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| Status |
Public on Oct 01, 2015 |
| Title |
4C-seq: ind12_Kc_1 |
| Sample type |
SRA |
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| Source name |
cultured fruit fly cells
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: Kc
restriction enzyme(s): DpnII, Csp6I
replicate: biological 1
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| Growth protocol |
S2 cells were cultured in Schneider's medium (Gibco) supplemented with 10% FCS and 0.05% Pluronic F-68 (Sigma-Aldrich) on shaking incubators at 27C at a density of 2-16 million/ml.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
4C-seq in S2 and Kc cells was carried out as described by Splinter et al.63 with minor modifications as following: 50-100 million S2 cells or Kc cells, fixed, were used for two biological replicates. DpnII (NEB) was used as the primary and Csp6I (ThermoScientific) as the secondary restriction enzyme. For each viewpoint, two 50ul PCR reactions (8 cycles with 5C annealing temperature, followed by 18 cycles with 63C) with 160ng of template each were prepared and the combined products cleaned up by a one-step purification using 1.6 volumes of AMPure XP magnetic beads (Beckmann Coulter) according to manufacturer's instructions. These viewpoint libraries were eluted in 20ul elution buffer (10mM Tris-HCl pH 8.5) and the molarities for each individual sample were estimated using the bioanalyzer DNA 7500 kit (Agilent Technologies). All different viewpoint libraries for one biological replicate were mixed equimolarly and sequenced on separate lanes on an Illumina HiSeq2500 DNA sequencer.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
ligated DNA
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| Data processing |
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.10
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3
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| Submission date |
Jan 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Fidel Ramirez |
| Organization name |
Max Planck Institute for Immunobiology and Epigenetics
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| Department |
Bioinformatics Unit
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| Street address |
Stübeweg 51
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| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
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| Platform ID |
GPL17275 |
| Series (1) |
| GSE58821 |
High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila |
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| Relations |
| BioSample |
SAMN03274375 |
| SRA |
SRX826259 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1575614_counts_ind12_Kc_1.bw |
282.9 Kb |
(ftp)(http) |
BW |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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