|
Status |
Public on Jul 03, 2013 |
Title |
TAB-Seq_mm_fc_6wk |
Sample type |
SRA |
|
|
Source name |
Frontal cortex from 6 week old male mouse brain
|
Organism |
Mus musculus |
Characteristics |
strain: C57Bl/6 genotype: wild type tissue: brain (frontal cortex) cell type(s): all age: 6 weeks (P40) 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 using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. TAB-Seq libraries were generated as descibed previously [Yu M. et al., Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell 149, 1368-1380 (2012)].
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
Other: TAB-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
|
|
|
Submission date |
Jun 25, 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 |
GPL13112 |
Series (1) |
GSE47966 |
Global epigenomic reconfiguration during mammalian brain development |
|
Relations |
SRA |
SRX314960 |
BioSample |
SAMN02213474 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr1.txt.gz |
277.6 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr10.txt.gz |
185.9 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr11.txt.gz |
186.8 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr12.txt.gz |
168.3 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr13.txt.gz |
169.9 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr14.txt.gz |
168.1 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr15.txt.gz |
149.3 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr16.txt.gz |
137.4 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr17.txt.gz |
136.5 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr18.txt.gz |
128.8 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr19.txt.gz |
88.6 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr2.txt.gz |
263.5 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr3.txt.gz |
222.1 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr4.txt.gz |
221.1 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr5.txt.gz |
218.3 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr6.txt.gz |
212.9 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr7.txt.gz |
203.7 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr8.txt.gz |
186.4 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chr9.txt.gz |
183.2 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chrL.txt.gz |
76.1 Kb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chrP.txt.gz |
5.0 Kb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chrX.txt.gz |
184.2 Mb |
(ftp)(http) |
TXT |
GSM1173795_allC.TAB-Seq_mm_fc_6wk.chrY.txt.gz |
2.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |