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Sample GSM2643059 Query DataSets for GSM2643059
Status Public on Jul 01, 2017
Title ChIPseq_CTCF_1385_M_CK-KO_neuronal
Sample type SRA
 
Source name adult mouse cortex
Organism Mus musculus
Characteristics antibody: CTCF
age: adult
gender: M
genotype: CK-KO
cell type: neuronal
Extracted molecule genomic DNA
Extraction protocol Nuclei were extracted from mouse brain tissue with or without formaline fixation. Neuronal nuclei were collected by FACS. Cromatin was fragmented by Mnase digestion (histone ChIP) or sonication (CTCF ChIP), and immunoprecipitated by different antibodies.
ChIP DNA was end repaired (End-it DNA Repair kit; Epicentre) and A tailed (Klenow Exo-minus; Epicentre). Adaptors (Illumina) were ligated to the ChIP-DNA (Fast-Link kit; Epicentre) and then PCR amplified using Illumina TruSeq ChIP Library Prep Kit. Library DNA with expected size (NChIP, ~275bp; XChIP, 350bp to 500bp) was selected by Pippin.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description ChIPseq_CTCF_neuronal_KOvsWT_1kb_001_annotated.txt
Data processing RNA-seq: The sequenced RNAseq data were aligned to the Mouse (mm10) reference genome using Tophat2 short-read aligner. Reads were counted using HTSeq against the Gencode vM4 Mouse annotation. Genes were filtered based on the criteria that all replicates in either condition must have at least 5 reads per gene. On the resulting filtered transcript, a pairwise differential analysis between Setdb1 conditional mutant vs control cortex was performed using the voom-limma R package, which converts counts into precision weighted log2 counts per million and determines differentially expressed genes using a linear model. Significantly differentially expressed genes were identified using a cutoff of Benjamini-Hochberg adjusted p-value less than 0.05.
ChIP-seq: The sequenced ChIP-seq data was first checked for quality using the various metrics generated by FastQC (v0.11.2). Raw sequencing reads were then aligned to the Mouse (mm10) reference genome using default settings of Bowtie (v2.2.0). Uniquely mapped reads were retained and the alignments were subsequently filtered using the SAMtools package (v0.1.19) to remove duplicate reads. Differential analysis between mutant and control samples was performed using diffReps with window size 1000 bp and moving step size 500 bp, and FDR<5% as significance cutoff.
insituHiC: The processing of the raw 2x125bp read pair in-situ HiC FASTQ files was performed using the HiC-Pro analysis pipeline. In brief, HiC-Pro performs four major tasks: aligning short reads, filtering for valid pairs, binning, and normalizing contact matrices. HiC-Pro implements the truncation-based alignment strategy using Bowtie v2.2.318, mapping full reads end-to-end or the 5’ portion of reads preceding a GATCGATC ligation site that results from restriction enzyme digestion with MboI followed by end ligation. Invalid interactions such as same-strand, dangling-end, self-cycle, and single-end pairs are not retained. Binning was performed in 20kb non-overlapping, adjacent windows across the genome and resulting interaction matrices were obtained.
Genome_build: mm10
Supplementary_files_format_and_content: text files of differential expression genes (RNAseq), differential binding regions (ChIPseq) and interaction counts (insituHiC)
Supplementary_files_format_and_content: ChIPseq_CTCF_neuron_KO_vs_WT_1kb_001b.annotated.txt: text file of differential binding regions
Supplementary_files_format_and_content: ChIPseq_H3K27ac_neuron_KO_vs_WT_1kb_001a.annotated.txt: text file of differential binding regions
Supplementary_files_format_and_content: ChIPseq_H3K9me3_neuron_KO_vs_WT_1kb_001a.annotated.txt: text file of differential binding regions
Supplementary_files_format_and_content: RNAseq_Setdb1-CK-KO_KO_vs_WT_gencode_vM4.txt: text file of differential expression genes
Supplementary_files_format_and_content: insituHiC_432_M_WT_neuronal_20000.HiCPro.interaction.txt: text file of interaction raw counts
Supplementary_files_format_and_content: insituHiC_513_M_CK-KO_neuronal_20000.HiCPro.interaction.txt: text file of interaction raw counts
Supplementary_files_format_and_content: insituHiC_9836_M_WT_neuronal_20000.HiCPro.interaction.txt: text file of interaction raw counts
Supplementary_files_format_and_content: insituHiC_9837_M_CK-KO_neuronal_20000.HiCPro.interaction.txt: text file of interaction raw counts
Supplementary_files_format_and_content: insituHiC_20000.HiCPro.bed: bed file of interaction bins
 
Submission date May 26, 2017
Last update date May 15, 2019
Contact name Eddie Loh
Organization name Icahn School of Medicine at Mount Sinai
Department Department of Neuroscience
Street address 1425 Madison Avenue
City New York
ZIP/Postal code 10029
Country USA
 
Platform ID GPL13112
Series (1)
GSE99363 Genome-wide maps of gene transcription and chromatin state in mouse Setdb1 wildtype and CK-cre conditional knockout brain.
Relations
BioSample SAMN07172523
SRA SRX2863192

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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