NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2052012 Query DataSets for GSM2052012
Status Public on May 31, 2016
Title carcass_WT_i9
Sample type SRA
 
Source name carcass
Organism Mus musculus
Characteristics tdg_genotype: wild-type
mouse_id: i9
mouse_litter: pair_b
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.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
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.
 
Submission date Feb 01, 2016
Last update date May 15, 2019
Contact name Dario Beraldi
E-mail(s) dario.beraldi@cruk.cam.ac.uk
Organization name Cambridge Research Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platform ID GPL19057
Series (1)
GSE77447 In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine
Relations
BioSample SAMN04450852
SRA SRX1556071

Supplementary file Size Download File type/resource
GSM2052012_carcass_WT_i9.bed.gz 232.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap