NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7097917 Query DataSets for GSM7097917
Status Public on Nov 10, 2023
Title Ctrl, bio2
Sample type SRA
 
Source name Thymus
Organism Mus musculus
Characteristics tissue: Thymus
replicate: Rep2
technical replicate: 1
genotype: C57BL/6
Extracted molecule total RNA
Extraction protocol Probe hybridization and all subsequent steps were performed as per 10X User guide for Visium CytAssist Spatial Gene Expression (CG000495).
Subsequently, probe extension was carried out and the ligation product was eluted, and a pre-amplification step performed. A subset of the pre-amplification product was used for library construction.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Base calling was performed using RTA 3.4.4, demultiplexing was performed using spaceranger v2.0.0 (Bcl2fastq 2.20.0), and alignment was performed using spaceranger v2.0.0 (STAR2.7.2a). Sequenced reads were aligned to the 10x Genomics provided mouse reference sequence (refdata-gex-mm10-2020-A) and probe set (Visium_Mouse_Transcriptome_Probe_Set_v1.0_mm10-2020-A).
Assembly: mm10
Supplementary files format and content: jpg; aligned tissue images
Supplementary files format and content: jpg; aligned fiducials
Supplementary files format and content: tiff; cytassist image
Supplementary files format and content: jpg; detected tissue images
Supplementary files format and content: png; tissue images
Supplementary files format and content: csv; spatial enrichment
Supplementary files format and content: csv; tissue positions
Supplementary files format and content: h5; matrix file
Supplementary files format and content: json; scalefactors
Library strategy: Spatial Transcriptomics
 
Submission date Mar 14, 2023
Last update date Nov 10, 2023
Contact name Remy Bosselut
E-mail(s) bosselur@helix.nih.gov
Phone 240-760-6866
Organization name National Cancer Institute, National Institute of Health
Department Laboratory of Immune Cell Biology
Lab Bosselut
Street address 9000 Rockville Pike, Building 37
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL24247
Series (2)
GSE207572 Zfp281 and Zfp148 control CD4+ T cell thymic development and Th2 functions
GSE227332 The transcription factor Zfp281 serves redundantly with Zfp148 to support CD4+ T cell development and functions [Thymus Visium]
Relations
BioSample SAMN33760093
SRA SRX19676889

Supplementary file Size Download File type/resource
GSM7097917_Ctrl_bio2_aligned_fiducials.jpg.gz 2.6 Mb (ftp)(http) JPG
GSM7097917_Ctrl_bio2_aligned_tissue_image.jpg.gz 1.0 Mb (ftp)(http) JPG
GSM7097917_Ctrl_bio2_cytassist_image.tiff.gz 21.3 Mb (ftp)(http) TIFF
GSM7097917_Ctrl_bio2_detected_tissue_image.jpg.gz 1002.5 Kb (ftp)(http) JPG
GSM7097917_Ctrl_bio2_filtered_feature_bc_matrix.h5 22.3 Mb (ftp)(http) H5
GSM7097917_Ctrl_bio2_raw_feature_bc_matrix.h5 30.8 Mb (ftp)(http) H5
GSM7097917_Ctrl_bio2_scalefactors_json.json.gz 194 b (ftp)(http) JSON
GSM7097917_Ctrl_bio2_spatial_enrichment.csv.gz 909.5 Kb (ftp)(http) CSV
GSM7097917_Ctrl_bio2_tissue_hires_image.png.gz 3.1 Mb (ftp)(http) PNG
GSM7097917_Ctrl_bio2_tissue_lowres_image.png.gz 238.1 Kb (ftp)(http) PNG
GSM7097917_Ctrl_bio2_tissue_positions_list.csv.gz 60.7 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap