|
| Status |
Public on Feb 25, 2019 |
| Title |
T4ph_mNETseq_siPCF11_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
T4ph_mNETseq_siPCF11
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa cells
genotype/treatment: PCF11 knock-down (5 nM)
antibody: Pol II T4ph (active motif, 61361, clone 6D7)
molecule subtype: Pol II bound RNA
|
| Treatment protocol |
siRNAs from Dharmacon were transfected for 48 hrs according to RNAiMAX reagent protocol at the concentrations indicated.
|
| Growth protocol |
HeLa cells were maintained in DMEM with 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nascent RNAs were purified from Pol II IP products of solubilized chromatin (Nojima et al., Nature Protocols, 2016, PMID: 2684442).
Libraries were prepared according to the protocols of TruSeq Small RNA Library Preparation kit (RS-200-0012, Illumina).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
wtPCF5nM-p318T4NET_S4
|
| Data processing |
library strategy: Mammalian Native elongating transcript sequencing (mNET-seq)
reads in FASTQ files were trimmed with cutadapt using following settings: -a TGGAATTCTCGG -A GATCGTCGGACT -e 0.05 -m 10 --times 1
trimmed reads were mapped with STAR 2.5b to hg19
last transcribed nucleotides positions from each read were retrieved using in house developed script based on R Bioconductor libraries similarily to (Nojima et al., 2016)
Those positions were further used to calculate genome-wide, sequencing depth normalized coverage utilized for downstream analysis and visualization
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files: genome-coverage files for all samples
|
| |
|
| Submission date |
Nov 29, 2018 |
| Last update date |
Feb 25, 2019 |
| Contact name |
Kinga Kamieniarz-Gdula |
| Organization name |
University of Oxford
|
| Department |
Sir William Dunn School of Pathology
|
| Street address |
South Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE123104 |
Selective roles of vertebrate PCF11 in premature and full-length transcript termination (mNET-seq) |
| GSE123105 |
Selective roles of vertebrate PCF11 in premature and full-length transcript termination |
|
| Relations |
| BioSample |
SAMN10497919 |
| SRA |
SRX5078070 |
