 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 15, 2024 |
| Title |
C&R,Zf5,Gaf,Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryo,NC14
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Embryo,NC14
genotype: sfGFP-ZLD
antibody: GAF
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryos were staged to NC12-NC13 and were placed and briefly dried on a double-sided tape . Using a sterile 18 gauge metal needle, embryos were popped into pools of the wash buffer previously described in Panday, A. 2022. Extracted contents were quickly moved in the wash buffer into a 1.5ul tube and temporarily stored at room temperature while samples were collected. Nuclei were collected by slow centrifugation at room temperature at 1500 RCF for 10 minutes.
Cut & Run libraries were made using NEBNext Ultra II NGS library kit and size selected using AMPure XP beads using manufacturer’s protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
For ATAC-seq and CUT&RUN, reads were aligned to the Berkeley Drosophila Genome Project (version six) reference genome using bowtie2 with the ‘--sensitive-local’ setting. Samtools was used to convert from .sam to .bam, index, sort, and remove duplicate, unmapped, and multi-mapped reads. For Cut and Run, peaks were called using macs2 using the ‘-f BAMPE’, ‘-g 129789873’, and ‘--bw 300’ settings using IgG as a control. For ATAC-seq, no IgG was used as a control and --nomodel --nolambda settings were used. Consensus peaks were called using the ‘diffbind’ package in R. Peaks were annotated using the CHIPseeker package and ‘TxDb.Dmelanogaster.UCSC.dm6.ensGene’ annotation. Bigwig files were generated using the Bamcoverage function from the deeptools package using the a ‘--binSize 20’, ‘--smoothLength 60’, ‘--centerReads’, ‘--normalizeUsing RPKM’, ‘--effectiveGenomeSize 142573017’.
Assembly: DM6
Supplementary files format and content: .bw files with averaged RPKM with a bine size of 20
Library strategy: Cut and Run
|
| |
|
| Submission date |
Apr 15, 2024 |
| Last update date |
Apr 16, 2024 |
| Contact name |
Mustafa Mir |
| E-mail(s) |
MIRM@chop.edu
|
| Organization name |
Children's Hospital of Philadelphia
|
| Street address |
3501 Civic Center Boulevard, CTRB 9030
|
| City |
philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL25244 |
| Series (2) |
| GSE263999 |
A fine kinetic balance of interactions directs transcription factor hubs to genes [Cut and Run] |
| GSE264096 |
A fine kinetic balance of interactions directs transcription factor hubs to genes |
|
| Relations |
| BioSample |
SAMN40976916 |
| SRA |
SRX24269285 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8208557_sfGFPzldwt_Gaf1.bw |
12.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
