|
| Status |
Public on Jan 16, 2024 |
| Title |
FOXP3_GFP_Tom_WPRE_Sample2 |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
cell type: splenocytes
genotype: Foxp3tm9(EGFP/cre/ERT2)Ayr/J x Ai14-tdTomato
treatment: tamoxifen - chronic hypoxia 5 days - replicate 2
|
| Treatment protocol |
Mice were fed a diet from Envigo (TD.140229 TAM Diet 2020, 500, B) containing 500 mg tamoxifen/kg diet for 2 wk. The dose was 80 mg/kg body weight per day. After at least 3 days receiving regular diet, mice were exposed to 380 mmHg (inspired PO2= 70 mmHg) for 5 days (chronic hypoxia) or left under normoxia (~630 mmHg in Albuquerque, NM, inspired PO2= 122 mmHg).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell concentrations and viability were determined using the Cell Countess II FL (ThermoFisher) prior to calculating cell counts and loading the suspension into the Next GEM Chip G and Chromium Controller (10x Genomics) per the manufacturer’s protocol for GEM formation. The 10x Chromium Next GEM 3’ protocol was used to create 3’ libraries; briefly, cells were lysed and barcoded within each GEM prior to first strand cDNA synthesis, also within each GEM. After GEM’s are broken, cells are pooled prior to library completion as described in the manufacture’s protocol. Library quality was assess after cDNA synthesis and after completion on the BioAnalyzer using a DNA High Sensitivity Chip (Agilent). Prior to sequencing, Agilent Tape Station 4200 and Invitrogen Qubit 4.0 reagents were used determine final library concentrations prior to dilution, normalization and pooling at 4nM. qPCR was used to determine cluster efficiency.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Illumina NovaSEQ 6000 at University of Colorado Anschutz Medical Campus Genomics Shared Resource Cancer Center, demultiplexed with bcl2fastq v2.20.0.422 with “--barcode-mismatches” set to 1
Aligned and counted with CellRanger v3.1.1
Assembly: mm10
Supplementary files format and content: CellRanger (v3.2.2) output files
|
| |
|
| Submission date |
Dec 02, 2022 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Laura Gonzalez Gonzalez Bosc |
| E-mail(s) |
lgonzalezbosc@salud.unm.edu
|
| Organization name |
University of New Mexico Health Sciences Center
|
| Department |
Cell Biology and Physiology
|
| Lab |
LGBosc Lab
|
| Street address |
Msc 084750, Brf 237J
|
| City |
Albuquerque |
| State/province |
NM |
| ZIP/Postal code |
87131-0001 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE219259 |
Single-cell RNA-seq uncovers unique gene expression profiles in the spleen of hypoxic mice |
|
| Relations |
| BioSample |
SAMN31839898 |
| SRA |
SRX18352163 |
