|
| Status |
Public on May 15, 2017 |
| Title |
RNAseq_A5-ProE-shNT-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Human primary adult proerythroblasts (ProEs)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD34+ HSPC-derived proerythroblasts
developmental stage: bone marrow
shRNA: shNT
|
| Treatment protocol |
NA
|
| Growth protocol |
Human primary adult HSPCs and erythroblasts were expanded and differentiated ex vivo using a serum-free two-phase liquid culture system.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq analysis using the illumina NextSeq500, 0.1-2 ug of total RNA was processed for library generation using the TruSeq RNA Sample Preparation v2 Kit (illumina) following the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ProE-shNT-rep1
|
| Data processing |
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) by TopHat.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilo base pair per million total reads).
Differential gene expression analyses were performed using DEseq.
Genome_build: hg19
Supplementary_files_format_and_content: text file of gene read count values
Supplementary_files_format_and_content: text file of gene RPKM values
|
| |
|
| Submission date |
Sep 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Xu |
| E-mail(s) |
Jian.Xu@UTSouthwestern.edu
|
| Phone |
214-648-6125
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Children's Research Institute
|
| Street address |
6000 Harry Hines Blvd. NL12.138B
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75235 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE86910 |
RNA-seq transcriptonal profiling in human primary adult erythroid progenitor cells (ProEs) after shRNA-mediated depletion of TFAM and PHB2 expression |
| GSE86912 |
Quantitative Proteomic and Transcriptomic Analysis Reveals Post-Transcriptional Regulation of Mitochondrial Biogenesis during Erythropoiesis |
|
| Relations |
| BioSample |
SAMN05771137 |
| SRA |
SRX2163110 |
