|
| Status |
Public on Nov 14, 2019 |
| Title |
Bone irradiation EC Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Femur/Tibia
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
treatment: 9 Gy irradiation
age: 8-12 weeks
genotype: Cdh5-mTnG
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Adult mouse bone samples were crashed with pestle, treated with collagenase IV, and digested to single cells. These single cell suspension were stained for FACS sorting. FACS sorted cell population were directly lysis into RLT buffer and RNA were extracted using RNeasy plus Micro Kit (Qiagen)
Double strand cDNA was synthesized using SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara) and sequencing library was constructed with Nextera XT DNA Library preparation kit (illumina). TruSeq Stranded Total RNA kit (Illumina) was used for the library preparation of total BMC and Lin- samples.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
whole bone GFP+ cells
BM_EC_9GY_fpkms.txt
9GY-1
|
| Data processing |
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
Tophat (v2.1.1) used for alignment
HTSeq-count (v0.6.1) used for transcriptome abundance measurement
DESeq2(v1.18.1) used for differential gene expression analyses
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Jun 06, 2018 |
| Last update date |
Nov 14, 2019 |
| Contact name |
Hyun-Woo Jeong |
| E-mail(s) |
zionjeong@gmail.com
|
| Phone |
+4917631115236
|
| Organization name |
Max-Planck-Institute for Molecular Biomedicine
|
| Department |
Dept. Tissue Morphogenesis
|
| Lab |
Adams
|
| Street address |
Roentgenstr.20
|
| City |
Muenster |
| State/province |
NRW |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE115422 |
Transcriptome profiling of adult mouse bone marrow endothelial cells |
|
| Relations |
| BioSample |
SAMN09375357 |
| SRA |
SRX4174987 |
