|
| Status |
Public on Feb 20, 2020 |
| Title |
RNA-seq_K562_dCas9-cBio-sgSE_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Human K562 cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: K562 cells
|
| Treatment protocol |
G1E-ER4 cells were treated with 10-7 M β-estradiol to induce erythroid differentiation.
|
| Growth protocol |
Human K562 cells were cultured in IMDM supplemented with 10% heat-inactivated fetal bovine serum (FBS). G1E-ER4 cells were cultured in IMDM medium containing 15% FBS, 50 ng/mL recombinant SCF, and 2 U/ml recombinant human erythropoietin (EPO).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq analysis using the illumina NextSeq500, 200ng of total RNA was processed for library generation using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq_RPKM.txt
|
| Data processing |
Sequencing reads were aligned to human genome assembly hg19 or mm10 by STAR.
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).
Genome_build: hg19, mm10
Supplementary_files_format_and_content: text file of gene FPKM values
|
| |
|
| Submission date |
Nov 05, 2019 |
| Last update date |
Feb 20, 2020 |
| 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 |
GPL18573 |
| Series (2) |
| GSE139116 |
RNA-seq transcriptonal profiling in human K562 cells and G1E-ER4 cells with or without dCas9 and sgRNAs |
| GSE139117 |
Analysis of CRE-mediated chromatin interactions by CAPTURE2.0 |
|
| Relations |
| BioSample |
SAMN13207885 |
| SRA |
SRX7101443 |
