 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 30, 2017 |
| Title |
OP9 Flat3 |
| Sample type |
SRA |
| |
|
| Source name |
OP9 Flat
|
| Organism |
Mus musculus |
| Characteristics |
strain: (C57BL/6xC3H)F2-op/op
cell line: OP9
cell type: Foetal calvaria stromal line
culture conditions: Maintained in flat culture submersed below media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from these samples with Qiagen RNeasy minikit (QIAGEN) including DNase I treatment (QIAGEN).
RNA sequencing libraries were prepared with a TruSeq RNA Library Preparation Kit (Illumina) and multiplexed.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing reads were processed using the RNA-seq analysis pipelines of Geneprof (Halbritter et al., 2012)
Sequencing reads were aligned with TopHat (Trapnell et al., 2009) v1.2.0 (2012-11-14).
The mRNA levels per gene were quantified by a custom script in Geneprof which accounts for multi-mapping reads. Briefly, all uniquely mapped reads overlapping with each annotated gene (Ensembl 58 Mouse Genes, NCBIM37) were summed, while ambiguously mapped genes were divided into fractions, weighted proportionally to the number of uniquely mapped genes in each possible gene assignment.
Read counts were then scaled per million (RPM)
Differential expression was with DESeq (Anders and Huber, 2010) (2011-03-15)
Genome_build: mm9
Supplementary_files_format_and_content: matrix contains normalised sequencing reads per million (RPM), the log2 fold change and adjusted p-value (output of DESeq) from comparisons between groups
|
| |
|
| Submission date |
Aug 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander Medvinsky |
| Organization name |
University of Edinburgh
|
| Department |
MRC Centre for Regenerative Medicine
|
| Street address |
5 Little France Drive
|
| City |
Edinburgh |
| ZIP/Postal code |
EH16 4UU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE102858 |
A molecular roadmap of the aorta-gonad-mesonephros region reveals BMPER as a novel regulator of HSC maturation [OP9] |
| GSE102859 |
A molecular roadmap of the aorta-gonad-mesonephros region reveals BMPER as a novel regulator of HSC maturation |
|
| Relations |
| BioSample |
SAMN07522775 |
| SRA |
SRX3110505 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
