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| Status |
Public on Jul 03, 2013 |
| Title |
hmC-gluc-IP-Seq_mm_fc_fetal |
| Sample type |
SRA |
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| Source name |
Frontal cortex from fetal mouse brain
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
genotype: wild type
tissue: brain (frontal cortex)
cell type(s): all
age: E13
gender: male/female
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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 cells using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. hmC-gluc-IP-Seq sequenging libraries were generated by biotin-glucosyl tagging and enrichment of hmC according to the following procedure. The Hydroxymethyl Collector Kit (Active Motif, Carlsbad, CA, USA) was used to selectively tag hmC bases within genomic DNA fragments (100-200 bp) with glucose and biotin moieties to form biotin-N3-5-gmC (biotin-gmC), as described previously [Song C.-X. et al., Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine, Nature Biotechnology 29, 68–72 (2011)]. Genomic DNA fragments containing biotin-gmC were then enriched and purified by high-affinity capture using streptavidin magnetic beads. Enriched DNA containing biotin-gmC was used to generate Illumina DNA sequencing libraries with the TruSeq DNA Sample Prep Kit v2 (Illumina, San Diego, CA).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Other: hmC-gluc-IP-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
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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 |
SRX314965 |
| BioSample |
SAMN02213471 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1173800_hmC-gluc-IP-Seq_mm_fc_fetal.mapped.bam |
22.2 Gb |
(ftp)(http) |
BAM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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