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| Status |
Public on Jul 12, 2018 |
| Title |
3-4h_nucleosome_rep1 |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: W1118
Stage: 3-4h AEL
enzyme: Mnase (Worthington Biochemical Corporation, catalog# LS004797)
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| Treatment protocol |
Embryos were dechorionated with 50% solution of bleach for 3 minutes and were cross-linked in a 1:3 mix of ChIP-fixed buffer with 1.8% formaldehyde and heptane for 15 min on a shaker with speed at 300 rpm. The aqueous and organic phase was replaced with PBST plus 0.25 mM glycine to cease cross-linked reaction, and fixed embryos were rinsed by PBST for 3 times. The cross-linked embryos were homogenized by Douce all-class tissue grinder, and filtered large residual tissue by Miracloth to get nuclei suspension.
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| Growth protocol |
Embryos were collected on grape juice plates with yeast paste from embryo collection cages for 1 hr, and then allowed to develop for 3 and 14 additional hours before being harvested. So the collected embryos are 3-4h and and 14-15h old, respectively.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
1.Nucleosome DNA fragment extraction, chromatin are digested by MNase and nucleosome was dissolved through sonication with 3 cycles of 20s duration with at least 40s pauses between cycles at the power setting of 6 (out of 20) on a Misonix sonicators XL-2000. Then nucleosome DNA was extracted by phenol–chloroform and dissolved in ddH2O. 2. H1 binding DNA fragment extraction, generated chromatin fragments between 100 and 500 bp through sonication with 7 cycles and 5 cycles on 3-4h and 14-15h embryonic nuclei, separately. Then immunoprecipitated DNA-H1 complexes were captured by anti-H1 antibody (Active Motif, 39707) dose as specification described in 20-25ug chromatin.Immunoprecipitated DNAs were obtained by extraction with phenol chloroform after incubated on metal bath under the condition of 65 ℃ over night.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
ChIP-seq raw reads were cleaned by removing adaptor sequence and low-quality sequences, then mapped to dm3 whole genome using bowtie v0.12.7 with parameters: -p 8 -m 1 -v 2
The uniquely mapped nucleosomal reads were used to identify genome-wide nucleosome positions through the peak-calling tool GeneTrack
Aligned dH1 reads were converted into tdf format use igvtools.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited files for nucleosome positions includes nucleosome name, location (chromatin, start, end), the number of reads aligned on predicted nucleosme (rc), fuzziness of predicted nucleosme (fuzziness, the standard deviation of tag locations around the nucleosome dyad).Tdf files are binary files which represented the dH1 enrichment at genomic loci.
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| Submission date |
Jul 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Hu |
| E-mail(s) |
hujian5241@126.com
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| Organization name |
Tongji University
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| Street address |
1239,Siping Road
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL13304 |
| Series (2) |
| GSE101327 |
Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos[ChIP-Seq] |
| GSE101330 |
Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos |
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| Relations |
| BioSample |
SAMN07346913 |
| SRA |
SRX2998861 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2701103_3-4h_AEL_predicted_nucleosome_rep1.tab.gz |
6.3 Mb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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