|
| Status |
Public on Sep 15, 2024 |
| Title |
BM_KO3_Mono |
| Sample type |
RNA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: ACKR1 KO
cell type: Mono
mouse id: KO3
|
| Treatment protocol |
Femurs were flushed with PBS, bone marrow cells were stained with lineage markers for NECs, PMNs, and Monos for 30 minutes at 4 °C. On average, 2 x 106 NECs, 1 x 106 PMNs, and 0.5 x 106 Monos were sorted using a FACSAria II instrument (BD Biosciences, Germany). Sorted populations were snap-frozen on dry ice and stored at -80°C.
|
| Growth protocol |
ACKR1-deficient mice generated with 129P2/OlaHsd ES cells were backcrossed for more than 10 generations onto a C57BL/6J background and maintained as a heterozygous breed. All experimental procedures were performed with 8- to 12-week-old male mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was carried out using the RNeasy Mini Kit (Qiagen, Germany) following the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
The preparation of fragmented Biotin-labeled sense-strand cDNA was carried out using the Affymetrix GeneChip® WT PICO Reagent kit (ThermoFisher, Germany) following the manufacturer's instructions. 2 ng total RNA per sample was spiked with polyadenylated transcripts, subjected to reverse transcription into cDNA, and subsequently converted into cRNA through in vitro transcription.
|
| |
|
| Hybridization protocol |
cRNA (> 20 µg) was subjected to hybridization at 45 °C for 16 hours on separate Affymetrix Clariom D Arrays for Mouse, previously known as Affymetrix Mouse Transcriptome Array 1.0 (ThermoFisher, Germany). Microarrays underwent two binding cycles involving anti-Biotin antibodies and a Streptavidin-phycoerythrin conjugate.
|
| Scan protocol |
GeneChips were scanned using Affymetrix GeneChip® 3000 Scanner (ThermoFisher, Germany).
|
| Description |
Gene expression data from murine bone marrow nucleated erythroid cells (NEC), monocytes (Mono), and polymorphonuclear neutrophils (PMN)
|
| Data processing |
Probe intensities were analyzed with Transcriptome Analysis Console (TAC) software v4.0.2 (ThermoFisher, Germany) following an assessment of quality control metrics. Affymetrix probes were annotated to the mouse genome GRCm38/mm10. Analysis was conducted with TAC default settings and quantile normalization method.
|
| |
|
| Submission date |
Feb 16, 2024 |
| Last update date |
Sep 15, 2024 |
| Contact name |
Johan Duchene |
| E-mail(s) |
[email protected], [email protected]
|
| Phone |
+4989440054757
|
| Organization name |
LMU
|
| Department |
IPEK
|
| Street address |
Pettenkoferstrasse, 9
|
| City |
Munich |
| State/province |
- Please Select - |
| ZIP/Postal code |
80336 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20775 |
| Series (1) |
| GSE256021 |
129-derived passenger mutations confound phenotype of ACKR1-deficient mice |
|
