DOI: 10.5061/dryad.cjsxksnb5
title: PHRF1 promotes the class switch recombination of IgA in CH12F3-2A cells-Dataset

description:  PHRF1 is an E3 ligase that promotes TGF-B signaling by
 ubiquitinating a homeodomain repressor TG-interacting factor (TGIF). The
 suppression of PHRF1 activity by PML-RAR facilitates the
 progression of acute promyelocytic leukemia (APL). PHRF1 also contributes
 to non-homologous end-joining in response to DNA damage by linking
 H3K36me3 and NBS1 with DNA repair machinery. However, its role in class
 switch recombination (CSR) is not well understood. In this study, we
 report the importance of PHRF1 in IgA switching in CH12F3-2A cells and
 CD19-Cre mice. Our studies revealed that Crispr-Cas9 mediated PHRF1
 knockout and shRNA-silenced CH12F3-2A cells reduced IgA production, as
 well as decreased the amounts of PARP1, NELF-A, and NELF-D. The
 introduction of PARP1 could partially restore IgA production in PHRF1
 knockout cells. Intriguingly, IgA, as well as IgG1, IgG2a, and IgG3,
 switchings were not significantly decreased in PHRF1 deficient splenic B
 lymphocytes isolated from CD19-Cre mice. The levels of PARP1 and NELF-D
 were not decreased in PHRF1-depleted primary splenic B cells. Overall, our
 findings suggest that PHRF1 may modulate IgA switching in CH12F3-2A cells.
description: The file is the result of RNA-seq analysis in "PHRF1
 promotes the class switch recombination of IgA in CH12F3-2A cells".
 The samples include normal CH12F3-2A cells and PHRF1 gene
 knockout CH12F3-2A cells. RNA was extracted and sequenced by
 next-generation sequence. The raw data is analyzed with KEGG pathway
 enricment.
description: The file is compatible with Microsoft Excel.
description: # Title of Dataset: *** PHRF1 promotes the class switch recombination of
 IgA in CH12F3-2A cells-Dataset ## Description of the Data and file
 structure The file is the result of RNA-seq analysis in "PHRF1
 promotes the class switch recombination of IgA in CH12F3-2A cells".
 The samples include normal CH12F3-2A cells and PHRF1 gene knockout
 CH12F3-2A cells. RNA was extracted and sequenced by next-generation
 sequence. The raw data is analyzed with the bioinformatic tool. File
 Cr\_wt\_Comparison\_CH12F3\_FC\_over\_2 is RNA seq data from 3 normal
 CH12F3-2A cells (WT) and 3 PHRF1 gene knockout CH12F3-2A cells (Cr). The
 raw data is analyzed with CLC Genomics Workbench v10. The comparison
 report contains the following information: Name: Gene name. Chromosome:
 Chromosome of gene Region: Region of gene Gene length: The length of gene.
 Exon length: The total length of exon. Exon: The number of exon. Gene ID:
 Gene ID Gene Description: Description of gene EntrezGene ID: The gene ID
 in NCBI Biotype: The type of gene. Transcripts annotated: The number of
 transcripts GO Biological Process: Biological process of GO GO Cellular
 Component: Cellular component of GO GO Molecular Function: Molecular
 function of GO KEGG Pathway: KEGG pathway of gene Target-based of Drugs
 from KEGG (Human): Target-based of Drugs with genes from KEGG in human.
 Fold Change: For a two-group experiment the 'Fold Change' tells
 you how many times bigger the mean expression value in group 2 is relative
 to that of group 1. If the mean expression value in group 2 is bigger than
 that in group 1 this value is the mean expression value in group 2 divided
 by that in group 1. If the mean expression value in group 2 is smaller
 than that in group 1 the fold change is the mean expression value in group
 1 divided by that in group 2 with a negative sign. Thus, if the mean
 expression levels in group 1 and group 2 are 10 and 50 respectively, the
 fold change is 5, and if the and if the mean expression levels in group 1
 and group 2 are 50 and 10 respectively, the fold change is -5. For
 experiments with more than two groups, the 'Fold Change' column
 contains the ratio of the maximum of the mean expression values of the
 groups to the minimum of the mean expression values of the groups,
 multiplied by -1 if the group with the maximum mean expression value
 occurs before the group with the minimum mean expression value (with the
 ordering: group 1, group 2, ...). Adjust Pvalue (Benjamini-Hochberg):
 Adjust p-value from DESeq2 (R package: v. 1.30.1). The smaller, the more
 significant FPKM. This is the expression value measured in FPKM. Mean. The
 mean of FPKM Total exon fragments: Total exon fragments of gene File
 KEGG　Pathway\_list is Pathway enrichment Analysis report. RNA-Seq data is
 analyed by KEGG Orthology system -Pathway and Gene -orthology group
 http://www.genome.jp/kegg/ko.html (version: 2016/05/24). The report
 contains the following information: PathwayID: Pathway ID in KEGG
 database. Pathways description: Description of pathway. Number of DEGs
 with pathway annotation: Genes involved in the term Number of DEGs with
 pathway annotation %: percentage of the gene involved in the term Up
 regulated: Number of the up regulated genes Down regulated: Number of the
 down regulated genes Number of All genes with pathway annotation: All
 Genes involved in the term Number of All genes with pathway annotation %:
 Percentage of all Genes involved in the term P-Value: Modified Fisher
 Extact P-Value, EASE Score. (The smaller, the more enriched.) Q-value:
 Q-value by q-value (R package: v1.38.0). Ref1: Bass JDSwcfAJ, Dabney A and
 Robinson D (2015). qvalue: Q-value estimation for false discovery rate
 control. Ref2:
 https://bioconductor.org/packages/release/bioc/html/qvalue.html
 Bonferroni: To globally correct enrichment P-values to control (Bonferroni
 correction) Benjamini: To globally correct enrichment P-values to control
 (Benjamini & Hochberg’s) FDR: To globally correct enrichment
 P-values to control (False discovery rate) Gene(Up): Gene list of up
 regulated genes Gene(Down): Gene list of down regulated genes ##
 Sharing/access Information Links to other publicly accessible locations of
 the data: https://doi.org/10.5061/dryad.cjsxksnb5 Was data derived from
 another source? No