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Sample GSM6944050 Query DataSets for GSM6944050
Status Public on Jan 08, 2024
Title HEK293 cells, triple KD, rep2
Sample type SRA
 
Source name HEK293
Organism Homo sapiens
Characteristics cell line: HEK293
genotype: triple KD
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from cells with Quick-RNA MicroPrep kit (Zymo). Polyadenylated RNA was then isolated using Dynabeads™ mRNA Purification Kit. Purification was done twice to increase purity.
Strand-specific libraries were generated using KAPA Stranded RNA-seq Library Preparation Kit (Roche)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Illumina base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCh38 assembly) using STAR 2.7.9a
Reads counted on GENCODE release 29 gene models using STAR 2.7.9a
Read alignments (.bam files) converted to bigWigs using bamCoverage 3.5.1
Assembly: hg38
Supplementary files format and content: Two-column tab-delimited text file with gene identifier and raw read count columns
Supplementary files format and content: Raw RNA-seq coverage in bigWig format, separate files for plus and minus strands
 
Submission date Jan 19, 2023
Last update date Jan 09, 2024
Contact name IBRAHIM AVSAR ILIK
E-mail(s) ilik@molgen.mpg.de
Organization name Max-Planck-Institut für molekulare Genetik
Lab OWL Aktas
Street address Ihnestraße 63-73
City Berlin
State/province Berlin
ZIP/Postal code 14195
Country Germany
 
Platform ID GPL24676
Series (2)
GSE223257 Autonomous transposons tune their sequences to ensure somatic suppression [polyA_HEK293]
GSE223263 Autonomous transposons tune their sequences to ensure somatic suppression.
Relations
BioSample SAMN32798218
SRA SRX19076268

Supplementary file Size Download File type/resource
GSM6944050_coverage_HEK293_triple_rep2_fwd_raw.bw 104.8 Mb (ftp)(http) BW
GSM6944050_coverage_HEK293_triple_rep2_rev_raw.bw 103.1 Mb (ftp)(http) BW
GSM6944050_read_counts_GRCh38_HEK293_triple_rep2.txt.gz 241.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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