|
| Status |
Public on Dec 20, 2018 |
| Title |
TriplexRNASeq_nuclear_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa S3 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
|
| Growth protocol |
HeLa S3 cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS, 1% penicillin/streptomycin and 2% Na-pyruvate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Chromatin was purified and chromatin-associated nucleic acids were isolated. Following the fragmentation of RNA, long DNA and DNA-associated RNA were separated from free RNA by Solid Phase Reversible Immobilization (SPRI)-based paramagnetic bead size selection. Alternatively, DNA-associated RNA was immunopurified using Anti-DNA antibody (DNA-IP).
Recovered RNAs from biological replicates were subjected rRNA depletion (except DNA-IP samples) using the NEBNext rRNA depletion kit (NEB). RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina (NEB).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Enriched nuclear RNA
Human cervix carcinoma
|
| Data processing |
Illumina Nextseq500 Platform was used
Adapter sequences were removed from the sequence reads by Trim galore with default parameters. Their quality was check by FASTQC. RNA sequence reads were aligned to human genome version hg38 using STAR with stringent parameters, allowing maximal one mismatch. Duplicate reads were filtered out.
As TriplexRNA-seq protocols enrich fragmented RNA associated with DNA, we adapted the ChIP-seq based differential peak caller THOR, taking into account reads in one DNA strand. Estimation of fragment sizes was based on Agilent Bioanalyzer profiles of libraries. Differential peak calling was performed for selected pairs of fractions (adjusted p-value < 10-500 and fold change (FC) > 1 in log2; Negative Binomial test). Peaks enriched in DNA-IP (vs. nuclear) and SPRI-size selection (vs. nuclear) are defined as DNA-associated RNA or TriplexRNA regions. Chromatin-associated and nuclear RNA are defined as peaks enriched in these fractions as compared to RNAs isolated by DNA-IP.
Genome_build: hg38
|
| |
|
| Submission date |
Oct 04, 2018 |
| Last update date |
Dec 20, 2018 |
| Contact name |
Ivan G. Costa |
| E-mail(s) |
ivan.costa@rwth-aachen.de
|
| Organization name |
Institute for Computational Genomics
|
| Department |
RWTH Aachen Medical Faculty
|
| Street address |
Pauwelsstr. 19
|
| City |
Aachen |
| State/province |
NRW |
| ZIP/Postal code |
52074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE120849 |
Isolation and genome-wide characterization of cellular DNA:RNA triplex structures IV |
| GSE120850 |
Isolation and genome-wide characterization of cellular DNA:RNA triplex structures |
|
| Relations |
| BioSample |
SAMN10177508 |
| SRA |
SRX4799318 |
