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Sample GSM2872559 Query DataSets for GSM2872559
Status Public on Sep 27, 2018
Title NT2D1_PRMT6_KO-2_-RA_rep3
Sample type SRA
 
Source name embryonal carcinoma cell line
Organism Homo sapiens
Characteristics cell line: NT2/D1
cell type: pluripotent embryonal carcinoma cell line
genotype/variation: CRISPR/Cas9-mediated deletion of PRMT6
atra: -
Treatment protocol 1 µM all-trans retinoic acid (ATRA) for 3 days.
Growth protocol NT2/D1 cells were cultured in DMEMI supplemented with 10% FCS.
Extracted molecule total RNA
Extraction protocol RNA was prepared using RNA-Mini-Kit (Seqlab, Göttingen, Germany).
Library preparation was done with Illumina TruSeq stranded mRNA Kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description CRISPR/Cas9-mediated deletion of PRMT6 in NT2/D1 cells.
Processed data file: PRMT6_CT_KO+-ATRA_raw_tagcounts.txt
Data processing Illumina RTA 1.8.66.4 software used for basecalling.
Sequenced reads were trimmed for adaptor using Illumina bcl2fastq, then mapped to hg19 whole genome using Tophat2.
Exon counts were aggregated for each gene to build a read count table using SubRead function featureCount.
Counts for each gene were normalized by DESeq2 according to instructions by authors.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: PRMT6_CT_KO+-ATRA_raw_tagcounts.txt: Tab-delimited text file includes raw counts for each Sample.
 
Submission date Dec 01, 2017
Last update date May 15, 2019
Contact name Uta Maria Bauer
E-mail(s) bauer@imt.uni-marburg.de
Organization name Philipps University Marburg
Department Institute of Molecular Biology and Tumor Research
Lab AG Bauer
Street address Hans-Meerwein-Str. 2
City Marburg
State/province Hessen
ZIP/Postal code 35043
Country Germany
 
Platform ID GPL18460
Series (2)
GSE107611 Transcriptome analysis of PRMT6 knock-out in NT2/D1 cells
GSE107612 Genomic location of PRMT6-dependent H3R2 methylation is decisive for the transcriptional outcome of associated genes
Relations
BioSample SAMN08120296
SRA SRX3437624

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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