RNA Sequencing Analysis of Gene Expression Profiles in Cic-null B-1a and Follicular B (Fo B) cells
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ABSTRACT:
PROVIDER: PRJNA686176 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13269775_1.fastq.gz | Fastqsanger.gz | |||
| SRR13269775_2.fastq.gz | Fastqsanger.gz | |||
| SRR13269776_1.fastq.gz | Fastqsanger.gz | |||
| SRR13269776_2.fastq.gz | Fastqsanger.gz | |||
| SRR13269777_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Purpose: The goal of this study is to compare and examine the transcriptional profiles in control versus Cic-deficient B cells, specifically splenic B-1a and Fo B cells, by mRNA sequencing. Methods: Splenic B-1a (IgM+, CD19+, CD5+, CD43+) and Fo B (B220+, CD93-, CD23+, CD21lo-mid) cells were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using TRIzol Reagent (GeneAll), according to the manufacturer’s instructions. The DNA library for mRNA sequencing was generated using SMART-seq v4 Ultra Input RNA Kit (Clontech, for B-1a cells) and TruSeq RNA Sample Prep Kit v2 (Illumina, for Fo B cells). DNA libraries were multiplexed and pooled for sequencing on the Illumina Hiseq 4000 platform. Results: Trimmed reads were mapped to mouse reference genome (mm10 RefSeq) with HISAT2, a splice-aware aligner, and transcripts were assembled by StringTie with aligned reads, for known transcripts, novel transcripts, and alternatively spliced transcripts. A total of 712 genes were differentially expressed in Cic-null B-1a cells (325 upregulated and 387 downregulated), while 357 genes were differentially expressed in Cic-deficient Fo B cells (180 upregulated and 178 downregulated) when compared with their respective control cells (fold change >1.2 and P < 0.05). Several known CIC target genes, including Etv1, Etv4, Etv5, Spry4, Spred1, Spred2, Dusp4, Dusp6, and Per2, were included in the list of the upregulated differentially expressed genes (DEGs) in either Cic-null B-1a or Fo B cells or both, validating the reliability of RNA sequencing results. Conclusions: Our study presents the first comparative gene expression analysis of B-1a and Fo B cells from control and B cell-specific Cic-deficient mice. We concluded that CIC deficiency promotes B-1a cell development through enhancing the BCR signaling pathway. The data reported here also provide references for the gene expression profiles of murine B-1a and Fo B cells.
2021-12-16 | GSE163455 | GEO
Project description:Purpose: B-1a cells have a distinct BCR repertoire compared with that of B-2 cells. To examine whether CIC loss affects the BCR repertoire in B-1a cells, we analyzed mRNA sequences of immunoglobulin heavy (Igh) and light (Igk and Igl) chain genes in B-1a cells from 12-week-old control and Cicf/f;Cd19-Cre mice. Methods: Peritoneal cavity B-1a cells (IgM+, CD19+, CD5+, CD43+) were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using TRIzol Reagent (GeneAll), according to the manufacturer’s instructions. Long Read iR-Profile Reagent System (iRepertoire) was used to generate NGS libraries covering BCR chains including Igh, Igk, and Igl. Briefly, nested inside and outside primers selectively amplified all V- and C- regions and incorporated communal adaptors. Following clean up, only target amplicons, which contain 5’ and 3’ communal adaptors, were exponentially amplified. Amplified libraries were multiplexed for sequencing on the Illumina Miseq platform. Sequence reads were de-multiplexed according to the barcode sequences. Results: Trimmed reads were mapped to germline V, D and J reference sequences downloaded from the IMGT database. IgH diversity and the usage of variable (V) segments in heavy (Ighv) chain and light (Igkv and Iglv) chain genes were comparable between control and Cic-null B-1a cells. Analysis of non-templated (N)-nucleotide addition at V(D)J junctions revealed that Cic-null B-1a cells have a higher proportion of zero to two N-nucleotides-containing-BCRs than control cells. Conclusions: Our study presents the first comparative BCR repertoire analysis of wild-type and Cic-null B-1a cells. We concluded that CIC deficiency does not dramatically alter the BCR repertoire in B-1a cells.
2021-12-16 | GSE164147 | GEO
Project description:BCR repertoire analysis of wild-type and Cic-null B-1a cells
| PRJNA689304 | ENA
Project description:Purpose: The goal of this study is to compare and examine the transcriptional profiles in Cd19-Cre (control) versus Cicf/f;Cd19-Cre (Cic-null) MZB cells,by mRNA sequencing. Methods: MZB cells (CD19+CD93-CD21+CD23-) were sorted by a MoFlo-Astrios (Beckman Coulter). Total RNA was extracted using TRIzol Reagent (GeneAll), according to the manufacturer’s instructions. . A library for mRNA sequencing was prepared using the Truseq Stranded mRNA/Total Library Prep Kit (Illumina) according to the manufacturer’s instructions. Sequencing was performed with Novaseq 6000 (Illumina). Results: Tophat (v2.0.13) was used to map reads for each sample to the mm10 RefSeq reference genome. The aligned results were then added to Cuffdiff (v2.2.0) to identify the differentially expressed genes (DEGs). In total, 775 genes were differentially expressed in Cic-null MZB cells (505 upregulated and 270 downregulated) compared to control cells (Log2 fold-change > 0.5 and P < 0.01). Conclusions: Our study presents the first comparative gene expression analysis of MZB cells from control and B cell-specific Cic-deficient mice. We concluded that CIC deficiency attenuates MZB cell development through downregulation of the NOTCH signaling pathway. The data reported here also provide references for the gene expression profiles of murine MZB cells through TPM.
2024-04-29 | GSE264654 | GEO
Project description:T follicular helper (Tfh) cells provide signals to initiate and maintain the germinal center (GC) reaction and are crucial for the generation of robust antibody responses. We found that hypoxia inducible factor-1 (HIF-1a) is an inhiibitor of Tfh generation in a mouse model of acute viral infection, and that HIF-1a mediates its effects by suppressing mTORC1 activity.
2021-12-10 | GSE144467 | GEO
Project description:Upon immunization with a T cell dependent antigen naive follicular B cells (Fo) are activated and a germinal center reaction is induced. Within the next 2 weeks large germinal centers develop where the process of affinity maturation takes place. To analyze the gene expression profile of resting and activated B cells, follicular B cells (Fo), B cells from early (GC1) and late germinal centers (GC2) were isolated and their gene expression profile compared.
2011-03-29 | GSE28237 | GEO
Project description:We report the global gene expression in follicular (FO) B cells and age/autoimmunity-associated B cells (ABCs). We found that Fc-receptor like (Fcrl) 5 was highly expressed in ABCs isolated from 50-week-old mice, compared to FO B cells. This study provides a basis for understanding the relationship between autoimmune diseases and Fcrl5 expression in B cells.
2023-09-14 | GSE237540 | GEO
Project description:Upon immunization with a T cell dependent antigen naive follicular B cells (Fo) are activated and a germinal center reaction is induced. Within the next 2 weeks large germinal centers develop where the process of affinity maturation takes place. To analyze the gene expression profile of resting and activated B cells, follicular B cells (Fo), B cells from early (GC1) and late germinal centers (GC2) were isolated and their gene expression profile compared. Gene expression profiles of Fo versus GC1 and GC2 B cells, respectively. Naïve Fo B cells were isolated from non-immunized BALB/c mice. Germinal center B cells sorted from spleen cell suspensions of BALB/-c mice immunized with the T cell dependent antigen 2-phenyl Oxazolone. GC1 B cells were isolated 7 days after primary immunization. GC2 cells were isolated 15 days after primary immunization. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in duplicates for each of the three groups to the GeneChip arrays. Group1: Fo, Group2: GC1, Group3: GC2. Lists of differentially regulated genes were created using High Performance Chip Data Analysis (HPCDA) with Bioretis database (http://www.bioretis-analysis.de). Worldwide data sharing is possible via Bioretis, please ask the authors.
2011-03-29 | E-GEOD-28237 | biostudies-arrayexpress
Project description:We have analyzed miRNA expression profile in FO and MZ B cells to identified differentially expressed miRNAs between this two subsets that could be potencially involved in the regulation of terminal B cell differentiation Spleens from CD19-Creki/+Dicerfl/+ and CD19-Creki/+Dicerfl/fl mice were collected and after erythrocyte lysis, splenocytes were stained with anti-B220, anti-CD21 and anti-CD23 antibodies. B220+CD21brightCD23+ (MZ) and B220+CD21+CD23bright (FO) B cell populations were sorted and total RNA of purified populations was extracted with TRIzol. miRNA microarray hybridations were performed on Mouse miRNA Microarray platform (Agilent Technologies).
2011-11-01 | E-GEOD-25139 | biostudies-arrayexpress
Project description:Immature B cells in spleens of mouse and human differentiate into at least two subsets of mature B cells, the follicular (FO) B cells and the marginal zone (MZ) B cells, but functions, maturation and other properties of these cells are largely unknown. To solve these questions, in this study, we performed transcriptome analyses of FO and MZ B cells sorted from spleens of normal unimmunized mice using gene chips. By comparison of gene expression profiles between FO and MZ B cells, we identified 1226 genes that are expressed higher in FO B cells than in MZ B cells. On the other hand, 1734 genes were found to be expressed higher in MZ B cells than in FO B cells. We noticed that some of differentially expressed genes have been reportedly characterized in FO and MZ B cells, suggesting the reliability of the analysis. By using FACS analyses, we confirmed that CD36, CD68, and CD49e are expressed on MZ B-cells but not on FO B-cells. These results revealed new phenotypic and functional properties of FO and MZ B cells, and set a molecular basis for further studying differentiation and functions of these mature B cells. Experiment Overall Design: one follicular B cells replicate and one marginal zone B cells replicate were analyzed.
2008-06-12 | E-GEOD-3599 | biostudies-arrayexpress