|
| Status |
Public on Jun 04, 2020 |
| Title |
st3-4_Input_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
preblastoderm embryos nc9-13
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: w- OR
tissue: preblastoderm embryos nc9-13
technique: Mnase-ChIP-seq
|
| Growth protocol |
D. melanogaster flies were maintained in standard Drosophila medium at 25oC.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIPseq: Dechorionated embryos were fixed using 0.1% Formaldehyde for 15min at RT. After fixation, they were hand picked for the desired developmental stage and frozen at -80oc until further use. Nuclei were isolated using short covaris sonication followed by chromatin digestion using Micrococcal nuclease and 10 cycles of sonication in a Bioruptor Pico. The lysate was clarified by centrifugation before immunoprecipitation, washes, elution by reverse crosslinking at 65deg for 16h. After RNaseA and proteinaseK treatment, the DNA from input and immunoprecipitation was purified using phenol-chloroform extraction and ethanol precipitation.
NEB Next Ultra II
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
ChIP-seq: Data processing was done using the bioRxiv. 2018, DOI: 10.1101/407312 pipeline. The DNA-mapping followed by the ChIp-seq pipeline were used. The default parameters were used.
Genome_build: dm6
Supplementary_files_format_and_content: ChIP-seq: bigwig normalized to Input, 1x coverage using bamCompare from deepTools, chrX was excluded for scalefactor calculation
|
| |
|
| Submission date |
Apr 25, 2019 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Asifa Akhtar |
| E-mail(s) |
akhtarlab_data@ie-freiburg.mpg.de
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Chromatin Regulation
|
| Lab |
Akhtar Lab
|
| Street address |
Stuebeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE130334 |
H4K16ac developmental dynamics during Drosophila development [DNA] |
| GSE130335 |
Intergenerationally maintained Histone H4 lysine 16 acetylation is instructive for future gene activation |
|
| Relations |
| BioSample |
SAMN11507275 |
| SRA |
SRX5736459 |
