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| Status |
Public on Sep 08, 2022 |
| Title |
P2_NOTCH |
| Sample type |
SRA |
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| Source name |
primary CLL cells
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| Organism |
Homo sapiens |
| Characteristics |
patient: P2
treatment: notch
igm: NO_IGM
disease: TRI12
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
raw_expressions.csv
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| 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.
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| Submission date |
May 14, 2020 |
| Last update date |
Sep 08, 2022 |
| Contact name |
Irina Mohorianu |
| E-mail(s) |
data-submissions@stemcells.cam.ac.uk
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| Organization name |
University of Cambridge
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| Department |
Wellcome-MRC Cambridge Stem Cell Institute
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| Street address |
Puddicombe Way
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| City |
Cambridge |
| ZIP/Postal code |
CB2 0AW |
| Country |
United Kingdom |
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| 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 |
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| Relations |
| BioSample |
SAMN14927883 |
| SRA |
SRX8343668 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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