|
| Status |
Public on Jan 17, 2019 |
| Title |
NaïvePLZF siRNA-C RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow derived hMSC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human Mesenchymal Stem Cells
passages: p4-p10
|
| Treatment protocol |
Differentiation was induced using StemPro osteogenesis (Gibco A10072-01), differentiation kit as per manufacturer’s instructions. Cells were harvested at the indicated time points for ChIP, RNA, 4C-seq and protein using appropriate buffers as described below.
|
| Growth protocol |
Cells were cultured according to manufacturer’s instructions (Lonza, CAt.No-PT-2501) using mesenchymal stem cell growth medium (MSCGM) (Lonza MSCGM™: PT-3238) supplemented with one MSCGM™ SingleQuots™ (PT-4105).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA representing the indicated time points were purified from hMSC using RNeasy Plus Mini kit (QIAGEN 74106)
For RNA sequencing, samples were processed using a True Seq RNA Sample preparation kit (Illumina # 15025062) following the manufacturer’s instructions. Samples were multiplexed and sequenced in HiSeq2000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Genome_build: hg19
Data received from RNA sequencing were mapped and analyzed by using Genomatix software and the Genomatix Mapper algorithm (Expression Analysis for RNASeq Data, GGATM) (Genomatix Software GmbH, Germany) according to their guidelines.
Normalised gene expression was calculated using following formula (by the software): NE = c * #reads / (#reads * length) where NE is the normalized expression or enrichment value, #reads: the reads (sum of base pairs) of falling into either the transcript or the cluster region, #reads: all mapped reads (in base pairs), length: the transcript or cluster length in base pairs and c a normalization constant set to 10^7.
Differential expression and significance was calculated and corrected for multiple testing using Genomatix's implementation of the DeSeq algorithm (Anders S, Huber W. Genome Biology, 11, R106 (2010)). This was done as pair-wise and transcript-based analyses in a strand-unspecific manner.
|
| |
|
| Submission date |
Jan 16, 2019 |
| Last update date |
Jan 24, 2019 |
| Contact name |
Mads Lerdrup |
| E-mail(s) |
[email protected]
|
| Phone |
+45 23636776
|
| Organization name |
University of Copenhagen
|
| Department |
Department of Cellular and Molecular Medicine
|
| Lab |
Center for Chromosome Stability
|
| Street address |
Blegdamsvej 3C
|
| City |
Copenhagen N |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE125167 |
PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells (RNA-seq) |
| GSE125168 |
PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells |
|
| Relations |
| BioSample |
SAMN10755632 |
| SRA |
SRX5254876 |
