|
| Status |
Public on Apr 13, 2023 |
| Title |
Mouse brain spatial transcriptomics, E12, ampicillin control, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryonic brain
developmental stage: E12
treatment: ampicillin control
slide: V10F06-005
slide area: A1
|
| 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_V10F06-005-A1_2114503_e12
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 |
| E-mail(s) |
jeremy.crawford@stjude.org
|
| 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 |
|
| Relations |
| SRA |
SRX19972167 |
| BioSample |
SAMN34176283 |
