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| Status |
Public on Nov 01, 2022 |
| Title |
attp2_1wk_3 (ATAC-seq) |
| Sample type |
SRA |
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| Source name |
Heart
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Heart
age: 1 week
strain: attp2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hearts were exposed and removed, and transferred to 1ml glass douncer with Nuclei EZ Prep kit detergent. Hearts were sheared with 20 loose and 15 tight strokes, then transferred to eppendorf for remainder of SigmaAldrich Nuclei EZ prep kit instructions. Samples were permeabilized in cold nuclear permeabilization buffer ((0.2% IGEPAL-CA630 (I8896, Sigma), 1 mM DTT (D9779, Sigma), Protease inhibitor (05056489001, Roche), and 5% BSA (A7906, Sigma) in PBS (10010-23, Thermo Fisher Scientific)) for 5 minutes on a rotator at 4°C followed by centrifugation for 5 min at 500g at 4°C. After decanting supernatant, the pellet was resuspended in cold tagmentation buffer ((33 mM Tris-acetate (pH = 7.8) (BP-152, Thermo Fisher Scientific), 66 mM K-acetate (P5708, Sigma), 11 mM Mg-acetate (M2545, Sigma), 16% DMF (DX1730, EMD Millipore) in molecular biology grade water (46000-CM, Corning)) followed by incubation with Tagmentation enzyme (FC-121-1030; Illumina) at 37°C with shaking at 500 rpm for 30 min. Tagmented DNA was purified using MinElute PCR purification kit (28004, QIAGEN).
The resulting libraries were amplified using NEBNext High-Fidelity 2X PCR Master Mix (M0541, NEB) with primer extension at 72°C for 5 minutes, denaturation at 98°C for 30 s, followed by 8 cycles of denaturation at 98°C for 10s, annealing at 63°C for 30s and extension at 72°C for 60s. After purification of amplified libraries using MinElute PCR purification kit (28004, QIAGEN), double sided size selection was performed using SPRIselect beads (B23317, Beckman Coulter) with 0.55X beads and 1.5X to sample volume.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were aligned using bowtie2, converted to uncompressed BAM files, sorted and index using: bowtie2-X2000 --mm --local -1 $fastq1 -2 $fastq2 | samtools view -Su /dev/stdin | samtools sort & index > xxx.PE2SE.bam &.bai 2> align.log. Poorly mapped, (<30 mapping score), duplicate, multimapped, and mitochondrial reads were removed using samtools and picard. Tn5 adapters were removed by truncating + end reads by 4 base pairs and – end reads by 5 base pairs, and then written to final output BAMs.
BAM files were sorted and indexed with samtools. Peakcalling was performed using MACS2 using the following commands: callpeak -f BAMPE -g dm - -q 0.01 --nomodel --shift -100 --extsize 200 --keep-dup all.
Genome_build: dm6
Supplementary_files_format_and_content: narrow peak
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| Submission date |
Oct 14, 2021 |
| Last update date |
Nov 02, 2022 |
| Contact name |
Adam Jeffrey Engler |
| E-mail(s) |
[email protected]
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| Phone |
858-246-0678
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| Organization name |
UC San Diego
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| Department |
Bioengineering
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| Street address |
9500 Gilman Drive, MC 0412
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL19132 |
| Series (2) |
| GSE185923 |
Age-dependent Lamin remodeling induces cardiac dysfunction via dysregulation of cardiac transcriptional programs [ATAC-Seq] |
| GSE185968 |
Age-dependent Lamin remodeling induces cardiac dysfunction via dysregulation of cardiac transcriptional programs |
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| Relations |
| BioSample |
SAMN22306784 |
| SRA |
SRX12622236 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5627298_X1wk_Ctl_Trip_12.05.20.final.bam.sorted.bam_peaks.narrowPeak.gz |
315.9 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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