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| Status |
Public on Jul 19, 2016 |
| Title |
GAFm_MNase |
| Sample type |
SRA |
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| Source name |
GAF mutant
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| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: GAF mutant
tissue: Imaginal discs and salivary glands
developmental stage: 3rd instar stage
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| Growth protocol |
Fly grew at 25 degree C, harvest at 3rd instar stage
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
MNase-digested chromatin was prepared as described previously (Petesch and Lis 2008; Gilchrist et al. 2009; Gilchrist et al. 2010) except that 200 µl chromatin was digested with 20 units MNase (Worthington) for 3 hours at 25 degrees C. Following gel purification, mono-nucleosome sized fragments (100-200 bp) were subjected to paired-end sequencing using the Illumina paired-end protocol.
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A’ bases were added to the 3’ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. This fragment range corresponds to a ChIP fragment range of about 200 -300bp. Size selected fragments were PCR amplified for 12 cycles . Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment.
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer |
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| Data processing |
Raw sequences were aligned to Drosophila Release 5.47 genome sequence by using mapping software CLC Genomics Workbench vision 7
Unique read pairs identifying both ends of fragments >=120 bp and =<180 bp in length were selected
The center of each read was used to identify as its position, and were smoothed with 10bp bin.
Reads were adjusted by using formula described in supplemental material and methods.
Genome_build: Dmel_Release_5.4
Supplementary_files_format_and_content: The processed data files contain the center position bp of each nucleosome read at each single-base pair position for +/- 500 bp surrounding the TSS of each indicated gene.
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| Submission date |
Jul 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Der-Hwa Huang |
| E-mail(s) |
mbdhuang@ccvax.sinica.edu.tw
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| Organization name |
Academia Sinica
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| Department |
Insititute of Molecular Biology
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| Lab |
N420
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| Street address |
128, Sec2, Academia Rd.
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| City |
Nankang, Taipei |
| State/province |
Taiwan |
| ZIP/Postal code |
11529 |
| Country |
Taiwan |
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| Platform ID |
GPL9058 |
| Series (2) |
| GSE70633 |
GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes. [MNase-seq] |
| GSE70634 |
GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes. |
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| Relations |
| BioSample |
SAMN03847019 |
| SRA |
SRX1085199 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1815465_GAFm_MNase_pair_merge.txt.gz |
6.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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