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| Status |
Public on May 31, 2016 |
| Title |
brain_WT_Q3 |
| Sample type |
SRA |
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| Source name |
hindbrain
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| Organism |
Mus musculus |
| Characteristics |
tdg_genotype: wild-type
mouse_id: Q3
mouse_litter: Q
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryonic tissues were lysed in RLT plus buffer (Qiagen), homogenised via centrifugation through a QIAshreddred column (Qiagen) at full speed for two minutes in a microcentrifuge. DNA and RNA were isolated using AllPrep DNA/RNA kit (Qiagen) following the manufacturer’s instructions.
Sequencing libraries were generated using the NEBNext library preparation modules. 16 cycles of PCR amplification were performed with the Illumina PCR Master Mix and PCR Primer Cocktail. Prior to sequencing, libraries were quantified by qPCR (KAPA Biosystems) and their fragment size profile analysed by TapeStation (Agilent). Sequencing was performed on an Illumina Nextseq 500, run in paired-end mode with 100 read cycles.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Raw sequence reads were trimmed to remove poor quality reads, adapter contamination, and the first 6 base pairs, using Trim Galore http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trimmed sequencing reads were aligned to mouse genome assembly NCBIM37 (mm9) using Bowtie2. Peaks were called in the SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) using the MACS peak caller, with a p-value cutoff of 1x10-5 and a fragment size of 200 base pairs
Genome_build: NCBIM37
Supplementary_files_format_and_content: Bed files of positions of 5fC peaks.
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| Submission date |
Feb 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dario Beraldi |
| E-mail(s) |
dario.beraldi@cruk.cam.ac.uk
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| Organization name |
Cambridge Research Institute
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| Street address |
Robinson Way
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| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE77447 |
In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine |
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| Relations |
| BioSample |
SAMN04450847 |
| SRA |
SRX1556066 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2052002_brain_WT_Q3.bed.gz |
146.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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