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Sample GSM6711859 Query DataSets for GSM6711859
Status Public on Aug 10, 2023
Title ABCG2+ L3.6pl, MM-102, replicate 2
Sample type SRA
 
Source name L3.6pl
Organism Homo sapiens
Characteristics cell line: L3.6pl
cell type: Pancreatic adenosquamous carcinoma
genotype: Mutation; HGNC; 6407; KRAS; Simple; p.Gly12Asp (c.35G>A); ClinVar=VCV000012582; Zygosity=Unspecified (from parent cell line).
treatment: MM-102
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from ABCG2+ L3.6pl tumorspheres with Trizol reagent and purified using Direct-zol RNA miniprep kit according to the manufacturer’s instructions.
Ribosomal RNA was depleted using NEBNEXT rRNA Depletion Kit v2 (Human/Mouse/Rat) (New England Biolabs, cat. E7400S) as per the manufacturer’s instructions. RNA-seq libraries were prepared using NEBNEXT Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, cat. E7760S) according to the manufacturer’s instructions. Fragment size distribution of cDNA libraries was determined using Agilent 4150 TapeStation system (Agilent Technologies). RNA-sequencing of 3 biological replicates per each treatment condition was performed at CD Genomics (New York, USA) using an Illumina NovaSeq6000 S4 sequencing platform.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description ABCG2+ L3.6pl cells
MM102_rep_2
Data processing Raw reads were cleaned using fastp v0.23.2 with default parameters.
Cleaned reads were confirmed high-quality using FastQC v0.11.9.
cleaned reads were mapped to the human genome hg38 using STAR v2.7.3a.
The mapped reads were quantified using featureCounts v2.0.0.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample
 
Submission date Nov 04, 2022
Last update date Aug 10, 2023
Contact name Siwei Deng
E-mail(s) siwei.deng@hotmail.com
Organization name University of Oxford
Department Radcliffe Department of Medicine
Street address Old Rd, Headington
City Oxford
ZIP/Postal code OX3 7LD
Country United Kingdom
 
Platform ID GPL24676
Series (2)
GSE217331 Targeting an RNA polymerase II-associated PHF5A transcriptional subcomplex with a KMT2A-WDR5 inhibitor impairs self-renewal and tumorigenicity of pancreatic cancer stem cells III
GSE217332 Targeting an RNA polymerase II-associated PHF5A transcriptional subcomplex with a KMT2A-WDR5 inhibitor impairs self-renewal and tumorigenicity of pancreatic cancer stem cells
Relations
BioSample SAMN31202215
SRA SRX17989178

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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