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| Status |
Public on Jul 01, 2017 |
| Title |
4C Kc SXL 1 [Sample 70] |
| Sample type |
SRA |
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| Source name |
Kc cells
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: Kc
gender: female
treatment: SXL RNAi
4c viewpoint (chrx): 12.7 MB
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
4C-seq was carried out on S2-DRSC cells (DGRC stock: 181) and Kc167 (DGRC stock: 1) in biological duplicates. RNAi was performed as described previously (Straub et al., 2005 and Alekseyenko et al., 2012)). After 7 days of RNA interference, cells were re-suspended in fresh medium and fixed with 1% formaldehyde for 10 min at room temperature. Fixing was quenched by adding glycine (final concentration 125 mM) and by cooling on ice. Cells were collected in a cooled centrifuge, snap frozen in liquid nitrogen and stored at -80°C.
4C-seq templates were generated on ~60 million fixed cells per replicate using 4-cutter restriction enzymes DpnII and NlaI, as described previously (Ghavi-Helm et al., 2014). Libraries were amplified using 100 ng 4C-seq templates and Pfu Turbo DNA polymerase in 8 PCR replicates, which were pooled for later analysis. Primers were designed to allow a multiplexing of 48 samples (for 12 viewpoints and 4 conditions) on a sequencing lane. Biological replicates were sequenced on two separate lanes of an Illumina NextSeq 500 sequencer.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Library strategy: 4C-Seq
4C-seq data processing was based on the FourCSeq Bioconductor package (Klein et al., 2015). Fastq files were de-multiplexed using a python script available in the package and aligned to the reference genome (BDGP 5.74) using bowtie2 (2.0.2) with "-local" settings. Reads were filtered for mapping quality (mapq > 1) and non-digested, self-ligated fragments were removed. Reads were counted for each valid DpnII fragment and obtained read counts per fragment. Bedgraphs were generated using the "writeTrackFiles" function.
Genome_build: BDGP 5.74
Supplementary_files_format_and_content: Bedgraph format. Hi-C PC1 values; 4C-seq, ChIP-seq and RNA-seq signals.
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| Submission date |
Jan 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tamas Schauer |
| E-mail(s) |
tamas.schauer@helmholtz-munich.de
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| Organization name |
Helmholtz Zentrum München
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| Department |
Institute of Epigenetics and Stem Cells
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| Street address |
Feodor-Lynen-Straße 21
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| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
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| Platform ID |
GPL19132 |
| Series (1) |
| GSE94115 |
The Drosophila Dosage Compensation Complex activates target genes via chromosome looping within the active compartment |
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| Relations |
| BioSample |
SAMN06274372 |
| SRA |
SRX2520616 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2469491_counts_27839_Kc.SXL_1.bedGraph.gz |
214.1 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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