|
Status |
Public on Jul 03, 2013 |
Title |
MethylC-Seq_hs_hues6 |
Sample type |
SRA |
|
|
Source name |
HUES6 human embryonic stem cell line
|
Organism |
Homo sapiens |
Characteristics |
tissue: embryonic stem cells cell type(s): embryonic stem cells gender: female
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was purified from tissue, sorted cells or nuclei using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. MethylC-Seq libraries were constructed as descibed previously [Lister R. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells, Nature 471, 68-73 (2011)], except library amplification was performed with either PfuTurboCx Hotstart DNA polymerase (Agilent Technologies, Santa Clara, CA, USA) or KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA, USA).
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|
|
Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
Bisulfite-Seq
|
Data processing |
Data were mapped to the Homo sapiens reference genome (hg18) or the Mus musculus reference genome (mm9). MethylC-Seq, TAB-Seq, CMS-IP and hmC-gluc-IP-Seq analyses were performed as described in Lister, Mukamel et al. Global epigenomic reconfiguration during mammalian brain development. Science (2013). RNA-Seq RPKM data were generated using Bowtie2 and Tophat2. Gene expression values were calculated using Cufflinks2. genome build: hg18 Supplementary_files_format_and_content: The processed data for the allC.MethylC-Seq_<sample>.<chr>.txt files contain a row of headers indicating the chromosome, position, strand, methylation class, methylation count, and total coverage. This is a tab-delimited file.
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|
|
Submission date |
Jun 25, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Joseph R Ecker |
E-mail(s) |
ecker@salk.edu
|
Phone |
8584534100
|
Organization name |
HHMI-Salk-Institute
|
Department |
Genomic Analysis Laboratory
|
Lab |
Ecker lab
|
Street address |
10010 North Torrey Pines Road
|
City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92037 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE47966 |
Global epigenomic reconfiguration during mammalian brain development |
|
Relations |
SRA |
SRX314943 |
BioSample |
SAMN02213481 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr1.txt.gz |
279.9 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr10.txt.gz |
163.4 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr11.txt.gz |
164.4 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr12.txt.gz |
163.1 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr13.txt.gz |
113.7 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr14.txt.gz |
109.5 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr15.txt.gz |
100.6 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr16.txt.gz |
102.5 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr17.txt.gz |
104.3 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr18.txt.gz |
91.5 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr19.txt.gz |
78.4 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr2.txt.gz |
290.6 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr20.txt.gz |
79.8 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr21.txt.gz |
42.6 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr22.txt.gz |
47.7 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr3.txt.gz |
239.2 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr4.txt.gz |
220.2 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr5.txt.gz |
214.0 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr6.txt.gz |
204.3 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr7.txt.gz |
189.3 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr8.txt.gz |
174.8 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chr9.txt.gz |
140.4 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chrL.txt.gz |
102.9 Kb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chrX.txt.gz |
173.2 Mb |
(ftp)(http) |
TXT |
GSM1173778_allC.MethylC-Seq_hs_hues6.chrY.txt.gz |
901.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |