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| Status |
Public on Nov 07, 2013 |
| Title |
pharate_wing_faire |
| Sample type |
SRA |
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| Source name |
pharate appendage
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: y;cn,bw,sp
developmental stage: stage P14 pharate adult
tissue: pharate wing
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| Treatment protocol |
Staged samples were fixed for 10 minutes at 25C, quenched with glycine, washed with Buffer A at 4C, Dounce homogenized in Buffer A, and filtered through 60uM Nitex.
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| Growth protocol |
Bottles were flipped every 12 hours, and aged at 25C until the designated time.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were pelleted, resuspended in FAIRE lysis buffer, and subjected to bead beating with 2mm tungsten beads. Chromatin was sonicated to a size range of 500bp-2kb, and phenol-chloroform extracted.
1-100ng DNA was prepared for sequencing on an Illumina GAII or HiSeq 2000 machine at the UNC High-Throughput Sequencing Facility.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
FAIRE-seq
pharate_wing_faire_rep1
pharate_wing_faire_rep2
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| Data processing |
Basecalls performed with CASAVA version 1.7
FAIRE-seq GAII reads were filtered with Tagdust, and aligned to the Drosophila reference genome (version dm3) using Bowtie (version 0.12.3) with up to four possible alignments (m), and up to two mismatches in the seed (n) permitted.
FAIRE-seq HiSeq reads were first filtered with Tagdust. The first 8 bases were trimmed with fastx_trimmer to remove the internal Index. The last 6 bases were trimmed with fastx_trimmer to make HiSeq reads equivalent in length to GAII reads. Trimmed reads were aligned to the Drosophila reference genome (version dm3) using Bowtie (version 0.12.3) with up to four possible alignments (m), and up to two mismatches in the seed (n) permitted.
FAIRE-seq signal files were generated by extending each read to a total of 110bp, and the number of reads overlapping each base in the genome was counted.
FAIRE data were normalized by subtracting Input signal from FAIRE at each base, and z-scores were generated using the mean and standard deviation for each chromosome arm.
FAIRE peaks were called using MACS2 with Input as control, a shift size of 125bp, and a q-value cutoff of 1.00e-2.
RNA-seq GAII reads were filtered with Tagdust, and aligned to the Drosophila reference genome (version dm3) using TopHat (version 1.1.4) and default parameters.
RNA-seq HiSeq reads were first filtered with Tagdust. The first 8 bases were trimmed with fastx_trimmer to remove the internal index. The last 6 bases were trimmed with fastx_trimmer to make HiSeq reads equivalent in length to GAII reads. Trimmed reads were aligned to the Drosophila reference genome (version dm3) using TopHat (version 1.1.4) and default parameters.
Genome_build: dm3
Supplementary_files_format_and_content: FAIRE processed data files are in wig format, and contain Input-subtracted FAIRE z-scores, smoothed with a 200bp sliding window average and 10bp step size.
Supplementary_files_format_and_content: RNA processed data files are matrices of gene names with their associated FPKM values calculated with Cuffdiff from the Tophat-aligned reads and using a RefSeq genome annotation file.
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| Submission date |
Jun 14, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel J McKay |
| E-mail(s) |
dmckay1@email.unc.edu
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| Organization name |
The University of North Carolina at Chapel Hill
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| Department |
Biology, Genetics
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| Lab |
McKay Lab
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| Street address |
3344 Genome Sciences Building
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7100 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE38727 |
A common set of DNA regulatory elements shapes Drosophila appendages |
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| Relations |
| SRA |
SRX155030 |
| BioSample |
SAMN01055242 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM948720_pharate_wing_FAIRE_POOL.wig.gz |
21.5 Mb |
(ftp)(http) |
WIG |
| GSM948720_pharate_wing_FAIRE_peaks.bed.gz |
282.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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