|
| Status |
Public on Oct 21, 2020 |
| Title |
NIPA KO untreated, replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
NIPA KO untreated
|
| Organism |
Mus musculus |
| Characteristics |
age: older than 20 months
genotype: NIPA KO
treatment: untreated
|
| Treatment protocol |
BMCs out of femurs were flushed in DMEM (+10% FCS) followed by lysis of erythrocytes for 5 minutes at room temperature and staining for Lineage markers (B220, CD3, CD4, CD8a, CD11b, GR1, TER119), cKIT and SCA1. LSK (Lineage-, SCA1+, cKIT+) cells were sorted by Beckman Coulter MoFlo XDP and cultured in BM media (DMEM, 30% fetal calf serum, 10ng/ml mIL-3, 10ng/ml mIL-6, 50ng/ml mSCF) in a 96-well plate for 30 minutes at 37°C with 5% CO2. Either not treated or 4 Gray irradiated LSK cells were harvested after 3 hours of culture and cell pelletts were stored at -80°C.
|
| Growth protocol |
Nipa WT and Nipa KO mice older than 20 months were at least ten-generation C57BL/6-backcrossed, mouse housing was in accordance with national and institutional guidelines for animal care and experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA was performed by RNeasy Micro Kit (Quiagen) according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.
|
| |
|
| Hybridization protocol |
Labeled fragments were hybridized to Affymetrix Mouse Gene ST 2.0 arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.
|
| Scan protocol |
After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.
|
| Description |
Gene expression data from aged NIPA KO mouse
|
| Data processing |
CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.
|
| |
|
| Submission date |
Oct 09, 2017 |
| Last update date |
Oct 21, 2020 |
| Contact name |
Geoffroy Andrieux |
| Organization name |
University clinics Freiburg
|
| Street address |
Breisacherstr 153
|
| City |
Freiburg |
| ZIP/Postal code |
79110 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE104735 |
Expression data from untreated and irradiated Nipa WT and Nipa KO hematopoietic stem cells (HSCs) |
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