|
Status |
Public on Jul 31, 2014 |
Title |
Sample 1367 phase G2 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.
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|
|
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, 6th Floor
|
City |
SEATTLE |
State/province |
WA |
ZIP/Postal code |
98121 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
|
Relations |
BioSample |
SAMN02894438 |
SRA |
SRX635258 |