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| Status |
Public on Jan 18, 2018 |
| Title |
Nascent strands reads from CCRF-CEM parental cells CPTATRi |
| Sample type |
SRA |
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| Source name |
Leukemic lymphoblasts
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| Organism |
Homo sapiens |
| Characteristics |
strain: CCRF-CEM
cell type: Cultured cancer cell line
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| Treatment protocol |
Cells were treated with DMSO, 100 nM camptothecin, or 100 nM camptothecin with 2 uM VE-821 for 4 hours.
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| Growth protocol |
Cancer cells were grown in RPMI1640 medium, 10% FBS
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from asynchronous cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. DNA from asynchronous cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004.
Illumina Genomic DNA protocol (Illumina Paired-END DNA Sample Prep Kit).
Illumina paired-end sequencing
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
Nascent DNA
Nascent strand DNA with camptothecin 100 nM and VE-821 (ATR inhibitor) 2 uM treatment for 4 hours
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| Data processing |
For peak calling, the SICER program and MACS2 program were used. Nascent strand reads were called by comparison to genomic reads of corresponding cell line. SICER algorithm was used with the following parameters: Window size 200 bp, Fragment size 150 bp, Gap size 600 bp, and FDR 0.01. MACS2 broad peak algorithm was also used for peak findings and quantification of signal value with the following parameters: q-value 0.01, Bandwidth 300, mfold 5-50 and Redundancy/duplicate threshold ‘auto’.
Illumina single read 105bp or 125bp sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks
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| Submission date |
Jul 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Junko Murai |
| E-mail(s) |
junko.murai@nih.gov
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| Organization name |
NCI
|
| Street address |
37 Convent Dr.
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| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL10999 |
| Series (2) |
| GSE101515 |
SLFN11 blocks stressed replication forks independently of ATR (NS-Seq) |
| GSE101516 |
SLFN11 blocks stressed replication forks independently of ATR |
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| Relations |
| BioSample |
SAMN07357707 |
| SRA |
SRX3009229 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2705265_CEMCPTATRNS_SICER24.bed.gz |
2.1 Mb |
(ftp)(http) |
BED |
| GSM2705265_CEMNSCPTATR_vs_genCEM_MACS2_result.bed.gz |
6.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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