 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 02, 2020 |
| Title |
ATAC shOpa_14d rep3 |
| Sample type |
SRA |
| |
|
| Source name |
embryos
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: embryos
age at harvest: nc14D (nc14+45min)
genotype: Opa shRNAi
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Individual embryos were collected on agar plates from females of the following genotypes: wild-type/control (i.e y w females crossed to sh_opa males), mutant (i.e.MTD-Gal4 x sh_opa), or ectopically-expressing opa (i.e. MTD-Gal4 x UAS-opa). Nuclear morphology was observed under a compount microscope at 20x magnification.Single sh_opa and control embryos were assayed at nc14D (nc14+45’), whereas UAS-opa and control embryos were assayed at nc14B (nc14+20’). Temperatures for sample collection were maintained at 26C to minimize variation in cell cycle timing. Under these conditions, cell cycle times were indistinguishable. Cell cycles were timed from the onset of anaphase of the previous cell cycle. Each embryo was hand-selected and hand-dechorionated for the analysis.
Fragmentation and amplification of ATAC-seq libraries were performed essentially as described previously (Buenrostro et al., 2015). RNA-seq libraries were constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770) following the manufacturer’s instructions.
Prepared libraries were subject to paired-end sequencing using an Illumina NovaSeq.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
ATAC-seq data, the raw 151bp paired-end fastq data were trimmed to before aligned to drosophila dm6 reference genome assembly using Bowtie2 aligner. Aligned bam files were subject to further sorting and duplicate removal using samtools before downstream analysis.
RNA-seq data, the raw 151bp paired-end fastq data were trimmed before aligned to drosophila dm6 reference genome/gene annotation using TOPHAT2. Aligned bam files were subject to gene quantification and differential analysis using cufflinks and cuffdiff pipelines.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig for ATACseq, gene statistics table for RNAseq
|
| |
|
| Submission date |
Jun 26, 2020 |
| Last update date |
Aug 04, 2020 |
| Contact name |
Theodora Koromila |
| E-mail(s) |
koromila@caltech.edu
|
| Phone |
6266776854
|
| Organization name |
California Institute of Technology
|
| Street address |
1200 E Califonia Blvd
|
| City |
Pasadena |
| State/province |
CA |
| ZIP/Postal code |
91125 |
| Country |
USA |
| |
|
| Platform ID |
GPL25244 |
| Series (2) |
| GSE153328 |
Opa is a late-acting, pioneer factor that coordinates with Zelda to broadly regulate gene expression in early embryos (ATAC-seq, RNA-seq) |
| GSE153329 |
Opa is a late-acting, pioneer factor that coordinates with Zelda to broadly regulate gene expression in early embryos |
|
| Relations |
| BioSample |
SAMN15377064 |
| SRA |
SRX8622122 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4640584_S11.bw |
60.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
