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| Status |
Public on Apr 15, 2024 |
| Title |
ATAC,Zf5,rep2 |
| Sample type |
SRA |
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| Source name |
Embryo,NC14
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Embryo,NC14
genotype: 5th Zinc Finger of Zelda deleted
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryos were staged at NC12-NC13; placed on double-sided tape and rinsed before they were placed in 1.5 mL tube caps. Embryos were macerated with an 18-gauge needle in lysis buffer containing 10mM Tris-HCl pH7.5; 10mM NaCl, 3mM MgCl2; 0.1% Igepal-630.
ATAC libraries were prepared using Illumina Tagment DNA Enzyme and Buffer Small Kit with Nextera DNA CD indexes following manuafactor's protocol and previously described methods from Blythe, SA and Buenrostro JD.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Apr 10, 2024 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Mustafa Mir |
| E-mail(s) |
MIRM@chop.edu
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| Organization name |
Children's Hospital of Philadelphia
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| Street address |
3501 Civic Center Boulevard, CTRB 9030
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| City |
philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL25244 |
| Series (2) |
| GSE263718 |
A fine kinetic balance of interactions directs transcription factor hubs to genes [ATAC-Seq] |
| GSE264096 |
A fine kinetic balance of interactions directs transcription factor hubs to genes |
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| Relations |
| BioSample |
SAMN40923029 |
| SRA |
SRX24218448 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8197214_ATAC_Znf5_2.bw |
28.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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