|
| Status |
Public on Jan 07, 2020 |
| Title |
S2-Input |
| Sample type |
SRA |
| |
|
| Source name |
embryonic cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2
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 lamin-DNA complexes were isolated with specific antibody
Libraries were prepared according to Illumina's instructions for HiSeq 2000 for KC or S2 cells and NextSeq 500/550 High Output Kit when brains were analyzed.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
control for S2 libraries
|
| 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.
For visualization, each individual library was normalized to 10 million reads per library and then track for each library subtracting its corresponding Input 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
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 21, 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) |
| GSE136115 |
Core components of the nuclear pore bind distinct states of chromatin and contribute to Polycomb repression II |
| GSE136117 |
Core components of the nuclear pore bind distinct states of chromatin and contribute to Polycomb repression |
|
| Relations |
| BioSample |
SAMN12615070 |
| SRA |
SRX6747981 |
