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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 16, 2023 |
| Title |
NC, 64C, ATAC-seq, rep2 |
| Sample type |
SRA |
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| Source name |
FACS purified germ cell
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: FACS purified germ cell
Sex: female
developmental stage: 64C NC
genotype: otu-Gal4, mata-gal4, nos-gal4, UASz-tdTomato
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| Growth protocol |
flies were grown on standard food plus wet yeast paste for 3-6 days
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq libraries were prepared with either the Illumina Nextera™ DNA Sample Preparation Kits or using the Illumina DNA Prep kit with a modified protocol. Briefly, sorted nuclei were resuspended in the Tagmentation Buffer 1 (TB1), then incubated with DNA Tagment DNA Enzyme (TDE1) for 30 min at 37℃ before stopping the reaction by incubating overnight at 65˚C with Tagment Stop Buffer (TSB). The reaction was then digested with RNAase for 1 hour, then Proteinase K for 2 hours.
Tagmented DNA was extracted with phenol/chloroform and amplified with Enhanced PCR Mix (EPM) and i7/i5 index primers for 10 PCR cycles. Amplified DNA was cleaned up with the Sample Purification Beads (SPB) from the Illumina Kit or AMPure XP beads (Beckman Coulter). Libraries were assessed for quantity and fragment size using an Agilent Bioanalyzer, then sequenced on an Illumina NextSeq 500 to yield 75 bp, single-end reads.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ATAC-seq of FACS-purified Drosophila melanogaster germ cells
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| Data processing |
Reads were mapped with Bowtie2 (2.3.2). SAM output was filtered for MAPQ (>= 30) and to retain only reads on the major chromosome scaffolds (2L, 2R, 3L, 3R, 4, X and Y), sorted, converted to BAM, and indexed with SAMtools (1.6). A BigWig file was generated from the sorted filtered BAM using DeepTools (3.1.3; -p max -bs 1 --effectiveGenomeSize 127324632 --normalizeUsing CPM).
Assembly: Genome and Gene Annotation Set: BDGP6.22.Ensembl.98 (dm6, Ensembl release 98, NCBI: GCA_000001215.4). For samples with mouse cell spike-ins, a "hybrid genome assembly" was constructed by combining the BDGP6.22.Ensembl.98 dm6 Drosophila genome assembly with the mm10 mouse genome assembly from which 'hybrid genome' bowtie2 indexes were constructed.
Supplementary files format and content: RNAseq: STAR-RSEM output of estimated expression ; ChIPseq: bigWig ; HMM state paths: bedGraph with states 1 (depleted), 2 (no-change), and 3 (enriched). HMM gene annotations: BED-like tab-sepatated file with description in column names ;
Supplementary files format and content: AllDataTable.csv: aggregated data table of processed data of ATACseq, H3K27ac ChIPseq, H3K27me3 ChIPseq, and RNAseq from GSC to stage 9 nurse cells (NCs)
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| Submission date |
Apr 18, 2023 |
| Last update date |
Aug 16, 2023 |
| Contact name |
Allan C Spradling |
| E-mail(s) |
spradling@carnegiescience.edu
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| Phone |
(410) 246-3015
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| Organization name |
Carnegie Institution for Science
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| Department |
HHMI Lab at Embryology
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| Lab |
Spradling
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| Street address |
3520 San Martin Drive
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21218 |
| Country |
USA |
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| Platform ID |
GPL19132 |
| Series (1) |
| GSE229943 |
Chromatin and gene expression changes during female Drosophila germline stem cell development. |
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| Relations |
| BioSample |
SAMN34232819 |
| SRA |
SRX20000257 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7181640_NC_064C.2.ATAC.chr.bw |
74.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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