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Sample GSM4552737 Query DataSets for GSM4552737
Status Public on Sep 08, 2022
Title P5_CNT.replicate1
Sample type SRA
 
Source name primary CLL cells
Organism Homo sapiens
Characteristics patient: P5
condition: ctr
replicate: replicate1
disease: DEL13
Extracted molecule total RNA
Extraction protocol RNA was extracted post cell sorting using the RNeasy Plus Micro Kit (Qiagen)
HiSeq4000
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description raw_expression.csv
Data processing the quality checking of the sequencing output was performed with FastQC, and summarised using MultiQC; additional checks include PCAs, Jaccard Similarity Indices and MA plots
the trimming was done using Trim Galore (option –paired)
the alignment of reads against the reference genome (hg38, version GRCh38.p13) was performed using tophat (option –no-coverage-search)
The count matrix was obtained using featureCounts version v1.5.0
DE analysis performed on quantile and TMM normalised expression levels with edgeR version 3.28.0; a noise filtering of 50 was applied, briefly is the maximum expression of a gene, across all samples was <50, then the gene was excluded from subsequent analyses
the enrichment analysis was performed using g:profiler (Reimand et al., Nucleic Acids Research, 2016)
Genome_build: hg38 (version GRCh38.p13)
Supplementary_files_format_and_content: raw.csv, raw count matrix.
 
Submission date May 14, 2020
Last update date Sep 08, 2022
Contact name Irina Mohorianu
E-mail(s) data-submissions@stemcells.cam.ac.uk
Organization name University of Cambridge
Department Wellcome-MRC Cambridge Stem Cell Institute
Street address Puddicombe Way
City Cambridge
ZIP/Postal code CB2 0AW
Country United Kingdom
 
Platform ID GPL20301
Series (2)
GSE150584 Gene expression profile of primary CLL cells transduced with a retrovirus expressing mutated NOTCH1
GSE150610 Gene expression profile of primary CLL cells transduced with a mutated NOTCH1
Relations
BioSample SAMN14923997
SRA SRX8342450

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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