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Sample GSM4556588 Query DataSets for GSM4556588
Status Public on Feb 04, 2022
Title rna-seq from Tumor_WT_7
Sample type SRA
 
Source name A549 tumor
Organism Homo sapiens
Characteristics hdlbp: WT
replicate: replicate 7
Growth protocol A549 cells were grown in DMEM + 10%FCS
Extracted molecule polyA RNA
Extraction protocol RNA was extracted using Trizol
Next Ultra Directional RNA Library Prep Kit (NEB)
polyA+ RNA-Seq single end
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Basecalls were converted to fastq files using Bcl2Fastq (2.16.0.10). Reads were demultiplexed and 3’adapter sequences removed by Flexbar (v2.5). Read counts per gene and TPM values were obtained by RSEM (v.1.2.20) (Li and Dewey, 2011) using default parameters and Bowtie (v.1.1.2) (Langmead et al., 2009) as transcriptome alignment program.
Raw read counts were normalized using DESeq2 (Love et al., 2014) and pairwise comparisons between and within fractions performed using standard parameters.
Genome_build: hg19
Supplementary_files_format_and_content: processed_data_A549_tumor.txt: tab delimited matrix of read counts per mRNA for all samples, log2-transformed fold changes and p-adjusted values from DESeq2 output from pairwise comparisons, as well as normalized read counts per mRNA (norm. prefix).
 
Submission date May 15, 2020
Last update date Feb 04, 2022
Contact name Markus Landthaler
E-mail(s) markus.landthaler@mdc-berlin.de
Organization name MDC Berlin
Department Berlin Institute of Medical Systems Biology
Street address Robert-Roessle Str. 10
City Berlin
ZIP/Postal code 13125
Country Germany
 
Platform ID GPL20301
Series (2)
GSE148262 HDLBP binds ER-targeted mRNAs by multivalent interactions to promote protein synthesis of transmembrane and secreted proteins
GSE150691 Vigilin/HDLBP promotes translation of endoplasmic reticulum-targeted mRNAs (A549 HDLBP KO and WT)
Relations
BioSample SAMN14934331
SRA SRX8350439

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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