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Status |
Public on Mar 30, 2021 |
Title |
RVKM-Empty |
Sample type |
SRA |
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|
Source name |
RVKM-Empty transfected and in vitro cultured activated B cells
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Organism |
Mus musculus |
Characteristics |
cell type: Naive B cells strain: C57BL/6
|
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 |
total RNA |
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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
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
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|
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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
|
Street address |
Haidian District
|
City |
Beijing |
ZIP/Postal code |
100084 |
Country |
China |
|
|
Platform ID |
GPL23479 |
Series (1) |
GSE169416 |
Transcription factor Ascl2 promotes geminal center B cell responses through directly regulating AID transcription |
|
Relations |
BioSample |
SAMN18437813 |
SRA |
SRX10418013 |