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Sample GSM7360736 Query DataSets for GSM7360736
Status Public on May 16, 2024
Title 12527_E2F1_Cfa6.66_ins_BioRep2
Sample type SRA
 
Source name Brainstem
Organism Canis lupus familiaris
Characteristics genotype: ins
cell type: Brainstem
chip antibody: E2F1 (Cell Signalling Technologies; cat# 3742S, Lot 8; concentration 48ug/ml)
Extracted molecule genomic DNA
Extraction protocol We extracted nuclei from flash frozen brainstem tissue using the Active Motif High sensitivity kit (Active Motif). Briefly, we re-suspended 50mg of flash-frozen tissue in Tissue fixation solution (4.35ml Molecular grade water, 0.5ml Active Motif 10x PBS, and 140ul 37% (v/v) formaldehyde). We rotated the tube for 8 minutes, added 51.5ul of Active Motif Stop Solution, and followed by 5 minutes of rotation.
ChIP-seq libraries were prepared using the Active Motif High sensitivity kit complemented with the Active Motif Next Gen DNA library Prep kit and Active Motif Next Gen Indexing kit with 15 PCR cycles. 1 ng of DNA was used as starting material for input and ip samples. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed to remove barcodes and reads with a qulaity cutoff score of greater than 20 (q>20) were reatined using Trim Galore v0.0.6
ChIP-seq reads were aligned to the canfam3 genome using Bowtie version 1.1.2. Only uniquely mapping reads with distinctive "unqiue molecular identifier" sequences were retained.
To create ChIP-seq coverage plots, we used deeptools v3.5.1 and normalized all libraries to the largest library size. ChIP-seq reads were extended 100bp.
Peaks were called uing MACS v2.2.0 with the significance cut-off q-value <=0.05 and 0.1 for E2F1 and H3K27ac Chip libraries, respectively.
Bigwig files were generated in deeptools v3.5.1. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2.2.0. broadPeak files were generated with MACS v2.2.0, with the q cutoff as 0.1 and --broad-cutoff as 0.1.
Assembly: canFam3.1
Supplementary files format and content: bigWig, narrowPeak/broadPeak (except for Input sample)
 
Submission date May 16, 2023
Last update date May 16, 2024
Contact name Dhriti Tandon
E-mail(s) dtandon@princeton.edu
Organization name Princeton University
Department Ecology and Evolutionary Biology
Lab vonHoldt Lab
Street address 106A Guyot Hall
City Princeton
State/province New Jersey
ZIP/Postal code 08544
Country USA
 
Platform ID GPL25760
Series (1)
GSE232642 Altered Chromatin State Drives Hypersocial Behaviors in Canids
Relations
BioSample SAMN35116905
SRA SRX20377936

Supplementary file Size Download File type/resource
GSM7360736_12527_E2F.bw 47.3 Mb (ftp)(http) BW
GSM7360736_12527_macs2_E2F_narrowPeak.bed.gz 1.6 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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