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Sample GSM6436180

Query DataSets for GSM6436180

Status

Public on Aug 10, 2022

Title

SI_bulk1

Sample type

SRA

Source name

small intestine

Organism

mouse gut metagenome

Characteristics

tissue: small intestine
Sex: male
age: 6 weeks
strain: C57BL/6

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.

Library strategy

OTHER

Library source

transcriptomic

Library selection

other

Instrument model

Illumina NovaSeq 6000

Description

bulk.taxa.tsv
TS2010CLZM

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

Submission date

Aug 08, 2022

Last update date

Aug 10, 2022

Contact name

seqcore sii

E-mail(s)

[email protected]

Organization name

Shanghai Jiao Tong University School of Medicine

Street address

Southern Chongqing Road