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Sample GSM2691888 Query DataSets for GSM2691888
Status Public on Apr 05, 2018
Title MOLM-13_6nM_NVP-2_rep-1_exp-2
Sample type SRA
 
Source name MOLM-13_6nM_NVP-2_rep-1_exp-2
Organism Homo sapiens
Characteristics treatment: 6nM NVP-2, 90 min
cell line: MOLM-13
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 SAMN07322761
SRA SRX2985785

Supplementary file Size Download File type/resource
GSM2691888_Sample41_tcount.tsv.gz 1.1 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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