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Sample GSM4552931 Query DataSets for GSM4552931
Status Public on Sep 08, 2022
Title P1_CTR_IGM
Sample type SRA
Source name primary CLL cells
Organism Homo sapiens
Characteristics patient: P1
treatment: ctr
igm: IGM
disease: TRI12
Extracted molecule total RNA
Extraction protocol RNA was extracted using the RNeasy Plus Micro Kit (Qiagen)
Libraries were prepared using the NEBNext Ultra™ II DNA Library Prep Kit for Illumina
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description raw_expressions.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
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)
GSE150595 Gene expression profile of primary CLL cells transduced with a mutated form on NOTCH1 following IgM stimulation
GSE150610 Gene expression profile of primary CLL cells transduced with a mutated NOTCH1
BioSample SAMN14927888
SRA SRX8343663

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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