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Sample GSM5311379 Query DataSets for GSM5311379
Status Public on Apr 03, 2024
Title HEL-WT1
Sample type SRA
 
Source name erytroleukemia cell
Organism Homo sapiens
Characteristics cell line: HEL cells
treatment: Untreated
genotype: Wild-type
Extracted molecule total RNA
Extraction protocol RNA was extracted using Direct-zol RNA Microprep (ZYMO RESEARCH, R2061) and cDNA synthesized by qScript cDNA Super-Mix (Quanta bio, #95048-100), according to the manufacturer’s instructions.
RNA-seq library prep was carried out using the Illumina TruSeq Total Total Stranded kit (RS-122-2201) with Ribo-Zero rRNA reduction following the manufacturer’s protocol without modification.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing FASTQ data were processed with cutadapt v1.15 (--nextseq-trim=20 -m 18) to remove low quality reads.
Gene level counts were estimated using RSEM v1.3.0 and STAR v2.6.0c alignment to the human hg19 transcriptome (GENCODE V19 annotation).
RUVseq v1.12.0 was sed adjusted gene counts by removing unwanted variance using exogenous ERCC spike-in RNA.
DESeq2 version 1.18.1 and R (version 3.4.1) were used for sample normalization and differential expression analysis with a q value < 0.25 and an FC > 2.0 (Wald test).
 
Submission date May 13, 2021
Last update date Apr 03, 2024
Contact name Hidehiro Itonaga
E-mail(s) itoman820hide@outlook.jp
Phone 3052436351
Organization name Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami
Department Department of Biochemistry and Molecular Biology
Lab Nimer Lab
Street address 1501 NW 10th Ave
City Miami
State/province FL
ZIP/Postal code 33136
Country USA
 
Platform ID GPL24676
Series (1)
GSE174432 RNA Sequencing Analysis of Wild Type and Non-phosphorylatable CARM1 mutation knock-in HEL cells
Relations
BioSample SAMN19184747
SRA SRX10875409

Supplementary file Size Download File type/resource
GSM5311379_WT_01_merged.rsem.cpm.fwd.bw 34.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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