|
| Status |
Public on May 01, 2018 |
| Title |
HSC saline treated young rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HSC saline treated young
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: young adult
treated with: saline
tissue: bone marrow
cell type: hematopoietic stem cells (HSCs)
|
| Treatment protocol |
For long-term administration of β3-adrenergic agonist BRL37344 (Sigma) was dosed at 2.4 mg Kg-1 day-1, using subcutaneously implanted Alzet osmotic pumps (model 2006; DURECT Corporation) into young (2 month old) and old (15-20 month old) mice . Six weeks following implantation of the first pump, an additional pump was implanted for a total of 12 weeks of continuous drug delivery. Control animals were implanted with Alzet pumps containing saline (PBS; Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from ~2000 sorted HSCs was extracted using the RNAeasy Plus Micro kit (Qiagen), and assessed for integrity and purity using an Aligent 2100 Bioanalyzer (Agilent Technologies).
Complementary DNA libraries were then generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) and the Nextera XT DNA Sample preparation Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
J703_AHW5G3BGXY_CGTACTAG-ATAGAGAG_2-HSC-Y-S
|
| Data processing |
Library adaptor sequences were trimmed using trim galore ( https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ )
Then reads were aligned to the mouse genome (mm10) using Spliced Transcripts Alignment to a Reference (STAR 2.5.3a)
Aligned reads were then quantified to transcriptome (mm10 - Ensembl Transcripts release 83), normalized and differentially expressed genes were identified using Partek Flow
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file contains gene counts for individual samples generated by Partek Flow
|
| |
|
| Submission date |
Jan 24, 2018 |
| Last update date |
May 01, 2018 |
| Contact name |
Paul Frenette |
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research
|
| Street address |
1301 Morris Park Avenue , Room 101
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE109546 |
Loss of adrenergic nerves in bone marrow drives hematopoietic stem cell niche aging |
|
| Relations |
| BioSample |
SAMN08389688 |
| SRA |
SRX3594756 |
