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Sample GSM7549618 Query DataSets for GSM7549618
Status Public on Apr 18, 2024
Title PB_classical monocytes,SF3B1wt LR-MDS, patient 2
Sample type SRA
 
Source name PBMCs
Organism Homo sapiens
Characteristics disease: LR-MDS
tissue: PBMCs
cell type: classical monocytes (CD14+ CD16-)
gender: male
genotype: SF3B1wt, EZH2mut, CBLmut
treatment: none
Treatment protocol none
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).
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
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
 
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
Street address Fetscherstrasse 74
City Dresden
ZIP/Postal code 01307
Country Germany
 
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
Relations
BioSample SAMN36307252
SRA SRX20898192

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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