|
| Status |
Public on Jul 14, 2022 |
| Title |
h3k4me3_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
fly heads
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: fly heads
genotype: Actin-gal4/+ (W1118) control
chip antibody: H3K4me3
|
| Growth protocol |
All flies were raised at 25°C in 12-hour light: 12-hour dark cycles on standard diets
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Chromatin immobilization and barcoding performed as previously described (Gutin, J. et al. Fine-Resolution Mapping of TF Binding and Chromatin Interactions. Cell Rep. 22, 2797–2807 (2018).)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
h3k4me3.narrowPeak
|
| Data processing |
ChIP-seq reads were aligned by bowtie2 software to the full genome sequence of Drosophila melanogaster (UCSC version dm3)
Duplicate reads were removed using the samtools rmdup function and uniquely mapped reads were kept (samtools view -q 10).
Peak calling was performed with the callpeak function of the MACS2 tool with a q-value<0.05
For visualization, bigwig files were created by deepTools (a python tool) with bamCoverage function and normalization parameter set to RPKM
Genome_build: dm3
Supplementary_files_format_and_content: bigwig file for each replica and bed peaks file per protein (antibody), MACS2 narrowPeak peaks file
|
| |
|
| Submission date |
Mar 23, 2021 |
| Last update date |
Jul 14, 2022 |
| Contact name |
Neta Herman |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
Hebrew University Of Jerusalem, Migal
|
| Department |
Gentics, Nutrition
|
| Lab |
Shagiv Shifman; Opatovsky Itai
|
| Street address |
Kiryat Shemona
|
| City |
Jerusalem, Kiryat Shemona |
| ZIP/Postal code |
1101202 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE169407 |
The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes [ChIP_seq_flyheads] |
| GSE169415 |
The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes |
|
| Relations |
| BioSample |
SAMN18437713 |
| SRA |
SRX10418028 |
