|
| Status |
Public on Apr 27, 2016 |
| Title |
MSI2 shRNA knock down - control 1 |
| Sample type |
SRA |
| |
|
| Source name |
Cord blood stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: control
cell type: Cord blood stem cells
|
| Treatment protocol |
Human lineage depleted CD34+ cord blood cells were FACS purified and cultured for 12 hours cells in StemSpan medium (Stem Cell Techonologies) supplemented with growth factors Interleukin 6 (20 ng/ml), Stem cell factor (100 ng/ml), Flt3 ligand (100 ng/ml) and Thrombopoietin (20 ng/ml). Lentivirus (Musashi-2 overexpression or knockdown) was then added in the same medium at a multiplicity of infection of 30–100 for 24 hours. Cells were given 2 days post transduction before flow-sorting for GFP expression.
|
| Growth protocol |
Human lineage depleted CD34+ cord blood cells were FACS purified and cultured for 12 hours cells in StemSpan medium (Stem Cell Techonologies) supplemented with growth factors Interleukin 6 (20 ng/ml), Stem cell factor (100 ng/ml), Flt3 ligand (100 ng/ml) and Thrombopoietin (20 ng/ml). Lentivirus (Musashi-2 overexpression or knockdown) was then added in the same medium at a multiplicity of infection of 30–100 for 24 hours. Cells were given 2 days post transduction before flow-sorting for GFP expression.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from transduced cells (~1x10^5) was isolated using TRIzol LS as recommended by the manufacturer (Invitrogen) and then further purified using RNeasy columns (Qiagen). Libraries were subjected to standard Illumina sequencing protocols.
standard Illumina Truseq RNA-seq protocol followed
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads for all samples were mapped to the human genome using Casava (Ver 1.8.2) with default paramters
RPKM values and reads counts were calculated using Casava
Analysis of differntial gene expression was performed thorugh ratio analysis and R (Deseq package)
Genome_build: hg19
Supplementary_files_format_and_content: KH_ratios_results.xlsx: This file contains the results of a ratio analysis of gene expression
Supplementary_files_format_and_content: KH_DESeq_results.xlsx: This file contains the results of a gene expression analysi performed using the DEseq R package
|
| |
|
| Submission date |
Jul 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Wilhelm |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Montreal
|
| Street address |
2950 Chemin Polytechnique
|
| City |
Montreal |
| ZIP/Postal code |
H1J 3R4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE70685 |
Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells |
|
| Relations |
| BioSample |
SAMN03853081 |
| SRA |
SRX1090966 |
