|
| Status |
Public on Feb 06, 2019 |
| Title |
697_Ctrl_RNA_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
pre-B leukemic 697 cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pre-B leukemic cell line
cell line: parental 697
|
| Treatment protocol |
The cells were treated with 0.5 ug/ml TPA for 0~ 24 hr before DNA or RNA extraction.
|
| Growth protocol |
The human pre-B leukemia 697 cell line was grown in RPMI1640 (Sigma) supplemented with 10% fetal bovine serum at 37 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extrated using Rneasy Mini kit (Qiagen)
Multiplexing libraries were prepared for sequencing using Illumina standard protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the HG19 human genome assembly using bowtie version 1.12 with with parameters "-n 2 -m 1 -l 36 --best". RNA-seq reads were alined to the HG19 human genome sequence using TopHat with the default parameters.
Potential PCR duplicates in ChIP-seq reads were removed using samtools rmdup command.
Tiled data files (TDF) were generated by igvtools with parameters "-z 5 -w 10 -e 200" for ChIP-seq ; "-z 5 -w 10" for RNA-seq.
The gene expression profiling was analyzed by HOMER software
Genome_build: HG19
Supplementary_files_format_and_content: Tiled data files (TDF) and tab-delimited text files include RPKM values for each RNA-seq samples.
|
| |
|
| Submission date |
Feb 05, 2019 |
| Last update date |
Feb 12, 2019 |
| Contact name |
Wei-Yi Chen |
| E-mail(s) |
chenwy@nycu.edu.tw
|
| Phone |
+886-2-2826-7328
|
| Organization name |
National Yang Ming Chiao Tung University
|
| Department |
Institute of Biochemistry and Molecular Biology
|
| Street address |
No. 155, Sec 2, Linong St.
|
| City |
Taipei |
| ZIP/Postal code |
112 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE126083 |
Genome-wide maps of chromatin state and gene expression in control and TPA-stimulated pre-B leukemic 697 line |
|
| Relations |
| BioSample |
SAMN10873024 |
| SRA |
SRX5333215 |
