|
| Status |
Public on Aug 25, 2022 |
| Title |
Wild Type Mouse Embryonic Fibroblast, rep2 (ATAC-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Embryonic Fibroblast
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse Embryonic Fibroblast
strain: BALB/c
genotype: Wild Type
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were shipped in frozen medium 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 preperation and sequencing was performed by Novogene. Co Ltd using standard illumina protocols
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT.bw
|
| Data processing |
Raw reads quality trimmed using trim-galore with default settings and assessed with fastqc
Surviving paired reads were then aligned against the mouse reference genome mm10 using bwa-mem
Resulting BAM alignments were then processed through PICARD tools (http://broadinstitute.github.io/picard), to clean, sort and deduplicate (PCR and Optical duplicates).
RPKM normalized bamCoverage files were produced using deeptools2 for replicate-merged bams of each conditions
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigwig files containing RPKM normalized ATAC signal for merged replicates of each condition
|
| |
|
| Submission date |
Mar 18, 2022 |
| Last update date |
Aug 25, 2022 |
| 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 (2) |
| GSE198988 |
ATAC-Seq analysis of wild-type and nm1-knockout mouse embryonic fibroblasts |
| GSE198990 |
Wild-type and nm1-knockout mouse embryonic fibroblasts |
|
| Relations |
| BioSample |
SAMN26804622 |
| SRA |
SRX14506063 |
