|
| Status |
Public on Jan 12, 2020 |
| Title |
UCB-1 control |
| Sample type |
SRA |
| |
|
| Source name |
huCD34+ HSPCs_control
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: umbilical cord blood derived stem and progenitor cells (HSPCs)
passage: 1
treated with: vehicle (control)
|
| Treatment protocol |
All cells were incubated at 37°C in 5%CO2. Freshly isolated huCD34+ HSPCs were split into 2 parts and seeded at a density of 1x10^5/ml. One part of cells (target) were immediately treated with G-CSF (100ng/ml) the other part of cells (control) was treated with vehicle. Addition of G-CSF or vehicle was repeated every 2nd day.
|
| Growth protocol |
huCD34+ HSPCs were routinely isolated from umbilical cord blood using CD34 MicroBead Kit (Miltenyi). Typically 1x10^5 cells were seeded into 12well plates and grown in IMDM medium containing 10% FBS supplemented with IL-6 (50ng/ml), SCF (50ng/ml) and FLT3-L (50ng/ml). From day 4 on cells were cultured in IMDM supplemented with IL-3 (10ng/ml), SCF (25ng/ml) and FLT3-L (25ng/ml).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol reagent.
TruSeq Small RNA Library Prep Kit v2 (Illumina) was used for the construction of sequencing libraries. smallRNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
Each library was indexed in order to multiplex sequencing runs on the Illumina HIScanSQ platform
50bp sequencing reads were collected and adaptor sequences were trimmed from raw sequences using cutadapt software
remaining read data for each sample were aligned to the most recent human (hsa-only) mature sequences of miRASE database v21 (miRBase.org) using bowtie aligner
Mapped reads for each miRNA were counted with R/Bioconductor programming environment by application of the ShortRead library
Supplementary_files_format_and_content: abundance measurements
|
| |
|
| Submission date |
Jan 12, 2017 |
| Last update date |
Jan 12, 2020 |
| Contact name |
Gerhard Behre |
| Organization name |
Leipzig University Hospital
|
| Department |
Division of Hematology and Oncology
|
| Street address |
Johannisallee 32A
|
| City |
Leipzig |
| ZIP/Postal code |
04103 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15456 |
| Series (1) |
| GSE93550 |
Next Generation Sequencing of miRNome of G-CSF treated huCD34+ HSPCs |
|
| Relations |
| BioSample |
SAMN06220148 |
| SRA |
SRX2488080 |
