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Status |
Public on Jul 03, 2013 |
Title |
MethylC-Seq_mm_fc_male_7wk_neun_neg |
Sample type |
SRA |
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Source name |
NeuN- nuclei isolated from frontal cortex from 7 week old male mouse brain
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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
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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.
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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 |
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Description |
Bisulfite-Seq
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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.
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Submission date |
Jun 25, 2013 |
Last update date |
Sep 09, 2019 |
Contact name |
Joseph R Ecker |
E-mail(s) |
ecker@salk.edu
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Phone |
8584534100
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Organization name |
HHMI-Salk-Institute
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Department |
Genomic Analysis Laboratory
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Lab |
Ecker lab
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Street address |
10010 North Torrey Pines Road
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City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92037 |
Country |
USA |
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Platform ID |
GPL13112 |
Series (1) |
GSE47966 |
Global epigenomic reconfiguration during mammalian brain development |
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Relations |
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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