GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3901940 Query DataSets for GSM3901940
Status Public on Jan 01, 2020
Title Wild type MEFs [WT_2]
Sample type SRA
Source name connective tissue - MEFs
Organism Mus musculus
Characteristics strain: BALB/c
genotype: wild type
Growth protocol All MEFs were cultured in DMEM with high glucose, 10% fetal bovine serum, and 100 U/ml penicillin and 100 µg/ml streptomycin (all from Millipore-Sigma), in a humidified incubator with 5% CO2 at 37°C
Extracted molecule genomic DNA
Extraction protocol Samples with 50,000 cells per condition were shipped in frozen medium (DMEM with 50 % FBS and 10% DMSO) on dry ice to Novogene (Beijing, China). All subsequent processing was performed by Novagene using standard DNA extraction and library preperation protocols
All processing was performed by Novagene (Beijing, China). Cell nuclei were isolated, mixed with Tn5 Transposase with two adapters and tagmentation was performed for 30 minutes at 37⁰C. The fragmented DNA was purified and amplified with limited PCR cycle using index primers. Llibraries were prepared according to recommended Illumina NovaSeq6000 protocols.
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
Description Actb +/+
Data processing Raw reads were analyzed using FastQC and quality trimmed using Trimmomatic with the parameters “trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36”
Surviving paired reads were then aligned against the mouse reference genome (GRCm38) using Burrows-Wheeler Aligner BWA-MEM 9
BAM alignments were cleaned, sorted and deduplicated (PCR and Optical duplicates) with PICARD tools
RPKM normalized bamCoverage files were produced using deeptools2
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: bigwig files containing RPKM normalized ATAC-Seq signal for each sample
Submission date Jun 24, 2019
Last update date May 11, 2020
Contact name Piergiorgio Percipalle
Organization name New York University Abu Dhabi
Department Biology Department, Science Division
Street address Saadiyat Campus, Abu Dhabi
City Abu Dhabi
State/province Abu Dhabi
ZIP/Postal code 129188
Country United Arab Emirates
Platform ID GPL24247
Series (1)
GSE133196 ATAC-Seq analysis of Mouse Embryonic Fibroblasts (MEFs) to understand the role of β-actin in regulating chromatin states
BioSample SAMN12125635
SRA SRX6353988

Supplementary file Size Download File type/resource 115.0 Mb (ftp)(http) BW
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