkref function.
cellRanger count function was used to process the fastq files using default parameter settings.
Assembly: CSHL_Jam_final
Supplementary files format and content: raw h5 file including feature count per sample
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| Submission date |
Sep 25, 2023 |
| Last update date |
May 06, 2024 |
| Contact name |
Tony Schountz |
| E-mail(s) |
tony.schountz@colostate.edu
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| Organization name |
Colorado State University
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| Street address |
3185 Rampart Rd
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| City |
Fort Collins |
| ZIP/Postal code |
80523 |
| Country |
USA |
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| Platform ID |
GPL33786 |
| Series (1) |
| GSE243982 |
Deciphering bat influenza H18N11 infection dynamics in Jamaican fruit bats on a single cell level |
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| Relations |
| BioSample |
SAMN37538774 |
| SRA |
SRX21884208 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7802739_ML9dpi1_filtered_feature_bc_matrix.h5 |
2.0 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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