|
Status |
Public on Jul 03, 2013 |
Title |
MethylC-Seq_hs_fc_fetal |
Sample type |
SRA |
|
|
Source name |
Cerebral cortex from fetal human brain
|
Organism |
Homo sapiens |
Characteristics |
tissue: brain (cerebral cortex) cell type(s): all age: 20 weeks (gestational) gender: male
|
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 14, 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 |
SAMN02204164 |
SRA |
SRX306253 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr1.txt.txt.gz |
245.8 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr10.txt.txt.gz |
144.8 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr11.txt.txt.gz |
144.5 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr12.txt.txt.gz |
141.0 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr13.txt.txt.gz |
95.0 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr14.txt.txt.gz |
95.2 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr15.txt.txt.gz |
89.4 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr16.txt.txt.gz |
95.6 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr17.txt.txt.gz |
97.3 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr18.txt.txt.gz |
78.4 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr19.txt.txt.gz |
76.0 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr2.txt.txt.gz |
249.9 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr20.txt.txt.gz |
73.1 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr21.txt.txt.gz |
37.5 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr22.txt.txt.gz |
46.4 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr3.txt.txt.gz |
202.8 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr4.txt.txt.gz |
182.1 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr5.txt.txt.gz |
181.5 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr6.txt.txt.gz |
173.3 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr7.txt.txt.gz |
164.3 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr8.txt.txt.gz |
150.7 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chr9.txt.txt.gz |
123.4 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chrL.txt.txt.gz |
96.7 Kb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chrX.txt.txt.gz |
126.2 Mb |
(ftp)(http) |
TXT |
GSM1163695_allC.MethylC-Seq_hs_fc_fetal.chrY.txt.txt.gz |
13.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |