|
| Status |
Public on Nov 10, 2018 |
| Title |
HeLa_RNAseq_totalRNA |
| Sample type |
SRA |
| |
|
| Source name |
cervical cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
|
| Growth protocol |
HeLa cells (from ATCC) were cultured in DMEM (HyClone, SH30243.01) supplemented with 10% FBS (HyClone, SH30084.03) and 100 U ml-1 penicillin-streptomycin (HyClone, SV30010) and maintained in a incubator at 37˚C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were UV-crosslinked and lysed, and RNA-protein complexes were isolated with magnetic beads.
cDNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
total RNA
|
| Data processing |
Library strategy: PBS-R
Illumina Casava1.7 software used for basecalling.
The reads were mapped to the hg19 human reference genome using the HISAT aligner.
Bowtie2 and RSEM were used to analyze gene expression, and MACS was used for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: AllSamples_FPKM txt file include FPKM values for each Sample, and RPBS_peaks txt file include peaks information of protein binding sites on RNAs.
|
| |
|
| Submission date |
Oct 29, 2018 |
| Last update date |
Nov 10, 2018 |
| Contact name |
Liu Fenglin |
| E-mail(s) |
liufl@ioz.ac.cn
|
| Phone |
15001248122
|
| Organization name |
Chinese Academy of Sciences
|
| Street address |
Courtyard 1, Beichen West Road
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE121919 |
Genome-wide identification of protein binding sites on RNAs in mammalian cells [PBS-R] |
|
| Relations |
| BioSample |
SAMN10341907 |
| SRA |
SRX4949959 |
