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Sample GSM4484777 Query DataSets for GSM4484777
Status Public on Apr 20, 2021
Title ATAC-seq_WT rep1
Sample type SRA
 
Source name Esophagus
Organism Mus musculus
Characteristics tissue: Esophagus
sample identification: C1
strain: CD1
genotype: wild type
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 low 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 Apr 17, 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 SAMN14614711
SRA SRX8133395

Supplementary file Size Download File type/resource
GSM4484777_ATAC-seq_WT_rep1_NormC1.bigwig 83.5 Mb (ftp)(http) BIGWIG
GSM4484777_ATAC_narrowPeaksC1.txt.gz 2.1 Mb (ftp)(http) TXT
GSM4484777_sortcAVE8-C1128-1.8C1.bam.tdf 151.0 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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