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Sample GSM2231457

Query DataSets for GSM2231457

Status

Public on Mar 14, 2018

Title

H3K4me1 Ngn3-low #2

Sample type

SRA

Source name

Pancreas

Organism

Mus musculus

Characteristics

embryonic day: E13.5
cell type: dorsal pancreas; Ngn3-low
chip antibody: H3K4me1 (Millipore, 07-436)

Extracted molecule

genomic DNA

Extraction protocol

Low-cell-number ChIP-seq followed the method described by Brind'Amour et al. We used approximately 1.5 × 10e4 cells per ChIP with 1 ng antibodies of H3K4me3 (Abcam, ab8580), H3K27me3 (Millipore, 07-449), H3K4me1 (Millipore, 07-436), H3K27ac (Active motif, 39133), respectively.
Library preparation was conducted with “Ultra DNA Library Prep Kit for Illumina” (NEB. E7370).

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 2500

Description

H3K4me1_Ngn3-low.bdg.gz

Data processing

The sequencing reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5) with default parameters, and we only retained reads with a mapping quality ≥ 30 for subsequent analyses.
PCR duplicate reads were removed using samtools (v1.3.1) with the commands “samtools sort in_bam | samtools rmdup -s - out_bam”.
Reads of two biological replicates were pooled.
Tag density was calculated and stored in the bedGraph format using Homer with the parameters “makeUCSCfile out_dir –o out.bdg –name sample_name -color track_color –fragLength 150 –avg -fsize 1e20”.
genome build: mm10
processed data files format and content: bedGraph files were generated using Homer (v4.7.2); Scores represent read count per bp per 1 × 10e7 reads.

Submission date

Jul 12, 2016

Last update date

May 15, 2019

Contact name

Cheng-ran Xu

Organization name

Peking University

Department

School of Basic Medical Sciences

Street address

NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA