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| Status |
Public on Aug 10, 2022 |
| Title |
LI_bulk3 |
| Sample type |
SRA |
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| Source name |
large intestine
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| Organism |
mouse gut metagenome |
| Characteristics |
tissue: large intestine
Sex: male
age: 6 weeks
strain: C57BL/6
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| Extracted molecule |
total RNA |
| Extraction protocol |
10x Genomics, Visium Spatial, Rev B for ST and TRIzol Reagent (#15596026, InvitrogenTM) for total RNA isolation extraction
The spatial gene libraries were constructed using Visium Spatial Library Construction kit (10X Genomics,PN-3000394). The cDNA was break into fragments of about 200-300bp, add poly(A) tails and connected the P7 adapter, 3’ end sequencing was performed using Illumina Novaseq 6000 sequencer with a sequencing depth of at least 100,000 reads per spot with pair-end 150 bp (PE150) reading strategy.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
bulk.taxa.tsv
TS2010CLZM
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| Data processing |
SpaceRanger 1.0.0
blastn 2.10.1+
phyloseq 1.32.0
Seurat 4.0.1
Assembly: mm10-3.0.0
Supplementary files format and content: rds was created from Seurat object in R
Supplementary files format and content: tsv was generated from blast output
Library strategy: Spatial Transcriptomics
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| Submission date |
Aug 08, 2022 |
| Last update date |
Aug 10, 2022 |
| Contact name |
seqcore sii |
| E-mail(s) |
seqcore_sii@126.com
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| Organization name |
Shanghai Jiao Tong University School of Medicine
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| Street address |
Southern Chongqing Road
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| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
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| Platform ID |
GPL32553 |
| Series (1) |
| GSE210738 |
Spatial transcriptomics revealing host-microbe interactions |
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| Relations |
| BioSample |
SAMN24114615 |
| SRA |
SRX13425802 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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