|
| Status |
Public on Jun 12, 2018 |
| Title |
Parental_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Parental
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HL-60
genotype/variation: parental cells
|
| Growth protocol |
HL-60 were grown in DMEM supplemented with 10% FBS, at 37 °C in a humidified atmosphere with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Adapter sequences were removed by using SeqPrep, and then poor quality reads filtered by sickle(version 1.200) for quality control
Quality filtered reads were then mapped to GRCh38 using TopHat (v2.0.4)
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . RSEM was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
GO functional enrichment and KEGG pathway analysis were carried out by Goatools and KOBAS
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file of expression analysis result of EdgeR and annotation
|
| |
|
| Submission date |
Jun 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
wang yujie |
| E-mail(s) |
wangyj@rainbow-genome.com
|
| Phone |
+86 18200353339
|
| Organization name |
Shanghai JiaYin Biological technology co., LTD
|
| Street address |
Chi Feng road No:65
|
| City |
shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200082 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE100484 |
mRNA profiles of JMJD3 overexpression- and JMJD3 knockout- HL-60 cells |
| GSE101891 |
JMJD3 facilitates C/EBPβ-centered transcriptional program to exert oncorepressor activity in AML |
|
| Relations |
| BioSample |
SAMN07278825 |
| SRA |
SRX2957410 |
