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| Status |
Public on Mar 16, 2020 |
| Title |
Neutrophils, MKL1 pt 2 |
| Sample type |
SRA |
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| Source name |
venous blood
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| Organism |
Homo sapiens |
| Characteristics |
cell type: neutrophil
genotype: MKL1-deficient
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| Extracted molecule |
total RNA |
| Extraction protocol |
Neutrophils were isolated by percoll gradient and 1-3 x 106 freshly purified neutrophils were suspended in RNAlater (RLT) lysis buffer. From this lysate RNA was purified using the QIAamp RNA Blood Mini Kit (Qiagen, Hilden, Germany).
cDNA was synthesized with SuperScript™ VILO™ cDNA Synthesis Kit (Thermofisher Scientific, Waltham, Massachusetts, USA) in an Ampliseq plate from the Ion AmpliSeq™ Kit for Chef DL8 (Thermofisher Scientific). The Ion AmpliSeq™ Transcriptome Human Gene Expression Panel, Chef Ready Kit (Thermofisher Scientific) was used to produce amplicons from 20,000 RefSeq genesLibrary preparation was done on the Ion Chef sytem (Thermofisher Scientific) . Libraries were sequenced on the Genestudio S5 (Thermofisher Scientific).
Targeted RNA-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent S5 |
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| Data processing |
The data were analyzed by the RNAseq plugin from the Torrent Suite software
The RNA output was analyzed in Rstudio 1.0.456/R version 3.5.3. using limma-voom
Moderated t-tests were performed taking into account biological and technical replicates;
Benjamini-Hochberg multiple comparison adjusted p <0.05 and a log fold change ≥1 was considered significant and relevant. The median of technical replicates per experimental condition were used for visualization in a heatmap using the Complexheatmap package
Genome_build: hg19
Supplementary_files_format_and_content: read counts
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| Submission date |
Jul 22, 2019 |
| Last update date |
Mar 16, 2020 |
| Contact name |
Evelien Sprenkeler |
| E-mail(s) |
e.sprenkeler@sanquin.nl
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| Organization name |
Sanquin Research
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| Department |
Department of Blood Cell Research
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| Street address |
Plesmanlaan 125
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| City |
Amsterdam |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
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| Platform ID |
GPL23934 |
| Series (1) |
| GSE134644 |
MKL1 deficiency results in a severe neutrophil motility defect due to impaired actin polymerization |
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| Relations |
| BioSample |
SAMN12336366 |
| SRA |
SRX6486562 |
| 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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