|
| Status |
Public on Aug 24, 2017 |
| Title |
RNA-seq_K562_FB-dCas9-BirA_sgHS1-5-rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Human K562 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
|
| Growth protocol |
Human K562 cells were cultured in IMDM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin.
|
| 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 |
| |
|
| 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) using Cufflinks.
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 |
May 22, 2017 |
| 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) |
| GSE88817 |
In situ CAPTURE of chromatin interactions by biotinylated dCas9 |
| GSE99179 |
RNA-seq transcriptonal profiling in human K562 cells with or without dCas9 and sgRNAs |
|
| Relations |
| BioSample |
SAMN07152448 |
| SRA |
SRX2841207 |
