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Sample GSM1974836 Query DataSets for GSM1974836
Status Public on Dec 21, 2019
Title ZNF599_KO2
Sample type SRA
 
Source name HeLa cell line
Organism Homo sapiens
Characteristics cell line: HeLa
genotype: ZNF599 -/-
sequencing: single-end
Growth protocol HeLa cells were cultured in DMEM (Sigma) supplemented with 10% fetal calf serum (Biochrom) and 50 µg/ml gentamycine (PAA).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from HeLa cells in biological quadruplicates using the nucleospin triprep kit (Macherey-Nagel).
Smart-seq2 (Picelli et al. 2013) from 5ng of RNA
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing base-calls were performed with Illumina bcl2fastq
demultiplexing was done using the assignRG package
cDNA reads were mapped to the hg19 genome assembly using NGM (v.4.12) Sedlazeck et al. 2013 and minimum sequence identity of 0.9
reads were assigned to gene features using the Rsubread package Liao et al. 2014
Genome_build: hg19
Supplementary_files_format_and_content: .txt gene-wise read-counts per sample
 
Submission date Dec 17, 2015
Last update date Dec 21, 2019
Contact name Martha Smets
E-mail(s) smets@bio.lmu.de
Organization name Ludwig-Maximilians University Munich
Department Department Biology II
Street address Großhaderner Str. 2
City Martinsried
ZIP/Postal code 82152
Country Germany
 
Platform ID GPL18460
Series (1)
GSE76129 ZNF599 and DNMT3A coordinately control nuclear envelope organization by repression of SUN4 expression
Relations
BioSample SAMN04349620
SRA SRX1490512

Supplementary file Size Download File type/resource
GSM1974836_ZNF599_KO2.bam.count_counttable.txt.gz 190.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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