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Sample GSM5267708

Query DataSets for GSM5267708

Status

Public on Jun 28, 2021

Title

Scx-Flag input-2

Sample type

SRA

Source name

forelimb cells

Organism

Mus musculus

Characteristics

age: E13.5
antibody: none input

Extracted molecule

genomic DNA

Extraction protocol

Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with anti-FLAG antibody.
Sequencing libraries were generated using Rubicon ThruPLEX DNA sequencing kit (Rubicon Genomics, Ann Arbor MI).

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 2500

Description

Scx ChIPseq Input_vs_ChIP

Data processing

ChIP-seq reads were aligned to UCSC mouse genome mm10 using STAR aligner (ver. 2.7.4) [1]. To match the sequencing depth across samples, aligned reads were down-sampled to 30 million. After deduplication, peaks were called for each Scx ChIP-seq data using Homer (ver. 4.11) [2] against a matching input sample. To identify reproducible and unified Scx peaks, we performed differential analysis comparing Scx samples versus input samples. First, Scx peaks from the three biological replicates were pooled and merged into a preliminary peak set. Second, read count were measured in all the Scx samples and input samples within the peak set. Finally, exact test was performed using edgeR [3] comparing Scx and input samples. Final Scx peaks were defined by log2 fold-change (log2FC) over input > 2 and FDR < 0.01. De novo motif search within the Scx peaks were performed using Homer.
mm10
excel file, list of all peaks

Submission date

Apr 27, 2021

Last update date

Jun 28, 2021

Contact name

HAN LIU

E-mail(s)

han.liu@cchmc.org

Organization name

CINCINNATI CHILDREN'S HOSPITAL

Department

DEVELOPMENTAL BIOLOGY