|
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 |