|
| Status |
Public on Jan 01, 2015 |
| Title |
RNAseq_F-shEZH1_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Human primary fetal live proerythroblasts (ProEs), shEZH1
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: fetal liver
cell type: CD34+ HSPC-derived proerythroblasts
shRNA: shEZH1
|
| Treatment protocol |
NA
|
| Growth protocol |
Primary maturing fetal liver erythroblasts were generated ex vivo using a serum-free two-phase liquid culture system.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq analysis using the Illumina HiSeq 2500, 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 HiSeq 2500 |
| |
|
| Description |
mRNA
|
| Data processing |
Sequencing reads were aligned to human genome assembly hg18 (NCBI version 36) 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 kilobase pair per million total reads).
Differential gene expression analyses were performed using DEseq.
Genome_build: hg18 (NCBI36)
Supplementary_files_format_and_content: Tab-delimited text file of gene RPKM values.
|
| |
|
| Submission date |
Jul 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Xu |
| E-mail(s) |
Jian.Xu@stjude.org
|
| Phone |
9015955208
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Pathology
|
| Street address |
262 Danny Thomas Place, MS 345
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE59089 |
RNA-seq transcriptional profiling in primary human erythroid progenitor cells upon shRNA-mediated knockdown of PRC2 core subunits |
| GSE59090 |
ChIP-seq and RNA-seq analysis of PRC2 core subunits in primary human erythroid progenitor cells |
|
| Relations |
| BioSample |
SAMN02902846 |
| SRA |
SRX646143 |
