|
| Status |
Public on Apr 20, 2021 |
| Title |
ATAC-seq_K5SmoM2Sox9cKO rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Esophagus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Esophagus
sample identification: X1
genotype: Krt5-SmoM2-Sox9fl/fl
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissues were digested, sorted in 1ml PBS 3% FBS. Nuclei were isolated to proceed to transposase reaction (Illumina). DNA was purified using the MinElute purification kit.
DNA libraries were PCR amplified (NEBNext High-Fidelity 2x PCR Master Mix, New England Biolabs), indexed using primers described by Buenrostro et al. (2013), and double size selected (from 150 to 1200 bp) using AmpureXP magnetic beads (Beckman) following the manufacturer's recommendations. The multiplexed libraries were loaded on a NovaSeq 6000 (Illumina) using a S2 flow cell and paired-end sequences were produced using a 200 Cycle Kit.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
The cells have been sorted based on high EpCam expression
|
| Data processing |
ATACseq paired-end reads of 50 bp were trimmed for adaptor sequences (using Trimmomatic).
ATAC-seq paired-end reads were then aligned to the mouse GRCm38 genome (using Bowtie2)
Mitochondrial reads and reads aligned to scaffolds and undefined chromosomes were excluded from downstream analysis.
Duplicated reads were removed by Picard tools.
Read start sites were adjusted to represent the center of the transposon binding event as described in Li et al., 2009.
Peak calling was performed on each individual sample using Macs2.
TDF files were generated using igv.
bigWig files were generated using bamCoverage from deepTools in Galaxy.
Genome_build: mm10
Supplementary_files_format_and_content: TDF binary files generated using igv. BigWig indexed binary file format generated using deepTools (bin size=50pb, scaling factor=1.0), files normalized for sequencing depth.
|
| |
|
| Submission date |
Dec 05, 2020 |
| Last update date |
Apr 21, 2021 |
| Contact name |
Alizee Vercauteren Drubbel |
| E-mail(s) |
alizeevd@gmail.com
|
| Organization name |
Université Libre de Bruxelles
|
| Lab |
Beck lab
|
| Street address |
808 route de Lennik
|
| City |
Anderlecht |
| ZIP/Postal code |
1070 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE148872 |
ATAC sequencing of esophageal cells from wild type and Krt5SmoM2 mice |
| GSE148876 |
RNA-seq and ATAC-sequencing of esophageal cells after HH pathway activation |
|
| Relations |
| BioSample |
SAMN17006609 |
| SRA |
SRX9635503 |
