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| Status |
Public on Aug 26, 2020 |
| Title |
CBS2 [Nanopore] |
| Sample type |
SRA |
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| Source name |
Mouse hippocampus
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| Organism |
Mus musculus |
| Characteristics |
tissue: hippocampus
strain: C57BL/6
developmental stage: 2 months old
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The Visium Spatial Tissue Optimization Slide & Reagent kit (10X Genomics, Pleasanton, CA, USA) was used to optimize permeabilization conditions for mouse brain tissue. Spatially barcoded full-length cDNA was generated using Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics) following the manufacturer’s protocol. Tissue permeabilization was performed for 6 and 9 min (CBS1, CBS2) and 12 min (MOB). cDNA amplification was conducted with 12 (CBS) and 17 (MOB) cycles.
10µl of cDNA library followed 10x Genomics Visium library preparation protocol of fragmentation, adapter ligation, and indexing. The libraries were sequenced on a NextSeq500 (Illumina), with 28 bases from read 1 and 91 from read 2.
Nanopore sequencing libraries were prepared with the LSK-109 kit from Oxford Nanopore (1 µg cDNA) following the instructions from the manufacturer. PromethION flowcells were loaded with 200 ng library each. PCR amplifications for Nanopore library preparations were made with Kapa Hifi Hotstart polymerase (Roche Sequencing Solutions): initial denaturation, 3 min at 95°C; cycles: 98°C for 30 sec, 64°C for 30 sec, 72°C for 5 min; final elongation: 72°C for 10 min, primer concentration was 1 µM.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
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| Description |
Visium Spatial Transcriptomics of mouse hippocampus of adult mouse.
spot barcode in the bam files is the SAM tag BC, and the UMI is SAM tag U8
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| Data processing |
The Space Ranger pre-release was used to perform Visium Spatial Transcriptomics Illumina profiling.
Processing of Nanopore reads for scNaUMI-seq is describe at https://github.com/ucagenomix/Sicelore
Genome_build: mm10
Supplementary_files_format_and_content: Space Ranger filtered gene barcodes matrices. SiT gene/isoform/junction/editing matrices.
Supplementary_files_format_and_content: The rds files refer to the final statistical analysis of the 3 samples, consisting of an analysis using Illumina and Nanopore sequencing.
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| Submission date |
Jul 06, 2020 |
| Last update date |
Aug 31, 2022 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
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| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
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| Street address |
660 route des lucioles
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| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
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| Platform ID |
GPL26624 |
| Series (1) |
| GSE153859 |
The spatial landscape of gene expression isoforms in tissue sections |
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| Relations |
| BioSample |
SAMN15458071 |
| SRA |
SRX8673336 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4656182_CBS2-SiT.tar.gz |
53.7 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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