|
| Status |
Public on Dec 31, 2015 |
| Title |
HepG2 Heat Shock 2 |
| Sample type |
SRA |
| |
|
| Source name |
HepG2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human liver hepatocellular carcinoma cells
antibody name: Rabbit anti-m6A (Abcam #ab151230)
cell line: HepG2
|
| Treatment protocol |
For heat shock treatment, cells were transferred to a 42C incubator for 1h and then placed back at 37C for 6h.
|
| Growth protocol |
Cells were grown in standard growth media for each cell line
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent. RNA was then subjected to DNAseI treatment to remove any contaminating DNA. mRNA was then isolated using oligo(dT) Dynabeads (Invitrogen).
Library construction was performed using the miCLIP method to map m6A residues at single-nucleotide resolution: Linder et al, Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nature Methods, 2015 Aug;12(8):767-72.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Barcodes used were NNNGGTTNN (HSreplicates1), NNNTTGTNN (HSrep2), NNNCAATNN (CTLrep1), and NNNACCTNN (CTLrep2)
Alignment to hg19 was performed using novoalign
Genome_build: hg19
Supplementary_files_format_and_content: m6A sites were identified from single reads using CIMS (C2T transitions, p=0.1). Metagene profiles were performed using hg19 genomic annotations. For HEK control samples, miCLIP data from Linder et al (2015) were used.
|
| |
|
| Submission date |
Dec 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kate Meyer |
| E-mail(s) |
[email protected]
|
| Phone |
9196849562
|
| Organization name |
Duke University School of Medicine
|
| Department |
Biochemistry
|
| Street address |
307 Research Drive Box 3711
|
| City |
D |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE73405 |
m6A in 5’ untranslated regions promotes cap-independent translation of mRNA |
|
| Relations |
| BioSample |
SAMN04377524 |
| SRA |
SRX1508524 |
