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Sample GSM1422159 Query DataSets for GSM1422159
Status Public on Jul 31, 2014
Title Sample 1364 phase S2 HT-1080
Sample type SRA
 
Source name HT-1080
Organism Homo sapiens
Characteristics tissue: connective tissue
cell line: HT-1080
Growth protocol http://www.atcc.org/products/all/CCL-121.aspx#culturemethod Generally followed ATCC growth protocol, with a targeted HPRT knockout to avoid a contaminating tetraploid population (CL12)
Extracted molecule genomic DNA
Extraction protocol http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwRepliSeq
Sequencing libraries were generated with Illumina RNA-Seq library kit, Illumina TruSeq v2.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description Library strategy: RepliSeq
Data processing Basecalls performed with Illumina RTA version 1.12.4.2
Uniquely mapping high-quality reads were mapped to the genome minus the Y chromosome. Replication signals within each six cell cycle fraction were derived from the density of sequence tags mapping within a 50 kb sliding window (stepped 1 kb across the genome); these densities were normalized to 4 million tags per genome. To avoid variation due to copy number or sequence bias, cell cycle-specific replication signals at each location were determined as a percentage of the sum of the six normalized tag density signals (Percentage-normalized Signal).
To transform the six fraction replication signals into one track (Wavelet-smoothed Signal), the percentage-normalized signals at each location were used to calculate a weighted average value based on the average DNA content of each fraction according to flow cytometry [higher values correspond to earlier replication; formula=(0.917*G1b)+(0.750*S1)+(0.583*S2)+(0.417*S3)+(0.250*S4)+(0*G2)]. These weighted average data were smoothed by wavelet transformation [J7 level, corresponding to a scale of 128 kb; see Thurman et al.(2007)].
Replication initiation zones were flagged by determining local maxima in the wavelet-smoothed data (Peaks) and, similarly, replication termination zones were flagged by local minima (Valleys).
Genome_build: hg19
Supplementary_files_format_and_content: normalized signal, bed, per fraction signal; wavelet smoothed signal, bigWig, scores represent an entire signal profile of all six fractions of the cycle; peaks/valleys, bed, scores replication initiation and termination zones.
 
Submission date Jun 27, 2014
Last update date May 15, 2019
Contact name John A Stamatoyannopoulos
E-mail(s) jstam@altius.org
Organization name Altius Institute / University of Washington
Department Genome Sciences
Lab Stamatoyannopoulos
Street address 2211 Elliott Avenue, 4th Floor
City SEATTLE
State/province WA
ZIP/Postal code 98121
Country USA
 
Platform ID GPL11154
Series (1)
GSE58907 RepliSeq of HT-1080 cell line
Relations
BioSample SAMN02894440
SRA SRX635255

Supplementary file Size Download File type/resource
GSM1422159_pn.HT1080_CL12-1364.S2.20.25000.1000.perc-norm.36.hg19.bed.gz 20.8 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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