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Sample GSM3890764 Query DataSets for GSM3890764
Status Public on Jul 25, 2019
Title Wild-type replicate 1 for RNA-seq
Sample type SRA
Source name HEK293T
Organism Homo sapiens
Characteristics cell line: HEK293T
genotype: Wild-type
Growth protocol 6.4x10^6 cells of HEK293T WT or XRN1-null cells were plated on 15 cm dishes 24 hrs before harvesting.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and a library prepared using the TruSeq RNA Sample Prep Kit (Illumina). For Ribo-Seq, the original procedure of Ingolia et al (2012) Nature Protocols was followed with modifications from Calviello et al (2016) Nature Methods.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Description messenger RNA
Data processing Illumina software used for basecalling.
Adapters removed with Flexbar, ribosomal-derived reads were removed using Bowtie2
Remaining reads were then mapped on hg19 using Tophat2
Ribo-seq reads were analyzed for three-nucleotide periodicity using the RiboTaper
Read count analysis was done with an R/Bioconductor package QuasR
Differential gene expression analysis with an R/Bioconductor package edgeR
Translational efficiency (TE) was estimated using the statistical framework and analysis as implemented in the RiboDiff program
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file for readcounts; tab-delimited file for differential expression analysis; tab-delimtied file for translational efficiency analysis
Submission date Jun 13, 2019
Last update date Jul 25, 2019
Contact name Eugene Valkov
Phone 497071601357
Organization name Max Planck Institute for Developmental Biology
Department Biochemistry
Lab Abt. II
Street address Max-Planck-Ring 5
City Tuebingen
State/province Baden-Wuerttemberg
ZIP/Postal code 72076
Country Germany
Platform ID GPL21290
Series (1)
GSE132725 Transcriptome and ribosome profiling of XRN1-null HEK293T human cell line generated by CRISPR/Cas9 gene editing
BioSample SAMN12056132
SRA SRX6069655

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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