|
| Status |
Public on Sep 01, 2016 |
| Title |
gd7_zld_1 |
| Sample type |
SRA |
| |
|
| Source name |
gd7 embryos
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: 2-4 hr after egg deposition
barcode-kit: Custom GenScript Zld (aa 1117-1327)
library-kit: NEB-next-ChIP
|
| Treatment protocol |
Embryos were dechorionated for 1 min with 100% bleach and then cross-linked for 15 min with 1.8% formaldehyde (final concentration in water phase).
|
| Growth protocol |
Adult flies were used in population cages for embryo collections and embryos were collected on apple juice plates for 2 h at 25°C in cages and then matured at 25°C for another 2 h (2-4 h after egg deposition (AED)).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq experiments were performed as described (He et al 2011, Nature Genet, He et al 2015, Nature Biotech) with the following differences: ~100 mg embryos were used per IP. After incubation of magnetic beads with antibodies, H3K27ac IP samples were washed 3 times by rotating tubes for 3 min at 4°C to reduce background.
Several different methods were used for library construction, please refer to the supplemental material of Koenecke et al 2016, Genome Research or Koenecke and Johnston, 2016, Genome Biol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ChIP-seq for Zelda in gd7 (replicate 1)
|
| Data processing |
RNA-Seq
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were aligned to FlyBase r5.57 genome and gene annotations using Tophat v2.0.14.
Differential gene expression was determined using cuffdiff (Cufflinks v2.2.1) between the three mutant genotypes (Toll10b, Toll rm9/rm10, gd7)
----------------------------------------------
ATAC-Seq
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Read pairs were trimmed to 25 bp each and aligned to the UCSC Drosophila melanogaster dm3 genome with Bowtie 1.1.2 with a maximum insert size of 1000 bp, keeping only uniquely aligning reads
Genome_build: UCSC dm3
BigWig files contain per-base coverage of all aligned read pairs
----------------------------------------------
ChIP-Seq
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were aligned to the UCSC dm3 reference genome using bowtie v1.1.1 retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were extended to each library's estimated insert size
Genome-wide coverage counts were calculated and saved in BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base
|
| |
|
| Submission date |
Aug 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Julia Zeitlinger |
| E-mail(s) |
[email protected]
|
| Organization name |
Stowers Institute for Medical Research
|
| Lab |
Zeitlinger Lab
|
| Street address |
1000 E 50th St
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE68983 |
Genome-wide analysis of enhancers in Drosophila DV patterning |
|
| Relations |
| BioSample |
SAMN05595773 |
| SRA |
SRX2035280 |
