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Sample GSM1039530 Query DataSets for GSM1039530
Status Public on Jul 02, 2013
Title rhesus_E31_input
Sample type SRA
Source name rhesus_E31
Organism Macaca mulatta
Characteristics developmental stage: gestational day E31
tissue: forelimb and hindlimb autopod
Treatment protocol Human samples were obtained from the Human Developmental Biological Resource (HDBR).
Growth protocol Normal Gestatation
Extracted molecule genomic DNA
Extraction protocol For each ChIP-Seq, limb bud tissue was crosslinked with 1% formaldehyde at room temperature and stored at -80°C. Chromatin was extracted and sheared by sonication. Soluble chromatin was combined with Protein G Dynabeads prebound with appropriate antibodies at 4C overnight. Beads were collected with magnet and washed 5x. Chromatin was eluted with TE+1%SDS at 65C for 10 minutes. Crosslinks were reversed at 65C overnight, and then chromatin was purified with the PCR cleanup kit (Qiagen).
Standard Paired End Illumina Multiplexing protocols
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Signal tracks for input (ie big wigs) were not generated as they were not used in any analysis.
Data processing Basecalls with CASAVA-1.8.2
ChIP-seq and RNA-Seq reads were aligned to the hg19, rheMac2, or mm9 genome assembly using Bowtie (0.12.7) with the -m1 flag.
Aligned ChIP-Seq reads in each sample were scanned along the genome in 500bp windows at 25bp step-size. For each window, the total number of reads from H3K27ac and control experiment were counted respectively. Raw read number in control experiment was then scaled to match the sequencing depth of H3K27ac experiment. The number of expected reads in a window based on uniform distribution of total mapped reads along a specific chromosome was also calculated. Then the significance of enrichment was calculated using a Poisson model where the null model is the larger number of control or expected read counts in the window. Significantly enriched windows (p-value≤10-5) within 1kb of each other were then merged.
Signal plots were generated by extending reads to 300bp and counting number of reads at each position in wiggle format. Wiggle tracks were then converted to bigwig using wigToBigWig from the Kent utilities.
Genome_build: hg19, rheMac2, or mm9
Supplementary_files_format_and_content: No raw data are provided for human samples. Human alignments were anonymized by removing sequence information and converting to bed format
Supplementary_files_format_and_content: Enriched Region files are in bed format.
Supplementary_files_format_and_content: Bigwig files were generated with wigToBigWig with the -clip flag.
Submission date Nov 20, 2012
Last update date May 15, 2019
Contact name Justin Cotney
Organization name UConn Health
Department Genetics and Genome Sciences
Lab Cotney Lab
Street address 400 Farmington Ave.
City Farmington
State/province CT
ZIP/Postal code 06030-6403
Country USA
Platform ID GPL14954
Series (1)
GSE42413 The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb
SRA SRX205513
BioSample SAMN01817948

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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