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| Status |
Public on Aug 07, 2023 |
| Title |
Skin - Gut axis, scRNAseq 2 |
| Sample type |
SRA |
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| Source name |
whole colon
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| Organism |
Mus musculus |
| Characteristics |
tissue: whole colon
cell type: section of the large intestine
strain: C57BL/6 back ground mouse
treatment: N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly collected whole colon were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissues were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2.5 mg/mL Collagenase D and 30 ng/mL DNAse1) and incubated at 37 °C for 40 min. Tissues were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
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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 |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (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 files and matrix files
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| Submission date |
Mar 21, 2023 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Tatsuya Dokoshi |
| E-mail(s) |
ta1983@hotmail.com
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| Organization name |
Univeristy of California, San Diego
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| Department |
Department of Dermatology
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| Street address |
9500 Gilman
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| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
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| Relations |
| BioSample |
SAMN33845198 |
| SRA |
SRX19741531 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7109550_K14_colon_v7.tar.gz |
73.4 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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