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| Status |
Public on Aug 01, 2016 |
| Title |
Mouse set 0 36S Input |
| Sample type |
SRA |
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| Source name |
Lin-Sca1-cKit+ cells
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| Organism |
Mus musculus |
| Characteristics |
genotype: Gfi1 36S/wt
mouse strain: C57BL/6
antibodies: na
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde. Cell lysis was performed using the following buffers: total cell lysis - 5mM PIPES pH 8, 85mM KCl, 0.5% NP-40, 1X protease inhibitor cocktail, 1mM PMSF, and nuclear lysis – 50mM Tris, 10mM EDTA, 1% SDS, 1X protease inhibitor cocktail, 1mM PMSF. After sonication (Covaris E220 sonicator), immunoprecipitation was performed using Protein A/G Dynabeads (Life Technologies)
Sequencing libraries were prepared from immunoprecipitated chromatin using the TruSeq DNA kit from Illumina according to the manufacturer’s instructions and sequenced using the TruSeq PE Clusterkit v3-cBot-HS
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Homer_mouse_set0_pos.txt
Homer_mouse_set0_neg.txt
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| Data processing |
ChIP-Seq reads were aligned to mm10 using Bowtie2 v2.10
.bam files were converted into .sam files using samtools
The annotatePeaks.pl function of the Homer software was used to quantify read densities around gene Transcription Start Sites.
Genome_build: mm10
Supplementary_files_format_and_content: Each processed data file is the result of a call to annotatepeaks.pl in the Homer software and covers an entire set of samples. Each line in the file represents one ensembl transcript with each column representing a sinble bin of 25bp. The first column is the Ensembl Transcript ID, the next 101 match the 36S H3 sample, the next 101 match the 36 H3K9Ac, then 36N H3, then 36N H3K9Ac. There is one output file for transcripts on the positive strand and one for transcripts on the negative strand. In the positive file, the genomic area covered is -500bp to +200bp relative to the TSS. In the negative file, the genomic area covered is -2000bp to +500bp relative to the TSS.
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| Submission date |
Jul 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Möröy Tarik |
| E-mail(s) |
tarik.moroy@ircm.qc.ca
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| Organization name |
Insititut de Recherches Cliniques
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| Street address |
110 Pine avenue West
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| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H2W 1R7 |
| Country |
Canada |
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| Platform ID |
GPL9250 |
| Series (1) |
| GSE71254 |
Effect of Gfi1 36N variant on genome-wide H3K9 Acetylation patterns |
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| Relations |
| BioSample |
SAMN03945240 |
| SRA |
SRX1125335 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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