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Sample GSM7173407 Query DataSets for GSM7173407
Status Public on Apr 13, 2023
Title Mouse brain spatial transcriptomics, E12, S. pneumoniae + ampicillin challenge, replicate 2
Sample type SRA
Source name embryonic brain
Organism Mus musculus
Characteristics tissue: embryonic brain
developmental stage: E12
treatment: S. pneumoniae + ampicillin challenge
slide: V10F06-004
slide area: B1
Extracted molecule polyA RNA
Extraction protocol Whole heads from E12 embryos were used for analysis with a Visium spatial transcriptomics kit (10X Genomics, PN-1000184). Immediately after dissection, samples were frozen in isopentane chilled by liquid nitrogen, embedded in OCT (Sakura, 4583), and then stored at 280°C. Then, 10-mm sagittal sections were obtained beginning at the periphery to the midline according to 10X Genomics-suggested practices. Tissue permeabilization was optimized to 12 min. A single section was then obtained from each of four mice per condition, and two sections were placed on each Visium slide (i.e., one section from each condition).
Libraries were prepared according to manufacturer recommendations and sequenced on an Illumina NovaSeq platform with a sequencing configuration of 28-10-10-120 (R1-i7-i5-R2) at 200 million clusters per library.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description JCC350_V10F06-004-B1_2114500_e12-Tx
10x Genomics Visium
Data processing Sections were imaged on a Nikon Eclipse Ni-E scope.
Slide fiducials and tissue coverage areas were manually annotated using Loupe Browser (10X Genomics).
Data were analyzed using SpaceRanger (v1.2.1; 10X Genomics) using the corresponding mm10 reference, with the reverse read trimmed to 90 bp.
Assembly: mm10
Supplementary files format and content: H&E stained section images are included as processed data files in the .tif format.
Supplementary files format and content: Slide fiducials and tissue coverage manual annotations are included as processed data files in the .json format.
Supplementary files format and content: Filtered outputs from CellRanger (filtered_feature_bc_matrix) are included as processed data files in the .h5 format.
Submission date Apr 13, 2023
Last update date Apr 14, 2023
Contact name Jeremy Chase Crawford
Organization name St. Jude Children's Research Hospital
Department Department of Host-Microbe Interactions
Street address MS 221, 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38105-3678
Country USA
Platform ID GPL24247
Series (1)
GSE229699 Bacterial TLR2/6 Ligands Block Ciliogenesis, Derepress Hedgehog Signaling, and Expand the Neocortex
BioSample SAMN34176284
SRA SRX19972166

Supplementary file Size Download File type/resource
GSM7173407_JCC350_V10F06-004-B1.json.gz 74.6 Kb (ftp)(http) JSON
GSM7173407_JCC350_V10F06-004-B1_2114500_e12-Tx_filtered_feature_bc_matrix.h5 7.0 Mb (ftp)(http) H5
GSM7173407_JCC350_V10F06_004_B1_HE.tif.gz 24.8 Mb (ftp)(http) TIFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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