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Sample GSM1173787 Query DataSets for GSM1173787
Status Public on Jul 03, 2013
Title MethylC-Seq_mm_fc_male_7wk_neun_neg
Sample type SRA
Source name NeuN- nuclei isolated from frontal cortex from 7 week old male mouse brain
Organism Mus musculus
Characteristics strain: C57Bl/6
genotype: wild type
tissue: brain (frontal cortex)
cell type(s): non-neurons (NeuN-, predominantly glia)
age: 7 weeks (P49)
gender: male
Growth protocol The mouse lines C57Bl/6 and S100b-eGFP (B6;D2-Tg(S100B-EGFP)1Wjt/J), both from Jackson Laboratories, ME were bred and maintained in our animal facility in 12 h light/dark cycles with food ad libitum. To produce the S100b-eGFP animals used for FACS, animals were crossed to C57BL/6 to produce heterozygotes for eGFP expression. Tet2-/- mice were produced by targeted disruption of the Tet2 gene. Animals were weaned in groups of 3-4 per cage, and used at the postnatal time-points indicated. Three animals obtained from separate litters were processed together for DNA and RNA isolations.
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: mm9
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 25, 2013
Last update date Sep 09, 2019
Contact name Joseph R Ecker
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 GPL13112
Series (1)
GSE47966 Global epigenomic reconfiguration during mammalian brain development
Reanalyzed by GSE137098
BioSample SAMN02213490
SRA SRX314952

Supplementary file Size Download File type/resource
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr1.txt.gz 267.1 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr10.txt.gz 177.9 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr11.txt.gz 177.6 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr12.txt.gz 160.9 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr13.txt.gz 162.5 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr14.txt.gz 161.0 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr15.txt.gz 142.6 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr16.txt.gz 131.5 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr17.txt.gz 130.3 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr18.txt.gz 123.3 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr19.txt.gz 84.7 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr2.txt.gz 252.8 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr3.txt.gz 214.1 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr4.txt.gz 212.5 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr5.txt.gz 209.8 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr6.txt.gz 205.1 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr7.txt.gz 195.4 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr8.txt.gz 179.4 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chr9.txt.gz 176.3 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chrL.txt.gz 95.0 Kb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chrX.txt.gz 182.3 Mb (ftp)(http) TXT
GSM1173787_allC.MethylC-Seq_mm_fc_male_7wk_neun_neg.chrY.txt.gz 2.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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