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| Status |
Public on Apr 23, 2015 |
| Title |
SNS-Seq (pool) from Bg3 cells, replicate 1 |
| Sample type |
SRA |
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| Source name |
SNS-Seq (pool) from Bg3 cells, replicate 1
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| Organism |
Drosophila melanogaster |
| Characteristics |
material: Short nascent leading strands
celll line: ML-DmBG3-c2
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| Growth protocol |
Drosophila S2-DRSC cells and ML-DmBG3-c2 cells were cultured at 25 °C in 145 mm plates (Greiner) at a density of 1.5 x 10^6 cells/ml in Schneider’s Insect Cell Medium (Sigma S0146) and Shields and Sang M3 insect medium (Sigma S3652) with 10 μg/ml insulin (Sigma), respectively, supplemented with 10 % FBS (Pansera ES).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
SNS fragments were isolated essentially as described in (Cayrou et al. 2011). Adjustments were made according to SW-41 Ti rotor specifications (Beckman-Coulter) and centrifugation was carried out at 4 °C and 26700 rpm for 21 hours. DNA fragments of 0.5-2.5 kb were collected, purified and subjected to up to five rounds of T4 PNK (Fermentas) phosphorylation and lambda Exonuclease (Fermentas) digestion. SNS were then prepared for sequencing by digesting the RNA-primer, second strand synthesis (NEBNext mRNA Second Strand Synthesis) and purified with AMPure XP beads (Beckman-Coulter).
DNA libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina) following manufacturer’s instructions.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Bg3origins.txt
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| Data processing |
S2 and Bg3 SNS-Seq reads were quality filtered and aligned to the dm3 Drosophila reference genome using Bowtie2 version 2.2.0 (Langmead et al., 2012) allowing one mismatch in seed alignment (-N 1 -L 22).
The output was converted from SAM format to BAM using samtools version 0.1.19 (Li et al., 2009), and BAM files were sorted and indexed.
Origin peaks were called using MACS version 1.4.1 (Zhang et al., 2008) with parameters -g dm -m 5,30 for each replicate. Only peaks supported by unique alignments were considered further. For single fraction SNS-Seq data, technical replicates for each fraction were pooled prior to peak calling.
Genome_build: dm3
Supplementary_files_format_and_content: All processed data files are tab-separated TXT files containing genomic coordinates of the origin peaks. In addition, S2 and Bg3 origins also contain a column with the estimated origin efficiency.
Supplementary_files_format_and_content: S2origins.txt: Origin peaks in S2 cells
Supplementary_files_format_and_content: Bg3origins.txt: Origin peaks in Bg3 cells
Supplementary_files_format_and_content: F4origins.txt: Origin peaks in S2 cells, from short SNS
Supplementary_files_format_and_content: F5origins.txt: Origin peaks in S2 cells, from intermediate SNS
Supplementary_files_format_and_content: F6origins.txt: Origin peaks in S2 cells, from long SNS
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| Submission date |
Feb 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Federico Comoglio |
| E-mail(s) |
federico.comoglio@bsse.ethz.ch
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| Organization name |
ETH Zurich
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| Department |
Department of Biosystems Science and Engineering
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| Lab |
Epigenomics Lab
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| Street address |
Mattenstrasse, 26
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| City |
Basel |
| State/province |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE65692 |
High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins |
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| Relations |
| BioSample |
SAMN03332026 |
| SRA |
SRX867349 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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