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| Status |
Public on May 24, 2024 |
| Title |
Wing disc, HWT, HiC, rep2 |
| Sample type |
SRA |
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| Source name |
wing disc
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| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: HWT
tissue: wing disc
developmental stage: 3LW
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| Growth protocol |
Stocks were maintained on standard cornmeal food at 25˚C. H3.2HWT and H3.2K9R larvae were cultured as previously described in Penke 2016. Briefly, one hundred fifty yw; ∆HisC, twi-Gal4/CyO virgin females and seventy-five yw; ∆HisC, UAS-2xEYFP/CyO; H3.2HWT/ H3.2HWT or H3.2K9R/ H3.2K9R males were put in a cage and allowed to lay eggs on a grape juice agar plates. GFP-positive L1 larvae were transferred to vials of standard food and allowed to grow at 25˚C. Wandering third instar (L3) GFP-positive larvae were used for experiments. HP1acontrol and HP1achromo larvae were cultured by establishing vials with ten w1118; Df(2L)BSC228/CyO, Tb, RFP virgin females and, to produce HP1acontrol, a single yw; +; + male, or a single w1118; HP1achromo/CyO, Tb, RFP male (Table S3). After three days, genomic DNA from sacrificed w1118; HP1achromo/CyO, Tb, RFP males was sequenced to confirm the genotype the HP1achromo allele, which exhibits occasional instability. The remaining females were flipped daily and non-tubby third larval instar wandering females were used for experiments.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Each in situ Hi-C replicate was performed using 60 wing imaginal discs dissected from female H3.2HWT, H3.2K9R, HP1-chromo, and HP1-control wandering L3 larvae. Discs were fixed in 1xPBS with 4% paraformaldehyde for 20min, transferred to tubes in a minimal volume of 1xPBS plus 0.15% Triton X-100, and used as input for the Arima Hi-C kit v00 protocol (A410030), following manufacturer’s instructions that were last revised March 2018.
Hi-C libraries were amplified using the KAPA Hyper Prep kit (KK8502).
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Sequenced PEx150
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| Data processing |
These data were merged, aligned, filtered, and balanced by juicer. Only reads with MAPQ > 30 were kept.
Assembly: dm6
Supplementary files format and content: juicer
Supplementary files format and content: peakfile
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| Submission date |
May 24, 2023 |
| Last update date |
May 24, 2024 |
| Contact name |
Daniel McKay |
| Organization name |
University of North Carolina at Chapel Hill
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| Street address |
250 Bell Tower Drive
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
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| Platform ID |
GPL21306 |
| Series (2) |
| GSE233384 |
Heterochromatic 3D genome organization is directed by HP1a and H3K9-dependent and independent mechanisms [Hi-C] |
| GSE234277 |
Heterochromatic 3D genome organization is directed by HP1a and H3K9-dependent and independent mechanisms. |
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| Relations |
| BioSample |
SAMN35356797 |
| SRA |
SRX20508977 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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