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Status |
Public on May 16, 2024 |
Title |
12517_E2F1_Cfa6.66_ins_BioRep1 |
Sample type |
SRA |
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Source name |
Brainstem
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Organism |
Canis lupus familiaris |
Characteristics |
genotype: ins cell type: Brainstem chip antibody: E2F1 (Cell Signalling Technologies; cat# 3742S, Lot 8; concentration 48ug/ml)
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NovaSeq 6000 |
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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)
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Submission date |
May 16, 2023 |
Last update date |
May 16, 2024 |
Contact name |
Dhriti Tandon |
E-mail(s) |
dtandon@princeton.edu
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Organization name |
Princeton University
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Department |
Ecology and Evolutionary Biology
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Lab |
vonHoldt Lab
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Street address |
106A Guyot Hall
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City |
Princeton |
State/province |
New Jersey |
ZIP/Postal code |
08544 |
Country |
USA |
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Platform ID |
GPL25760 |
Series (1) |
GSE232642 |
Altered Chromatin State Drives Hypersocial Behaviors in Canids |
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Relations |
BioSample |
SAMN35116906 |
SRA |
SRX20377935 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7360735_12517_E2F.bw |
49.5 Mb |
(ftp)(http) |
BW |
GSM7360735_12517_macs2_E2F_narrowPeak.bed.gz |
1.6 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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