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Sample GSM2685800 Query DataSets for GSM2685800
Status Public on Jul 19, 2017
Title Control ChIP Input1 Rep2
Sample type SRA
 
Source name mesenchymal cells
Organism Gallus gallus
Characteristics breed: Lohmann Selected Leghorn
tissue: limb buds
cell type: mesenchymal cells
developmental stage: E4.5
time of culture: 5 days
condition: RCAS-BP(A)-empty
antibody: none
Treatment protocol Prior to seeding, mesenchymal cells were infected with empty RCAS-BP(A) retroviral particles carrying no recombinant protein.
Growth protocol Mesenchymal cells were isolated from limb buds of E4.5 chick embryos and were plated as 10-µL droplets at a concentration of 2.10^7 cells/mL. Cells were maintained in culture for 5 days at 37°C in DMEM/Ham’s F-12 (1:1) medium (Biochrom) supplemented with 10% FBS (Biochrom), 0.2% chicken serum (Sigma-Aldrich), 1% L-glutamine (Lonza) and 1% penicillin/streptomycin (Lonza).
Extracted molecule genomic DNA
Extraction protocol Mesenchymal cells harvested from 8 cultures were cross-linked in 1% FA for 10 min on ice. Following cell lysis and nuclei isolation, nuclear extracts were sonicated to fragment chromatin between 200 and 500 bp. 10 µg of chromatin extracts were mixed with 4 µg/4 µL of corresponding antibody. Antibody-histone-DNA complexes were pulled down by using 40 µL of magnetic beads (Dynabeads protein G; Thermo Fischer). Enriched complexes were eluted from the beads. Reverse cross-linking was performed overnight at 65°C. DNA was purified by successive treatments with RNase A and Proteinase K followed by ethanol precipitation.
ChIP and input librairies were prepared by using the NEBNext Ultra DNA Library Preparation kit for Illumina (New England Biolabs). 50-bp single-end reads were generated by using a HiSeq 1500 sequencer (Illumina).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Data processing ChIP-seq single-end reads were filtered on their quality by using the FASTX-Toolkit (median quality value of minimum 28).
Filtered reads were mapped against the chicken genome galGal4 by using BWA (default parameters).
Uniquely mapped reads were extracted and duplicated reads were removed by using the tool rmdup from SAMtools.
Peak calling was performed as suggested by the ENCODE consortium and the Roadmap Epigenomics project by using MACS2 (--bw 400; -g 1.0e9; --to-large). Narrow peaks were called by using a p-value (-p) of 0.01. Broad peaks were called by using an additional broad-peak p-value (-p 0.01; --broad; --broad-cutoff) of 0.1.
Broad peaks that contain at least one narrow peak were extracted by using BEDtools intersect.
Genome_build: galGal4
Supplementary_files_format_and_content: Broad peaks called by MACS2 in ENCODE broadPeak format; Narrow peaks called by MACS2 in ENCODE narrowPeak format.
 
Submission date Jun 26, 2017
Last update date May 15, 2019
Contact name Mickael Orgeur
Organization name Max Planck Institute for Molecular Genetics
Department Development and Disease
Street address Ihnestrasse 63-73
City Berlin
ZIP/Postal code 14195
Country Germany
 
Platform ID GPL21476
Series (2)
GSE100514 Genome-wide strategies identify downstream target genes of connective tissue-associated transcription factors [ChIP-seq Histones]
GSE100517 Genome-wide strategies identify downstream target genes of connective tissue-associated transcription factors
Relations
BioSample SAMN07280083
SRA SRX2959172

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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