|
| Status |
Public on Dec 31, 2013 |
| Title |
short-hairpin Drosha (shDr) day 0 (D0) rep2 |
| Sample type |
SRA |
| |
|
| Source name |
CD34+ HSPCs
|
| Organism |
Homo sapiens |
| Characteristics |
source tissue: umbilical cord blood
treatment: transduced with the lentivector encoding a short-hairpin RNA targeting Drosha
cell culture: serum-free MEM containing SCF, TPO, FLT-3L, IL-3 and IL-6
time-points collected: day 0 (immediately after sorting)
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted (D0), collected, washed and gently centrifuged. Cell pellets were lysed in Ambion's miRVana RNA extraction lysis buffer and applied to kit columns. Total RNA was eluted and concentrations were assessed using a nanodrop spectrophotometer. Bioanalysis of total RNA to assess quality and subsequent size fractionation by gel electrophoresis was done at Medomics, Inc. (Azusa, CA).
The guidelines provided in the user guide by Applied Biosystems were followed. Total RNA samples were used to generate cDNA libraries. Each cDNA had adapters on both ends giving a total of approximately 42 extra baseparis. The fragments were size selected on gels by excising fragments in the of 55 to 90 bp (target size 60-80 bp). These size-selected cDNAs were then sequenced on the SOLiD 4.0 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Description |
short-hairpin Drosha (shDr) day 0 (D0)
|
| Data processing |
The csfasta files were processed by cutadapt v0.9.3 to remove the 3'-adapter, Then the trimmed reads were aligned to hg19 genome with Bowtie v0.12.7 with default options.
The miRNA expression levels were counted using customized R script using miRBase v16
All counts were scaled to the total number of aligned reads across all samples
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format containing the log2 transformed scaled counts
|
| |
|
| Submission date |
May 30, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiwei Wu |
| E-mail(s) |
xwu@coh.org
|
| Organization name |
City of Hope National Medical Center
|
| Department |
Computational and Quantitative Medicine
|
| Street address |
1500 E. Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL13393 |
| Series (1) |
| GSE47519 |
Global miRNA expression status of human hematopoietic stem–progenitor cells modulates myelopoiesis |
|
| Relations |
| BioSample |
SAMN02183415 |
| SRA |
SRX288060 |
