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Sample GSM7720321

Query DataSets for GSM7720321

Status

Public on May 05, 2024

Title

YKO

Sample type

SRA

Source name

Heart

Organism

Mus musculus

Characteristics

tissue: Heart
genotype: Ythdc1 CKO

Treatment protocol

Ythdc1flox/flox and Ythdc1CKO mice were fed with normal chow diet for 15 days old

Extracted molecule

genomic DNA

Extraction protocol

Nuclei was extracted from heart samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min.
Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated.

Library strategy

ATAC-seq

Library source

genomic

Library selection

other

Instrument model

Illumina NovaSeq 6000

Data processing

Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ≥13), non mitochondrial chromosome, and properly paired reads (longer than 18 nt).
All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel --keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
Peaks were merged with ‘bedtoolsmerge’ for differential peak analysis. Differential peak calling was performed using our own R script. Only peaks with foldchange more than 0.5 were considered as differential peaks. Using the same method, genes associated with different peaks were identified and also do GO and KEGG enrichment analysis.
Assembly: Ensemble_GRCm38.p6
Supplementary files format and content: YKO_vs_YFF_peak_compare_table.txt

Submission date

Aug 21, 2023

Last update date

May 05, 2024

Contact name

lei shi

E-mail(s)

shilei2021@yeah.net

Organization name

jilin university

Street address

changchun