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Status |
Public on Jul 28, 2017 |
Title |
Repli-seq F121-9 hybrid mouse cells - Early S fraction - Rep 1 |
Sample type |
SRA |
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Source name |
mESC
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Organism |
Mus musculus |
Characteristics |
strain background: F1 CASTx129 hybrid mouse (clone F121-9) cell line/type: ES cells s phase fraction: Early S fraction replicate: 1
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Growth protocol |
46C mESCs were cultured in mESC media supplemented with LIF. F121-9 ESC were cultured in N2B27+2i+LIF media.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Genome-wide replication timing profiles were constructed as previously described (Hiratani et al. 2008; Ryba et al. 2011). Briefly, cells were pulse labeled with BrdU and separated into early and late S-phase fractions by flow cytometry and processed either by NGS. Sequencing libraries of BrdU-substituted DNA from early and late fractions were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2500 |
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Description |
processed data file: F121-9_nesc_r1_R_T_.bedGraph F121-9_nesc_r1_R_T_Loess.bedGraph F121-9_nesc_r1_R_T_qnorm.bedGraph F121-9_nesc_r1_T_clip_129_genparsed_mm10w50000gt100snp_unified_qnorm_loess0-01.bedGraph F121-9_nesc_r1_T_clip_cas_genparsed_mm10w50000gt100snp_unified_qnorm_loess0-01.bedGraph
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Data processing |
Reads are mapped on mm10 using bowtie2. F121-9 cells have also been parsed, between cas and 129 genome (“*cas*” and “*129*” files) Coverage data are calculated from mapped reads using samtools and bedtools Base 2 log of early to late coverage ratio is calculated on 50kb windows (“*_T_.bg” files) Log Ratio data are quantile normalized using R package preprocessCore (“*_T_qnorm.bg” files) Data are smoothed using R Loess function (“*_T_Loess.bg” files, and “*unified_qnorm_loess0-01.bg” files for allele specific data) Genome_build: mm10 Supplementary_files_format_and_content: processed data are coverage data on mm10 genome, they can be visualized using a genome viewer. To visualize them using UCSC genome viewer, add a bedgraph file header (see UCSC website for description of the header)
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Submission date |
Feb 20, 2017 |
Last update date |
May 15, 2019 |
Contact name |
David M Gilbert |
Organization name |
Florida State University
|
Department |
Biology
|
Lab |
Gilbert
|
Street address |
319 Stadium Drive
|
City |
Tallahassee |
State/province |
FL |
ZIP/Postal code |
32306-4295 |
Country |
USA |
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Platform ID |
GPL17021 |
Series (2) |
GSE95091 |
Repli-seq: genome-wide analysis of replication timing by next-generation sequencing |
GSE95092 |
genome-wide analysis of replication timing by repli-chip and repli-seq |
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Relations |
BioSample |
SAMN06349388 |
SRA |
SRX2577311 |