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| Status |
Public on Mar 14, 2018 |
| Title |
H3K4me1 Ngn3-high #1 |
| Sample type |
SRA |
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| Source name |
Pancreas
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| Organism |
Mus musculus |
| Characteristics |
embryonic day: E13.5
cell type: dorsal pancreas; Ngn3-high
chip antibody: H3K4me1 (Millipore, 07-436)
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| 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).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
H3K4me1_Ngn3-high.bdg.gz
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| 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.
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| Submission date |
Jul 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Cheng-ran Xu |
| Organization name |
Peking University
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| Department |
School of Basic Medical Sciences
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| Street address |
NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA
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| City |
Beijing |
| State/province |
- |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE84324 |
Dynamics of chromatin marks and the role of JMJD3 during pancreatic endocrine cell fate commitment |
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| Relations |
| BioSample |
SAMN05385883 |
| SRA |
SRX1941083 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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