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| Status |
Public on Oct 02, 2023 |
| Title |
ChIP_Input Cnd-GFP cut14-208 replicate 4 |
| Sample type |
SRA |
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| Source name |
fission yeast cut14-208mutant cells
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| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: condensin cut14-208 mutant
antibody: Total fraction prior to IP
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| Treatment protocol |
Fission yeast cells mixed with budding yeast cells (SMC3-GFP) at a ratio of 5:1
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| Growth protocol |
cells exponentailly growing in synthetic PMG medium at 30°C were arrested in metaphase by depletion of the Slp1 protein (APC co-activator) for 2hours, shifted at 36°C for 1 hour, fixed with formaldehyde 1% and processed for calibrated ChIP-seq using budding yeast cells expressing SMC3-GFP for internal calibration
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
cnd2 tagged with GFP
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| Data processing |
Process fastq file with fastp (version 0.20.1)
Concatenate the fission yeast genome and the budding yeast (calibration) genome and prefix every chromosomes in the calibration genome with the string calib
Map fastq files on the concatenated genome with bowtie2 (versio 2.3.4.1).
Sort and index bam files with samtools (version 1.11)
Split bam files into bam of reads mapping exclusively on the fission yeast genome and bam of reads mapping exclusively on the calibration genome
Remove duplicated reads with picard (version 2.18.11).
Bam files are converted to bigwig format and and bedgraph format using deeptools (version 3.5.1)
Read numbers in IP samples were normalized according to the internal calibration signal provided by budding yeast SMC3-GFP, using the method of Hu et al. [Hu, B., Petela, N., Kurze, A., Chan, K.-L., Chapard, C., and Nasmyth, K. (2015). Biological chromodynamics: a general method for measuring protein occupancy across the genome by calibrating ChIP-seq. Nucleic Acids Res. 43, e132.].
To analyze the coverage information at repetitive regions of the genome, we calculated the IP/WCE ratio for each base, as described in the git repository https://gitbio.ens-lyon.fr/LBMC/Bernard/condensin_cal_ChIPseq.git
Assembly: fission yeast genome version ASM294v2 extented with TEL2R DNA sequence.
Supplementary files format and content: ip.bw files are normalized IPs; wce.bw files are normalized Total (Input); IP.OR.bw files are base per base ratios of ip.bw/wce.bw
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| Submission date |
May 15, 2023 |
| Last update date |
Oct 02, 2023 |
| Contact name |
Pascal BERNARD |
| E-mail(s) |
[email protected]
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| Organization name |
CNRS
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| Department |
LBMC
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| Lab |
ENS de Lyon
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| Street address |
46 allée d'Italie
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| City |
Lyon |
| ZIP/Postal code |
F-69364 |
| Country |
France |
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| Platform ID |
GPL28961 |
| Series (1) |
| GSE196149 |
Condensin positioning at telomeres by shelterin proteins drives sister-telomere disjunction in anaphase |
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| Relations |
| BioSample |
SAMN35085946 |
| SRA |
SRX20344849 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7349846_T6305_Ch163_wce.OR.bigwig |
21.8 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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