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| Status |
Public on Nov 02, 2015 |
| Title |
NextSeq_H3_lo_CB_DMSO3 |
| Sample type |
SRA |
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| Source name |
Cord blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Cord blood
immunprecipitation: Total H3
mnase for chromatin digestion: Low
treatment: DMSO
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mint-ChIP: Cells were lysed and native chromatin was digested using Mnase. Subsequently, nucleosomes were indexed by adapter ligation and pooled for immunoprecipiation of H3K9ac (Active Motif, 39917), H3K9me2 (Abcam, ab1220) and total H3 (Abcam, ab1791).
Mint-ChIP: Immunoprecipitated DNA was amplified by in vitro transcription, followed by reverse transcription. Resulting fragments, tagged on both ends, were amplified by PCR using primers compatible with Illumina sequencing.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ChIP-seq
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| Data processing |
Provided fastq files are already demultiplexed according to adapter barcode and trimmed.
Alignment: BWA paired-end alignment to hg19
Filter1: Remove all unmapped reads and reads with X0 > 2 from bam files
Filter2: Remove all PCR duplicates using PicardTools MarkDuplicates with REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT
Filter3: Of pairs with identical R1 starting position alignment, keep only the pair with the longest fragment size.
Make tdf files using igvtools count --includeDuplicates --pairs
Genome_build: hg19
Supplementary_files_format_and_content: For visualization in IGV, tdf files are provided.
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| Submission date |
Jun 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter van Galen |
| E-mail(s) |
petervangalen@gmail.com, pvangalen@bwh.harvard.edu
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| Organization name |
Brigham and Women's Hospital / Broad Institute of MIT and Harvard
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| Department |
Hematology
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| Lab |
Van Galen Lab
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| Street address |
4 Blackfan Circle
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| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE69516 |
EHMT1 and EHMT2 inhibition induce fetal hemoglobin expression [ChIP-seq] |
| GSE71422 |
EHMT1 and EHMT2 inhibition induce fetal hemoglobin expression |
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| Relations |
| BioSample |
SAMN03759627 |
| SRA |
SRX1047399 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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