|
| Status |
Public on May 20, 2019 |
| Title |
BSPC.H3K9M.1362 |
| Sample type |
SRA |
| |
|
| Source name |
hematopoietic stem and progenitor cells (Lin-, cKit+ bone marrow cells)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57B6/129 hybrid
tissue: Bone marrow
genotype/variation: K9M
|
| Treatment protocol |
Both male and females were used in this study at 6-8 weeks of age and were induced by adding 2 mg/ml doxycycline to drinking water.
|
| Growth protocol |
Mice used in this study were housed and bred in Specific Pathogen Free (SPF) rooms located in the AAALAC-accredited Center for Comparative Medicine vivarium at Massachusetts General Hospital. Mice were housed in ventilated cages on a standard 12:12 light cycle. All procedures involving mice adhered to the guidelines of the approved Massachusetts General Hospital Institutional Animal Care and Use Committee (IACUC) protocol no. 2006N000104.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was purified using the RNeasy plus mini kit (Qiagen) using the provided protocol. RNA-Seq libraries were constructed using the SMARTer v3 kit (Clontech) and sequenced on Illumina HiSeq2500 instrument, resulting in approximately 30 million reads per sample on average.
RNA-Seq libraries were constructed using the SMARTer v3 kit (Clontech)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome mm9 using STAR
Transcript abundance was calculated using Htseq
Genome_build: mm9
Supplementary_files_format_and_content: count
|
| |
|
| Submission date |
Feb 20, 2019 |
| Last update date |
May 21, 2019 |
| Contact name |
Justin Brumbaugh |
| Organization name |
University of Colorado Boulder
|
| Department |
Molecular, Cellular, and Developmental Biology
|
| Street address |
347 UCB
|
| City |
Boulder |
| State/province |
CO |
| ZIP/Postal code |
80309 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE126826 |
Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo [RNA] |
| GSE126829 |
Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo |
|
| Relations |
| BioSample |
SAMN10976784 |
| SRA |
SRX5398962 |
