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| Status |
Public on Jun 30, 2016 |
| Title |
ATAC-seq from H1-KD rep1 |
| Sample type |
SRA |
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| Source name |
H1-KD OSC
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Ovarian Somatic Cells (OSC)
variation: RNAi H1
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| Treatment protocol |
Transfection of siRNAs was performed using Cell Line 96-well Nucleofector Kit SF and 96-well Shuttle Device (Lonza).
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| Growth protocol |
Cells were grown at 26 degrees on OSC medium (Fly Extract added M3 medium).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq samples were extracted as described (Buenrostro et al., 2013; Buenrostro et al., 2015).
ATAC-seq libraries were constructed as described (Buenrostro et al., 2013; Buenrostro et al., 2015).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
processed_ATACseq.txt
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| Data processing |
Library strategy: ATAC-Seq
ATAC-seq analysis was performed as previously described (Buenrostro et al., 2013) with some modifications. Adaptors were removed using Cutadapt software, and reads with lengths shorter than 50 bp were removed. Reads were first aligned to dm3 genome using Bowtie2.0.6 (Langmead and Salzberg, 2012) with the parameter –X 4000, to allow fragments up to 4 kbp long. MACS2 (Zhang et al., 2008) was used for peak calling with the parameters –g dm –nomodel –nolambda –extsize 239 –keep-dup all. MACS2 bdgdiff was used to compare samples, and CEAS (Shin et al., 2009) was used to annotate the peaks. To analyze the ATAC-seq reads mapped to transposons, reads mapped to the genome concordantly were extracted and mapped to Repbase transposon consensus sequences (Jurka, 1998) using the same parameters as for genome mapping.
Genome_build: dm3
Supplementary_files_format_and_content: Normalized read counts mapped to each transposon consensus sequence (Tab delimited format, txt).
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| Submission date |
May 13, 2016 |
| Last update date |
Jul 03, 2021 |
| Contact name |
Yuka W. Iwasaki |
| E-mail(s) |
iwasaki@keio.jp
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| Organization name |
Keio University School of Medicine
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| Department |
Department of Molecular Biology
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| Lab |
Siomi Lab
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| Street address |
35 Shinanomachi, Shinjuku-ku,
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| City |
Tokyo |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
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| Platform ID |
GPL16479 |
| Series (1) |
| GSE81434 |
Piwi modulates chromatin accessibility by regulating multiple factors including histone H1 to repress transposons |
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| Relations |
| BioSample |
SAMN04999509 |
| SRA |
SRX1760715 |
| 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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