|
| Status |
Public on Jan 07, 2020 |
| Title |
Nup107.rep2 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2
cell type: Embryonic cells
genotype/variation: wild type
chip antibody: Nup107 (this study)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates from embryonic cells were clarified from sonicated nuclei and Nup-DNA complexes were isolated with specific antibody.
Libraries were prepared according to Illumina's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were aligned to genome assembly dm3 using Bowtie2 (version 2.2.9) with default parameters and “--local” to allow soft clipping of ends.
Alignments were further processed by SAMtools (version 0.1.19) to remove low quality alignments (“-q 10”), PCR duplicates (“rmdup -s”) and mitochondrial reads.
Reads that passed filter were used to call peaks with MACS2 (v2.1.0, “--qvalue 0.05 --mfold 2 50 --broad”).
Peaks that overlapped between biological replicates were retained for each antibody.
For visualization, each individual library was normalized to 10 million reads per library and then track for each library subtracting its corresponding IgG control was generated using BEDtools (“genomecov”) and Deeptools (“bigwigCompare –ratio=subtract --binSize=10”).
BigWig files were then converted from bedGraph files using command "bedGraphToBigWig".
Genome_build: dm3 (BDGP Release 5)
Supplementary_files_format_and_content: BedGraph files were generated for each library using Bedtools 'genomecov' with scale normalized to 10 million reads per library. IgG were then subtracted from IP bedGraph files using Deeptools 'bigwigCompare'. BigWig files were converted from bedGraph files.
|
| |
|
| Submission date |
Aug 08, 2019 |
| Last update date |
Jan 07, 2020 |
| 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 (2) |
| GSE135610 |
Core components of the nuclear pore bind distinct states of chromatin and contribute to Polycomb repression I |
| GSE136117 |
Core components of the nuclear pore bind distinct states of chromatin and contribute to Polycomb repression |
|
| Relations |
| BioSample |
SAMN12541616 |
| SRA |
SRX6685748 |
