|
| Status |
Public on Jan 03, 2018 |
| Title |
HeLa WT-1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa WT
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HeLa
genotype/variation: Wild type
|
| Treatment protocol |
PA+EIPA means (50mM) propionate plus (25uM) EIPA.
|
| Growth protocol |
HeLa cells were cultured in Dulbecco's modified Eagle's medium (DMEM), 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit from QIAGEN.
Integrity and quantity of RNA was evaluated by Agilent 2100, following the manufacturer’s instructions. The mRNA and non-coding RNAs are enriched by removing rRNA using RNaseH. Mixed with the fragmentation buffer, target RNA were fragmented into short fragments and cDNA was synthesized using the RNA fragments as templates by N6 random primer, followed by end reparation and ligated with adapters. The quantity and quality of the cDNA libraries were assessed using an Agilent 2100 BioAnalyzer (Agilent Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Sequencing reads that contained adapters and/or had low quality, aligned to rRNA were filtered off before mapping.
We aligned clean reads to the hg19 UCSC RefSeq (RNA sequences, GRCh37) using bowtie2.
Gene level expression was performed by transforming mapped transcript reads to FPKM using RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Dec 24, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Yonglun Luo |
| E-mail(s) |
alun@biomed.au.dk
|
| Phone |
0045-22411944
|
| Organization name |
Aarhus University
|
| Street address |
Wilhelm Meyers Allé 4
|
| City |
aarhus |
| ZIP/Postal code |
8000 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
|
| Relations |
| SRA |
SRX3509840 |
| BioSample |
SAMN08242802 |
