|
| Status |
Public on Aug 10, 2016 |
| Title |
polyA-K.rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
buffer: K
|
| Growth protocol |
HeLa cells were obtained from the European Collection of Animal Cell Cultures and grown in Dulbecco’s Modified Eagle Media (Sigma) supplemented with 10% fetal bovine serum (Sigma).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) with gDNA eliminator and quantified with Qubit 2.0
Custom library construction was developed for Illumina sequencing (compatible with TruSeq adapters and 6nt index barcoding sequences)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
replicate 3
|
| Data processing |
fastq files were trimmed for low quality tails and illumina adapters using trim_galore and aligned to the reference genome using tophat2
bam files from the alignment were cleaned (q > 30) using samtools
bedgraph coverage files were calculated using bedtools and scoring regions saved as bed files were identified using a customized procedure involving convolution-based filtering and linear model developed in R
Genome_build: hg19
Supplementary_files_format_and_content: aligned files; bedGraph files: ocverage file; bed files: scoring regions with the detected RNA G-quadruplexes.
|
| |
|
| Submission date |
Jan 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Giovanni Marsico |
| E-mail(s) |
persego@gmail.com
|
| Organization name |
CRUK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE77282 |
rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome |
|
| Relations |
| BioSample |
SAMN04444456 |
| SRA |
SRX1549462 |
