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Sample GSM2691426 Query DataSets for GSM2691426
Status Public on Feb 19, 2018
Title LOUCY_Untreated_Exp1_Rep1
Sample type SRA
 
Source name Leukemia cell line
Organism Homo sapiens
Characteristics cell line: LOUCY
treatment: Untreated
experiment number: 1
Growth protocol Cells were grown in RPMI-1640 (Gibco) supplemented with 10% FCS (HyClone) and 1% penicillin/streptomycin (PAA Laboratories)
Extracted molecule polyA RNA
Extraction protocol RNA was extracted using the RNeasy Mini Kit (Qiagen).
Libraries were constructed using the Smart-seq2 method (Picelli et al., Full-length RNA-seq from single cells using Smart-seq2. Nat Protocols 2014). cDNA was generated using SuperScript II (Invitrogen) and oligo-dT30VN primers (Biomers.net), pre-amplified using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) and purified using Agencourt AMPure XP (Beckman Coulter). Tagmentation and library preparation was performed using the Nextera XT DNA Library Preparation Kit (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing FASTQ files were aligned to the human genome (hg38) using STAR version 2.5.1b.
Reads mapping to gene exons were counted using the Subread (version 1.4.5-p1) featureCounts tool and the hg38 annotation.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using edgeR (version 3.10.5). Only genes detected at greater than 1 count per million (cpm) in at least 4 samples were included for analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Table of RPKM values for all samples for all genes expressed at greater than 1 cpm in at least 4 samples
 
Submission date Jun 30, 2017
Last update date May 15, 2019
Contact name Christopher Booth
Organization name University of Oxford
Department Weatherall Institute of Molecular Medicine
Street address John Radcliffe Hospital
City Oxford
State/province Oxfordshire
ZIP/Postal code OX3 9DS
Country United Kingdom
 
Platform ID GPL18573
Series (2)
GSE100694 Ezh2 and Runx1 Mutations Collaborate to Initiate Lympho-Myeloid Leukemia in Early Thymic Progenitors [Human cell line RNA-seq]
GSE100695 Ezh2 and Runx1 Mutations Collaborate to Initiate Lympho-Myeloid Leukemia in Early Thymic Progenitors
Relations
BioSample SAMN07304696
SRA SRX2975030

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record

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