|
| Status |
Public on Jul 03, 2013 |
| Title |
MethylC-Seq_hs_mfg_35do |
| Sample type |
SRA |
| |
|
| Source name |
Middle frontal gyrus from 35 day old male human brain (UMB_759)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain (middle frontal gyrus)
cell type(s): all
age: 35 days
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).
|
| |
|
| 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.
|
| |
|
| Submission date |
Jun 18, 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 |
SAMN02206500 |
| SRA |
SRX309596 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr1.txt.gz |
322.4 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr10.txt.gz |
187.6 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr11.txt.gz |
190.0 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr12.txt.gz |
187.0 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr13.txt.gz |
130.2 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr14.txt.gz |
125.5 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr15.txt.gz |
115.2 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr16.txt.gz |
117.7 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr17.txt.gz |
120.1 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr18.txt.gz |
104.6 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr19.txt.gz |
91.4 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr2.txt.gz |
332.7 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr20.txt.gz |
91.3 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr21.txt.gz |
48.9 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr22.txt.gz |
55.4 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr3.txt.gz |
273.2 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr4.txt.gz |
252.4 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr5.txt.gz |
244.7 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr6.txt.gz |
233.8 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr7.txt.gz |
217.5 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr8.txt.gz |
200.6 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chr9.txt.gz |
161.8 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chrL.txt.gz |
93.3 Kb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chrX.txt.gz |
189.1 Mb |
(ftp)(http) |
TXT |
| GSM1167004_allC.MethylC-Seq_hs_mfg_35do.chrY.txt.gz |
20.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
