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| Status |
Public on Mar 26, 2015 |
| Title |
Cerebellum_cKO_dnmt3a_BS-seq_1 |
| Sample type |
SRA |
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| Source name |
Cerebellum
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| Organism |
Mus musculus |
| Characteristics |
genotype: Dnmt3a flx/flx Tg(Nes-cre)1Kln/J
background: C57BL/6
age: 10-11 weeks
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| Growth protocol |
Brain tissue was taken from wild-type mice maintained under standard housing conditions.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from the cerebellum of dnmt3a flx/flx, or dnmt3a flx/flx Nestin-cre mice at the indicated ages. For bisulfite treatment, 25-100 ng of genomic DNA 0.25-1 ng of unmethylated lambda DNA was added and libraries were generated using the Ovation Ultralow Methyl-Seq Library System (Nugen). Bisulfite treatment was performed using the EpiTect bisulfite conversion kit (Qiagen) following manufacturer’s instructions.
Libraries were constructed using TruSeq reagents (Illumina) and sequenced on the Miseq instrument (Illumina).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Reads were mapped to the mm9 genome using BS seeker, allowing up to four mismatches. Duplicate reads were removed and only uniquely mapping reads were kept. For Dnmt3a data, reads containing 3 consecutive mCH were discarded in attempt to remove unconverted reads.
Genome_build: mm9
Supplementary_files_format_and_content: text file containing processed data for bisulfite sequencing. One file each CN dinucleotide. Each file summarizes information for the pooled data from 4 replicates for each brain regions. Each line indicates a cytosine in the genome with the following information listed for each column: Chromosome, Base on the plus strand (G or C), nucleotide position, Di or Trinucleotide context (CG, CHH or CHG), specific dinucleotide (CG, CA,CC,CT), fraction of reads non-converted base-calls at this position , number of reads non-converted bases at this position (# of C basecalls), total number of reads for the base at this position (# of C and T base-calls).
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| Submission date |
Mar 25, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Harrison Wren Gabel |
| E-mail(s) |
gabelh@pcg.wustl.edu
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| Organization name |
Harvard Medical School
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| Department |
Neurbiology
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| Lab |
Michael Greenberg
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| Street address |
220 longwood avenue
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| City |
brookline |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (2) |
| GSE60077 |
Length-dependent gene misregulation in Rett syndrome |
| GSE67292 |
Length-dependent gene misregulation in Rett syndrome (Bisulfite-Seq 2) |
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| Relations |
| BioSample |
SAMN03447212 |
| SRA |
SRX968947 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1643932_CB1_CA_cKO_dnmt3a.txt.gz |
18.9 Mb |
(ftp)(http) |
TXT |
| GSM1643932_CB1_CC_cKO_dnmt3a.txt.gz |
12.8 Mb |
(ftp)(http) |
TXT |
| GSM1643932_CB1_CG_cKO_dnmt3a.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
| GSM1643932_CB1_CT_cKO_dnmt3a.txt.gz |
18.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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