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| Status |
Public on May 24, 2024 |
| Title |
Wing disc, HP1a-control, FAIREseq, rep2 |
| Sample type |
SRA |
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| Source name |
wing disc
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: wing disc
genotype: HP1a-control
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| Growth protocol |
Stocks were maintained on standard cornmeal food at 25˚C. 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 |
A minimum of 50 wing imaginal discs per replicate were dissected from wandering female L3 w1118; HP1achromo/Df or w1118; Df/+ (HP1acontrol) larvae and used as input for FAIRE-seq, as described previously (Uyehara 2022).
Libraries were prepared for sequencing using Takara ThruPLEX DNA-Seq Kit with Takara DNA Unique Dual Index Kit and paired-end sequenced at the UNC High Throughput Sequencing Facility with an Illumina Hi-Seq 4000.
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| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Files were merged at the fastq level. Adapters were trimmed using bbmap version 38.71 and parameters ktrim=k ref=adapters rcomp=t tpe=t tbo=t hdist=1 mink=11. Trimmed reads were aligned to dm6 using bowtie2 version 2.3.4.1 and default parameters with --seed 123. Sam files were then converted to bam files and reads were filtered using samtools version 1.9 such that only reads with a MAPQ greater than 5 were kept. Duplicates were marked using picard version 2.2.4 and removed using samtools. Bam files for biological reps were pooled using samtools. All bam files were converted to bed files using bedtools version 3.36. Read depth was calculated and rpgc-normalized bigWigs were generated from bed files using deeptools version 2.4.1.
Assembly: dm6
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| Submission date |
Jul 10, 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) |
| GSE234277 |
Heterochromatic 3D genome organization is directed by HP1a and H3K9-dependent and independent mechanisms. |
| GSE236965 |
Heterochromatic 3D genome organization is directed by HP1a and H3K9-dependent and independent mechanisms[FAIRE-seq] |
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| Relations |
| BioSample |
SAMN36390764 |
| SRA |
SRX20969174 |
| 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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