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Status |
Public on Jan 26, 2021 |
Title |
S_KO_LPS_SMRT_rp1 |
Sample type |
SRA |
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Source name |
RAW264.7 cells
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Organism |
Mus musculus |
Characteristics |
cell type: Macrophage strain: BALB/c antibody: SMRT agent: LPS time point: 2 hours
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Treatment protocol |
RAW264.7 cells were treated with or without LPS treatment (2 hours)
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Growth protocol |
CRISPR/cas9-mediated enhancer/promoter knockout or lentivius-mediated gene knockdown RAW264.7 cells were maintained normal 10% FBS DMEM medium
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Extracted molecule |
genomic DNA |
Extraction protocol |
Fresh cells were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 30 min, followed by 1% formaldehyde for 10 min at room temperature. Nuclei were isolated, sonicated and incubated with magnetic bead-antibody complexes. ChIPed DNA was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
NextSeq 550 |
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Description |
ChIP-seq_Sample
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Data processing |
ChIP-seq raw files (fastq or txt files, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept. Genome_build: mm9 Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak. ChIP-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept. Genome_build: mm9 Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak. GRO-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using bwa with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept. Genome_build: mm9 Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak. 4C-seq raw files (fastq, paired-end) were performed by the standard 4Cseqpipe protocol. The primer sequences were trimmed from the raw reads. The trimmed reads were mapped to the mm9 reference fragmented genome. The contact intensity was normalized by the fragment counts. The cis-interacting DNA contact profiles around the baits were plotted in the same chromosome window. Genome_build: mm9 Supplementary_files_format_and_content: 4C-seq analysis does not provide processed data file. RNA-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition. Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes. Genome_build: mm9 Supplementary_files_format_and_content: Bedgraph files contain the tags for each condense gene ATAC-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. MACS2 was used for the peak calling. The differential changed peaks was done in R using edgeR. Genome_build: mm9 Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak.
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Submission date |
Oct 22, 2020 |
Last update date |
Jan 26, 2021 |
Contact name |
Zhiqiang Huang |
E-mail(s) |
zhiqiang.huang@ki.se, zhiqiang.huang@nju.edu.cn
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Organization name |
Nanjing University
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Department |
Medical School
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Street address |
Hankou 22
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City |
Nanjing |
State/province |
Jiangsu |
ZIP/Postal code |
210093 |
Country |
China |
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Platform ID |
GPL21626 |
Series (1) |
GSE130383 |
The corepressors GPS2 and SMRT control enhancer and silencer function linked to eRNA transcription during inflammatory activation of macrophages |
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Relations |
BioSample |
SAMN16516902 |
SRA |
SRX9344814 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4848538_S_KO_LPS_SMRT_rp1.UCSC.bedGraph.gz |
85.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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