|
| Status |
Public on Jan 08, 2015 |
| Title |
KC2 bio rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Cervical cancer cells
passages: 10-15
ip antibody: Anti-m6A antibody
|
| Treatment protocol |
4-thiouridine was added to growth media to a final concentration of 200 mM and treated for 16 hrs.
|
| Growth protocol |
HeLa cell was grown in Gibco DMEM media supplemented with 10% FBS and 1% pen-strep (Life Technologies).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by TRIzol and mRNA was isolated by FastTrack MAG mRNA isolation kit.
Libraries were constructed by Illumina TruSeq Small RNA Sample Prep Kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Photo-crosslinking-assisted-m6A-seq with anti-m6A antibody
|
| Data processing |
Adapters were trimed by FASTX and also the first and last bases were removed because of the quality.
Then the reads were mapped onto the human genome (hg19) using bowtie with at most two mismatches allowed
PARalyzer was used for peak calling using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains the m6A sites
|
| |
|
| Submission date |
Feb 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
zhike lu |
| E-mail(s) |
zhikelu@gmail.com
|
| Organization name |
University of Chicago
|
| Department |
department of chemistry
|
| Street address |
5801 South Ellis Avenue
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE54921 |
High Resolution N6-Methyladenosine (m6A) Map Using Photo-crosslinking-Assisted m6A Sequencing |
|
| Relations |
| BioSample |
SAMN02640641 |
| SRA |
SRX469996 |
| Named Annotation |
GSM1326565_KC2_4SU2_clusters_reads50.peaks.bed.gz |
