|
| Status |
Public on Aug 14, 2019 |
| Title |
Sample:C1 |
| Sample type |
SRA |
| |
|
| Source name |
endothelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/KaLwRijHsd
healthy vs. myeloma-bearing: healthy
cell type: endothelial cells
|
| Treatment protocol |
No treatments given.
|
| Growth protocol |
8-10 week-old C57Bl/KaLwRij mice were inoculated IV with PBS vehicle or 1 x10e6 5TGM1-GFP cells, and prospectively culled on day +23 from tumour inoculation.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Bones were flushed, washed, crushed, collagenase digested and bone lining niche cells were FACS sorted. 100 cells per sample were sorted into 4µl lysis buffer (Gooding et al., Nature Communications 2019).
RNA was extracted and libraries constructed according to SmartSeq2 protocol (Picelli et al., Nature Protocols 2014).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: healthy_v_myeloma-bearing_rpkm_table.txt
|
| Data processing |
Reads were aligned with STAR version 2.4.0, to the GRCm38 (mm10) genome build.
Reads were quantified as read counts using the featureCounts function from the Subread package version 1.4.5-p1.
Reads were quantified by edgeR as rpkm (reads per kilobase per million).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: All processed data for all expressed genes in all cell types is combined into rpkm table healthy_v_myeloma-bearing_rpkm_table.txt, such that normalised transcript abundance can be compared across tissues and between conditions.
|
| |
|
| Submission date |
Aug 11, 2019 |
| Last update date |
Aug 14, 2019 |
| Contact name |
Sarah Gooding |
| E-mail(s) |
sarah.gooding@rdm.ox.ac.uk
|
| Phone |
00441865222410
|
| Organization name |
Oxford University
|
| Department |
Weatherall Institute of Molecular Medicine
|
| Lab |
Drakesmith Lab
|
| Street address |
John Radcliffe Site, Headley Way
|
| City |
Oxford |
| State/province |
Oxon |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE135691 |
RNASeq of bone lining niche cell components from healthy vs. myeloma-bearing mice |
| GSE135786 |
Transcriptomic profiling of the myeloma bone-lining niche identifies BMP signalling as a target for bone disease |
|
| Relations |
| BioSample |
SAMN12558159 |
| SRA |
SRX6695966 |
