ATAC-Seq of pDC Transcriptomes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA738890 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14094960_1.fastq.gz | Fastqsanger.gz | |||
| SRR14094960_2.fastq.gz | Fastqsanger.gz | |||
| SRR14094961_1.fastq.gz | Fastqsanger.gz | |||
| SRR14094961_2.fastq.gz | Fastqsanger.gz | |||
| SRR14094962_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:ATAC-Seq of Wild Type pDC Transcriptomes (CpG 0h, 2h)
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Project description:ATAC-Seq of Batf-deficient pDC Transcriptomes (CpG 0h, 2h)
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Project description:Purpose: The goals of this study are to compare the pDC chromatin structure (ATAC-seq) at steady state and at 2h after CpG activation. Methods: Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay. The cells were then thawed in a 37°C water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al., 2013), with some modifications based on (Corces et al., 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina). Results: Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cut off of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations. For differential analysis, reads were counted in all merged peak regions (using Subread), and the replicates for each condition were compared using DESeq2. Conclusions: Our study represents a detailed analysis of naive and activated pDC chromatin that analyzes the global murine TF reservoir as defined by Hu et al. in the AnimalTFdb (Hu et al. , 2019, Nucleic Acids Res 47, D33-D38). Our results show that pDC activation substantially altered the chromatin structure making it more or less accessible to specific TF families.
2021-04-01 | GSE171075 | GEO
Project description:Purpose: The goals of this study are to compare the pDC chromatin structure (ATAC-seq) at steady state and at 2h after CpG activation. Methods: Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay. The cells were then thawed in a 37°C water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al., 2013), with some modifications based on (Corces et al., 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina). Results: Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cut off of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations. For differential analysis, reads were counted in all merged peak regions (using Subread), and the replicates for each condition were compared using DESeq2. Conclusions: Our study represents a detailed analysis of naive and activated pDC chromatin that analyzes the role of the transcription factor BATF for chromatin structure in pDCs.
2024-01-12 | GSE178410 | GEO
Project description:ChIP-Seq of Wild Type pDC Transcriptomes (CpG 0h, 2h)
| PRJNA721219 | ENA
Project description:Genome-wide chromatin accessibility analysis in colorectal cancer PDC (ATAC-Seq)
| PRJNA684606 | ENA
Project description:Dendritic cells (DC) are professional antigen presenting cells that comprise different subsets: classical DC type 1 and 2 (cDC1 and cDC2, respectively) and plasmacytoid DC (pDC). In this study cDC1 or pDC were obtained in a two-step in vitro culture system according to Felker et al., J. Immunol. 185, 5326-5335, 2010. Briefly, mouse bone marrow cells were first amplified with a specific cytokine cocktail and then induced to differentiate into DC with Flt3 ligand. cDC1 are CD11c+ CD11b+ XCR1+ and pDC are CD11c+ CD11b- B220+ and thus cDC1 and pDC were obtained by FACS sorting and subjected to Omin-ATAC-seq analysis. As an example of practical application of HINT-ATAC, we performed Omin-ATAC-seq experiments of cDC and pDC cell populations and used HINT-ATAC to detect footprints within ATAC-seq peaks of each of these two cells. Next, we estimated changes in binding activity for all factors with a motif in JASPAR. Cell-specific TF activity is measured by the depth of footprints and number of reads flanking regions. Two known cDC factors, BATF3 and HES1, are detected. In summary, we demonstrated that HINT-ATAC is capable of identifying relevant factors for dendritic cell specification.
2019-01-15 | GSE118221 | GEO
Project description:During hematopoiesis, cells originating from the same stem cell reservoir differentiate into distinct cell types. The mechanisms enabling common progenitors to differentiate into distinct cell fates are not fully understood. Here, we identify chromatin-regulating and cell-fate-determining transcription factors (TF) governing dendritic cell (DC) development by annotating the enhancer and promoter landscapes of the DC lineage. Combining these analyses with detailed over-expression, knockdown and ChIP-Seq studies, we show that Irf8 functions as a plasmacytoid DC epigenetic and fate-determining TF, regulating massive, cell-specific chromatin changes in thousands of pDC enhancers. Importantly, Irf8 forms a negative feedback loop with Cebpb, a monocyte-derived DC epigenetic fate-determining TF. We show that using this circuit logic, differential activity of TF can stably define epigenetic and transcriptional states, regardless of the microenvironment. More broadly, our study proposes a general paradigm that allows closely related cells with a similar set of signal-dependent factors to generate differential and persistent enhancer landscapes. Here we profiled accessible chromatin of moDC and pDC using ATAC-seq assay, developed by Buenrostro et al. (2013)
2014-12-14 | E-GEOD-62703 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2021-06-18 | GSE178412 | GEO
Project description:ATAC-seq in oesophageal cell lines, OE33 (OAC), FLO1 (OAC), HET1A (Normal)
2016-09-12 | E-MTAB-4209 | biostudies-arrayexpress