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| Status |
Public on Jul 03, 2013 |
| Title |
MethylC-Seq_mm_fc_tet2ko |
| Sample type |
SRA |
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| Source name |
Frontal cortex from 8 week old Tet2-/- mouse brain
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
genotype: Tet2-/-
tissue: brain (frontal cortex)
cell type(s): all
age: 8 weeks
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 |
May 15, 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 |
| SRA |
SRX314958 |
| BioSample |
SAMN02213449 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr1.txt.gz |
268.1 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr10.txt.gz |
178.8 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr11.txt.gz |
180.0 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr12.txt.gz |
161.6 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr13.txt.gz |
163.2 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr14.txt.gz |
161.5 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr15.txt.gz |
143.7 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr16.txt.gz |
132.0 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr17.txt.gz |
131.3 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr18.txt.gz |
123.9 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr19.txt.gz |
85.4 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr2.txt.gz |
254.6 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr3.txt.gz |
214.4 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr4.txt.gz |
214.0 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr5.txt.gz |
211.4 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr6.txt.gz |
205.9 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr7.txt.gz |
196.9 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr8.txt.gz |
180.8 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chr9.txt.gz |
177.8 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chrL.txt.gz |
96.4 Kb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chrX.txt.gz |
179.4 Mb |
(ftp)(http) |
TXT |
| GSM1173793_allC.MethylC-Seq_mm_fc_tet2ko.chrY.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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