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| Status |
Public on Mar 25, 2020 |
| Title |
e11.5_mouse_forelimb_WT_HOXA11_ChIPseq_rep1 |
| Sample type |
SRA |
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| Source name |
forelimb bud
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| Organism |
Mus musculus |
| Characteristics |
age: e11.5
strain: mixed background C57Bl/6 x 129
genotype: WT
chip antibody: HOXA11 sigma: sab1304728
tissue: forelimb buds
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
HOXA11 ChIP was performed in forelimb buds of CD1 (wild type) and Prx1Cre; RosaHoxa11/Hoxa11 (RA11KI) mice at E11.5 in the same conditions as previously described for HOX13 ChIP 7. Chromatin was cross-linked using a combination of disuccinimidyl glutarate (DSG) and formaldehyde and sonicated using Fisher Scientific, Model 100 sonic dismembrator to obtain fragments between 100-600 bp. Protein A and Protein G Dynabeads (Invitrogen) were incubated for 6 hours at 4C with 5ug HOXA11 (SAB1304728, Sigma) antibody. The chromatin was coupled to the beads overnight at 4C. The immunoprecipitated samples were then sequentially washed in low salt (1% Triton, 0,1% SDS, 150 mM NaCl, 20 mM Tris (pH8), 2 mM EDTA), high salt (1% Triton, 0,1% SDS, 500 mM NaCl, 20 mM Tris pH8, 2 mM EDTA), LiCl (1% NP-40, 250 mM LiCl, 10 mM Tris (pH8), 1 mM EDTA) and TE buffer (50 mM NaCl, 10 mM Tris (pH8), 1 mM EDTA). The DNA was then purified on QIAquick columns (Qiagen).
Library and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations and sequenced on Illumina Hiseq 2500 in a 50 cycles paired-end configuration.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
ChIP-seq reads were aligned to the mm10 genome using bowtie v.2.3.1 with the following settings: bowtie2 -p 8 --fr --no-mixed --no-unal –x.
Sam files were converted into tag directories using HOMER v4.9.1 and into bam files using Samtools v1.4.1 view function.
bigwig files were generated using HOMER; Scores represent reads normalized per 10000000 reads
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files
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| Submission date |
Dec 07, 2018 |
| Last update date |
Jan 29, 2021 |
| Contact name |
ALEXANDRE MAYRAN |
| E-mail(s) |
alexandre.mayran@epfl.ch
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| Organization name |
EPFL
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| Street address |
Station 19
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| City |
LAUSANNE |
| State/province |
Waadt |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE123480 |
HOX13-dependent chromatin accessibility underlies the transition towards the digit development program[ChIP-seq] |
| GSE123482 |
HOX13-dependent chromatin accessibility underlies the transition towards the digit development program |
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| Relations |
| Reanalyzed by |
GSE165761 |
| BioSample |
SAMN10532343 |
| SRA |
SRX5105273 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3504924_HoxA11_WT_rep1.ucsc.bigWig |
1.2 Gb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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