|
| Status |
Public on Dec 27, 2019 |
| Title |
CD34negCD19posROR1posCB96-Late S Fraction |
| Sample type |
SRA |
| |
|
| Source name |
cord blood pool 96 CD34-CD19+ROR1+ fraction
|
| Organism |
Homo sapiens |
| Characteristics |
s phase fraction: Late S fraction
gender: not applicable
replicate: 1
|
| Treatment protocol |
Asynchronous cells were labeled with 100 micromolar BrdU for 2 hours at 37˚C in RPMI 1640+ 10% FBS
|
| Growth protocol |
Cell lines were cultured in RPMI1640+10-20% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genome-wide replication timing profiles were constructed as previously described (Hiratani et al. 2008; Ryba et al. 2011; Marchal et al., 2017). Briefly, cells were pulse labeled with BrdU and separated into early and late S-phase fractions by flow cytometry and processed by either microaray or NGS.
Sequencing libraries of BrdU-substituted DNA from early and late fractions were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Genome-wide RT profiles were constructed by Repli-chip, Repli-seq, Capture Repli-seq and deep whole genome sequencing (WGS). Replication timing profiles were scaled and pooled for analysis as previously described (Ryba et al., 2011; Marchal et al., 2018). Briefly, Log2 transformed early/late replication timing ratios were quantile normalized and loess smoothed in R
Genome_build: HG38
Supplementary_files_format_and_content: processed data are 50kb windows in HG38 genome.
|
| |
|
| Submission date |
Apr 26, 2019 |
| Last update date |
Dec 27, 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 |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE130373 |
Replication timing alterations in leukemia reflect stable clinically-relevant changes in genome architecture [Repli-Seq] |
| GSE130374 |
Replication timing alterations in leukemia reflect stable clinically-relevant changes in genome architecture |
|
| Relations |
| BioSample |
SAMN11515032 |
| SRA |
SRX5758057 |
