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| Status |
Public on Jul 18, 2011 |
| Title |
ZLD cycle 8 |
| Sample type |
SRA |
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| Source name |
Embryos
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Oregon R
tissue: embryo
developmental stage: mitotic cycles 8-9
antibody: anti-ZLD
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The chromatin obtained was fragmented to sizes ranging from 100-300 bp using a Bioruptor for a total of processing time of 140 min (15s on, 45s off), with power setting at H. We used 3.7 µg chromatin from cycle 8, 6.6 µg for cycle 13 and 6 µg for stage 5 in the chromatin immunoprecipitation reaction using the affinity purified anti-ZLD antibody, following the procedure described previously (Li-XY et al, PLoS Biology, 2008). The sequencing libraries were prepared from the ChIP and Input DNA samples, and subjected to ultra-high throughput sequencing on a Solexa GAIIx platform as previously described (Bradley-RK et al, PLoS Biology, 2010), except that the DNA fragments ranged from 200-350 bp in size.
ZLD antibody purification -
As described in Harrison-MM et al. (Dev. Biology, 2010), rabbits were immunized with GST fused to amino acids 1117-1487 of ZLD and purified against the same portion of the protein fused to maltose binding protein (MBP). As this portion of ZLD includes the zinc-finger DNA-binding domain, we further purified these antibodies using MBP fused to the four zinc fingers, amino acids 1318-1444. For our experiments, we recovered the antibodies that failed to bind to this MBP fusion protein and confirmed by immunoblot that these antibodies could recognize the full-length ZLD, but not the DNA-binding domain alone.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
ChIP for Zelda at wt Dmel embryo (Oregon R) at mitotic cycles 8-9 (hand sorted)
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| Data processing |
Alignment: Sequenced reads were mapped to the April 2006 assembly of the D. melanogaster genome, (UCSC version dm3, BDGP Release 5) using Bowtie (version 0.12.5). Sequenced reads were trimmed to 36 bp and mapped to the genomes using the Bowtie command-line options -n 2 -l 36 -m 2, thereby keeping for further analyses only tags that mapped uniquely to the genome with at most two mismatch.
Peaks: Each read was extended to 150 bp based on its orientation, and the total number of reads per time point was normalized to 10,000,000 reads. Peak calling was then performed using a Model-based Grizzly Peak algorithm (http://eisenlab.org/software/grizzly)
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| Submission date |
Jul 18, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Tommy Kaplan |
| E-mail(s) |
tommy@cs.huji.ac.il
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| Organization name |
Hebrew University
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| Department |
School of Computer Science and Engineering
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| Street address |
Givat Ram Campus
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| City |
Jerusalem |
| ZIP/Postal code |
91904 |
| Country |
Israel |
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| Platform ID |
GPL11203 |
| Series (1) |
| GSE30757 |
Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition |
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| Relations |
| SRA |
SRX084383 |
| BioSample |
SAMN00672508 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM763060_ZLD.1hr.peaks.bed.gz |
136.7 Kb |
(ftp)(http) |
BED |
| GSM763060_ZLD.1hr.raw.bedgraph.gz |
53.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM763060_s_6_sequence.dm3.bed.gz |
185.5 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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