NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5239716 Query DataSets for GSM5239716
Status Public on Apr 13, 2021
Title HIGM2 unswitched memory B cells replicate 1
Sample type SRA
 
Source name Blood / PBMCs
Organism Homo sapiens
Characteristics genotype: AICDA-/-
cell type: unswitched memory B cells
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using Maxwell SimplyRNA kit
RNA-sequencing libraries from total mRNA were prepared and purified using Illumina Stranded mRNA Prep, Ligation kit (Illumina)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description higm_memory_R1
Data processing Raw sequence reads were initially processed using FastQC (Babraham Institute, Cambridge, UK)
Adapter sequences and poor quality reads were removed using TrimGalore that uses Cutadapt for trimming
Quality-filtered reads were then mapped to the human genome (hg19) using STAR and uniquely mapped reads were retained
Read counts were calculated using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: dds_matrix.txt (DESeq2 count matrix)
 
Submission date Apr 13, 2021
Last update date Apr 14, 2021
Contact name Esteban Ballestar
Organization name Josep Carreras Research Institute (IJC)
Lab Epigenetics and Immune Disease
Street address Ctra de Can Ruti, Camí de les Escoles s/n
City Badalona, Barcelona
State/province N/A = Not Applicable
ZIP/Postal code 08916
Country Spain
 
Platform ID GPL18573
Series (2)
GSE172011 Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction
GSE172012 The DNA methylome and transcriptome of hyper-IgM syndrome type 2 B cells
Relations
BioSample SAMN18736330
SRA SRX10595871

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.