|
Status |
Public on Jul 03, 2013 |
Title |
MethylC-Seq_hs_fc_female_53yr_NeuN_neg |
Sample type |
SRA |
|
|
Source name |
NeuN- nuclei isolated from dorsal prefrontal cortex from 53 year old female human brain (UMB_579)
|
Organism |
Homo sapiens |
Characteristics |
tissue: brain (dorsal prefrontal cortex) cell type(s): non-neurons (NeuN-, predominantly glia) age: 53 years 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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|
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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 |
BioSample |
SAMN02213488 |
SRA |
SRX314939 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr1.txt.gz |
310.8 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr10.txt.gz |
180.8 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr11.txt.gz |
183.2 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr12.txt.gz |
180.1 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr13.txt.gz |
125.8 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr14.txt.gz |
121.2 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr15.txt.gz |
111.1 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr16.txt.gz |
113.2 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr17.txt.gz |
115.3 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr18.txt.gz |
101.1 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr19.txt.gz |
87.2 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr2.txt.gz |
321.4 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr20.txt.gz |
88.1 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr21.txt.gz |
47.2 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr22.txt.gz |
53.0 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr3.txt.gz |
264.0 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr4.txt.gz |
243.7 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr5.txt.gz |
236.4 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr6.txt.gz |
225.8 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr7.txt.gz |
209.5 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr8.txt.gz |
193.7 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chr9.txt.gz |
155.6 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chrL.txt.gz |
86.8 Kb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chrX.txt.gz |
192.8 Mb |
(ftp)(http) |
TXT |
GSM1173774_allC.MethylC-Seq_hs_fc_female_53yr_NeuN_neg.chrY.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |