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| Status |
Public on Dec 23, 2019 |
| Title |
Delineating functional enhancers (cis-regulome) in LPS-activated murine splenic B cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
LPS activated murine splenic B cells (aB) were subjected to FAIRE-Seq, STARR-Seq, Hi-C, ChIP-seq, Nascent-RNA-seq and RNAseq to compile cis-regulome.
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| Overall design |
Splenic B cells were isolated from C56BL/6J mice (6-8 weeks of age) using B cell isolation kit from Miltenyi (Catalog # 130-090-862) and cultured in complete RPMI with 10% FCS. Purified B cells (250,000 cells/ml) were activated with LPS (10ug/ml, Salmonella typhimurium, Sigma Catalog # L6143). At 72h post-activation B cells were subjected to FAIRE-Seq, Hi-C, ChIP-seq, Nascent-RNA-seq (EU pulse-labeling) and RNAseq. STARR-Seq was performed by transfecting FAIRE-Seq plasmid library at 48h or 60h post LPS-activation. RNA was isolated at 72h post-activation and processed for STARR-Seq. STARR-Seq_24h refers to transfection of library at 48h and STARR-Seq_12h refers to transcfection at 60h. By computational integration of FAIRE-seq and STARR-seq datasets (HOMER peak calls) we identified approximately 10,000 functional enhancers in LPS-activated B cells. These enhancers were connected to active promoters identified by RNA-seq using Hi-C. Integrated datsets yielded a functional mammalian cis-regulome for activated B cells. Cis-regulome was further analyzed using ChIP-seq for 3 histone marks H3K4me1, H3K4me3 and H3K27ac. Nascent RNA-Seq was used for localizing eRNAs and determining rates of gene transcription. Resting B-cells (rB) were used as controls.
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| Web link |
https://www.nature.com/articles/s41590-019-0565-0
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| Contributor(s) |
Singh H, Chaudhri VK |
| Citation(s) |
31873292 |
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| Submission date |
Oct 24, 2018 |
| Last update date |
Jan 09, 2020 |
| Contact name |
Harinder Singh |
| E-mail(s) |
chaudhri.vk@gmail.com
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| Organization name |
CCHMC
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| Department |
Immunobiology
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| Lab |
Harinder Singh
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| Street address |
3333 Burnet Ave
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| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (34)
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| Relations |
| BioProject |
PRJNA498316 |
| SRA |
SRP166787 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE121753_CD43Neg_BCells_RNAseq.txt.gz |
586.0 Kb |
(ftp)(http) |
TXT |
| GSE121753_FAIREseq_aB_peaks.bed.gz |
638.3 Kb |
(ftp)(http) |
BED |
| GSE121753_H3K27ac_aB_SuperEnhancers.bed.gz |
556 b |
(ftp)(http) |
BED |
| GSE121753_H3K27ac_aB_peaks.bed.gz |
224.9 Kb |
(ftp)(http) |
BED |
| GSE121753_H3K4me3_aB_peaks.bed.gz |
160.3 Kb |
(ftp)(http) |
BED |
| GSE121753_HiC_Filtered_Enhancer_Promoter_Interactions.txt.gz |
886.8 Kb |
(ftp)(http) |
TXT |
| GSE121753_STARRseq_aB_peaks.bed.gz |
153.8 Kb |
(ftp)(http) |
BED |
| GSE121753_STARRseq_aB_peaks_overlap_FAIREseqPeaks.bed.gz |
105.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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