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| Status |
Public on Dec 22, 2014 |
| Title |
CMa H3K4me3_ChIPSeq |
| Sample type |
SRA |
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| Source name |
CMa H3K4me3_ChIPSeq
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| Organism |
Mus musculus |
| Characteristics |
developmental stage: 2 month old
cell type: left ventricle cardiomyocytes
chip antibody: H3K4me3 (Active Motif, 39159)
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| Treatment protocol |
none
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| Growth protocol |
none
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Primary 1-day-old cardiomyocytes and 2-month-old cardiomyocytes have been isolated to single cells and purified after sequential enzymatic digestions using standard protocols. The chromatin obtained after nuclei isolation has been sonicated to obtain an average chromatin length of 300bp; immunoprecipitation was performed by incubating the chromatin at 4°C overnight with antibodies anti-H3K4me3, anti-H3K79me2, anti-H3K27me3 and anti-H3K9me3. After decrosslinking of the chromatin, the enriched DNA was extracted and control of quantity and quality was assessed before sequencing.
Sequencing libraries have been prepared and barcoded according to the Lifetech ChIP-Seq Alpha protocol and amplified with a total of 15 PCR cycles. All sequencing libraries have been quantified with the Qubit Fluorometer (Life Technologies), protocol DNA HS, and checked with the Agilent 2100 Bioanalyzer instrument, protocol DNA 1000
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB 5500 Genetic Analyzer |
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| Data processing |
Sequencing reads were generated by the Lifetech analysis software on the SOLiD 5500™ sequencing machine
The .csfasta and .qual files were generated from the 5500 .xsq files with the convertFromXSQ Lifetech conversion utility
Mapping to the genome reference was performed with BOWTIE version 0.12.8, accepting only alignments with a QV > 10
Peak calling was performed using SICER version 1.1 with the following settings: windows size=200, gap size=600, redundancy threshold=1, FDR=0.05 and MACS version 1.4.2 with the following settings: effective genome size=1.87e+09, band width=300, model fold=5,30, p-value cutoff= 1.00e-05
Occupancy and differential binding affinity analysis were assessed with the R Bioconductor package DiffBind version 1.2.0
Genome_build: mm9
Supplementary_files_format_and_content: *_MACS bed file were generated after running MACS peak calling software
Supplementary_files_format_and_content: *_SICER bed file were generated after running SICER peak calling software
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| Submission date |
Mar 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Paolo Kunderfranco |
| E-mail(s) |
Paolo.Kunderfranco@humanitasresearch.it
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| Organization name |
Humanitas Research Hospital
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| Department |
Research
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| Lab |
Bioinformatic Unit
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| Street address |
Via Rita Levi Montalcini 4
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| City |
Pieve Emanuele |
| State/province |
Milano |
| ZIP/Postal code |
20090 |
| Country |
Italy |
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| Platform ID |
GPL16790 |
| Series (1) |
| GSE45174 |
Genome-wide maps of chromatin histone methylation marks in neonatal and adult cardiomyocytes |
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| Relations |
| SRA |
SRX249503 |
| BioSample |
SAMN01978501 |
| Named Annotation |
GSM1098561_CMa_H3K4me3_SICER.bed.gz |
| Named Annotation |
GSM1098561_CMa_H3K4me3_MACS.bed.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1098561_CMa_H3K4me3_MACS.bed.gz |
76.3 Kb |
(ftp)(http) |
BED |
| GSM1098561_CMa_H3K4me3_SICER.bed.gz |
196.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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