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Sample GSM8208558 Query DataSets for GSM8208558
Status Public on Apr 15, 2024
Title C&R,Zf5,Gaf,Rep2
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
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
BioSample SAMN40976915
SRA SRX24269286

Supplementary file Size Download File type/resource 13.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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