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Status |
Public on Apr 18, 2024 |
Title |
PB classical monocytes, healthy donor 3 |
Sample type |
SRA |
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Source name |
PBMCs
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Organism |
Homo sapiens |
Characteristics |
disease: HD tissue: PBMCs cell type: classical monocytes (CD14+ CD16-) gender: female genotype: healthy donor treatment: none
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Treatment protocol |
none
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Growth protocol |
Monocytes (195000 – 500000 cells per 96-well in 250 µl RPMI 1640/PenStrep/5% heat-inactivated human serum) were cultivated for 4 hours in humidified atmosphere (5% CO2, 37°C).
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was isolated with TRIzol and Direct-zol™ RNA Microprep Ultra-low input RNA sequencing library was prepared by using SMART-Seq HT kit for full-length cDNA synthesis and amplification (Takara, San Jose, CA, USA), and Illumina Nextera XT (Illumina, San Diego, CA, USA) was used for sequencing library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). RNA-seq, 2x150 bp paired-end configuration
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Data processing |
Image analysis and base calling were conducted by the HiSeq Control Software. Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into FASTQ files and de-multiplexed using Illumina’s bcl2fastq Conversion Software v2.20. Sequencing quality of raw FASTQ files was checked using FastQC 0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapter trimming and quality filtering of sequence reads were performed using Seqtk and cutadapt. The adapter clipped reads were also aligned to ribosomal RNA sequences using Bowtie 2 (v2.4.1) and the mapped reads were discarded. After that, mapping against the human genome (GRCh38 version 32 [Ensembl 98]) was performed using STAR aligner v.2.7.9a. The R package EBSeq was used for normalization and to infer differential gene and isoform expressions. Assembly: GRCh38 version 32/Ensembl 98 Supplementary files format and content: Table containing normalized counts for biological replicates
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Submission date |
Jul 05, 2023 |
Last update date |
Apr 18, 2024 |
Contact name |
Susann Winter |
Organization name |
University Hospital Carl Gustav Carus, Faculty of Medicine Carl Gustav Carus, TU Dresden
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Street address |
Fetscherstrasse 74
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City |
Dresden |
ZIP/Postal code |
01307 |
Country |
Germany |
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Platform ID |
GPL20301 |
Series (1) |
GSE236535 |
Mutations in the splicing factor SF3B1 are linked to frequent emergence of HLA-DRlow/neg monocytes in lower-risk myelodysplastic neoplasms |
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Relations |
BioSample |
SAMN36307257 |
SRA |
SRX20898187 |
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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