|
| Status |
Public on Feb 20, 2024 |
| Title |
mLND3-1 |
| Sample type |
SRA |
| |
|
| Source name |
Mediastinal lymph node
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mediastinal lymph node
time: Day 3
treatment: House dust mite intranasal
|
| Treatment protocol |
naïve 1DERYFP CD4+ T cells (CD45.1+) were transferred into CD45.2+ recipients and were immunized with 25 µg of HDM intranasally daily for 3 days. Mediastinal lymph nodes (mLN) were isolated on day 4 and day 6, snap frozen and embedded in chilled optimal cutting temperature (OCT) compound (Tissue-Tek) on dry ice, and stored at -80 °C. Samples were cryosectioned (10 µm) at -20 °C on a cryostat (Leica) and mounted directly onto a 3 x 3 mm Curio Seeker Spatial Mapping Slide (Curio Biosciences)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tile was removed and placed in a 1.5ml Eppendorf LoBind tube with Hybridization Reaction Mix. Reverse transcription was performed to generate cDNA followed by tissue clearing and Curio Seeker Bead resuspension.
Second stand synthesis was done followed by cDNA amplification, which after purifiying was subjected to tagmentation (Nextera XT) and library generation
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
fresh frozen Spatial transcriptome sequencing
|
| Data processing |
For images of Seeker tile, serial sections were cut onto glass slides followed by staining and imaging as described.
Demultiplexed FastQ files were initially processed by the Curio Seeker bioinformatics pipeline
Assembly: mm10
Supplementary files format and content: MoleculesPerMatchedBead.mtx: Expression table Sparse Matrix (column=BeadBarcodes, row=Genes)
Supplementary files format and content: MatchedBeadLocation.csv: Spatial coordinates of Beadbarcodes
Supplementary files format and content: genes.tsv: Expression table genes
Supplementary files format and content: barcodes.tsv :Expression table BeadBarcode
Supplementary files format and content: image.tif: image of serial section
|
| |
|
| Submission date |
Oct 11, 2023 |
| Last update date |
Feb 20, 2024 |
| Contact name |
Amanda Catherine Poholek |
| E-mail(s) |
poholeka@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Department |
Pediatrics
|
| Street address |
4401 Penn Ave., Rangos Research Center 8129
|
| City |
Pittsburgh |
| State/province |
Pennsylvania |
| ZIP/Postal code |
15224 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (2) |
| GSE245111 |
Spatial microniches of IL-2 synergize with IL-10 to drive lung migratory Th2 cells in response to inhaled allergen [Curio] |
| GSE245112 |
Spatial microniches of IL-2 synergize with IL-10 to drive lung migratory Th2 cells in response to inhaled allergen |
|
| Relations |
| BioSample |
SAMN37776924 |
| SRA |
SRX22066364 |
