|
| 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 |
| E-mail(s) |
pp69@nyu.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN12125635 |
| SRA |
SRX6353988 |
