|
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, Camà 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 |