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Sample GSM5957390 Query DataSets for GSM5957390
Status Public on Aug 03, 2022
Title ChIP IP H3K27ac Phalange Rep1
Sample type SRA
 
Source name ChIP IP H3K27ac Phalange
Organism Gallus gallus
Characteristics developmental stage: HH32
tissue: phalange
chip antibody: H3K27ac
Growth protocol Chick White Leghorn embryonated eggs were incubated at 38.5ÂșC in fixed humidity for 7.5 days, followed by evaluation of developmental stage based on the Hamilton Hamburger classification (HH). The joint interzones and adjacent phalange samples were microdissected from hindlimb digit-3
Extracted molecule genomic DNA
Extraction protocol For the preparation of ChIPseq libraries, the histone-DNA complexes were immunoprecipitated with antibody.
For each sample, 100 specimens were collected from the 3rd hindlimb digit of developing chicken ebmryo (HH32) and pooled together. Further, samples were dissociated using Collagenase-II and passed through a 40-m cell strainer. The 1mln of cells were cross-linked and after series of washes the cell nuclei were further isolated. Subsequently, the nuclei were treated with SDS-containing lysis buffer, and chromatin was sheard obtaining the average size of 150 bp. For ChIP, 500 ng of sonicated chromatin was immunoprecipitated with 7.5 g of antibody. Input sample was collected prior to immunoprecipitation reaction. ChIP-seq libraries were prepared using QIAseq Ultra Low Input Library Kit (QIAGEN, Hilden, Germany). Briefly, DNA was end-repaired, adenosines were added to the 3 ends of dsDNA and adapters were ligated. Adapters containing DNA fragments were amplified by PCR using NEB starters. Mean library size was 300 bp. Libraries were run in the rapid run flow cell and were single-end sequenced (65 bp) on HiSeq 1500 (Illumina, San Diego, CA 92122 USA).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Description Transient_Cartilage_H3K27ac_IP_rep1_macs2_broad_peaks.broadPeak
Data processing In the ChIPseq primary analysis, the quality of reads was checked by FASTQC followed by removal of adapters using Trimmomatic tool.
Reads were mapped to the Gallus Gallus 6 reference genome using Bowtie2 followed by removal of PCR duplicates with Picard tool.
Peaks were called with MACS2.
In the RNAseq primary analysis, the quality of reads was validated with FASTQC and adapters were removed using Trimmomatic tool.
Reads were aligned to the Gallus Gallus 6 reference genome using using STAR
Reads were counted by gene using FeatureCounts
Identification of differentially expressed genes was performed using DESeq2
Assembly: gg6
Supplementary files format and content: (RNA-seq) DESeq2 normalized abundance measurements ouput
Supplementary files format and content: (ChIP-seq) MACS2 narrow peaks files
 
Submission date Mar 16, 2022
Last update date Aug 03, 2022
Contact name Karol Nowosad
E-mail(s) karolnowosad.lab@gmail.com
Organization name Erasmus MC
Street address Doctor Molewaterplein 40
City Rotterdam
ZIP/Postal code 3015 GD
Country Netherlands
 
Platform ID GPL21476
Series (1)
GSE198819 Identification of candidate regulatory elements controlling transcriptome during the formation of interphalangeal joints
Relations
BioSample SAMN26733778
SRA SRX14490269

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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