|
| Status |
Public on Mar 30, 2017 |
| Title |
Input-2 |
| Sample type |
SRA |
| |
|
| Source name |
brains
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: 3rd instar larva
tissue: brains
chip antibody: none
genotype/variation: wild type
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates from embryonic cells or 3rd instar brains were clarified from sonicated nuclei and histone-DNA or Nup-DNA complexes were isolated with specific antibody
Libraries were prepared according to Illumina's instructions for NextSeq® 500/550 High Output Kit v2 (FC-404-2005).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
control for Nup98 and H3K27ac ChIP
|
| Data processing |
Raw fastq files were trimmed to remove low quality base calls using Trimmomatic, with parameter "LEADING:3 TRAILING:3 SLIDINGWINDOW:3:3 MINLEN:30".
Trimmed reads were aligned to dm3 using Bowtie2, allowing for only uniquely aligned reads (MAPQ > 10) to be reported.
Duplicate reads and mitochondria reads were removed using Samtools and Bedtools.
Significant peaks were called using MACS2, with parameter "--qvalue 0.05 -m 2 50".
Bedgraphs were generated using the command "bedtools genomecov", library sizes were normalized to 10 million reads per sample.
BigWig files were then converted from bedgraph files using command "bedGraphToBigWig".
Genome_build: dm3
Supplementary_files_format_and_content: bigwig files were converted from bedgraph files, which were generated using Bedtools. Scores were normalized to 10 million reads per sample.
|
| |
|
| Submission date |
Feb 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yemin Lan |
| Organization name |
University of Pennsylvania
|
| Street address |
3400 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE94922 |
Nuclear Pores provide a scaffold for induced enhancer promoter contacts |
|
| Relations |
| BioSample |
SAMN06336855 |
| SRA |
SRX2564142 |
