|
| Status |
Public on May 20, 2019 |
| Title |
BSPC.WT.rep2 |
| 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: wildtype
|
| 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 |
genomic DNA |
| Extraction protocol |
60.000 cells were washed once with 100µl PBS and resuspended in 50µl lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.2% IGEPAL CA-630). The suspension of nuclei was then centrifuged for 10min at 500g at 4°C, followed by the addition of 50µl transposition reaction mix (25µl TD buffer, 2.5µl Tn5 Transposase and 22.5µl Nuclease Free H2O) and incubation at 37°C for 30min. DNA was isolated using MinElute Kit (Qiagen). Libraries were amplified by PCR (13 cycles). After the PCR reaction, the library was selected for fragments between 100 and 1000bp with AmpureXP beads (Beckman Coulter). Libraries were purified with Qiaquick PCR (Qiagen) and integrity checked on a Bioanalyzer before sequencing.
Libraries were amplified by PCR (13 cycles). After the PCR reaction, the library was selected for fragments between 100 and 1000bp with AmpureXP beads (Beckman Coulter). Libraries were purified with Qiaquick PCR (Qiagen) and integrity checked on a Bioanalyzer before sequencing.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| 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 hg19 using BWA
Normalized genome coverage bigWig files were generated by Deeptools
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
|
| |
|
| 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) |
| GSE126825 |
Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo [ATAC] |
| 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 |
SAMN10976806 |
| SRA |
SRX5398949 |
