|
| Status |
Public on May 12, 2022 |
| Title |
CTCF ChIP, WT[0], rep3 |
| Sample type |
SRA |
| |
|
| Source name |
0-14 hour old embryos
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: WT[0] (matched wildtype control)
tissue: whole embryo
age: 0-14 hour old
genotype: WT[0] (matched wildtype control)
replicate: 3
chip antibody: CTCF rabbit polyclonal (Kaushal et al. 2021)
|
| Treatment protocol |
Animals were not subjected to any particular treatment.
|
| Growth protocol |
standard Drosophila culture at 25°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
About 400 0-14 hour old embryos per biological replicate (three biological replicates prepared per genotype) were dechorionated, dounced in 5 ml crosslinking solution (50 mM Hepes pH 7.9, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 1.8% formaldehyde), and fixed for 15 minutes. Nuclei were sonicated in RIPA buffer in a Covaris S220 sonicator as described in Kaushal et al. 2021. 60 third instar larval central nervous systems per biological replicate (two biological replicates per genotype) were dissected in PBS and chromatin was prepared as in Kaushal et al. 2021.
NEBNext Ultra II DNA Library Prep kit for Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ChIP-seq library
|
| Data processing |
Reads were aligned against Drosophila melanogaster genome assembly release 6 (dm6) using MicMap (v2.2)
For samples that were sequenced twice, reads were merged with Samtools v1.10.
Samtools v1.10 was used to identify duplicate reads
Coverage (in reads per million) was evaluated after truncating each paired end read to the 50nt region centered on the its midpoint, ignoring duplicate reads.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files were generated using R package rtracklayer v1.42.2. Score represent coverage in reads per million.
|
| |
|
| Submission date |
Jul 19, 2021 |
| Last update date |
May 12, 2022 |
| Contact name |
Maria Cristina Gambetta |
| E-mail(s) |
mariacristina.gambetta@unil.ch
|
| Organization name |
University of Lausanne
|
| Department |
Center for Integrative Genomics
|
| Street address |
Genopode Building
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21306 |
| Series (2) |
| GSE180374 |
Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [ChIP-seq] |
| GSE180376 |
Essential role of Cp190 in physical and regulatory boundary formation in Drosophila |
|
| Relations |
| BioSample |
SAMN20306450 |
| SRA |
SRX11499368 |
