|
| Status |
Public on Sep 23, 2019 |
| Title |
Oga(Vav-Cre) 1 |
| Sample type |
SRA |
| |
|
| Source name |
Oga(Vav-Cre)
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype: Oga(Vav-Cre)
age: ~12 weeks
Sex: female
cell type: Lin-Sca+Kit+ Bone marrow cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bone marrow cells collected from 3 OgaVav-Cre and 3 wildtype female mice were sorted for Lin-Sca+Kit+ cells using a BD FACSAria Fusion Flow cytometer and the following antibodies: Lineage Cocktail FITC (R&D Biosystems), Sca-1(D7)APC (ebiosciences), c-Kit (2B8)PE (ebiosciences), FVD (ebiosciences). At least 2x10^4 cells were collected for each sample. RNA was extracted using RNeasy plus micro kit (Qiagen) following manufacturers protocol
RNA libraries were prepped using NEBNext Ultra RNA Library Prep Kit for Illumina and the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Treatment 1
KO-7886_S1
|
| Data processing |
ELAND aligner from Illumina in the CASAVA 1.8.2 package with the default parameter settings is used to align the fastq to the reference genome
Data was analyzed using the default parameter settings on Genomatix
Genome_build: mm9
Supplementary_files_format_and_content: RPKM
|
| |
|
| Submission date |
Jul 03, 2018 |
| Last update date |
Sep 23, 2019 |
| Contact name |
WeiPing Chen |
| E-mail(s) |
weipingChen@niddk.nih.gov
|
| Phone |
301-496-0175
|
| Organization name |
NIDDK/NIH
|
| Department |
GCL
|
| Lab |
Genomics Core Lab
|
| Street address |
Bldg 8, Room 1A11, NIDDK/NIH
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE116620 |
RNA-seq analysis of LSK from Oga(Vav-Cre) mice compared to wildtype |
|
| Relations |
| BioSample |
SAMN09579745 |
| SRA |
SRX4339352 |
