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Sample GSM7142289 Query DataSets for GSM7142289
Status Public on Jun 07, 2023
Title mouse brain coronal tissue section 4, PCI
Sample type SRA
 
Source name brain
Organism Mus musculus
Characteristics tissue: brain
genotype: C57BL/6J
treatment: PCI
Treatment protocol Improved immunostaining protocol presented in the accompanying publication Hahn et al.
Extracted molecule polyA RNA
Extraction protocol According to Visium Spatial Gene Expression User Guide (CG000239, Rev E).
Tissue permeabilization time: 8 min. After transfer of cDNA from slide, cDNA was amplified with 14 cycles and after adapter ligation, sample index PCR was performed in dependence of the sample with 16 to 17 cycles.
 
Library strategy OTHER
Library source other
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing bcl2fastq v2.20.0.422
spaceranger count (spaceranger-1.3.1)
spaceranger mat2csv (spaceranger-1.3.1)
Assembly: Mouse reference, mm10 (GENCODE vM23/Ensembl 98); pre-build for Cell Ranger (2020-A)
Supplementary files format and content: Tagged Image File Format
Supplementary files format and content: filtered feature-barcode matrix
Library strategy: 10X Visium Spatial Transcriptomics
 
Submission date Apr 03, 2023
Last update date Jun 07, 2023
Contact name Marco Groth
E-mail(s) dnaseq@leibniz-fli.de
Organization name Leibniz Institute on Aging - FLI
Department Core Facility - Next Generation Sequencing
Street address Beutenbergstra├če 11
City Jena
ZIP/Postal code 07747
Country Germany
 
Platform ID GPL24247
Series (1)
GSE228891 Protecting RNA Integrity for Spatial Transcriptomics While Improving Immunofluorescent Staining Quality
Relations
BioSample SAMN34062215
SRA SRX19859608

Supplementary file Size Download File type/resource
GSM7142289_V10T12-340_GM2728_A4_antibody-lables_8bit.tif.gz 456.1 Mb (ftp)(http) TIFF
GSM7142289_filtered_feature_bc_matrix_GM2728.csv.gz 9.4 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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