GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM5202112

Query DataSets for GSM5202112

Status

Public on Mar 30, 2021

Title

GC B cells, input

Sample type

SRA

Source name

GC B cells

Organism

Mus musculus

Characteristics

cell type: GC B cells
strain: C57BL/6
tag: none

Growth protocol

For RNA-seq, Naïve B cells were isolated from C57BL/6 mice, infected with RVKM-Empty/Ascl2 retrovirus and in vitro cultured with anti-IgM&anti-CD40. For ChIP-seq, GC B cells were isolated from draining LN after KLH immunization at 7 days.

Extracted molecule

genomic DNA

Extraction protocol

The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions. The ChIP assay was performed using ChIP-IT Express Chromatin Immunoprecipitation Kits (Active Motif) according to manufacturer’s instructions with slight modifications.
RNA-seq library was constructed for deep sequencing by BGI Genomics. ChIP-seq DNA library was constructed for deep sequencing by BGI Genomics.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

BGISEQ-500

Data processing

For RNA-seq, low quality reads and adaptor sequences were removed by Trim Galore,then clean reads were aligned to mm10 by bowtie2 with default parameter.
Differentially expressed genes were identified by at least 1.5fold change and fdr adjusted p-value 0.05
For ChIP-seq, all sequencing reads were mapped to the mouse genome mm10 by bowtie2, then PCR duplicates were removed using picard MarkDuplicates
For ChIP-seq, the uniquely mapped reads were used to call peak with MACS2 using a p value cutoff 0.01
Genome_build: mm10
Supplementary_files_format_and_content: expression data, bigwig file

Submission date

Mar 23, 2021

Last update date

Mar 30, 2021

Contact name

Chen Dong

Organization name

Tsinghua University

Department

Institute for Immunology and School of Medicine

Lab

Dongchen's lab