|
| Status |
Public on Apr 05, 2018 |
| Title |
OCI/AML-3_6nM_NVP-2_rep-2 |
| Sample type |
SRA |
| |
|
| Source name |
OCI/AML-3_6nM_NVP-2_rep-2
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: 6nM NVP-2, 90 min
cell line: OCI/AML-3
4su labeling time before harvest (min): 60
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using a commercial column purification kit and treated with iodoacetamide for alkylation of 4-thiouridine.
3'UTR sequencing libraries were generated from 500ng of alkylated total RNA using a commercial kit (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Shallow sequencing for observation of global effects on transcription.
|
| Data processing |
Library strategy: SLAM-seq
Raw reads were adapter trimmed using cutadapt through the trim_galore (v0.3.7) wrapper tool with adapter overlaps set to 3bp for trimming (--stringency 3).
Trimmed reads were processed using SlamDunk v0.2.4 running the full analysis procedure (slamdunk all) and aligning against the human genome (UCSC version GRCh38), trimming 12 bp from the 5’ end (-5 12), reporting up to 100 alignments for multimappers (-n 100) and activating multimapper retainment strategy (-m), filtering for variants with a variant fraction of 0.2 (-mv 0.2), filtering with a base-quality cutoff of 27 (-mbq 27) and stringency filter set to 2 (requiring ≥ 2 T>C conversions per read).
Genome_build: GRCh38
Supplementary_files_format_and_content: *tsv: Tab-delimited text files; SlamDunk v0.2.4 output containing UTR coordinates named by EntrezID, raw and normalized read counts, as well as T>C conversion statistics. For details see: http://t-neumann.github.io/slamdunk/docs.html
Supplementary_files_format_and_content: hg38_refseq_062016_ensemblv84_3UTR.bed
|
| |
|
| Submission date |
Jun 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthias Muhar |
| E-mail(s) |
matthias.muhar@imp.ac.at
|
| Organization name |
Research Institute for Molecular Pathology
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| State/province |
- |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL18460 |
| Series (2) |
| GSE100708 |
SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis [SLAM-seq] |
| GSE111463 |
SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis |
|
| Relations |
| BioSample |
SAMN07322747 |
| SRA |
SRX2985799 |
