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| Status |
Public on Aug 25, 2016 |
| Title |
HSPC_p300_ChIPSeq_1 |
| Sample type |
SRA |
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| Source name |
HPC7
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| Organism |
Mus musculus |
| Characteristics |
cell line: hematopoietic cell line HPC7
chip antibody: p300 (santa cruz sc-585 X, lot j2214)
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| Growth protocol |
HPC7 were grown in IMDM supplemented with 5%FBS, MTG, pen/Strep and 100ng/ml SCF
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested, washed with PBS and crosslinked with 1% Formaldehyde for 30 min at 37C.
Libraries were constructed with KAPA Hyper Prep Kit and Multiplexed with NextFlex Barcodes from Biooscientific
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7
Processed reads were slopped by 250bp
Duplicates were removed with Picard tools and bedgraphs were normalized to reads per million.
MACS version 1.4.2 was used for ChIP-sequencing peak discovery.
Bedtools, GenomicTools version 2.7.2, Seqminer and deepTools weee used for performing genomic interval mathematical operations, genomic interval annotation, ChIP-seq heatmap generation and ChIP-seq profile construction.
Genome_build: mm9
Supplementary_files_format_and_content: BigWigs of data normalized to reads per million
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| Submission date |
Dec 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Beatriz Aranda-Orgilles |
| Organization name |
NYU School of Medicine
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| Street address |
522 First Avenue
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| City |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE76053 |
Med12 and p300 chips in HSPCs |
| GSE76055 |
Regulation of enhancer dynamics by MED12 |
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| Relations |
| BioSample |
SAMN04338701 |
| SRA |
SRX1484890 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1973452_bowtie.HPC7_p300.dd.sort.slop.bw |
159.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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